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https://openalex.org/W4283741730
https://www.nature.com/articles/s41586-022-04911-x.pdf
English
null
Structural insights into dsRNA processing by Drosophila Dicer-2–Loqs-PD
Nature
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cc-by
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1State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China. 2Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China. 3Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. 4These authors contributed equally: Shichen Su, Jia Wang. ✉e-mail: hongweiwang@tsinghua.edu.cn; majb@fudan.edu.cn Article Article https://doi.org/10.1038/s41586-022-04911-x Dicer proteins normally function under the aid or regulation of certain cofactor proteins, more of which are distinct dsRBD proteins, to efficiently produce siRNAs or miRNAs. In Drosophila, there are two dicer protein isoforms. Dcr-1 requires Loquacious-PA/PB (Loqs-PA/PB) to produce miRNAs from precursor-miRNAs (pre-miRNAs). Dcr-2 requires Loqs-PD to produce siRNAs from dsRNAs and another double- stranded RNA-binding domain (dsRBD) protein R2D2 to load siRNAs into Argonaute2 (Ago2)1. In various eukaryotic species, including Schizosaccharomyces pombe, worm, fruit fly, plants and human, dicer proteins of the RNase III family enzyme are responsible for producing siRNAs from long dsRNAs. Dicer proteins are also responsible for the production of intrinsic microRNAs (miRNAs) that have essential roles in gene regulation of multiple cellular processes7,8. Dicer proteins normally function under the aid or regulation of certain cofactor proteins, more of which are distinct dsRBD proteins, to efficiently produce siRNAs or miRNAs. In Drosophila, there are two dicer protein isoforms. Dcr-1 requires Loquacious-PA/PB (Loqs-PA/PB) to produce miRNAs from precursor-miRNAs (pre-miRNAs). Dcr-2 requires Loqs-PD to produce siRNAs from dsRNAs and another double- stranded RNA-binding domain (dsRBD) protein R2D2 to load siRNAs into Argonaute2 (Ago2)1. Several structures of dicer proteins from different species have been reported in recent years, including human Dicer–TRBP in complex with a pre-miRNA substrate9, Arabidopsis DCL1 and DCL3 in complex with their substrates13,14, and Drosophila Dcr-2 in complex with dsRNA12. How- ever, the molecular mechanism of a full cycle of RNA substrate process- ing by dicer remains unclear, especially that by ATP-dependent dicer proteins. Here six cryo-electron microscopy (cryo-EM) structures of Drosophila Dcr-2–Loqs-PD in apo and in complex with dsRNA substrate in the absence or in the presence of ATP were captured, illuminating the continuous conformational changes of Dcr-2–Loqs-PD after binding to dsRNA and translocating until forming the active dicing state and cleav- ing the dsRNA substrate into an siRNA duplex in the post-dicing state. Previous structural studies suggest that canonical dicer proteins usually contain three modules: the N-terminal bottom module, the C-terminal core module and the cap module in the middle of the pro- tein sequence9,10. The core module comprises two RNase III domains— RNase IIIa and RNase IIIb, which are responsible for cleaving the duplex stem of dsRNAs—and has an additional one or two dsRBDs in the C-terminal region. Structural insights into dsRNA processing by Drosophila Dicer-2–Loqs-PD Shichen Su1,4, Jia Wang2,4, Ting Deng1, Xun Yuan3, Jinqiu He1, Nan Liu2, Xiaomin Li2, Ying Huang3, Hong-Wei Wang2 ✉ & Jinbiao Ma1 ✉ https://doi.org/10.1038/s41586-022-04911-x https://doi.org/10.1038/s41586-022-04911-x Received: 9 November 2021 Accepted: 25 May 2022 Published online: 29 June 2022 Open access Check for updates https://doi.org/10.1038/s41586-022-04911-x Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes1,2. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs)3,4. ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes5,6. Here we report the cryo-electron microscopy structures of Dcr-2–Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5′-phosphate-binding pocket. The overall conformation of Dcr-2–Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2–Loqs-PD. and the Platform domain, respectively. The bottom module comprises a RIG-I-like helicase domain and a dsRBD-like DUF283 domain. Although the RIG-I-like helicase domains are highly conserved in dicer proteins, only those that process long dsRNAs to produce consecutive siRNAs are ATP-dependent, such as Drosophila Dcr-2. By contrast, the human Dicer and Drosophila Dcr-1 proteins do not have ATP-hydrolysis activ- ity in their helicase domains. Previous studies demonstrated that the helicase domain of Drosophila Dcr-2 is also required to discriminate between the dsRNA termini for specific cleavage11,12. In various eukaryotic species, including Schizosaccharomyces pombe, worm, fruit fly, plants and human, dicer proteins of the RNase III family enzyme are responsible for producing siRNAs from long dsRNAs. Dicer proteins are also responsible for the production of intrinsic microRNAs (miRNAs) that have essential roles in gene regulation of multiple cellular processes7,8. Article 1 | Cryo EM structures of Dcr 2 Loqs PD in different dsRNA binding states. a, Schematic of Dcr-2, Loqs-PD and 50 bp dsRNA. Unless specified otherwise, the colour scheme of Dcr-2 and Loqs-PD is used throughout all of the figures. b, Cartoon model of Dcr-2–Loqs-PD in the apo state. The cap, core and base modules are labelled on the right. c, Cartoon model of Dcr-2–Loqs- PD–50 bp dsRNA dimer in the initial dsRNA-binding state (initial state). Molecule A is coloured, molecule B is shown in grey. d,e, Cartoon model of (Extended Data Fig. 1). We also designed and purified a 50 bp palindromic sequence dsRNA with a 3′ two-nucleotide overhang and a 5′ monophos- phate terminus as the substrate on the basis of previous studies11,16 (Fig. 1a). Using a different combination of assembly components and buffers with or without ATP, we solved a series of cryo-EM structures of Dcr-2–Loqs-PD during the dsRNA-processing cycle at resolutions ranging from 3.1 Å to 4.6 Å. These structures include the Dcr-2DDNN–Loqs-PD com- plex in the apo state and the dsRNA initial binding state without ATP; the dsRNA early-translocation and mid-translocation states and the active (Extended Data Fig. 1). We also designed and purified a 50 bp palindromic sequence dsRNA with a 3′ two-nucleotide overhang and a 5′ monophos- phate terminus as the substrate on the basis of previous studies11,16 (Fig. 1a). Using a different combination of assembly components and buffers with or without ATP, we solved a series of cryo-EM structures of Dcr-2–Loqs-PD during the dsRNA-processing cycle at resolutions ranging from 3.1 Å to 4.6 Å. These structures include the Dcr-2DDNN–Loqs-PD com- plex in the apo state and the dsRNA initial binding state without ATP; the dsRNA early-translocation and mid-translocation states and the active Article 1722 1 C terminus 359 344 10 20 30 40 50 50 40 30 20 10 2 1016 1169 1655 216 348 230 508 554 713 665 856 982 1268 1362 1420 1520 1609 5′-P-GAGACUUGGGCAAUGUGACUGCUGAUCAGCAGUCACAUUGCCCAAGUCUCUU-3′ 3′-UUCUCUGAACCCGUUACACUGACGACUAGUCGUCAGUGUAACGGGUUCAGAG-P-5′ Dcr-2 Loqs-PD 50 bp dsRNA Hel1 Hel2i Hel2 Pincer DUF283 Platform Connector RIIIDai RIIIDbi DP-linker PAZ CR-linker RNase IIIa RNase IIIb dsRBD 1 a a RIIIDai Platform Connector RIIIDa RIIIDb Hel2 DUF283 DP-linker PAZ Cap Core Base Loqs-PD Pincer (3.3 Å) Dcr-2DDNN–Loqs-PD (– ATP) Hel1 b RIIIDbi dsRBD Hel2i RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer Hel2 DUF283 Hel1 dsRNA CR-linker Molecule A Molecule B Loqs-PD + dsRNA Platform PAZ dsRNA dsRNA RIIIDa IDb RIIIDai DP-linker DP-linker PD DUF283 el1 Pincer + Mg2+ (4.0 Å) Platform PAZ siRNA RIIIDa RIIIDb RIIIDai Loqs-PD Hel2 DUF283 Hel1 Pincer Connector Connector Hel2 DUF283 Hel1 dsRNA RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer DNN–Loqs-PD RNA (– ATP) 3.1 Å) Dcr-2DDNN–Loqs-PD + dsRNA + ATP + Mg2+ (3.9 Å) d g CR-linker Dcr-2WT–Loqs-PD + dsRNA + ATP + Mg2+ (4.6 Å) D ing d ll of , core oqs- of Dcr-2–Loqs-PD–50 bp dsRNA complex in the early-translocation (d) and mid- translocation (e) state. f,g, Cartoon model of Dcr-2–Loqs-PD–50 bp dsRNA complex in the active dicing (f) and post-dicing (g) state. The siRNA in g is coloured in goldenrod. The post-dicing state is shown as a transparent cryo-EM map. The model in c–g is aligned by base region. The components and resolution of each state are labelled below. Article RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer Hel2 DUF283 Hel1 dsRNA CR-linker Molecule A Molecule B Dcr-2DDNN–Loqs-PD + dsRNA (– ATP) (3.1 Å) c d Hel2 DUF283 Hel1 dsRNA RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer Dcr-2DDNN–Loqs-PD + dsRNA + ATP + Mg2+ (3.9 Å) d CR-linker b d Molecule B Hel2 DUF283 Hel1 dsRNA RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer Dcr-2DDNN–Loqs-PD + dsRNA + ATP + Mg2+ (3.9 Å) CR-linker Dcr-2DDNN–Loqs-PD + dsRNA Platform PAZ dsRNA RIIIDa RIIIDb RIIIDai DP-linker Loqs-PD Hel2 DUF283 Hel1 Pincer + ATP + Mg2+ (4.0 Å) Connector f dsRBD Dcr-2DDNN–Loqs-PD + dsRNA Platform PAZ dsRNA RIIIDa RIIIDb RIIIDai DP-linker Loqs-PD Hel2 DUF283 Hel1 Pincer + ATP + Mg2+ (4.0 Å) Connector f dsRBD dsRNA DP-linker Platform PAZ siRNA RIIIDa RIIIDb RIIIDai Loqs-PD Hel2 DUF283 Hel1 Pincer Connector g Dcr-2WT–Loqs-PD + dsRNA + ATP + Mg2+ (4.6 Å) dsRNA DP-linker Platform PAZ siRNA RIIIDa RIIIDb RIIIDai Loqs-PD Hel2 DUF283 Hel1 Pincer Connector g Dcr-2WT–Loqs-PD + dsRNA + ATP + Mg2+ (4.6 Å) Dcr-2DDNN–Loqs-PD + dsRNA Loqs-PD Pincer + ATP + Mg2+ (4.2 Å) dsRNA Hel2 DUF283 Hel1 RIIIDa RIIIDb Connector RIIIDai Platform PAZ e CR-linker dsRBD f g e Loqs-PD Loqs-PD Dcr-2DDNN–Loqs-PD + dsRNA + ATP + Mg2+ (4.0 Å) -2 –Loqs-PD + dsRN + ATP + Mg2+ (4.0 Å) Fig. 1 | Cryo-EM structures of Dcr-2–Loqs-PD in different dsRNA-binding states. a, Schematic of Dcr-2, Loqs-PD and 50 bp dsRNA. Unless specified otherwise, the colour scheme of Dcr-2 and Loqs-PD is used throughout all of the figures. b, Cartoon model of Dcr-2–Loqs-PD in the apo state. The cap, core and base modules are labelled on the right. c, Cartoon model of Dcr-2–Loqs- PD–50 bp dsRNA dimer in the initial dsRNA-binding state (initial state). Molecule A is coloured, molecule B is shown in grey. d,e, Cartoon model of Dcr-2–Loqs-PD–50 bp dsRNA complex in the early-translocation (d) and mid- translocation (e) state. f,g, Cartoon model of Dcr-2–Loqs-PD–50 bp dsRNA complex in the active dicing (f) and post-dicing (g) state. The siRNA in g is coloured in goldenrod. The post-dicing state is shown as a transparent cryo-EM map. The model in c–g is aligned by base region. The components and resolution of each state are labelled below. Fig. 1 | Cryo-EM structures of Dcr-2–Loqs-PD in different dsRNA-binding Fig. https://doi.org/10.1038/s41586-022-04911-x The cap module can specifically recognize 3′-end two-nucleotide overhang and 5′-phosphate through the PAZ domain Nature  |  Vol 607  |  14 July 2022  |  399 399 Article RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer Hel2 DUF283 Hel1 dsRNA RIIIDai Platform Connector RIIIDa CR-linker RIIIDb Hel2 DUF283 DP-linker PAZ Cap Molecule A Molecule B Core Base Loqs-PD Pincer (3.3 Å) Dcr-2DDNN–Loqs-PD (– ATP) Dcr-2DDNN–Loqs-PD + dsRNA Dcr-2DDNN–Loqs-PD + dsRNA 1722 1 C terminus 359 344 10 20 30 40 50 50 40 30 20 10 2 1016 1169 1655 216 348 230 508 554 713 665 856 982 1268 1362 1420 1520 1609 Platform PAZ dsRNA dsRNA RIIIDa RIIIDb RIIIDai DP-linker DP-linker Loqs-PD Loqs-PD Hel2 DUF283 Hel1 Pincer Pincer + ATP + Mg2+ (4.2 Å) + ATP + Mg2+ (4.0 Å) Platform PAZ siRNA RIIIDa RIIIDb RIIIDai Loqs-PD Hel2 DUF283 Hel1 Pincer Hel1 dsRNA Hel2 DUF283 Hel1 RIIIDa RIIIDb Connector Connector Connector RIIIDai Platform PAZ Hel2 DUF283 Hel1 dsRNA RIIIDa RIIIDb DP-linker Connector Loqs-PD RIIIDai Platform PAZ Pincer 5′-P-GAGACUUGGGCAAUGUGACUGCUGAUCAGCAGUCACAUUGCCCAAGUCUCUU-3′ 3′-UUCUCUGAACCCGUUACACUGACGACUAGUCGUCAGUGUAACGGGUUCAGAG-P-5′ Dcr-2 Dcr-2DDNN–Loqs-PD + dsRNA (– ATP) (3.1 Å) Dcr-2DDNN–Loqs-PD + dsRNA + ATP + Mg2+ (3.9 Å) Loqs-PD 50 bp dsRNA Hel1 Hel2i Hel2 Pincer DUF283 Platform Connector RIIIDai RIIIDbi DP-linker PAZ CR-linker RNase IIIa RNase IIIb dsRBD 1 a b c d e f g RIIIDbi dsRBD Hel2i CR-linker CR-linker dsRBD Dcr-2WT–Loqs-PD + dsRNA + ATP + Mg2+ (4.6 Å) dsRBD Fig. 1 | Cryo-EM structures of Dcr-2–Loqs-PD in different dsRNA-binding states. a, Schematic of Dcr-2, Loqs-PD and 50 bp dsRNA. Unless specified otherwise, the colour scheme of Dcr-2 and Loqs-PD is used throughout all of the figures. b, Cartoon model of Dcr-2–Loqs-PD in the apo state. The cap, core and base modules are labelled on the right. c, Cartoon model of Dcr-2–Loqs- PD–50 bp dsRNA dimer in the initial dsRNA-binding state (initial state). Molecule A is coloured, molecule B is shown in grey. d,e, Cartoon model of Dcr-2–Loqs-PD–50 bp dsRNA complex in the early-translocation (d) and mid- translocation (e) state. f,g, Cartoon model of Dcr-2–Loqs-PD–50 bp dsRNA complex in the active dicing (f) and post-dicing (g) state. The siRNA in g is coloured in goldenrod. The post-dicing state is shown as a transparent cryo-EM map. The model in c–g is aligned by base region. The components and resolution of each state are labelled below. Conformational changes after dsRNA binding dsRNA binding to Dcr-2 induces a large conformational change of the helicase and DUF283 domains (Supplementary Videos 1 and 2). The N-terminal helicase domain of Dcr-2 belongs to the superfamily 2 group of helicase proteins, like RIG-I-like receptors (RLRs), and contains four subdomains: Hel1, Hel2i, Hel2 and Pincer18. However, in contrast to RLRs, of which the Pincer subdomain links the helicase domain to the protein’s C-terminal domain, the Pincer subdomain of Dcr-2 links the helicase domain to the DUF283 domain. After binding to a dsRNA substrate, the helicase domain together with the DUF283 domain trans- form from a stretched conformation (Fig. 3a) to a closed one (Fig. 3b), wrapping around the RNA helix (Supplementary Video 2). Notably, the DUF283 domain rotates about 150° around Hel1 and directly contacts the dsRNA (Fig. 3c). Meanwhile, the second α-helix of Pincer rotates together with DUF283, forming the traditional V-shaped structure and clamping Hel1 (Fig. 3b,c). These conformational changes reorient the DUF283 domain between Hel1 and Hel2i and tightly interact with the two subdomains (Extended Data Fig. 6h,i). Overall structures We used single-particle cryo-EM to study the structure and mecha- nism of Drosophila Dcr-2 in the dsRNA-processing cycle. We purified recombinant wild-type (WT) Dcr-2 and its catalytically inactive mutant Dcr-2(D1217N/D1476N) (hereafter Dcr-2(DDNN)), corresponding to Aquifex aeolicus RNaseIII (AaRNaseIII) D44N15, from insect cells, and mixed the Dcr-2 constructs with purified full-length Loqs-PD to form sta- ble WT Dcr-2–Loqs-PD and Dcr-2DDNN–Loqs-PD complexes, respectively 400  |  Nature  |  Vol 607  |  14 July 2022 a b c d F356 F354 Y347 I344 I359 I359 R522 I518 Y519 F356 R369 F354 Y347 D345 I344 Q349 T364 L232 His–Sumo–Loqs-PD F356D Y347A WT I359D Relative amount of Dcr-2 0 0.4 0.2 0.8 0.6 1.2 1.0 ** ** ** DUF283 E1333 RIIIDai Hel1 R9 Y214 Q12 F36 Hel1 R9 Y214 Q12 F36 Mg2+ ADP C N C His-tag pull-down Input Dcr-2: F356D 200 120 70 50 Y347A WT I359D + − − − − + − − − − − − − − + + − − − − − − + + − − − − − − + + + + + + + + + + Dcr-2 His–Sumo– Loqs-PD M222 M372 V503 V221 V223 I293 K340 e h i f g Hel2 Hel1 Pincer Loqs-PD Negative Positive N C Hel2i (kDa) Fig. 2 | The ATP-binding pocket and interactions between helicase domain and C terminus of Loqs-PD. a, Interactions between the ATP-binding site and RIIIDai from molecule B in the initial binding state. b, Details of the ATP-binding site in the early-translocation state. c, Overview of the Loqs-PD binding sites in the helicase domain of Dcr-2. Loqs-PD is shown as a transparent cryo-EM map. d, Surface presentation of the Loqs-PD binding region in the helicase domain. Loqs-PD is shown as a stick model. The surface is coloured by electrostatic potential. e–g, Details of the interactions of Dcr-2 with Ile359 (e), Phe354 and Phe356 (f), and Tyr347 (g) regions of C terminus of Loqs-PD. h, SDS–PAGE gels of the pull-down result for Dcr-2 with the WT and three variants of His-tagged Loqs-PD. Gel source data are provided in Supplementary Fig. 1. i, Quantification of the pull-down data in h. Data are mean ± s.d. n = 3 biologically independent experiments. Statistical analysis was performed using two-sided paired t-tests; **P < 0.01. The exact P values for WT versus Y347A, F356D and I359D are 0.0037, 0.0063 and 0.0091, respectively. Interaction between Loqs-PD and Dcr-2 In the absence of ATP, we found that Dcr-2–Loqs-PD tends to dimerize and forms an initial binding complex with dsRNA (Fig. 1c). The dimeri- zation interface involves the RIIIDai domain of one Dcr-2 and the Hel2 domain of the other Dcr-2, and mutation of residues in the dimerization interface results in dissociation of dimer (Fig. 1c and Extended Data Fig. 5f–k). The dimerization interface also disrupts the ATP-binding site of the helicase domain (Fig. 2a) that otherwise is well maintained to bind to ADP/ATP in the translocation and dicing states (Fig. 2b). The high-resolution (3.1 Å) cryo-EM structure of the initial binding complex is good enough for us to unambiguously identify the density of the C-terminal tail (amino acids 344–359) of Loqs-PD interacting with thehelicase domain of Dcr-2 (Fig. 2c and Extended Data Fig. 6f,g). The other portions of the Loqs-PD protein cannot be distinguished in the cryo-EM maps probably due to its flexible nature. The short Overall structures a b c d F356 F354 Y347 I344 I359 I359 R522 I518 Y519 F356 R369 F354 Y347 D345 I344 Q349 T364 L232 His–Sumo–Loqs-PD F356D Y347A WT I359D Relative amount of Dcr-2 0 0.4 0.2 0.8 0.6 1.2 1.0 ** ** ** DUF283 E1333 RIIIDai Hel1 R9 Y214 Q12 F36 Hel1 R9 Y214 Q12 F36 Mg2+ ADP C N C His-tag pull-down Input Dcr-2: F356D 200 120 70 50 Y347A WT I359D + − − − − + − − − − − − − − + + − − − − − − + + − − − − − − + + + + + + + + + + Dcr-2 His–Sumo– Loqs-PD M222 M372 V503 V221 V223 I293 K340 e h i f g Hel2 Hel1 Pincer Loqs-PD Negative Positive N C Hel2i (kDa) a b c d F356 F354 Y347 I344 I359 R52 I34 Q T3 DUF283 E1333 RIIIDai Hel1 R9 Y214 Q12 F36 Hel1 R9 Y214 Q12 F36 Mg2+ ADP C N V V2 e f g Hel2 Hel1 Pincer Loqs-PD Negative Positive N C Hel2i I359 R522 I518 Y519 F356 R369 F354 Y347 D345 I344 Q349 T364 L232 C M222 M372 V503 V221 V223 I293 K340 e h i f g a b c d F356 F354 I359 DUF283 E1333 RIIIDai Hel1 R9 Y214 Q12 F36 Hel1 R9 Y214 Q12 F36 Mg2+ ADP C Hel2 Hel1 Pincer Loqs Negative C h e a i b d g Positive Negative His–Sumo–Loqs-PD F Y His–Sumo–Loqs-PD Fig. 2 | The ATP-binding pocket and interactions between helicase domain ding pocket and interactions between helicase domain Phe356 (f), and Tyr347 (g) regions of C terminus of Loqs-PD. h, SDS–PAGE gels of the pull-down result for Dcr-2 with the WT and three variants of His-tagged Loqs-PD. Gel source data are provided in Supplementary Fig. 1. i, Quantification of the pull-down data in h. Data are mean ± s.d. n = 3 biologically independent experiments. Statistical analysis was performed using two-sided paired t-tests; **P < 0.01. The exact P values for WT versus Y347A, F356D and I359D are 0.0037, 0.0063 and 0.0091, respectively. Fig. 2 | The ATP-binding pocket and interactions between helicase domain and C terminus of Loqs-PD. a, Interactions between the ATP-binding site and RIIIDai from molecule B in the initial binding state. b, Details of the ATP-binding site in the early-translocation state. Overall structures c, Overview of the Loqs-PD binding sites in the helicase domain of Dcr-2. Loqs-PD is shown as a transparent cryo-EM map. d, Surface presentation of the Loqs-PD binding region in the helicase domain. Loqs-PD is shown as a stick model. The surface is coloured by electrostatic potential. e–g, Details of the interactions of Dcr-2 with Ile359 (e), Phe354 and and C terminus of Loqs-PD. a, Interactions between the ATP-binding site and RIIIDai from molecule B in the initial binding state. b, Details of the ATP-binding site in the early-translocation state. c, Overview of the Loqs-PD binding sites in the helicase domain of Dcr-2. Loqs-PD is shown as a transparent cryo-EM map. d, Surface presentation of the Loqs-PD binding region in the helicase domain. Loqs-PD is shown as a stick model. The surface is coloured by electrostatic potential. e–g, Details of the interactions of Dcr-2 with Ile359 (e), Phe354 and C-terminal tail extends and wraps over the surface of the Hel2i, Hel2 and Pincer domains (Fig. 2c,d), mainly through hydrophobic interac- tions and hydrogen bonds (Fig. 2e–g). The C-terminal end residue of Loqs-PD, Ile359, is accommodated by the hydrophobic pocket com- prised by Met222 from Hel2, Ile518 and Tyr519 from Pincer. Further- more, the C-terminal carboxyl group of Ile359 of Loqs-PD forms a salt bridge interaction with the side chain of Arg522 from Pincer (Fig. 2e). Two hydrophobic residues identified previously17, Phe354 and Phe356 of Loqs-PD, bind to the hydrophobic patch on the Hel2 domain, whereas the aromatic ring of Phe356 stacks with the side chain of Arg369 (Fig. 2f). Tyr347 of Loqs-PD inserts into a hydrophobic cage comprising Leu232, Ile293 and Thr364 right at the interface of the Hel2 and Hel2i domains (Fig. 2g). Mutations to any of the three hydrophobic residues (Y347A, F356D, I359D) of Loqs-PD notably reduced its interaction with Dcr-2 as shown in the pull-down assay (Fig. 2h,i), indicating their essential roles in Dcr-2–Loqs-PD interactions. dicing state in the presence of ATP; and Dcr-2WT–Loqs-PD complex in its post-dicing state (Fig. 1b–g and Extended Data Figs. 2 and 3). C-terminal tail extends and wraps over the surface of the Hel2i, Hel2 and Pincer domains (Fig. 2c,d), mainly through hydrophobic interac- tions and hydrogen bonds (Fig. 2e–g). The C-terminal end residue of Loqs-PD, Ile359, is accommodated by the hydrophobic pocket com- prised by Met222 from Hel2, Ile518 and Tyr519 from Pincer. Overall structures Further- more, the C-terminal carboxyl group of Ile359 of Loqs-PD forms a salt bridge interaction with the side chain of Arg522 from Pincer (Fig. 2e). Two hydrophobic residues identified previously17, Phe354 and Phe356 of Loqs-PD, bind to the hydrophobic patch on the Hel2 domain, whereas the aromatic ring of Phe356 stacks with the side chain of Arg369 (Fig. 2f). Tyr347 of Loqs-PD inserts into a hydrophobic cage comprising Leu232, Ile293 and Thr364 right at the interface of the Hel2 and Hel2i domains (Fig. 2g). Mutations to any of the three hydrophobic residues (Y347A, F356D, I359D) of Loqs-PD notably reduced its interaction with Dcr-2 as shown in the pull-down assay (Fig. 2h,i), indicating their essential roles in Dcr-2–Loqs-PD interactions. The cryo-EM structure of Dcr-2–Loqs-PD in the apo state at a resolution of 3.3 Å shows that Dcr-2 has the same L-shaped domain organization as human Dicer9, but with more structural elements solved (Fig. 1b). Similar to human Dicer, the N-terminal helicase region forms the base of the L-shaped structure and the DUF283 domain is located at the corner of the L and just below the catalytic active core. The previously unmodelled linker between the DUF283 and Platform domains (DP-linker) in human Dicer is now well resolved in Dcr-2 as a structural element that interacts with the RNase IIIa domain through two α-helices and one β-strand. The Platform and PAZ domains surrounding the Connector helix sit at the top of the core processing region. The intrinsic RNase III dimer comprising the RIIIDa and RIIIDb domains is located in the centre of the molecule with the insertion domains (RIIIDai and RIIIDbi) sitting in symmetric positions (Extended Data Figs. 4 and 5a–e). The C-terminal dsRBD interacts with the DP-linker and shields the RNase-activity centre (Extended Data Fig. 5e). Compared with the apo state, the overall structures of Dcr-2–Loqs-PD complex undergo major conformational changes when interacting with the dsRNA substrate, especially on the helicase and DUF283 domains (Extended Data Fig. 6a–e). By contrast, the structures in the active dic- ing and post-dicing states demonstrate further conformational changes in the PAZ–Platform module. These structures and their mechanistic insights are discussed in more detail in the sections below. Overall structures 344 I359 R522 I518 Y519 F356 R369 F354 Y347 D345 I344 Q349 T364 L232 His–Sumo–Loqs-PD F356D Y347A WT I359D Relative amount of Dcr-2 0 0.4 0.2 0.8 0.6 1.2 1.0 ** ** ** N C His-tag pull-down Input Dcr-2: F356D 200 120 70 50 Y347A WT I359D + − − − − + − − − − − − − − + + − − − − − − + + − − − − − − + + + + + + + + + + Dcr-2 His–Sumo– Loqs-PD M222 M372 V503 V221 V223 I293 K340 e h i f g ositive N Hel2i (kDa) Phe356 (f), and Tyr347 (g) regions of C terminus of Loqs-PD. h, SDS–PAGE gels of the pull-down result for Dcr-2 with the WT and three variants of His-tagged Loqs-PD. Gel source data are provided in Supplementary Fig. 1. i, Quantification of the pull-down data in h. Data are mean ± s.d. n = 3 biologically independent experiments. Statistical analysis was performed using two-sided paired t-tests; **P < 0.01. The exact P values for WT versus Y347A, F356D and I359D are 0.0037, 0.0063 and 0.0091, respectively. Article Distinctly, a loop specific for the Dicer Hel2i subdomain forms intimate contacts with the dsRNA substrate, which corresponds to the second helix in Hel2i of RLRs, extending into the major groove of dsRNA duplex (Fig. 3d and Extended Data Fig. 7d,f). Residues in this loop extensively interact with the backbone phosphates of the major groove that is widened subsequently (Fig. 3d), resulting in the dsRNA duplex bending around 10° towards the DUF283 domain (Fig. 3e). Moreover, the phosphate group of the 5′ strand terminus of the dsRNA is specifically recognized by Hel2i through a salt-bridge interaction between 5′-phosphate and Lys310 of Hel2i (Fig. 3d,g). The electrostatic potential surface suggests that there is a basic and con- served pocket around the 5′-phosphate of dsRNA in the Hel2i domain (Fig. 3h,i). Furthermore, the DUF283 domain recognizes the minor and major groove of the dsRNA terminal duplex through Gln580 from region 1 and Asn635/Lys642 from region 3 of the dsRBD fold, respec- tively (Fig. 3f). In summary, the conformational changes of the helicase Article Hel2 Hel2i dsRNA Bent by helicase Hel1 DUF283 ~10˚ ~8 bp ~17 bp DP-linker RIIIDa 3′-end-binding region in PAZ RIIIDb a d e g f b c ~25˚ dsRNA dsRBD Bent by helicase and dsRBD RIIIDb RIIIDbi Hel2i DUF283 Hel1 RIIIDa L1532 S1467 Q1469 N623 F587 T584 R1463 I675 Y1232 V1243 W1235 V672 E670 T667 R662 N660 E658 K666 R671 DP-linker ~29 bp RIIIDa RIIIDb DUF283 DUF283 Hel1 Hel2 Hel2i Pincer c f DUF283 Q580 K642 N635 3′ strand 5′ strand Hel2 Hel2i dsRNA Bent by helicase Hel1 DUF283 ~10˚ ~8 bp a b ~17 bp RIIIDa RIIIDb b a DP-linker 3′-end-binding region in PAZ c ~25˚ dsRNA dsRBD Bent by helicase and dsRBD c b a c f d f DUF283 Q580 K642 N635 3′ strand 5′ strand Bent by helicase d e f RIIIDb RIIIDbi Hel2i DUF283 Hel1 RIIIDa DP-linker g ~29 bp RIIIDa RIIIDb g f Q1469 N623 F587 T584 R1463 I675 Y1232 V1243 W1235 V672 E670 T667 R662 N660 E658 K666 R671 f i K273 K310 Variable Conserved 3′ strand 5′ strand i K273 K310 Variable Conserved 3′ strand 5′ strand i h 5′-P binding site Negative Positive 3′ strand 5′ strand g h Hel2i G1 Q313 K310 K273 5′-P i h g Fig. 4 | The relative rigid structures of the Dcr-2–Loqs-PD complex and further dsRNA bending in the translocation states. a, Distortion of dsRNA in the early-translocation state. The dsRNA is presented in surface mode. Dcr- 2–Loqs-PD is presented in cartoon mode. The translocation length of dsRNA (~8 bp) compared with the initial binding state is labelled. Domains interacting with dsRNA are opaque with a black outline. The axis of ideal A-form dsRNA extended from outside the helicase domain is shown by the black line. The helical axis of the helicase domain-bound dsRNA is shown by the red arrow. b, Overview of the mid-translocation state. The translocation length of dsRNA (~17 bp) is labelled in b as in a. The transparent cryo-EM map is shown in c. c, Distortion of dsRNA in the mid-translocation state is shown in the same mode as in a. The 3′-end binding region of PAZ in the mid-translocation state is labelled by the transparent orange circle. The axis of ideal A-form dsRNA extended from outside the helicase domain is shown by the black line. The helical axis of C-terminal dsRBD domain-bound dsRNA is shown by the red arrow. Article DUF283 is presented as transparent surface. The structures in a and b are aligned by the Hel1 domain. c, Superimposition of the helicase domain aligned by the Hel1 domain in the apo and initial binding states. The apo state is coloured with a similar but lighter colour compared with the initial binding state. The movement of DUF283 is labelled by the black arrow. d, The close-up view of the Hel2i–dsRNA interface. The special loop is coloured in dodger blue. The 5′ and 3′ strands of dsRNA are shown in lime green and light grey, helicase–DUF283 module and the dsRNA with precision and unambigu- ity at the residue level (Extended Data Fig. 7a). The dsRNA-recognition mode of the Hel1 and Hel2 subdomains is conserved with the RLR (Extended Data Fig. 7). Distinctly, a loop specific for the Dicer Hel2i subdomain forms intimate contacts with the dsRNA substrate, which corresponds to the second helix in Hel2i of RLRs, extending into the major groove of dsRNA duplex (Fig. 3d and Extended Data Fig. 7d,f). Residues in this loop extensively interact with the backbone phosphates of the major groove that is widened subsequently (Fig. 3d), resulting in the dsRNA duplex bending around 10° towards the DUF283 domain (Fig. 3e). Moreover, the phosphate group of the 5′ strand terminus of the dsRNA is specifically recognized by Hel2i through a salt-bridge interaction between 5′-phosphate and Lys310 of Hel2i (Fig. 3d,g). The electrostatic potential surface suggests that there is a basic and con- served pocket around the 5′-phosphate of dsRNA in the Hel2i domain (Fig. 3h,i). Furthermore, the DUF283 domain recognizes the minor and major groove of the dsRNA terminal duplex through Gln580 from region 1 and Asn635/Lys642 from region 3 of the dsRBD fold, respec- tively (Fig. 3f). In summary, the conformational changes of the helicase and DUF283 domains induced by dsRNA binding are coupled to the simultaneous recognitions of the major and minor groove of the dsRNA terminal duplex and the 5′-phosphate by Hel2i and DUF283, determin- ing the initial binding of dsRNAs to the specific terminal duplex feature. helicase–DUF283 module and the dsRNA with precision and unambigu- ity at the residue level (Extended Data Fig. 7a). The dsRNA-recognition mode of the Hel1 and Hel2 subdomains is conserved with the RLR (Extended Data Fig. 7). Article Hel2 Hel2i dsRNA Bent by helicase Hel1 DUF283 ~10˚ ~8 bp ~17 bp DP-linker RIIIDa 3′-end-binding region in PAZ RIIIDb a d e g f b c ~25˚ dsRNA dsRBD Bent by helicase and dsRBD RIIIDb RIIIDbi Hel2i DUF283 Hel1 RIIIDa L1532 S1467 Q1469 N623 F587 T584 R1463 I675 Y1232 V1243 W1235 V672 E670 T667 R662 N660 E658 K666 R671 DP-linker ~29 bp RIIIDa RIIIDb Fig. 4 | The relative rigid structures of the Dcr-2–Loqs-PD complex and further dsRNA bending in the translocation states. a, Distortion of dsRNA in the early-translocation state. The dsRNA is presented in surface mode. Dcr- 2–Loqs-PD is presented in cartoon mode. The translocation length of dsRNA (~8 bp) compared with the initial binding state is labelled. Domains interacting with dsRNA are opaque with a black outline. The axis of ideal A-form dsRNA extended from outside the helicase domain is shown by the black line. The helical axis of the helicase domain-bound dsRNA is shown by the red arrow. b, Overview of the mid-translocation state. The translocation length of dsRNA (~17 bp) is labelled in b as in a. The transparent cryo-EM map is shown in c. c, Distortion of dsRNA in the mid-translocation state is shown in the same mode as in a. The 3′-end binding region of PAZ in the mid-translocation state is labelled by the transparent orange circle. The axis of ideal A-form dsRNA extended from outside the helicase domain is shown by the black line. The helical axis of C-terminal dsRBD domain-bound dsRNA is shown by the red arrow. d, Overview of the interdomain contacts between DUF283 and the core region in the initial binding state. e, Magnified view of the interdomain contacts between the DUF283 and RIIIDb–RIIIDbi domains, corresponding to the orange-red box in d. f, Magnified view of the interdomain contacts between DUF283 with RIIIDa through the DP-linker, corresponding to the dark-blue box in d. g, Overview of the pre-dicing model. Model of the pre-dicing state based on the mid-translocation state with further RNA translocation. The translocation length of dsRNA (~29 bp) is labelled as in a. Recognition of dsRNA by helicase–DUF283 The near-atomic high resolution (3.1 Å) structure of the initial binding state enabled us to examine the interactions between the Nature  |  Vol 607  |  14 July 2022  |  401 401 Article d, Overview of the interdomain contacts between DUF283 and the core region in the initial binding state. e, Magnified view of the interdomain contacts between the DUF283 and RIIIDb–RIIIDbi domains, corresponding to the orange-red box in d. f, Magnified view of the interdomain contacts between DUF283 with RIIIDa through the DP-linker, corresponding to the dark-blue box in d. g, Overview of the pre-dicing model. Model of the pre-dicing state based on the mid-translocation state with further RNA translocation. The translocation length of dsRNA (~29 bp) is labelled as in a. Positive Variable Conserved Fig. 3 | Substantial conformational changes of the helicase and DUF283 domains induced by dsRNA binding and specific dsRNA recognitions. a,b, Overview of the helicase domain in the apo state (a) and the initial binding state (b). DUF283 is presented as transparent surface. The structures in a and b are aligned by the Hel1 domain. c, Superimposition of the helicase domain aligned by the Hel1 domain in the apo and initial binding states. The apo state is coloured with a similar but lighter colour compared with the initial binding state. The movement of DUF283 is labelled by the black arrow. d, The close-up view of the Hel2i–dsRNA interface. The special loop is coloured in dodger blue. The 5′ and 3′ strands of dsRNA are shown in lime green and light grey, respectively. e, Overview of DUF283 and Hel2i interacting with dsRNA in the initial binding state. The special loop of Hel2i (257–271) is coloured in blue. dsRNA is shown as surface. The axis direction of dsRNA termini bound by the helicase domain is shown by the red arrow, and the black line represents the axis of the free dsRNA. The bending angle is labelled at the top. f, Magnified view of the DUF283–dsRNA interface. dsRNA is coloured as in e. g, Details of dsRNA terminal recognition of Hel2i domain. h,i, The surface presentation of the helicase domain around the terminal binding region. The surface of the helicase domain is coloured by electrostatic potential (h) and sequence conservation (i). The 5′-phophate-binding site is marked by an orange dotted circle. The two residues involved in 5′-phosphate recognition are labelled in i. Fig. 3 | Substantial conformational changes of the helicase and DUF283 domains induced by dsRNA binding and specific dsRNA recognitions. a,b, Overview of the helicase domain in the apo state (a) and the initial binding state (b). 402  |  Nature  |  Vol 607  |  14 July 2022 Structural states during translocation e, Magnified view of the spring helix α1 of the superimposed structures in the mid-translocation state (grey) and the active dicing state (coloured) aligned by RIIIDs, corresponding to the orange-red box in d. The first half of α1 is coloured in red for the mid-translocation state and orange for the active dicing state, respectively. f, Cross-section of the processing centre of the superimposed mid-translocation state (grey) and active dicing state (coloured) aligned by RIIIDs. g, Overview of the post-dicing state. The display mode is the same as in a and c. The break in the dsRNA is labelled by the red arrow. h, Superposition of the structures in the active dicing and post-dicing state shown as a transparent cryo-EM map. The conformational change from the active dicing state to the post-dicing state is labelled by the black arrow. i, The distance between Gln580 of DUF283 and both RIIIDs (Glu1213 and Glu1472) in the post-dicing state as in d. The spring helix α1 is marked by orange-red arrow. Dcr-2–Loqs-PD complex in the early-translocation state has almost no conformational changes and no additional interactions with dsRNA, except that the cap and core modules shift about 3 Å away from the dsRNA (Extended Data Fig. 8a,b and Supplementary Video 1). The tra- jectory of dsRNA in the early-translocation state is same as in the initial binding state (Fig. 4a and Extended Data Fig. 8c). We captured another structure in the mid-translocation state, in which about 17 bp of a dsRNA duplex threads through the helicase domain further towards the cata- lytic centre of Dcr-2 (Fig. 4b). When superimposed onto structures of the initial binding and early translocation states, the cap–core modules sway back about 2 Å towards the dsRNA (Extended Data Fig. 8a,b and Supplementary Video 1). Importantly, in the mid-translocation state, the C-terminal dsRBD of Dcr-2 appears in the map and interacts with the dsRNA substrate (Extended Data Fig. 8d), resulting in further bending of the axis of the dsRNA about 25°, and the trajectory of the dsRNA is directly towards the PAZ domain (Fig. 4c and Supplementary Video 1). Removal of the C-terminal dsRBD of Dcr-2 completely abolished the cleavage ability of the enzyme on the dsRNA substrate and cryo-EM analysis revealed no further bending of the dsRNA during the translo- cation by the helicase domain (Extended Data Fig. Structural states during translocation Recent single-molecule analysis demonstrated that Dcr-2 translocates along the dsRNA after its helicase initially binds to the dsRNA termi- nus in the presence of ATP19. To capture the different steps during the translocation of Dcr-2–Loqs-PD along the dsRNA, we used cryo-EM to analyse the sample of Dcr-2DDNN–Loqs-PD in complex with the dsRNA substrate under conditions with ATP and Mg2+. Through single-particle classification, we captured two representative cryo-EM structures of Dcr-2–Loqs-PD in complex with the dsRNA substrate in transloca- tion states (Fig. 1d,e and Extended Data Fig. 3). In the first captured structure, termed the early-translocation state, about 8 bp of duplex threads through the helicase domain towards the catalytic centre of Dcr-2 (Fig. 1d). In comparison to the initial binding state (Fig. 1c), the 402  |  Nature  |  Vol 607  |  14 July 2022 402 RIIIDb RIIIDa 50.4 Å 31.1 Å DP-linker DUF283 Axis of ideal dsRNA Axis of dsRNA in active dicing state dsRBD and RIIIDa/b induced Helicase induced Active dicing state dsRBD b RIIIDb RIIIDa 50.4 Å 31.1 Å DP-linker DUF283 RIIIDb RIIIDa DUF283 DP-linker 40.1 Å 22.0 Å RIIIDai Platform DP-linker PAZ PAZ Axis of ideal dsRNA Axis of dsRNA in active dicing state 4 bp dsRNA dsRBD and RIIIDa/b induced Helicase induced Pre-dicing state Active dicing state RIIIDb dsRBD dsRBD dsRBD RIIIDbi dsRNA siRNA DP-linker RIIIDb RIIIDa Connector Spring helix Pre-dicing Active dicing RIIIDai Platform ~10 Å ~40º DP-linker dsRNA DP-linker PAZ DP-linker RIIIDb RIIIDa 43.5 Å 24.7 Å DP-linker DUF283 Spring helix RIIIDa RIIIDai Platform DP-linker PAZ RIIIDb dsRNA siRNA RIIIDai Platform Dicing site a d g h i e f b c RIIIDb dsRBD Pre-dicing Active dicing RIIIDbi Post-dicing Active dicing Fig. 5 | The conformational changes associated with transitions from the pre-dicing to active dicing and to post-dicing states. a, Overview of the Dcr- 2–Loqs-PD–50 bp dsRNA complex in the active dicing state. Dcr-2 (672–1722) is shown in surface mode. The siRNA region is coloured in gold. b, The distortion of dsRNA in the active dicing state. The axes of free dsRNA and active dicing dsRNA are coloured in yellow and hot pink, respectively. The torsion position induced by Dcr-2 is labelled. c, Overview of the pre-dicing model. The display mode is the same as in a. The conformational change from the pre-dicing state (c) to the active dicing state (a) is marked by purple, green and grey arrows in c. Structural states during translocation The conformational change from the pre-dicing state (c) to the active dicing state (a) is marked by purple, green and grey arrows in c. d, The distance between Cα atoms of Q580 from DUF283 and both RIIIDs (E1213 and E1472) in the pre-dicing (mid-translocation) and active dicing states. Cα atoms are labelled as spheres. RIIIDs are shown as transparent surface. The conformational change of DP-linker is marked by the orange-red box. e, Magnif mid-trans RIIIDs, co in red for t respectiv mid-trans RIIIDs. g, O a and c. Th the struct cryo-EM m post-dicin of DUF283 The spring RIIIDb RIIIDa DUF283 DP-linker 40.1 Å 22.0 Å RIIIDai Platform DP-linker PAZ Pre-dicing state RIIIDb dsRBD RIIIDbi dsRNA siRNA a d RIIIDa 50.4 Å DP-linker DUF283 PAZ A Axis of dsRNA in active dicing state 4 bp dsRNA dsRBD and RIIIDa/b induced se ed dicing state dsRBD DP-linker RIIIDb RIIIDa Connector Spring helix Pre-dicing Active dicing RIIIDai Platform ~10 Å ~40º DP-linker dsRNA DP-linker PAZ DP-linker RIIIDb RIIIDa 43.5 Å 24.7 Å DP-linker DUF283 Spring helix RIIIDai Platform i e f c RIIIDb dsRBD Pre-dicing Active dicing Post-dicing cing 3 e, Magnified view of the spring helix α1 of the superimposed structures in the mid-translocation state (grey) and the active dicing state (coloured) aligned by RIIIDs, corresponding to the orange-red box in d. The first half of α1 is coloured in red for the mid-translocation state and orange for the active dicing state, respectively. f, Cross-section of the processing centre of the superimposed mid-translocation state (grey) and active dicing state (coloured) aligned by RIIIDs. g, Overview of the post-dicing state. The display mode is the same as in a and c. The break in the dsRNA is labelled by the red arrow. h, Superposition of the structures in the active dicing and post-dicing state shown as a transparent cryo-EM map. The conformational change from the active dicing state to the post-dicing state is labelled by the black arrow. i, The distance between Gln580 of DUF283 and both RIIIDs (Glu1213 and Glu1472) in the post-dicing state as in d. The spring helix α1 is marked by orange-red arrow. Structural states during translocation d, The distance between Cα atoms of Q580 from DUF283 and both RIIIDs (E1213 and E1472) in the pre-dicing (mid-translocation) and active dicing states. Cα atoms are labelled as spheres. RIIIDs are shown as transparent surface. The conformational change of DP-linker is marked by the orange-red box. e, Magnified view of the spring helix α1 of the superimposed structures in the mid-translocation state (grey) and the active dicing state (coloured) aligned by RIIIDs, corresponding to the orange-red box in d. The first half of α1 is coloured in red for the mid-translocation state and orange for the active dicing state, respectively. f, Cross-section of the processing centre of the superimposed mid-translocation state (grey) and active dicing state (coloured) aligned by RIIIDs. g, Overview of the post-dicing state. The display mode is the same as in a and c. The break in the dsRNA is labelled by the red arrow. h, Superposition of the structures in the active dicing and post-dicing state shown as a transparent cryo-EM map. The conformational change from the active dicing state to the post-dicing state is labelled by the black arrow. i, The distance between Gln580 of DUF283 and both RIIIDs (Glu1213 and Glu1472) in the post-dicing state as in d. The spring helix α1 is marked by orange-red arrow. RIIIDb RIIIDa 50.4 Å 31.1 Å DP-linker DUF283 RIIIDb RIIIDa DUF283 DP-linker 40.1 Å 22.0 Å RIIIDai Platform DP-linker PAZ Axis of ideal dsRNA Axis of dsRNA active dicin state dsRBD a RIIIDa/b induced Helicase induced Pre-dicing state Active dicing state RIIIDb dsRBD dsRBD RIIIDbi dsRNA siRNA PAZ DP-linker RIIIDa RIIIDai Platform DP-linker PAZ RIIIDb dsRNA siRNA RIIIDai Platfor Dicing site a d g h b RIIIDbi Post-dicing Active dicing Fig. 5 | The conformational changes associated with transitions from the pre-dicing to active dicing and to post-dicing states. a, Overview of the Dcr- 2–Loqs-PD–50 bp dsRNA complex in the active dicing state. Dcr-2 (672–1722) is shown in surface mode. The siRNA region is coloured in gold. b, The distortion of dsRNA in the active dicing state. The axes of free dsRNA and active dicing dsRNA are coloured in yellow and hot pink, respectively. The torsion position induced by Dcr-2 is labelled. c, Overview of the pre-dicing model. The display mode is the same as in a. Structural states during translocation h, Superposition of the structures in the active dicing and post-dicing state shown as a transparent cryo-EM map. The conformational change from the active dicing state to the post-dicing state is labelled by the black arrow. i, The distance between Gln580 of DUF283 and both RIIIDs (Glu1213 and Glu1472) in the post-dicing state as in d. The spring helix α1 is marked by orange-red arrow. Fig. 5 | The conformational changes associated with transitions from the pre-dicing to active dicing and to post-dicing states. a, Overview of the Dcr- 2–Loqs-PD–50 bp dsRNA complex in the active dicing state. Dcr-2 (672–1722) is shown in surface mode. The siRNA region is coloured in gold. b, The distortion of dsRNA in the active dicing state. The axes of free dsRNA and active dicing dsRNA are coloured in yellow and hot pink, respectively. The torsion position induced by Dcr-2 is labelled. c, Overview of the pre-dicing model. The display mode is the same as in a. The conformational change from the pre-dicing state (c) to the active dicing state (a) is marked by purple, green and grey arrows in c. d, The distance between Cα atoms of Q580 from DUF283 and both RIIIDs (E1213 and E1472) in the pre-dicing (mid-translocation) and active dicing states. Cα atoms are labelled as spheres. RIIIDs are shown as transparent surface. The conformational change of DP-linker is marked by the orange-red box. e, Magnified view of the spring helix α1 of the superimposed structures in the mid-translocation state (grey) and the active dicing state (coloured) aligned by RIIIDs, corresponding to the orange-red box in d. The first half of α1 is coloured in red for the mid-translocation state and orange for the active dicing state, respectively. f, Cross-section of the processing centre of the superimposed mid-translocation state (grey) and active dicing state (coloured) aligned by RIIIDs. g, Overview of the post-dicing state. The display mode is the same as in a and c. The break in the dsRNA is labelled by the red arrow. h, Superposition of the structures in the active dicing and post-dicing state shown as a transparent cryo-EM map. The conformational change from the active dicing state to the post-dicing state is labelled by the black arrow. i, The distance between Gln580 of DUF283 and both RIIIDs (Glu1213 and Glu1472) in the post-dicing state as in d. The spring helix α1 is marked by orange-red arrow. Structural states during translocation PAZ in 4 bp dsRNA d dsRBD DP-linker RIIIDb RIIIDa Connector Spring helix Pre-dicing Active dicing RIIIDai Platform ~10 Å ~40º DP-linker dsRNA DP-linker RIIIDb RIIIDa 43.5 Å 24.7 Å DP-linker DUF283 Spring helix m i e f c RIIIDb dsRBD Pre-dicing Active dicing RIIIDai Platform DP-linker PAZ RIIIDb dsRBD RIIIDbi dsRNA siRNA a d b a c Axis of ideal dsRNA b RIIIDb RIIIDa DUF283 DP-linker 40.1 Å 22.0 Å Pre-dicing state d d Pre-dicing state Active dicing state PAZ DP-linker RIIIDai Platform h Post-dicing Active dicing RIIIDb RIIIDa 43.5 Å 24.7 Å DP-linker DUF283 Spring helix i RIIIDa RIIIDai Platform DP-linker PAZ RIIIDb dsRNA siRNA Dicing site g RIIIDbi i h g Post-dicing Active dicing Fig. 5 | The conformational changes associated with transitions from the pre-dicing to active dicing and to post-dicing states. a, Overview of the Dcr- 2–Loqs-PD–50 bp dsRNA complex in the active dicing state. Dcr-2 (672–1722) is shown in surface mode. The siRNA region is coloured in gold. b, The distortion of dsRNA in the active dicing state. The axes of free dsRNA and active dicing dsRNA are coloured in yellow and hot pink, respectively. The torsion position induced by Dcr-2 is labelled. c, Overview of the pre-dicing model. The display mode is the same as in a. The conformational change from the pre-dicing state (c) to the active dicing state (a) is marked by purple, green and grey arrows in c. d, The distance between Cα atoms of Q580 from DUF283 and both RIIIDs (E1213 and E1472) in the pre-dicing (mid-translocation) and active dicing states. Cα atoms are labelled as spheres. RIIIDs are shown as transparent surface. The conformational change of DP-linker is marked by the orange-red box. e, Magnified view of the spring helix α1 of the superimposed structures in the mid-translocation state (grey) and the active dicing state (coloured) aligned by RIIIDs, corresponding to the orange-red box in d. The first half of α1 is coloured in red for the mid-translocation state and orange for the active dicing state, respectively. f, Cross-section of the processing centre of the superimposed mid-translocation state (grey) and active dicing state (coloured) aligned by RIIIDs. g, Overview of the post-dicing state. The display mode is the same as in a and c. The break in the dsRNA is labelled by the red arrow. Structural states during translocation Domains shown no dicing activity, the complex halts in a stable state, of which the struc- ture was captured at a resolution (4 Å)—higher than the resolution of the structure in the mid-translocation state (4.2 Å). The C-terminal dsRBD in the active dicing state is also better defined for its interac- tions with the minor and major grooves of dsRNA mainly by residues of Arg1658, Lys1706 and Lys1702 (Extended Data Fig. 8k,l). The axis of dsRNA bound by the Dcr-2–Loqs-PD complex in the active dicing state is obviously distorted due to the interactions of dsRBD and RIIIDa/b (Fig. 5b). Moreover, compared with the structure in the pre-dicing state, the dsRNA in the active dicing state further threads about 4 bp through the helicase domain (Fig. 5a,c), resulting in the cap and core modules transforming about 10 Å away from the bottom module and rotating 40° (Fig. 5a,c and Supplementary Video 1). The keys for the conformational changes are the disruption of interactions between the DUF283 and RIIIDb domains (Fig. 5d), and the stretch of DP-linker in which a helix unwound about one turn (Fig. 5e and Supplementary Video 1), eliminating the misalignment between the bottom and cap– core modules of Dcr-2 and allowing the dsRNA duplex to shift about 10 Å (Fig. 5f) and position exactly in the catalytic active centre of the RIIID domains (Extended Data Fig. 8j). These conformational changes suggest that the ATP hydrolysis by the helicase domain is converted into a tension accumulated during the translocation of Dcr-2 on dsRNA, driv- ing the transformation of the pre-dicing state to the active dicing state. However, the translocation of the dsRNA’s terminus threading through the helicase domain towards the RNase active centre of Dcr-2 is clearly ATP driven, as none of the translocation intermediate states were observed in the sample without ATP (only the apo state or initial bind- ing state were observed). It is expected that a deeper translocated state has no further conformational changes until the dsRNA terminus is bound by the Platform–PAZ domains. Thus, on the basis of the struc- ture of mid-translocation state, we modelled the structure of a fully translocated state by threading a further 12 bp dsRNA through the helicase domain compared with the mid-translocation state (Fig. Structural states during translocation However, the translocation of the dsRNA’s terminus threading through the helicase domain towards the RNase active centre of Dcr-2 is clearly ATP driven, as none of the translocation intermediate states were observed in the sample without ATP (only the apo state or initial bind- ing state were observed). It is expected that a deeper translocated state has no further conformational changes until the dsRNA terminus is bound by the Platform–PAZ domains. Thus, on the basis of the struc- ture of mid-translocation state, we modelled the structure of a fully translocated state by threading a further 12 bp dsRNA through the helicase domain compared with the mid-translocation state (Fig. 4g and Supplementary Video 1), which is similar to the recently reported structures of Arabidopsis thaliana DCL-1 (AtDCL-1) in complex with a primary miRNA substrate13 (Extended Data Fig. 8g). However, when superimposing the modelled structure of the fully translocated state onto the active dicing structure of AtDCL3 in complex with a dsRNA substrate (Protein Data Bank (PDB): 7VG2) by the RIIIDa/b domains14, the interaction between the DUF283 and RIIIDb domains (Fig. 4d,e) has steric clashes with the dsRNA bound to the RNase active centre of RIIIDa/b of AtDCL3 in the active dicing state (Extended Data Fig. 8h), suggesting that this interaction would prevent the dsRNA substrate from accessing the RNase active centre of the RIIIDa/b domains dur- ing the translocation of Dcr-2 along dsRNA. This modelled structure is designated the pre-dicing state (Fig. 4g). Structural states during translocation Nature  |  Vol 607  |  14 July 2022 403 Article Platform PAZ PAZ PAZ Hel1 Hel2i Hel2i Hel2i RIIIDb dsRBD ds RIIIDa Pincer Initial dsRNA-binding state Apo state of Dcr-2–Loqs-PD Early-translocatio dsRNA loading Loqs-PD dsRBD2 dsRB d D1 dsRBD1 Connector DP-linker DUF283 DUF283 Pincer P Translocation Translocation siRNA DP-linker ATP + Mg2+ ATP + Hel2 Hel2 Hel1 Hel2 Hel1 Fig. 6 | The model of the Dcr-2–Loqs-PD complex in the dsRNA-processing cycle. The stars represent the mature ATP-binding site, with red and hollow representing whether or not ATP or ADP is bound. The sky-blue region in the Platform–PAZ domains is the dsRNA terminal recognition site. Domains shown Platform Platform Platform Platform Platform PAZ PAZ PAZ PAZ PAZ PAZ Hel1 Hel2i Hel2i Hel2i RIIIDb dsRBD dsRBD dsRBD RIIIDa Pincer Initial dsRNA-binding state Apo state of Dcr-2–Loqs-PD Mid-translocation state Pre-dicing state Post-dicing state Early-translocation state dsRNA loading Dcr-2–R2D2 Activation Active dicing state Loqs-PD dsRBD2 dsRB d D1 dsRBD1 Connector DP-linker DUF283 DUF283 DUF283 DUF283 DUF283 RIIIDa RIIIDa DP-linker DP-linker Pincer Pincer Translocation Translocation Translocation Dicing siRNA releasing and loading into Ago2 siRNA RIIIDa DP-linker DP-linker DP-linker DP-linker RIIIDa RIIIDa ATP + Mg2+ ATP + Mg2+ ATP + Mg2+ ATP + Mg2+ Hel2 Hel2 Hel1 Hel2 Hel1 RIIIDb dsRBD DUF283 Platform PAZ RIIIDb DUF283 Fig. 6 | The model of the Dcr-2–Loqs-PD complex in the dsRNA-processing cycle. The stars represent the mature ATP-binding site, with red and hollow representing whether or not ATP or ADP is bound. The sky-blue region in the Platform–PAZ domains is the dsRNA terminal recognition site. Domains shown in transparent mode with a dotted outline are not visible in that state. The triangles in RIIIDs represent the RNase active centre. The red arrows show the translocation direction. Translocation Translocation ATP + Mg2+ Platform Dcr-2–R2D2 Dicing siRNA releasing and loading into Ago2 in transparent mode with a dotted outline are not visible in that state. The triangles in RIIIDs represent the RNase active centre. The red arrows show the translocation direction. Fig. 6 | The model of the Dcr-2–Loqs-PD complex in the dsRNA-processing cycle. The stars represent the mature ATP-binding site, with red and hollow representing whether or not ATP or ADP is bound. The sky-blue region in the Platform–PAZ domains is the dsRNA terminal recognition site. Structural states during translocation 4g and Supplementary Video 1), which is similar to the recently reported structures of Arabidopsis thaliana DCL-1 (AtDCL-1) in complex with a primary miRNA substrate13 (Extended Data Fig. 8g). However, when superimposing the modelled structure of the fully translocated state onto the active dicing structure of AtDCL3 in complex with a dsRNA substrate (Protein Data Bank (PDB): 7VG2) by the RIIIDa/b domains14, the interaction between the DUF283 and RIIIDb domains (Fig. 4d,e) has steric clashes with the dsRNA bound to the RNase active centre of RIIIDa/b of AtDCL3 in the active dicing state (Extended Data Fig. 8h), suggesting that this interaction would prevent the dsRNA substrate from accessing the RNase active centre of the RIIIDa/b domains dur- ing the translocation of Dcr-2 along dsRNA. This modelled structure is designated the pre-dicing state (Fig. 4g). no dicing activity, the complex halts in a stable state, of which the struc- ture was captured at a resolution (4 Å)—higher than the resolution of the structure in the mid-translocation state (4.2 Å). The C-terminal dsRBD in the active dicing state is also better defined for its interac- tions with the minor and major grooves of dsRNA mainly by residues of Arg1658, Lys1706 and Lys1702 (Extended Data Fig. 8k,l). The axis of dsRNA bound by the Dcr-2–Loqs-PD complex in the active dicing state is obviously distorted due to the interactions of dsRBD and RIIIDa/b (Fig. 5b). Moreover, compared with the structure in the pre-dicing state, the dsRNA in the active dicing state further threads about 4 bp through the helicase domain (Fig. 5a,c), resulting in the cap and core modules transforming about 10 Å away from the bottom module and rotating 40° (Fig. 5a,c and Supplementary Video 1). The keys for the conformational changes are the disruption of interactions between the DUF283 and RIIIDb domains (Fig. 5d), and the stretch of DP-linker in which a helix unwound about one turn (Fig. 5e and Supplementary Video 1), eliminating the misalignment between the bottom and cap– core modules of Dcr-2 and allowing the dsRNA duplex to shift about 10 Å (Fig. 5f) and position exactly in the catalytic active centre of the RIIID domains (Extended Data Fig. 8j). These conformational changes suggest that the ATP hydrolysis by the helicase domain is converted into a tension accumulated during the translocation of Dcr-2 on dsRNA, driv- ing the transformation of the pre-dicing state to the active dicing state. Structural states during translocation 9), underlining the critical role of C-terminal dsRBD in ATP-dependent dsRNA process- ing by Dcr-2. During the translocation, the interactions between the DUF283 domain and RIIIDa/b domains (Fig. 4d), including relatively flexible interactions between the DUF283 and RIIIDb/RIIIDbi domains (Fig. 4e), and relatively rigid interactions between the DUF283 domain and RIIIDa through the DP-linker domain (Fig. 4f and Extended Data Fig. 8f), remain almost the same as in the initial binding state (Extended Data Fig. 8a). This suggests that the overall domain configuration of Dcr-2 is relatively rigid during the translocation process until the dsRNA terminus reaches the Platform–PAZ domains. Dcr-2–Loqs-PD complex in the early-translocation state has almost no conformational changes and no additional interactions with dsRNA, except that the cap and core modules shift about 3 Å away from the dsRNA (Extended Data Fig. 8a,b and Supplementary Video 1). The tra- jectory of dsRNA in the early-translocation state is same as in the initial binding state (Fig. 4a and Extended Data Fig. 8c). We captured another structure in the mid-translocation state, in which about 17 bp of a dsRNA duplex threads through the helicase domain further towards the cata- lytic centre of Dcr-2 (Fig. 4b). When superimposed onto structures of the initial binding and early translocation states, the cap–core modules sway back about 2 Å towards the dsRNA (Extended Data Fig. 8a,b and Supplementary Video 1). Importantly, in the mid-translocation state, the C-terminal dsRBD of Dcr-2 appears in the map and interacts with the dsRNA substrate (Extended Data Fig. 8d), resulting in further bending of the axis of the dsRNA about 25°, and the trajectory of the dsRNA is directly towards the PAZ domain (Fig. 4c and Supplementary Video 1). Removal of the C-terminal dsRBD of Dcr-2 completely abolished the cleavage ability of the enzyme on the dsRNA substrate and cryo-EM A comparison of the cryo-EM structures of the early- and mid- translocation states also demonstrates a very similar structure in their helicase domains, of which the ATP-hydrolytic pockets have an EM density for either ATP or ADP-Mg2+ (Fig. 2b and Extended Data Fig. 8e). The current resolution is yet not high enough to distinguish the nucleotide state or separate the ATP-hydrolytic steps in the complex. Online content Any methods, additional references, Nature Research reporting sum- maries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author con- tributions and competing interests; and statements of data and code availability are available at https://doi.org/10.1038/s41586-022-04911-x. It is well known that Dcr-2 is an ATP-dependent enzyme. However, we found that Dcr-2 forms a homodimer when binding to dsRNA a sub- strate in the absence of ATP. Although we cannot conclude whether the dimerization is an in vitro artifact or whether it is physiologically relevant, this finding helped us to solve near-atomic high-resolution structures of Dcr-2–Loqs-PD in the apo and initial binding states under conditions without ATP. Interestingly, the conformational changes of the helicase and DUF283 domains induced by dsRNA binding, which are similar to RLRs, do not require ATP hydrolysis, instead, forming an ATP-binding pocket (Fig. 2a). Although the translocation requires ATP hydrolysis, Dcr-2–Loqs-PD does not undergo major conformational changes. However, in comparison to the modelled pre-dicing state, substantial conformational changes in the dicing state accompanied by an additional 4 bp dsRNA threading through helicase domain (Fig. 5) suggested that the transformation of Dcr-2–Loqs-PD into the active dicing state requires ATP hydrolysis. Thus, both the translocation and activation of Dcr-2–Loqs-PD are ATP-dependent (Fig. 6). Note that the helicase domain is responsible for reducing non-specific cleav- age, indicating that the ATP-dependent translocation of dsRNA is the key property of Dcr-2 for controlling the precision of RNA processing (Extended Data Fig. 10c). 7. Ha, M. & Kim, V. N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509–524 (2014). 8. Kozomara, A. & Griffiths-Jones, S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42, D68–D73 (2014). 9. Liu, Z. et al. Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate. Cell 173, 1191–1203 (2018). 10. Taylor, D. W. et al. Substrate-specific structural rearrangements of human Dicer. Nat. Struct. Mol. Biol. 20, 662–670 (2013). 11. Sinha, N. K., Trettin, K. D., Aruscavage, P. J. & Bass, B. L. Drosophila Dicer-2 cleavage is mediated by helicase-and dsRNA termini-dependent states that are modulated by Loquacious-PD. Mol. Cell 58, 406–417 (2015). The DUF283 domain is a distinct domain that is found only in higher eukaryotic dicer proteins. The bioinformatic24 and structural25 stud- ies suggested that DUF283 has a non-canonical dsRBD fold, and functions in protein–protein interactions25 and dsRNA annealing26. siRNA releasing in post-dicing state To investigate the dynamic dicing process of Dcr-2, we mixed WT Dcr-2– Loqs-PD with a 50 bp dsRNA substrate, then added ATP and Mg2+ just before generating the cryo-EM samples. From such an enzymatically active sample, we were able to capture a complex structure in the post-dicing state at a relatively lower resolution (4.6 Å) (Figs. 1g and 5g). In this structure, a clear breakage of the dsRNA after the dicing near to the catalytic centre was observed (Fig. 5g) and exactly 21 bp away from the PAZ-domain-binding terminus (Extended Data Fig. 8m). The cleavage of dsRNA disrupts the binding site for the C-terminal dsRBD in the active dicing state (Fig. 5b and Extended Data Fig. 8k–m), and prob- ably results in the dsRBD becoming more flexible and losing its density We wondered how Dcr-2 is activated from the pre-dicing state to allow the dsRNA to reach the active centre of RIIIDa/b. We captured a struc- ture of Dcr-2–Loqs-PD in complex with 50 bp dsRNA in an active dicing state under the same conditions as for the translocation states (Figs. 1f and 5a and Extended Data Fig. 3), in which the terminus of dsRNA was bound by the Platform–PAZ domains through recognition of the 3′ two-nucleotide overhang and 5′-phosphate, respectively (Extended Data Fig. 8i). The dsRNA is held in the RNase active centre formed by RIIIDa and RIIIDb, and two metal ions are bound in the two catalytic sites (Extended Data Fig. 8j), suggesting that the structure is in the active dicing state. As the Dcr-2 used here is a double mutant that has 404  |  Nature  |  Vol 607  |  14 July 2022 404 in the averaged EM map of the post-dicing state (Fig. 5g,h), which may be also favourable to the release of cleaved siRNA products (Extended Data Fig. 8m and Supplementary Video 1). Compared with the struc- ture in the active dicing state, the cap–core module with siRNA in the post-dicing state rotated about 20° (Fig. 5h), which is derived from the partial restoration of the spring helix in the DP-linker, probably accom- panied by the release of the tension (Fig. 5i and Supplementary Video 1). The remaining dsRNA duplex bound by the helicase domain also returns to a conformation similar to the early-translocation state (Extended Data Fig. 8n), which enables the translocation of Dcr-2–Loqs-PD to enter the next processing cycle (Fig. 6 and Supplementary Video 1). Summary In conclusion, we used cryo-EM to solve the structures of Dicer-2 in complex with its cofactor Loqs-PD in its apo and initial dsRNA-binding states in the absence of ATP, and in multiple translocation and dicing states in the presence of ATP, deciphering the multiple ATP-dependent conformational changes during the full cycle of dsRNA processing by Dcr-2–Loqs-PD from initial dsRNA binding to dicing of the dsRNA substrate into the siRNA duplex (Fig. 6 and Supplementary Video 1). siRNA releasing in post-dicing state cleavage of dsRNA during the translocation. In the active dicing state, the interaction between DUF283 and RIIIDb is disrupted (Fig. 5d) and the DP-linker is stretched (Fig. 5e), allowing the dsRNA substrate to enter the active centres of RIIIDa/b for precise cleavage (Fig. 5f). Recent research suggested that ATP is required for recogni- tion and discrimination of dsRNA termini12,27. We have identified a 5′-phosphate-binding pocket in Hel2i in the initial binding state (Fig. 3g–i) under conditions without ATP. There are extensive studies on the 5′-triphosphate recognition by the C-terminal domain of RIG-I that has similar conformational change of helicase after dsRNA binding28,29. Dcr-2 may sense the 5′-triphosphate of RNAs using a similar binding pocket to that demonstrated previously12,27. Recent single-molecule analysis19 supports the conclusion from our structures in this study that terminal loading of dsRNA as the initial step and translocation along the dsRNA are required to activate the processive cleavage activity of Dcr-2. Discussion Dcr-2 is a Dicer protein that requires ATP hydrolysis to process long dsRNA and produce siRNA duplex in vivo20,21, although later studies showed that human Dicer does not require ATP to cleave the dsRNA in vitro22,23. Loqs-PD is a cofactor protein that comprises two dsRBDs that are responsible for recruiting siRNA precursor substrates for Dcr-2. The interactions between the C-terminal tail of Loqs-PD and Dcr-2 provide a structural basis for the specific requirement of Loqs-PD for endo-siRNA production3. Its strong interaction with the Dcr-2 helicase domain lends a proximate convenience for loading siRNA precursors onto the helicase domain for initial binding. The two dsRBDs increase the dsRNA-binding affinity of the helicase, making it easier for the complex to reach the initial binding state (Extended Data Fig. 10a,b). However, the dsRBDs were not observed in the density of the two-dimensional average of the initial binding state, suggesting that the dsRBDs of Loqs-PD have only an assisting role in the initial dsRNA binding of the helicase domain of Dcr-2, which is consistent with the single-molecule result from a previous study19. 1. Wilson, R. C. & Doudna, J. A. Molecular mechanisms of RNA interference. Annu. Rev. Biophys. 42, 217–239 (2013). 1. Wilson, R. C. & Doudna, J. A. Molecular mechanisms of RNA interference. Annu. Rev. Biophys. 42, 217–239 (2013). Article 28. Kowalinski, E. et al. Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA. Cell 147, 423–435 (2011). 29. Devarkar, S. C. et al. Structural basis for m7G recognition and 2′-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc. Natl Acad. Sci. USA 113, 596–601 (2016). 28. Kowalinski, E. et al. Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA. Cell 147, 423–435 (2011). 19. Naganuma, M., Tadakuma, H. & Tomari, Y. Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-2. Nat. Commun. 12, 4268 (2021). pattern recognition receptor RIG I by viral RNA. Cell 147, 423 435 (2011). 29. Devarkar, S. C. et al. Structural basis for m7G recognition and 2′-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc. Natl Acad. Sci. USA 113, 596–601 (2016). 29. Devarkar, S. C. et al. Structural basis for m7G recognition and 2′-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc. Natl Acad. Sci. USA 113, 596–601 (2016). 20. Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000). 21. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004). Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 22. Provost, P. et al. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864–5874 (2002). 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. Online content Our high-resolution structures of Dcr-2–Loqs-PD in the apo and initial binding states, as well as the translocation and dicing states, revealed that DUF283 has a central role in conformational changes: from the apo to initial binding state and from the pre-dicing to active dicing state. In the transition from the apo to the initial binding state, the DUF283 domain undergoes conformational changes in a manner similar to the C-terminal domain in RLRs (Fig. 3). Moreover, DUF283 interacts with RIIIDb and RIIIDa, blocking the access of dsRNA to the catalytic centre of RIIIDa/b (Extended Data Fig. 8h) and preventing non-specific 12. Sinha, N. K., Iwasa, J., Shen, P. S. & Bass, B. L. Dicer uses distinct modules for recognizing dsRNA termini. Science 359, 329–334 (2018). 13. Wei, X. et al. Structural basis of microRNA processing by Dicer-like 1. Nat. Plants 7, 1389–1396 (2021). 14. Wang, Q. et al. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science 374, 1152–1157 (2021). 15. Gan, J. et al. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124, 355–366 (2006). 16. Kandasamy, S. K. & Fukunaga, R. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc. Natl Acad. Sci. USA 113, 14031–14036 (2016). 16. Kandasamy, S. K. & Fukunaga, R. Phosphate binding pocket in Dicer 2 PAZ domain for high-fidelity siRNA production. Proc. Natl Acad. Sci. USA 113, 14031–14036 (2016). 17. Trettin, K. D., Sinha, N. K., Eckert, D. M., Apple, S. E. & Bass, B. L. Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc. Natl Acad. Sci. USA 114, E7939–E7948 (2017). 17. Trettin, K. D., Sinha, N. K., Eckert, D. M., Apple, S. E. & Bass, B. L. Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc. Natl Acad. Sci. USA 114, E7939–E7948 (2017). 18. Hansen, S. R., Aderounmu, A. M., Donelick, H. M. & Bass, B. L. Dicer's helicase domain: a meeting place for regulatory proteins. in Cold Spring Harb. Symp. Quant. Biol. Vol. 84 (eds Stewart, D. & Stillman, B.) 185–193 (Cold Spring Harbor Laboratory Press, 2019). Nature  |  Vol 607  |  14 July 2022 405 406  |  Nature  |  Vol 607  |  14 July 2022 406  |  Nature  |  Vol 607  |  14 July 2022 BS3/EDC-mediated cross-linking mass spectrometry Dcr-2 or its mutants was expressed using the Bac-to-Bac baculovirus expression system (Invitrogen) in sf9 cells at 27 °C. One litre of cells (2 × 106 cells per ml, medium from Expression Systems) was infected with 20 ml baculovirus at 27 °C. After growth at 27 °C for 48 h, the cells were collected, resuspended in buffer A (150 mM NaCl, 20 mM Tris-HCl pH  8.0, 10% glycerol, 20 mM imidazole) with 0.5 mM PMSF and protease inhibitors, and lysed by adding 0.5% Triton X-100 and shaken gently for 30 min at 4 °C. Dcr-2 was purified to homogeneity using Ni-NTA affin- ity, Hitrap Q column (Cytiva), 2nd Ni-NTA affinity and size-exclusion chromatography using the Superdex 200 10/300 Increase column (Cytiva) (in that order). g p y The purified complexes were incubated with 0.25 mM bis (sulfosuccinimidyl)suberate (BS3; Thermo Fisher Scientific, 21580) in the reaction buffer containing 50 mM HEPES pH 7.5, 80 mM NaCl and 5% glycerol at 25 °C for 2 h or 5 mM 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC; Thermo Fisher Scientific, PG82073) in the reaction buffer containing 50 mM HEPES pH 7.2, 80 mM NaCl and 5% glycerol at 25 °C for 2 h. Cross-linked complexes were further purified to remove oligomer and glycerol by size-exclusion chromatography. The proteins (10 μg) were precipitated and digested for 16 h at 37 °C by trypsin at an enzyme-to-substrate ratio of 1:50 (w/w). The tryptic digested peptides were desalted and loaded on an in-house packed capil- lary reverse-phase C18 column (40 cm length, 100 µM ID × 360 µM OD, 1.9 µM particle size, 120 Å pore diameter) connected to an Easy LC 1200 system. The samples were analysed with a 120 min high-performance liquid chromatography gradient from 6% to 35% buffer B (buffer A: 0.1% formic acid in water; buffer B: 0.1% formic acid in 80% acetonitrile) at 300 nl min−1. The eluted peptides were ionized and directly introduced into a Q-Exactive mass spectrometer using a nano-spray source. Survey full-scan MS spectra (m/z = 300–1,800) were acquired in the Orbitrap analyzer with resolution r = 70,000 at m/z = 400. Cross-linked peptides were identified and evaluated using pLink2 software30. Loqs-PD and its mutants were expressed in Escherichia coli BL21 (DE3). Loqs-PD was first purified by Ni-NTA affinity chromatography. Using protease ULP1 to remove the 6×His–SUMO tag, and dialysis was applied to remove imidazole. In vitro dsRNA cleavage assays Dicer-2–Loqs-PD cleavage assays were performed in cleavage buffer (50 mM HEPES pH 7.2, 100 mM NaCl, 1 mM DTT, 5 mM ATP) with dsRNA. Dcr-2–Loqs-PD and dsRNA were preincubated at 25 °C for 15 min, then added with ATP and MgCl2 to a final concentration of 5 mM to start the reactions. The reactions were stopped with equal volume of 2× formamide loading buffer (95% formamide, 20 mM EDTA, 0.1% SDS, 0.005% xylene cyanol, 0.005% bromophenol blue). Samples were sepa- rated by 12% denaturing PAGE, visualized on Typhoon FLA-9000 (GE Healthcare) system. BS3/EDC-mediated cross-linking mass spectrometry The sample was then applied to a second Ni-NTA chromatography and the flow-through was collected for size-exclusion chromatography using the Superdex 200 16/600 column (Cytiva). Fractions corresponding to the apo Loqs-PD were collected and con- centrated to about 10 mg ml−1. Data reporting No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. Methods centrifugation at 500i for 1 min, the supernatant was removed and the beads were washed five times using wash buffer (200 mM NaCl, 20 mM Tris pH 8.0, 5% glycerol, 20 mM imidazole, 0.1% NP-40) by centrifuga- tion, followed by SDS–PAGE analysis. Image processing and 3D reconstruction For all of the datasets, the image processing was adopted in similar steps. All of the raw dose-fractionated image stacks were 2× Fourier binned, aligned, dose-weighted and summed using MotionCorr2 (ref. 33). The following steps were then processed in RELION (v.3.1)34. The contrast transfer function parameters were estimated using CTFFIND4 (ref. 35). Approximately 2,000 particles were manually picked and 2D-classified to generate initial templates for automatic picking. A large number of particles were then automatically picked from raw micrographs on the basis of our templates. After one round of reference-free 2D Article 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/. 23. Zhang, H., Kolb, F. A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885 (2002). 24. Dlakić, M. DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold. Bioinformatics 22, 2711–2714 (2006). 25. Qin, H. et al. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction. RNA 16 474–481 (2010). 26. Kurzynska-Kokorniak, A. et al. Revealing a new activity of the human Dicer DUF283 domain in vitro. Sci. Rep. 6, 23989 (2016). 27. Singh, R. K. et al. Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self–nonself discrimination. eLife 10, e65810 (2021). © The Author(s) 2022 406  |  Nature  |  Vol 607  |  14 July 2022 Preparation of dsRNAs The dsRNAs were in vitro transcribed using T7 RNA polymerase. The pUC19 plasmids containing target sequences with 3′-HDV ribozyme sequences were linearized by EcoRI, extracted with phenol–chloroform and precipitated with isopropanol. The in vitro transcription reaction was performed at 37 °C for 5 h in the buffer containing 100 mM HEPES-K (pH 7.9), 10 mM MgCl2, 10 mM dithiothreitol (DTT), 6 mM NTP each, 2 mM spermidine, 200 μg ml−1 linearized plasmid and 100 μg ml−1 T7 RNA polymerase. For the 5′-monophosphate RNA, 40 mM GMP was added in the transcription reactions. EDTA at a final concentration of 20 mM was added to the samples containing palindromic tran- scripts. The samples were heated to 95 °C for 5 min and then slowly cooled to room temperature. The annealed transcripts were purified by 8% denaturing urea PAGE, eluted from gel slices and precipitated with isopropanol. After centrifugation, the RNA precipitant was collected, washed twice with 70% ethanol and air-dried, and the RNA was dissolved in ultrapure water. We next used T4 PNK (NEB, M0201) to remove the 2′,3′ cyclic phosphate at the 3′ end of the RNA. The FAM-labelled dsRNA was produced by Silencer siRNA Labeling kit-FAM according to the manufacturer’s instructions. Cryo-EM sample preparation and data collection We used the same specimen preparation and data collection method for all of the cryo-EM datasets. An aliquot of 4 μl of purified or reaction sample was applied to a custom-made graphene grid31 (Quantifoil Au 1.2/1.3, 300 mesh), which were glow-discharged (in a Harrick Plasma system) for 10 s at middle level after 2 min evacuation. The grids were then blotted by a couple of 55 mm filter papers (Ted Pella) for 0.5 s at 22 °C and 100% humidity, then flash-frozen in liquid ethane using the FEI Vitrobot Mark IV. Cryo-EM data were collected on different Titan Krios electron microscopes, all of which were operated at 300 kV, equipped with a Gatan K3 direct electron detector and a Gatan Quantum energy filter. All data were automatically recorded using AutoEMation32 or EPU (post-dicing state dataset) in counting mode and defocus values ranged from −1.5 μm to −2.0 μm. The other parameters of each dataset are provided in Extended Data Table 1. Protein expression and purification The gene encoding full-length Drosophila melanogaster Dcr-2 (UniProt: A1ZAW0) was cloned from the recombinant pFastBac-Dcr-2 plasmid (gifted by the Q. Liu laboratory). Full-length DmLoqs-PD (UniProt: M9MRT5) was PCR amplified from Drosophila cDNA and cloned into a modified pET28a (with a 6×His-SUMO tag). The constructs of WT Dcr-2, Loqs-PD and other mutations were generated using a standard PCR-based cloning strategy and cloned into the corresponding vectors, and their identities were confirmed by sequencing analysis. BS3/EDC-mediated cross-linking mass spectrometry Reporting summary Further information on research design is available in the Nature Research Reporting Summary linked to this paper. Author contributions J.M. and H.-W.W. conceived the study. J.H. and X.Y. initiated the project. S.S., J.W., J.M. and H.-W.W. designed experiments. S.S. and T.D. prepared the samples and performed the biochemical experiments, the mass spectrometry and analysed the data. S.S. and T.D. performed negative screening. J.W., S.S., N.L. and X.L. performed cryo-EM experiments and structure determination. J.M., S.S. and J.W. built the models. S.S. and J.W. refined the models. S.S., J.W., T.D., Y.H., J.M. and H.-W.W. analysed data. S.S., J.W., J.M. and H.-W.W. wrote the manuscript with input from the other authors. Model building and refinement 34. Zivanov, J. et al. New tools for automated high-reso determination in RELION-3. eLife 7, e42166 (2018). The highest resolution EM density map of dimer status was used for initial model building, in which the quality of density was sufficient for de novo model building in COOT38. The initial model was separated into three parts (helicase-LoqsPD, DUF283 and other domains) and docked into EM 3D density maps of other states in Chimera39 and then adjusted manually in ISOLDE40 in Chimerax41 and COOT. Finally, all of the models were refined against the EM map by PHENIX42 in real space with secondary structure and geometry restraints. The final models were validated in PHENIX software package. The model statistics are summarized in Extended Data Table 1. 35. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). 36. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). 37. Heymann, J. B. Single particle reconstruction and validation using Bsoft for the map challenge. J. Struct. Biol. 204, 90–95 (2018). 38. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). 38. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). 39. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). 40. Croll, T. I. ISOLDE: a physically realistic environment for model building into l l ti l t d it A t C t ll D St t Bi l 74 519 530 40. Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). 41. Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). 41. Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). 42. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). Article the UniProt database under accession codes A1ZAW0 and M9MRT5. Any other data or materials can be obtained from the corresponding authors on reasonable request. the UniProt database under accession codes A1ZAW0 and M9MRT5. Any other data or materials can be obtained from the corresponding authors on reasonable request. classification and several rounds of 3D classification, using the initial 3D reference models obtained by ab initio calculation in RELION v.3.1, particles from good 3D classes, with better overall structure features, were selected for 3D refinement. The final high-resolution homogene- ous refinement was performed in CryoSPARC36. The resolutions were determined by gold-standard Fourier shell correlation. Local resolu- tion distribution was evaluated using blocres command in the Bsoft software package37. The detailed image processing of each dataset is provided in Extended Data Figs. 2 and 3. 30. Lu, S. et al. Mapping native disulfide bonds at a proteome scale. Nat. Methods 12, 329–331 (2015). 31. Liu, N. et al. Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM. Biophys. Rep. 7, 227–238 (2021). 31. Liu, N. et al. Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM. Biophys. Rep. 7, 227–238 (2021). 32. Lei, J. & Frank, J. Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J. Struct. Biol. 150, 69–80 (2005). 33. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). Pull-down assays Pull-down assays were performed to detect Dcr-2–Loqs-PD interac- tions using His-tagged proteins purified from bacterial or insect cells. First, 1.25 μM His-tagged Loqs-PD and 0.6 μM untagged Dcr-2 were mixed and incubated on ice for 30 min. The protein mixture was then incubated with 15 μl Ni-NTA Agarose (Qiagen, 30210) in a total volume of 500 μl in the binding buffer (200 mM NaCl, 20 mM Tris pH 8.0, 5% glycerol, 20 mM imidazole) at 4 °C for 1 h with gentle rotation. After Statistics and reproducibility 42. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). For Extended Data Fig. 1a–c, experiments were repeated at least three times. For Extended Data Figs. 1d, 2a,f, 3a,j, 9a and 10a–c, experiments were repeated at least twice. Acknowledgements We thank Q. Liu for the Dcr-2 plasmid; J. Lei for assistance of data collection; and C. Peng, Y. Yin, C. Su and P. Wu for the mass spectrometry. We acknowledge the staff at the Tsinghua University Branch of the China National Center for Protein Sciences (Beijing) and Shuimu BioSciences for providing the cryo-EM facility support and the computational facility support. This research is supported by the National Natural Science Foundation of China (31971130 to J.M., 31825009 to H.-W.W., 32000849 to J.W. and 91940302 to Y.H.); the National Key R&D Program of China (2017YFA0503500 to X.L.); and the mRNA Innovation and Translation Center, Shanghai (to J.M.) and the Xplorer Prize (to H.-W.W.). 30. Lu, S. et al. Mapping native disulfide bonds at a proteome scale. Nat. Methods 12, 329–331 (2015). Data availability The atomic coordinates and structure factors in apo and initial dsRNA-binding states, early- and mid-translocation states, active dic- ing and post-dicing states in this study have been deposited at the RCSB PDB and Electron Microscopy Data Bank (EMDB) under EMD accession codes EMD-32236, EMD-32237, EMD-32238, EMD-32239, EMD-32240 and EMD-32241, and PDB accession codes 7W0A, 7W0B, 7W0C, 7W0D, 7W0E and 7W0F, respectively. The PDB and EMDB codes are also listed in Extended Data Table 1. Uncropped gel images are provided in Sup- plementary Fig. 1. Other structures used in this study were retrieved from PDB with accession code 7VG2 (AtDCL3), 2EZ6 (AaRNase III), 2FFL (GiDicer), 5ZAK (HsDicer), 6LXD (HsDrosha), 5F9H (HsRIG-I) and 7ELE (AtDCL1). The information of Dcr-2 and Loqs-PD is available in Competing interests The authors declare no competing interests. Competing interests The authors declare no competing interests. 31. Liu, N. et al. Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM. Biophys. Rep. 7, 227–238 (2021). Additional information Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41586-022-04911-x. Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41586-022-04911-x. Correspondence and requests for materials should be addressed to Hong-Wei Wang or Jinbiao Ma. Correspondence and requests for materials should be addressed to Hong-Wei Wang or Jinbiao Ma. Peer review information Nature thanks Ian Macrae and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Reprints and permissions information is available at http://www.nature.com/reprints. Extended Data Fig. 1 | Protein purification and dsRNA-processing activity of Dcr-2–Loqs-PD. a–b, Size exclusion chromatography results of Dcr-2– Loqs-PD and Dcr-2–Loqs-PD/50-bp dsRNA complex. c, SDS-PAGE of the protein fractions from b. d, Cleavage assays of Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM), in the cleavage assay buffer (25 °C). Products were resolved on a 12% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. Extended Data Fig. 1 | Protein purification and dsRNA-processing activity of Dcr-2–Loqs-PD. a–b, Size exclusion chromatography results of Dcr-2– Loqs-PD and Dcr-2–Loqs-PD/50-bp dsRNA complex. c, SDS-PAGE of the protein fractions from b. d, Cleavage assays of Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM), in the cleavage assay buffer (25 °C). Products were resolved on a 12% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. Extended Data Fig. 1 | Protein purification and dsRNA-processing activity of Dcr-2–Loqs-PD. a–b, Size exclusion chromatography results of Dcr-2– Loqs-PD and Dcr-2–Loqs-PD/50-bp dsRNA complex. c, SDS-PAGE of the protein fractions from b. d, Cleavage assays of Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM), in the cleavage assay buffer (25 °C). Products were resolved on a 12% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. Fig. 1 | Protein purification and dsRNA-processing activity Extended Data Fig. 1 | Protein purification and dsRNA-processing activity of Dcr-2–Loqs-PD. a–b, Size exclusion chromatography results of Dcr-2– Loqs-PD and Dcr-2–Loqs-PD/50-bp dsRNA complex. c, SDS-PAGE of the protein fractions from b. d, Cleavage assays of Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM), in the cleavage assay buffer (25 °C). Products were resolved on a 12% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. Article rticle ended Data Fig. 2 | Cryo-EM image processing workflow of Dcr- oqs-PD and its initial dsRNA-binding state. a, A representative cryo-EM ge of the Dcr-2–Loqs-PD complex in the apo-state. Additional information b, Representative views D class averages of the apo-state complex. c, Flowchart of cryo-EM data cessing of the Dcr-2–Loqs-PD complex. d, Gold-standard Fourier shell correlation (GSFSC) of the final map of Dcr-2–Loqs-PD. e, Particle dist and final electron density map coloured according to the local resolu Dcr-2–Lops-PD. f–j, Corresponding information as the apo-state for D Loqs-PD/dsRNA in the initial binding state. Extended Data Fig. 2 | Cryo-EM image processing workflow of Dcr- 2–Loqs-PD and its initial dsRNA-binding state. a, A representative cryo-EM image of the Dcr-2–Loqs-PD complex in the apo-state. b, Representative views of 2D class averages of the apo-state complex. c, Flowchart of cryo-EM data processing of the Dcr-2–Loqs-PD complex. d, Gold-standard Fourier shell correlation (GSFSC) of the final map of Dcr-2–Loqs-PD. e, Particle distribution and final electron density map coloured according to the local resolution of Dcr-2–Lops-PD. f–j, Corresponding information as the apo-state for Dcr-2– Loqs-PD/dsRNA in the initial binding state. ed Data Fig. 3 | Cryo-EM image processing workflow of Dcr- PD with dsRNA in the early- and mid-translocation, active dicing t-dicing states. a–i, Image processing information of Dcr-2DDNN– Loqs-PD/dsRNA in the translocation and active dicing states. Pleas we reconstructed three different maps from the same dataset. j–n processing information of Dcr-2WT–Loqs-PD/dsRNA in the post-dic Loqs-PD/dsRNA in the translocation and active dicing states. Please note that we reconstructed three different maps from the same dataset. j–n, Image processing information of Dcr-2WT–Loqs-PD/dsRNA in the post-dicing state. Extended Data Fig. 3 | Cryo-EM image processing workflow of Dcr- 2–Loqs-PD with dsRNA in the early- and mid-translocation, active dicing and post-dicing states. a–i, Image processing information of Dcr-2DDNN– Article Article icle ed Data Fig. 4 | Sequence and Structure alignments of RIIIDs. a, ce alignment of RIIIDs in different families of RNase III proteins seIII, GiDicer, DmDcr-2, HsDicer, HsDrosha). The secondary structure of seIII are at the top. The conserved residues interact with Mg2+ ions are d with red triangle. The RIIID insertion region is labelled by green box. ifex aeolicus; Gi, Giardia intestinalis; Dm, Drosophila melanogaster; Hs, i b St t fRIIID di t ( ) A RN III(PDB 2EZ6), GiDicer (PDB: 2FFL), DmDcr-2 (apo state), HsDicer (PDB: 5ZAK), HsDrosha (PDB: 6LXD) The helices adjacent to the insertion region are m according to their appearance in GiDicer, DmDcr-2, HsDicer, and HsDro insertion region of RIIIDs is coloured differently. RIIIDa insertion of Dro coloured in cyan. RIIIDa and RIIIDb insertions in Dicer family are colour cornflower-blue and pink, respectively. Extended Data Fig. 4 | Sequence and Structure alignments of RIIIDs. a, 2EZ6), GiDicer (PDB: 2FFL), DmDcr-2 (apo state), HsDicer (PDB: 5ZAK), HsDrosha (PDB: 6LXD) The helices adjacent to the insertion region are marked according to their appearance in GiDicer, DmDcr-2, HsDicer, and HsDrosha. The insertion region of RIIIDs is coloured differently. RIIIDa insertion of Drosha is coloured in cyan. RIIIDa and RIIIDb insertions in Dicer family are coloured in cornflower-blue and pink, respectively. Sequence alignment of RIIIDs in different families of RNase III proteins (AaRnaseIII, GiDicer, DmDcr-2, HsDicer, HsDrosha). The secondary structure of AaRNaseIII are at the top. The conserved residues interact with Mg2+ ions are labelled with red triangle. The RIIID insertion region is labelled by green box. Aa, Aquifex aeolicus; Gi, Giardia intestinalis; Dm, Drosophila melanogaster; Hs, Homo sapiens. b, Structures of RIIIDs corresponding to (a). AaRNase III (PDB: ExtendedDataFig 5|RIIIDinsertionsinteractwiththeregulatoryregions i marked ithbla kd tted ir le andthe rre p ndingre id e inthe Extended Data Fig. 5 | RIIID insertions interact with the regulatory regions of Dcr-2 and participate in dimer formation of the initial binding state. is marked with black dotted circles and the corresponding residues in the cartoon was labelled in red colour. f, Details of interactions at the dimer interface of the initial binding state. The interactions between RIIIDai and helicase domain are mainly hydrophilic. The residues involved in the interactions are shown as sticks. Cyan dashes represent the hydrogen bonds. g, The EM density of aa 1325–1339 of RIIIDai domain with fitted atomic models. Article h, Schematic summary of the inter-molecule cross-linking residues in the dimer of initial binding state from XL-MS result. The BS3 and EDC cross-linking sites are coloured in blue and red, respectively. i, The table of distance between cross-linking residues in monomer state or in dimer state. j, Close-up view of inter-molecule BS3 and EDC cross-linking residues in the initial binding state. The cross-linking site is coloured as in (h). k, Overlay view of the size exclusion chromatography results of Dcr-2WT, Dcr-2R1330A, and Dcr-2R1308A/R1309A/R1330A with Loqs-PD and dsRNA. g g y g of Dcr-2 and participate in dimer formation of the initial binding state. a, Overview of inter-region interactions of RIIIDai and RIIIDbi. Hel2, Hel2i, and C-terminal dsRBD are hidden in this panel. The core region except for the C-terminal dsRBD is shown in a cartoon model. Other parts of Dcr-2 is shown in transparent surface. b, Inter-region contacts of RIIIDai and the cap region, corresponding to the orange box in (a). The interactions between RIIIDai and the cap region are mainly hydrophobic. The residues involved in the interactions are shown as sticks. Cyan dashes represent the hydrogen bonds. c, Inter-region contacts of RIIIDb and RIIIDbi with the base region, corresponding to the cyan box in (a). The interactions between them are mainly hydrophilic. Residues and hydrogen bonds are marked as in (c). d, The EM density of aa 1273–1286 of RIIIDai domain with the fitted atomic model. e, Two different views of Dcr-2’s core region in the apo-state. The RNase active centre g, The EM density of aa 1325 1339 of RIIIDai domain with fitted atomic models. h, Schematic summary of the inter-molecule cross-linking residues in the dimer of initial binding state from XL-MS result. The BS3 and EDC cross-linking sites are coloured in blue and red, respectively. i, The table of distance between cross-linking residues in monomer state or in dimer state. j, Close-up view of inter-molecule BS3 and EDC cross-linking residues in the initial binding state. The cross-linking site is coloured as in (h). k, Overlay view of the size exclusion chromatography results of Dcr-2WT, Dcr-2R1330A, and Dcr-2R1308A/R1309A/R1330A with Loqs-PD and dsRNA. Article Extended Data Fig. 6 | The conformational change of the helicase domain nduced by dsRNA binding. a, Superposition of the apo state (grey) and the nitial binding state (coloured), aligned by RIIIDs. Article b, The RMSD values of esidues in (a) demonstrate the variation of the two state. The helicase domain s coloured as in Fig. 1a, and the cap-core region is coloured in grey. c, Superposition of the apo state (grey) and the initial binding state (coloured), aligned by the Hel1 domain. The DUF283-cap-core region is shown as EM density in the apo (grey) and initial binding (sky-blue) states, respectively. d, The BS3 cross-linking residues in the apo state (left panel) and the initial binding state (right panel) of the helicase domain. The cross-linked residues are linked by blue line (upper panel) and red dashes (lower panel). e, Summary of distances between BS3 cross-linking residues in the apo state and the initial binding state. The cross-linking sites specific in the apo state are marked in t orange square. The cross-linking sites specific in the initial binding state are marked in the green square. f, The C-terminal region of Loqs-PD is shown in stick model fitted in the EM density in transparency. g, The EDC cross-linking residues between the helicase domain and C-terminal region of Loqs-PD. h–i, Inter-domain contacts of DUF283 with the Hel1 domain (h) and the Hel2i domain (i) in the initial binding state. Extended Data Fig. 6 | The conformational change of the helicase domain induced by dsRNA binding. a, Superposition of the apo state (grey) and the initial binding state (coloured), aligned by RIIIDs. b, The RMSD values of residues in (a) demonstrate the variation of the two state. The helicase domain is coloured as in Fig. 1a, and the cap-core region is coloured in grey. c, Superposition of the apo state (grey) and the initial binding state (coloured), aligned by the Hel1 domain. The DUF283-cap-core region is shown as EM density in the apo (grey) and initial binding (sky-blue) states, respectively. d, The BS3 cross-linking residues in the apo state (left panel) and the initial binding state (right panel) of the helicase domain. The cross-linked residues are linked by blue line (upper panel) and red dashes (lower panel). e, Summary of distances between BS3 cross-linking residues in the apo state and the initial binding state. The cross-linking sites specific in the apo state are marked in the orange square. The cross-linking sites specific in the initial binding state are marked in the green square. Article f, The C-terminal region of Loqs-PD is shown in stick model fitted in the EM density in transparency. g, The EDC cross-linking residues between the helicase domain and C-terminal region of Loqs-PD. h–i, Inter-domain contacts of DUF283 with the Hel1 domain (h) and the Hel2i domain (i) in the initial binding state. linked by blue line (upper panel) and red dashes (lower panel). e, Summary of distances between BS3 cross-linking residues in the apo state and the initial binding state. The cross-linking sites specific in the apo state are marked in the orange square. The cross-linking sites specific in the initial binding state are marked in the green square. f, The C-terminal region of Loqs-PD is shown in stick model fitted in the EM density in transparency. g, The EDC cross-linking residues between the helicase domain and C-terminal region of Loqs-PD. h–i, Inter-domain contacts of DUF283 with the Hel1 domain (h) and the Hel2i domain (i) in the initial binding state. Extended Data Fig. 6 | The conformational change of the helicase domain induced by dsRNA binding. a, Superposition of the apo state (grey) and the initial binding state (coloured), aligned by RIIIDs. b, The RMSD values of residues in (a) demonstrate the variation of the two state. The helicase domain is coloured as in Fig. 1a, and the cap-core region is coloured in grey. c, Superposition of the apo state (grey) and the initial binding state (coloured), aligned by the Hel1 domain. The DUF283-cap-core region is shown as EM density in the apo (grey) and initial binding (sky-blue) states, respectively. d, The BS3 cross-linking residues in the apo state (left panel) and the initial binding state (right panel) of the helicase domain. The cross-linked residues are Extended Data Fig. 7 | DsRNA recognition by the helicase domain in the initial binding state. a, Schematic diagram showing the interactions between the helicase and dsRNA in the initial binding state. b–c, Close-up views of the Hel1-dsRNA (b), Hel2-dsRNA (c) interfaces. d, Overview of the helicase domain of Dcr-2 and HsRIG-I (PDB: 5F9H) in the dsRNA-binding state. The special loop of Hel2i in Dcr-2 and the corresponding helix α2 in RIG-I are coloured in blue. e, The dsRNA of initial binding state is shown in stick model fitted in the EM density in transparency. f, The special loop of Hel2i is shown in stick model fitted in the EM density in transparency. of Hel2i in Dcr-2 and the corresponding helix α2 in RIG-I are coloured in blue. e, The dsRNA of initial binding state is shown in stick model fitted in the EM density in transparency. f, The special loop of Hel2i is shown in stick model fitted in the EM density in transparency. Article of Hel2i in Dcr-2 and the corresponding helix α2 in RIG-I are coloured in blue. e, The dsRNA of initial binding state is shown in stick model fitted in the EM density in transparency. f, The special loop of Hel2i is shown in stick model fitted in the EM density in transparency. Extended Data Fig. 7 | DsRNA recognition by the helicase domain in the initial binding state. a, Schematic diagram showing the interactions between the helicase and dsRNA in the initial binding state. b–c, Close-up views of the Hel1-dsRNA (b), Hel2-dsRNA (c) interfaces. d, Overview of the helicase domain of Dcr-2 and HsRIG-I (PDB: 5F9H) in the dsRNA-binding state. The special loop Extended Data Fig. 7 | DsRNA recognition by the helicase domain in the initial binding state. a, Schematic diagram showing the interactions between the helicase and dsRNA in the initial binding state. b–c, Close-up views of the Hel1-dsRNA (b), Hel2-dsRNA (c) interfaces. d, Overview of the helicase domain of Dcr-2 and HsRIG-I (PDB: 5F9H) in the dsRNA-binding state. The special loop Article Extended Data Fig. 8 | Structural detail and comparison of different states of Dcr-2–Loqs-PD/50-bp dsRNA complex. a, Structural alignment of the initial binding, early-translocation and mid-translocation states of Dcr-2– Loqs-PD. The initial binding state is coloured in slate-blue. The early- and mid-translocation states are coloured in goldenrod and light-green, respectively. The colour scheme is used for (a–c). b, Structural comparison of the Connector helices, which represent the cap-core region positions in three states. The structures are aligned by their helicase domains. c, Superposition of the helicase domain in three states to display the trajectory of dsRNA. d, Overview of the mid-translocation state with transparent cryo-EM map. e, The density around the ATP-binding site in the early- and mid- translocation states. f, The interaction region of DUF283 and DP-linker (656–678) of initial binding state is shown in stick model fitted in the EM density in transparency. g,Structural comparisonofthepre-dicingstateandAtDCL1/pre-miRNA pre-dicing state and AtDCL3/40-bp dsRNA complex. RIIIDs and dsRNA a shown in cartoon mode. DUF283 is shown in cartoon mode with transpa surface. i, Close-up view of the PAZ-Platform domain recognizing the ter of dsRNA in the dicing state with transparent cryo-EM map. j, Close-up vi the processing centre of Dcr-2 in the active dicing state with transparent cryo-EM map. Two Mg2+ ions are labelled. Article pre-dicing state and AtDCL3/40-bp dsRNA complex. RIIIDs and dsRNA are shown in cartoon mode. DUF283 is shown in cartoon mode with transparent surface. i, Close-up view of the PAZ-Platform domain recognizing the terminus of dsRNA in the dicing state with transparent cryo-EM map. j, Close-up view of the processing centre of Dcr-2 in the active dicing state with transparent cryo-EM map. Two Mg2+ ions are labelled. k, Overview of the interactions between the core region and dsRNA with transparent cryo-EM map. l, Close-up view of the C-terminal dsRBD/dsRNA interactions. m, Superimposition of RNA in the active dicing state (grey) and the post-dicing state (coloured). The C-terminal dsRBD of the active dicing state is shown in cartoon mode. The siRNA turned about 20 degrees after cleavage. n, Comparison of structures of the post-dicing state (light grey) and the early-translocation state (coloured) aligned by the helicase domain. Conformational changes from the post-dicing state to the early-translocation state are indicated by arrows. Extended Data Fig. 8 | Structural detail and comparison of different states of Dcr-2–Loqs-PD/50-bp dsRNA complex. a, Structural alignment of the initial binding, early-translocation and mid-translocation states of Dcr-2– Loqs-PD. The initial binding state is coloured in slate-blue. The early- and mid-translocation states are coloured in goldenrod and light-green, respectively. The colour scheme is used for (a–c). b, Structural comparison of the Connector helices, which represent the cap-core region positions in three states. The structures are aligned by their helicase domains. c, Superposition of the helicase domain in three states to display the trajectory of dsRNA. d, Overview of the mid-translocation state with transparent cryo-EM map. e, The density around the ATP-binding site in the early- and mid- translocation states. f, The interaction region of DUF283 and DP-linker (656–678) of initial binding state is shown in stick model fitted in the EM density in transparency. g, Structural comparison of the pre-dicing state and AtDCL1/pre-miRNA complex (PDB: 7ELE), aligned by RIIIDs. h, Superposition the RIIIDs of Extended Data Fig. 8 | Structural detail and comparison of different states pre-dicing state and AtDCL3/40-bp dsRNA complex. RIIIDs and dsRNA are shown in cartoon mode. DUF283 is shown in cartoon mode with transparent surface. i, Close-up view of the PAZ-Platform domain recognizing the terminus of dsRNA in the dicing state with transparent cryo-EM map. j, Close-up view of the processing centre of Dcr-2 in the active dicing state with transparent cryo-EM map. Article k, Overview of the interactions between the core region and dsRNA with transparent cryo-EM map. l, Clo view of the C-terminal dsRBD/dsRNA interactions. m, Superimposition o in the active dicing state (grey) and the post-dicing state (coloured). The C-terminal dsRBD of the active dicing state is shown in cartoon mode. Th siRNA turned about 20 degrees after cleavage. n, Comparison of structu the post-dicing state (light grey) and the early-translocation state (colou aligned by the helicase domain. Conformational changes from the post- statetotheearly-translocationstateareindicatedbyarrows. Article Article Two Mg2+ ions are labelled. k, Overview of the interactions between the core region and dsRNA with transparent cryo-EM map. l, Close-up view of the C-terminal dsRBD/dsRNA interactions. m, Superimposition of RNA in the active dicing state (grey) and the post-dicing state (coloured). The C-terminal dsRBD of the active dicing state is shown in cartoon mode. The siRNA turned about 20 degrees after cleavage. n, Comparison of structures of the post-dicing state (light grey) and the early-translocation state (coloured) aligned by the helicase domain. Conformational changes from the post-dicing state to the early-translocation state are indicated by arrows. Extended Data Fig. 9 | The C-terminal dsRBD of Dcr-2 is crucial for bending and efficient cleavage of dsRNA. a, Cleavage assays were with 50-bp dsRNA (1.2 μM) with Dcr-2WT, Dcr-2E1676S/E1678S, and Dcr-2ΔdsRBD (1.2 μM) with ATP, in the cleavage assay buffer (25 °C). Products were resolved on a 16% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. b–c, The 2D class averages and 3D reconstruction of Dcr-2ΔdsRBD/Loqs-PD+dsRNA in presence of ATP and Mg2+. The density and model of dsRNA is coloured yellow and orange, separately. d–e, Structural model of the mid-translo state fitted in the 3D map of Dcr-2ΔdsRBD/Loqs-PD+dsRNA in two views. Extended Data Fig. 9 | The C-terminal dsRBD of Dcr-2 is crucial for bending and efficient cleavage of dsRNA. a, Cleavage assays were with 50-bp dsRNA (1.2 μM) with Dcr-2WT, Dcr-2E1676S/E1678S, and Dcr-2ΔdsRBD (1.2 μM) with ATP, in the cleavage assay buffer (25 °C). Products were resolved on a 16% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. b–c, The 2D class averages and 3D reconstruction of Dcr-2ΔdsRBD/Loqs-PD+dsRNA in the presence of ATP and Mg2+. The density and model of dsRNA is coloured in light yellow and orange, separately. d–e, Structural model of the mid-translocation state fitted in the 3D map of Dcr-2ΔdsRBD/Loqs-PD+dsRNA in two views. Extended Data Fig. 9 | The C-terminal dsRBD of Dcr-2 is crucial for bending and efficient cleavage of dsRNA. a, Cleavage assays were with 50-bp dsRNA (1.2 μM) with Dcr-2WT, Dcr-2E1676S/E1678S, and Dcr-2ΔdsRBD (1.2 μM) with ATP, in the cleavage assay buffer (25 °C). Products were resolved on a 16% polyacrylamide denaturing gel. For gel source data, see Supplementary Figure 1. b–c, The 2D Extended Data Fig. 10 | The base region plays a vital role in reducing nonspecific cleavage and dsRNA binding. Article a, Cleavage assays of Dcr-2, Dcr-2– Loqs-PD320–359, Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM). b, EMSA experiment of Dcr-2, Dcr-2–Loqs-PD320–359, Dcr-2–Loqs-PDFL with 50-bp dsRNA (0.2 μM). Molar ratio of protein and dsRNA are labelled. c, Cleavage assay of 50-bp dsRNA (1.2 μM) with Dcr-2WT, Dcr-2ΔHel, and Dcr-2ΔHel-DUF (3.6 μM). Substrate dsRNA and cleavage products are labelled by bracket arrows. For gel source data, see Supplementary Figure 1. (0.2 μM). Molar ratio of protein and dsRNA are labelled. c, Cleavage assay of 50-bp dsRNA (1.2 μM) with Dcr-2WT, Dcr-2ΔHel, and Dcr-2ΔHel-DUF (3.6 μM). Substrate dsRNA and cleavage products are labelled by bracket arrows. For gel source data, see Supplementary Figure 1. Extended Data Fig. 10 | The base region plays a vital role in reducing nonspecific cleavage and dsRNA binding. a, Cleavage assays of Dcr-2, Dcr-2– Loqs-PD320–359, Dcr-2–Loqs-PDFL (1.2 μM) with 50-bp dsRNA (1.2 μM). b, EMSA experiment of Dcr-2, Dcr-2–Loqs-PD320–359, Dcr-2–Loqs-PDFL with 50-bp dsRNA Data Table 1 | Cryo-EM data collection, processing, model refinement and validation statistics Extended Data Table 1 | Cryo-EM data collection, processing, model refinement and validation statistics
https://openalex.org/W2954252697
https://www.aclweb.org/anthology/W18-2809.pdf
English
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A Sound and Complete Left-Corner Parsing for Minimalist Grammars
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Proceedings of the Eighth Workshop on Cognitive Aspects of Computational Language Learning and Processing, pages 65–74 Melbourne, Australia, July 19, 2018. c⃝2018 Association for Computational Linguistics Abstract sisters of that element (top-down), if any. The following CFG trees have nodes numbered in the order they would be constructed by bottom-up, left-corner and top-down strategies: sisters of that element (top-down), if any. The following CFG trees have nodes numbered in the order they would be constructed by bottom-up, left-corner and top-down strategies: This paper presents a left-corner parser for minimalist grammars. The relation be- tween the parser and the grammar is trans- parent in the sense that there is a very sim- ple 1-1 correspondence between deriva- tions and parses. Like left-corner context- free parsers, left-corner minimalist parsers can be non-terminating when the grammar has empty left corners, so an easily com- puted left-corner oracle is defined to re- strict the search. 1 2 3 4 5 6 7 4 2 1 3 6 5 7 7 3 1 2 6 4 5 top-down left-corner bottom-up left-corner LC parsing is bottom-up on the leftmost leaf, but then proposes a completed parent of that node on condition that its predicted sister is found. For CFGs, LC parsing is well understood (Aho and Ullman, 1972; Rosenkrantz and Lewis, 1970). In a CF rule A →B C, the left cor- ner is of course always B. Johnson and Roark (2000) generalize from CFGs to unification-based grammars and show how to allow some selected categories to be parsed left-corner while others are parsed top-down. Extending these ideas to MGs, we must deal with movements, with rules that sometimes have their first daughter on the left and sometimes on the right, and with cate- gories that are sometimes empty and sometimes not. Left corner parsers were developed for some other discontinuous formalisms with similar prop- erties (van Noord, 1991; D´ıaz et al., 2002) but in all cases these parsers fall in the category of the arc-standard left corner parsing. Here we present a left corner parser that is of arc-eager type which is argued to be more cognitively plau- sible due to its higher degree of incrementality (Abney and Johnson, 1991; Resnik, 1992). A Sound and Complete Left-Corner Parsing for Minimalist Grammars Miloˇs Stanojevi´c University of Edinburgh Edinburgh EH8 9AB, UK m.stanojevic@ed.ac.uk Edward P. Stabler UCLA and Nuance Communications California, USA edward.stabler@nuance.com 2 Minimalist grammars We present a succinct definition adapted from Stabler (2011, §A.1) and then consider a sim- ple example derivation in Figure 1. An MG G=⟨Σ, B, Lex, C, {merge,move}⟩, where Σ is the vocabulary, B is a set of basic features, Lex is a finite lexicon (as defined just below), C ∈B is the start category, and {merge,move} are the gener- ating functions. The basic features of the set B are concatenated with prefix operators to specify their roles, as follows: ⊥:: T -r -l ⊤:: =T +r +l T a :: =A +l T -l a :: =T +r A -r b :: =B +l T -l b :: =T +r B -r With T as the start category, this grammar defines the copy language ⊥XX⊤where X is any string of a’s and b’s. Bracketing the reduplicated string with ⊥and ⊤allows this very simple grammar with no empty categories, and makes it easy to track how the positions of these elements is de- fined by the derivation tree on the left in Figure 2, with 6 movements numbered 0 to 4, with TP(0) moving twice. categories, selectees = B selectors = {=f | f ∈B} licensees = {-f | f ∈B} licensors = {+f | f ∈B}. Let F be the set of role-marked features, that is, the union of the categories, selectors, licensors and licensees. Let T={::, :} be two types, indicat- ing ‘lexical’ and ‘derived’ structures, respectively. Let C = Σ∗× T × F ∗be the set of chains. Let E = C+ be the set of expressions. An expression is a chain together with its ‘moving’ sub-chains, if any. Then the lexicon Lex ⊂Σ∗× {::} × F ∗ is a finite set. We write ǫ for the empty string. Merge and move are defined in Table 1. Note that each merge rule deletes a selection feature =f and a corresponding category feature f, so the result on the left side of the rule has 2 features less than the total number of features on the right. Simi- larly, each move rule deletes a licensor feature +f and a licensee feature -f. Note also that the rules have pairwise disjoint domains; that is, an instance of a right side of a rule is not an instance of the right side of any other rule. 1 Introduction An example derivation is shown in Figure 1. Grammar G1 is simple in a way that can be misleading, since the mechanisms that allow sim- ple wh-movement also allow remnant movements, that is, movements of a constituent out of which something has already moved. Without remnant movements, MGs only define context-free lan- guages (Kobele, 2010). So remnant movements are responsible for deriving copying and other sorts of crossing dependencies that cannot be en- forced in a CFG. Consider G2: 1 Introduction Minimalist grammars (MGs) (Stabler, 1997) were inspired by proposals in Chomskian syn- tax (Chomsky, 1995). MGs are strictly more expressive than context free grammars (CFGs) and weakly equivalent to multiple context free grammars (MCFGs) (Michaelis, 2001; Harkema, 2001a). The literature presents bottom-up and top- down parsers for MGs (Harkema, 2001b), which differ in the order in which derivations are con- structed, and consequently they may differ in their memory demands at each point in the parse. But partly because of those memory demands, parsers that mix top-down and bottom-up steps are often regarded as psycholinguistically more plausible (Hale, 2014; Resnik, 1992; Abney and Johnson, 1991). Among mixed strategies, left-corner parsing (LC) is perhaps the best known (Rosenkrantz and Lewis, 1970). A left-corner parser does not begin by guessing what’s in the string, as a top-down parser does. But it also does not just reduce elements of the input, as a bottom- up parser does. A left-corner parser looks first at what is in the string (completing the left-most constituent, bottom-up) and then predicting the A first approach to left-corner MG parsing, de- signed to involve a kind of psycholinguistically motivated search, has been presented (Hunter, 2017), but that proposal does not handle all MGs. In particular, remnant movement presents the main challenge to Hunter’s parser. The parser proposed here handles all MGs, and it is easily shown to be sound and complete via a simple 1-1 correspon- 65 ǫ :: =v c knows :: =c =d v ǫ :: =v +wh c likes :: =d =d v Aca :: d what :: d -wh Bibi :: d These 7 lexical items define an infinite language. An example derivation is shown in Figure 1. dence between derivations and parses. (However, as mentioned in the conclusion, the present pro- posal does not yet address the psycholinguistic is- sues raised by Hunter.) Following similar work on CFGs (Pereira and Shieber, 1987, §6.3.1), we show how to compute a left-corner oracle that can improve efficiency. And probabilities can be used in a LC beam-parser to pursue the most proba- ble parses at each step (Manning and Carpenter, 1997). These 7 lexical items define an infinite language. An example derivation is shown in Figure 1. These 7 lexical items define an infinite language. An example derivation is shown in Figure 1. These 7 lexical items define an infinite language. 2 Minimalist grammars The set of structures, everything you can derive from the lexicon using the rules, S(G)=closure(Lex,{merge,move}). The sentences L(G) = {s| s·C ∈S(G) for some type · ∈{:, ::}}, where C is the ‘start’ category. This example shows that simple mechanisms and simple lexical features can produce sur- prising patterns. Some copy-like patterns are fairly easy to see in human languages (Bresnan et al., 1982; Shieber, 1985), and many proposals with remnant derivations have become quite prominent in syntactic theory, even where copy-like patterns are not immediately obvious (den Besten and Webelhuth, 1990; Kayne, 1994; Koopman and Szabolcsi, 2000; Hinterh¨olzl, 2006; Grewendorf, 2015; Thoms and Walkden, 2018). Since remnant-movement analyses seem appropri- ate for some constructions in human languages, and since grammars defining those analyses are often quite simple, and since at least in many cases, remnant analyses are easy to compute, it would be a mistake to dismiss these derivations too quickly. For present purposes, the relevant and ob- vious point is that a sound and complete left corner parser for MGs must handle all such derivations. Example grammar G1 with start category c uses features +wh and -wh to trigger wh-movements: 66 Aca knows what Bibi likes:c ǫ::=v c 1 Aca knows what Bibi likes:v knows what Bibi likes:=d v knows::=c =d v 3 what Bibi likes:c Bibi likes:+wh c,what:-wh ǫ::=v +wh c 5 Bibi likes:v,what:-wh likes:=d v,what:-wh likes::=d =d v 7 what::d -wh 4 Bibi::d 6 Aca::d 2 cP c ǫ 1 vP dP Aca 2 v’ v knows 3 cP dP(0) what 4 c’ c ǫ 5 vP dP Bibi 6 v’ v likes 7 dP(0) Figure 1: Derivation tree from G1 on the left, and corresponding X-bar derived tree on the right. In the derivation tree, the binary internal nodes are applications of merge rules, while the unary node is an application of move1. Computing the derived X-bar structure from the derivation is briefly described in §5 below. Note that in the X-bar tree, P is added to each category feature when the complex is the ‘max- imal projection’ of the head, while primes indicate intermediate projections, and the moved constituent is ‘coindexed’ with its origin by marking both positions with (0). For the LC parser, the derivation tree (not the derived X-bar tree) is the important object, since the derivation is what shows whether a string is derived by the grammar. 2 Minimalist grammars But which daughter is ‘leftmost’ in the derivation tree is determined by the derived string positions, counted here from 1 to 7, left to right. Derived categories become left corners when they are completed, so for the nodes in the derivation tree, the leftmost daughter, in the sense relevant for LC parsing, is the one that is completed first in the left-to-right parse of the derived string. Aca knows what Bibi likes:c ǫ::=v c 1 Aca knows what Bibi likes:v knows what Bibi likes:=d v knows::=c =d v 3 what Bibi likes:c Bibi likes:+wh c,what:-wh ǫ::=v +wh c 5 Bibi likes:v,what:-wh likes:=d v,what:-wh likes::=d =d v 7 what::d -wh 4 Bibi::d 6 Aca::d 2 cP c ǫ 1 vP dP Aca 2 v’ v knows 3 cP dP(0) what 4 c’ c ǫ 5 vP dP Bibi 6 v’ v likes 7 dP(0) Aca knows what Bibi likes:c ǫ::=v c 1 Aca knows what Bibi likes:v knows what Bibi likes:=d v knows::=c =d v 3 what Bibi likes:c Bibi likes:+wh c,what:-wh ǫ::=v +wh c 5 Bibi likes:v,what:-wh likes:=d v,what:-wh likes::=d =d v 7 what::d -wh 4 Bibi::d 6 Aca::d 2 cP Figure 1: Derivation tree from G1 on the left, and corresponding X-bar derived tree on the right. In the derivation tree, the binary internal nodes are applications of merge rules, while the unary node is an application of move1. Computing the derived X-bar structure from the derivation is briefly described in §5 below. Note that in the X-bar tree, P is added to each category feature when the complex is the ‘max- imal projection’ of the head, while primes indicate intermediate projections, and the moved constituent is ‘coindexed’ with its origin by marking both positions with (0). For the LC parser, the derivation tree (not the derived X-bar tree) is the important object, since the derivation is what shows whether a string is derived by the grammar. But which daughter is ‘leftmost’ in the derivation tree is determined by the derived string positions, counted here from 1 to 7, left to right. Derived categories become left corners when they are completed, so for the nodes in the derivation tree, the leftmost daughter, in the sense relevant for LC parsing, is the one that is completed first in the left-to-right parse of the derived string. 3 Left corner MG parsing tion tree is terminal element 7. In Figure 2, we can see that ⊥occurs first in the input, and is pro- cessed in the very first step of the successful left corner parse, even though it is the deepest, right- most element in the derivation tree. A left corner parser uses an MG rule when the left- most element on the right side is complete, where by leftmost element we do not mean the one that appears first in the rules of Table 1. Rather, the leftmost element is the one that is completed first in the left-to-right parse. For MOVE rules, there is just one element on the right side, so that ele- ment is the left-corner. When the right side of a MOVE rule is complete, it is replaced by the corre- sponding left side. But matters are more interest- ing for MERGE rules, which have two constituents on their right sides. Because the first argument s of MERGE1 is lexical, it is always the left corner of that rule. But for MERGE2 and MERGE3, either argument can have moved elements that appear to the right, so which argument is the left corner de- pends on the particular grammar and even some- times on the particular derivation. The MERGE3 rule of MGs raises another tricky issue. After the output of this rule with the pre- dicted right corner is computed, we need to re- member it, sometimes for a number of steps, since left and right corners can be arbitrarily far apart. Even with the simple G1, we can get Aca knows what Bibi knows Aca knows Bibi knows. . . Aca likes. We could put the MERGE3 output into a special store, like the HOLD register of ATNs (Wanner and Maratsos, 1978), but here we adopt the equivalent strategy of keeping MERGE3 pre- dictions in the memory that holds our other com- pleted left corners and predicted elements. We call this memory a queue, since it is ordered like a stack, but the parser can access elements that are not on top, as explained below. 2 Minimalist grammars ⊥a b a b ⊤:T a b ⊤:+l T,⊥a b:-l ⊤:+r +l T,⊥a b:-l,a b:-r ⊤::=T +r +l T ⊥a b:T -l,a b:-r b:+l T -l,a b:-r,⊥a:-l b::=B +l T -l a b:B -r,⊥a:-l b:+r B -r,⊥a:-l,a:-r b::=T +r B -r ⊥a:T -l,a:-r a:+l T -l,a:-r,⊥:-l a::=A +l T -l a:A -r,⊥:-l a:+r A -r,⊥:-r -l a::=T +r A -r ⊥::T -r -l TP TP(4) TP(2) TP(0) ⊥ T’ T a AP(1) T’ T b BP(3) T’ BP(3) AP(1) TP(0) A’ A a TP(0) B’ B b TP(2) T’ T ⊤ TP(4) Figure 2: Derivation tree from G2 on the left, and corresponding derived tree on the right. Note that the empty TP(0) moves twice, first with MOVE2 and then landing with MOVE1. That TP is just the empty head, the only element of G2 with 2 licensees. Graf et al. (2016) show that all MG languages can be defined without moving any phrase more than once, but G2 is beautifully small and symmetric. ⊥a b a b ⊤:T a b ⊤:+l T,⊥a b:-l ⊤:+r +l T,⊥a b:-l,a b:-r ⊤::=T +r +l T ⊥a b:T -l,a b:-r b:+l T -l,a b:-r,⊥a:-l b::=B +l T -l a b:B -r,⊥a:-l b:+r B -r,⊥a:-l,a:-r b::=T +r B -r ⊥a:T -l,a:-r a:+l T -l,a:-r,⊥:-l a::=A +l T -l a:A -r,⊥:-l a:+r A -r,⊥:-r -l a::=T +r A -r ⊥::T -r -l TP TP(4) TP(2) TP(0) ⊥ T’ T a AP(1) T’ T b BP(3) T’ BP(3) AP(1) TP(0) A’ A a TP(0) B’ B b TP(2) T’ T ⊤ TP(4) TP TP(4) TP(2) TP(0) ⊥ T’ T a AP(1) T’ T b BP(3) T’ BP(3) AP(1) TP(0) A’ A a TP(0) B’ B b TP(2) T’ T ⊤ TP(4) Figure 2: Derivation tree from G2 on the left, and corresponding derived tree on the right. Note that the empty TP(0) moves twice, first with MOVE2 and then landing with MOVE1. That TP is just the empty head, the only element of G2 with 2 licensees. Graf et al. (2016) show that all MG languages can be defined without moving any phrase more than once, but G2 is beautifully small and symmetric. 2 Minimalist grammars , αk has -f as its first feature: g , g , or δ ∈F +, such that none of the chains α1, . . . , αi−1, αi+1, . . . , αk has -f as its first feature: (MOVE1) final move of t, so its -f chain is eliminated on the left (MOVE1) final move of t, so its -f chain is eliminated on the left ts : γ, α1, . . . , αi−1, αi+1, . . . , αk ← s : +fγ, α1, . . . , αi−1, t : -f, αi+1, . . . , αk (MOVE2) nonfinal move of t, so its chain continues with features δ s : γ, α1, . . . , αi−1, t : δ, αi+1, . . . , αk ← s : +fγ, α1, . . . , αi−1, t : -fδ, αi+1, . . . , αk Table 1: Rules for minimalist grammars from (Stabler, 2011, §A.1). Where a CFG has →, these rules have ←as a reminder that they are usually used ‘bottom-up’, as functions from the elements on their right sides to the corresponding value on the left. To handle movements, MGs show the strings s, t explicitly. And where CFG rules have categories, these rules have complexes, i.e. comma-separated chains. Intuitively, each chain is a string with a type and syntactic features, and each constituent on either side of these rules is a sequence of chains, an initial head chain possibly followed by moving chains. Table 1: Rules for minimalist grammars from (Stabler, 2011, §A.1). Where a CFG has →, these rules have ←as a reminder that they are usually used ‘bottom-up’, as functions from the elements on their right sides to the corresponding value on the left. To handle movements, MGs show the strings s, t explicitly. And where CFG rules have categories, these rules have complexes, i.e. comma-separated chains. Intuitively, each chain is a string with a type and syntactic features, and each constituent on either side of these rules is a sequence of chains, an initial head chain possibly followed by moving chains. 2 Minimalist grammars 67 merge is the union of the following 3 rules, each with 2 elements on the right, for strings s, t ∈Σ∗, for types · ∈{:, ::} (lexical and derived, respectively), for feature sequences γ ∈F ∗, δ ∈F +, and for chains α1, . . . , αk, ι1, . . . , ιl (0 ≤k, l) (MERGE1) lexical item s selects non-mover t to produce the merged st st : γ, α1, . . . , αk ← s :: =fγ t · f, α1, . . . , αk (MERGE2) derived item s selects a non-mover t to produce the merged ts ts : γ, α1, . . . , αk, ι1, . . . , ιl ← s : =fγ, α1, . . . , αk t · f, ι1, . . . , ιl (MERGE3) any item s selects a mover t to produce the merged s with chain t s : γ, α1, . . . , αk, t : δ, ι1, . . . , ιl ← s · =fγ, α1, . . . , αk t · fδ, ι1, . . . , ιl move is the union of the following 2 rules, each with 1 element on the right, for δ ∈F +, such that none of the chains α1, . . . , αi−1, αi+1, . . . , αk has -f as its first feature: (MOVE1) final move of t, so its -f chain is eliminated on the left ts : γ, α1, . . . , αi−1, αi+1, . . . , αk ← s : +fγ, α1, . . . , αi−1, t : -f, αi+1, . . . , αk (MOVE2) nonfinal move of t, so its chain continues with features δ s : γ, α1, . . . , αi−1, t : δ, αi+1, . . . , αk ← s : +fγ, α1, . . . , αi−1, t : -fδ, αi+1, . . . , αk move is the union of the following 2 rules, each with 1 element on the right, move is the union of the following 2 rules, each with 1 element on the right, for δ ∈F +, such that none of the chains α1, . . . , αi−1, αi+1, . . . 1Instead of requiring completions to happen when an ele- ment is added to the queue, the ‘arc-standard’ variant of LC parsing uses separate complete rules, which means that a con- stituent need not (and sometimes cannot) be connected to pre- dicted structure at the time when it is first proposed. 3 Left corner MG parsing The ‘arc-eager’ variant of LC parsing, which we will define here, adds additional variants of those 8 rules: instead of just putting the new element on top of the queue, the element created by a rule can also be used to complete a prediction on the queue, ‘connecting’ the new element with structure already built.1 Im- portantly, the following completion variants of the LC rules can search below the top element to find connecting elements: (4) We have introduced 8 LC rules so far. There is SHIFT, and there are 7 LC rules corresponding to the 5 MG rules in Table 1, because of the fact that the left corner of MERGE2 and MERGE3 can be either the first or second element on the right side of the rule. Each LC rule acts to put some- thing new on top of the queue. The ‘arc-eager’ variant of LC parsing, which we will define here, adds additional variants of those 8 rules: instead of just putting the new element on top of the queue, the element created by a rule can also be used to complete a prediction on the queue, ‘connecting’ the new element with structure already built.1 Im- portantly, the following completion variants of the LC rules can search below the top element to find connecting elements: (input, 0, ǫ). For any input of length n, we then attempt to apply the LC rules to get For any input of length n, we then attempt to apply the LC rules to get (ǫ, n, 0-n·c), where · is any type and c is the start category. The LC rules are these: where · is any type and c is the start category. The LC rules are these: (0) The SHIFT rule takes an initial (possibly empty) element w with span x-y from the begin- ning of the remaining input, where the lexicon has w :: γ, and puts x-y::γ onto the queue. (1) For an MG rule R of the form A ←B C with left corner B, if an instance of B is on top of the queue, lc1(R) removes B from the top of the queue and replaces it with an element C ⇒A. Since any merge rule can have the selector as its left corner, we have the LC rules LC1(MERGE1), LC1(MERGE2), and LC1(MERGE3). 3 Left corner MG parsing Queue could be treated as a multiset (since elements can be ac- cessed even if they are not on the top) but treating queue as an ordered structure allows easier defini- In the derivation shown in Figure 1, for exam- ple, there is one application of MERGE3, to com- bine likes with what, and in that case, the selectee lexical item what is the left corner because it is the 4th terminal element, while its sister in the deriva- 68 (2) For an MG rule R of the form A ←B C′ with completed left corner C and Cθ = C′θ, lc2(R) replaces C on top of the queue by (B ⇒ A)θ. For this case, where the second argument on the right side is the left corner, we have the LC rules LC2(MERGE2) and LC2(MERGE3). tion of oracle and easier definition of which con- stituent is triggering the next parser’s operation. (2) For an MG rule R of the form A ←B C′ with completed left corner C and Cθ = C′θ, It will be convenient to number string positions as usual: 0 Aca 1 knows 2 what 3 Bibi 4 likes 5. Substrings can then be given by their spans, so Aca in our example is represented by 0-1, knows is 1-2, and an initial empty element would have the span 0-0. (3) Similarly for MG rules A ← B, the only possible leftcorner is a constituent B where Bθ = B′θ, replacing B′ by Aθ. So we have LC1(MOVE1) and LC1(MOVE2) in this case. So the parser state is given by (remaining input, current position, queue), and we begin with and we begin with and we begin with (4) We have introduced 8 LC rules so far. There is SHIFT, and there are 7 LC rules corresponding to the 5 MG rules in Table 1, because of the fact that the left corner of MERGE2 and MERGE3 can be either the first or second element on the right side of the rule. Each LC rule acts to put some- thing new on top of the queue. 3 Left corner MG parsing c(R) If LC rule R creates a constituent B, and the queue has B′ ⇒A, where Bθ = B′θ, then c(R) removes B′ ⇒A puts Aθ onto the queue. c1(R) If LC rule R creates B ⇒A and we al- ready have C ⇒B′ on the queue, where Bθ = B′θ, then c1(R) removes C ⇒B′ and puts (C ⇒ A)θ onto the queue. Let’s be more precise about being ‘an instance’. When R is A ←B C, the top element B′ of the queue is an instance of B iff we can find a (most general) substitution θ such that B′θ = Bθ. In that case, lc(R) replaces B′ with (C ⇒A)θ. This computation of substitutions can be done by standard unification (Lloyd, 1987). For example, looking at MERGE1 in Table 1, note that the first constituent on the right specifies the feature f, the sequence γ, and the string s, but not the string t or the 0 or more moving chains α1, . . . , αk. So when LC1(MERGE1) applies, the unspecified el- ements are left as variables, to be instantiated by later steps. So when s :: =fγ (for some particu- lar s, f, γ) is on top of the queue, LC1(MERGE1) replaces it by c2(R) If LC rule R creates C ⇒B and we al- ready have B′ ⇒A on the queue, where Bθ = B′θ, c2(R) removes B′ ⇒A and puts (C ⇒A)θ onto the queue. c3(R) If LC rule R creates a constituent C ⇒B and we already have B′ ⇒A and D ⇒C′ on the queue, where Bθ = B′θ and Cθ = C′θ c3(R) removes B′ ⇒A and D ⇒C′ and puts (D ⇒ A)θ onto the queue. c3(R) If LC rule R creates a constituent C ⇒B and we already have B′ ⇒A and D ⇒C′ on the queue, where Bθ = B′θ and Cθ = C′θ c3(R) removes B′ ⇒A and D ⇒C′ and puts (D ⇒ A)θ onto the queue. These completion rules are similar to the ‘com- position’ rules of combinatory categorial grammar (Steedman, 2014). These completion rules are similar to the ‘com- position’ rules of combinatory categorial grammar (Steedman, 2014). (t · f, α1, . . . , αk ⇒st : γ, α1, . . . , αk). where underlined elements are variables. where underlined elements are variables. 2An implementation of this parser and our example grammars is provided at https://github.com/stanojevic/Left- Corner-MG-parser 3 Left corner MG parsing 69 That completes the specification of an arc-eager left corner parser for MGs. The rules are non- deterministic; that is, at many points in a parse, various different LC rules can apply. But for each n-node derivation tree, there is a unique sequence of n LC rule applications that accepts the derived string. This 1-1 correspondence between deriva- tions and parses is unsurprising given the defini- tion of LC. Intuitively, every LC rule is an MG rule, except that it’s triggered by its left corner, and it can ‘complete’ already predicted constituents. This makes it relatively easy to establish the cor- rectness of the parsing method (§5, below). and so there is a corresponding 17 step LC parse. For lack of space, we do not present that parse here. It is easy to calculate by hand (especially if you cheat by looking at the tree in Figure 2), but much easier to calculate using an implementation of the parsing method.2 1. shift [Aca,knows,what,Bibi,likes] 0-0::=v c 4 A left corner oracle The description of the parsing method above spec- ifies the steps that can be taken, but does not spec- ify which step to take in situations where more than one is possible. As in the case of CFG parsing methods, we could take some sequence of steps arbitrarily and then backtrack, if necessary, to ex- plore other options, but this is not efficient, in gen- eral (Aho and Ullman, 1972). A better alternative is to use ‘memoization’, ‘tabling’ – that is, keep computed results in an indexed chart or table so that they do not need to be recomputed – compare (Kanazawa, 2008; Swift and Warren, 2012). An- other strategy is to compute a beam of most prob- able alternatives (Manning and Carpenter, 1997). But here, we will show how to define an ora- cle which can tell us that certain steps cannot possibly lead to completed derivations, following similar work on CFGs (Pereira and Shieber, 1987, §6.3.1). This oracle can be used with memoizing or beam strategies, but as in prior work on CFG parsing, we find that sometimes an easily com- puted oracle makes even backtracking search effi- cient. Here we define a simple oracle that suffices for G1 and G2. For each grammar, we can effi- ciently compute a link relation that we use in this way: A new constituent A′ or B′ ⇒A′ can be put onto the queue only if A′ stands in the LINK rela- tion to a predicted category, that is, where the start category is predicted when the queue is empty, and a category B is predicted when we have B ⇒A on top of the queue. For many grammars, this use of a LINK oracle eliminates many blind alleys, sometimes infinite ones. The 14 node derivation tree in Figure 1 has this 14 step LC parse, indicating the rule used, the remaining input, and queue contents from top to bottom, with variables M and N for chain se- quences, Fs for features, for span positions, and [] represents the remaining input ǫ in the last 2 steps of the listing: 1. shift [Aca,knows,what,Bibi,likes] 0-0::=v c 3. shift [knows,what,Bibi,likes] 0-1::d (0-_.v _M => 0-_:c _M) 4. c1(lc2(merge2)) [knows,what,Bibi,likes] (1-_:=d v _M => 0-_:c _M) 5. shift [what,Bibi,likes] 1-2::=c =d v (1-_:=d v _M => 0-_:c _M) 6. c1(lc1(merge1)) [what,Bibi,likes] ( _ _ _ _ ) 6. 2. lc1(merge1) [Aca,knows,what,Bibi,likes] (0-_.v _M => 0-_:c _M) 5 Correctness, and explicit trees We sketch the basic ideas needed to demonstrate the soundness of our parsing method (every suc- cessful parse is of a grammatical string) and its completeness (every grammatical string has a suc- cessful parse). Notice that while the top-down MG parser in Stabler (2013) needed indices to keep track of relative linear positions of predicted con- stituents, no such thing is needed in the LC parser. This is because in LC parsing, every rule has a bottom-up left corner, and in all cases except for MERGE3, that left corner determines the linear or- der of any predicted sisters. Without any change in the LC method above, with this grammar, the final start category in the last step of the LC parse of Aca knows what Bibi likes will have as its argument an explicit representation of the derivation tree of Figure 1, but with binary internal nodes replaced by • and unary ones by ◦. A slightly different version of G1 will build the the derived X-bar tree for the example in Figure 1, or any other string in the infinite language of G1: For MERGE3, neither element on the right side of the rule, neither the selector nor the selectee, determines the relative position of the other. But the MERGE3 selectee has a feature sequence of the form: fγ-g, and this tells us that the linear posi- tion of this element will be to the left of the cor- responding +g constituent that is the left corner of move1. That is where the string part of the -g constituent ‘lands’. The Shortest Move Constraint (SMC) guarantees that this pairing of the +g and -g constituents is unique in any well formed deriva- tion, and the well-formedness of the derivation is guaranteed by requiring that constituents built by the derivation are connected by instances of the 5 MG rules in Table 1. ǫ :: =v(V) c(cP/[c/[ǫ/[],V]]) ǫ :: =v(V) +wh(W) c(cP/[W,c’/[c/[ǫ/[]],V]]) knows :: =c(C) =d(D) v(vP/[D,v’/[v/[knows/[]],C]]) likes :: =d(E) =d(D) v(vP/[D,v’/[v/[likes/[]],E]]) Aca :: d(dP/[Aca/[]]) Bibi :: d(dP/[Bibi/[]]) what :: d(dP(I)/[]) -wh(dP(I)/[what/[]]) ǫ :: =v(V) c(cP/[c/[ǫ/[],V]]) ǫ :: =v(V) +wh(W) c(cP/[W,c’/[c/[ǫ/[]],V]]) knows :: =c(C) =d(D) v(vP/[D,v’/[v/[knows/[]],C]]) likes :: =d(E) =d(D) v(vP/[D,v’/[v/[likes/[]],E]]) Aca :: d(dP/[Aca/[]]) Bibi :: d(dP/[Bibi/[]]) what :: d(dP(I)/[]) -wh(dP(I)/[what/[]]) Notice how this representation of the grammar uses a variable I to coindex the moved element with its original position. 5 Correctness, and explicit trees In the X-bar tree of Fig- ure 1, that variable is instantiated to 0. Note also how the variable W gets bound to the moved ele- ment, so that it appears in under cP, that is, where the moving constituent ‘lands’. See e.g. Stabler (2013, Appendix B) for an accessible discussion of how this kind of X-bar structure is related to the derivation, and see Kobele et al. (2007) for techni- cal details. (See footnote 2 for an implementation of the approach presented here.) Locating the relevant +g move1 constituent also sufficiently locates the MERGE3 selector with its feature sequence of the form =fγ. It can come from anywhere in the +g move1 constituent’s derivation that is compatible with its features. Consequently, when predicting this element, the prediction is put onto the queue when the +g con- stituent is built, where the compose rules can use it in any feature-compatible position. 4 A left corner oracle c1(lc1(merge1)) [what,Bibi,likes] (2-_.c _M => 0-_:c _M) 7 hif [ ibi lik ] ( _ _ _ _ ) 7. shift [Bibi,likes] 2-3::d -wh (2-_.c _M => 0-_:c _M) 8. lc2(merge3) [Bibi,likes] (_-_.=d _Fs_M => _-_:_Fs,2-3:-wh ) (2-_.c _M => 0-_:c _M) 9. shift [Bibi,likes] 3-3::=v +wh c (_-_.=d _Fs => _-_:_Fs,2-3:-wh ) (2-_.c _M => 0-_:c _M) 10. lc1(merge1) [Bibi,likes] (3-_.v _M => 3-_:+wh c _M) (_-_.=d _Fs => _-_:_Fs,2-3:-wh ) (2-_.c _N => 0-_:c _N) 11. shift [likes] 3-4::d (3-_.v _M => 3-_:+wh c _M) (_-_.=d _Fs => _-_:_Fs,2-3:-wh ) (2-_.c _N => 0-_:c _N) Let LINK(X, Y ) hold iff at least one of these conditions holds: (1) X is a left corner of Y , (2) Y contains a initial licensee -f and the first feature of Y is +f, or (3) X and Y are in the transitive closure of the relation defined by (1) and (2). To keep things finite and simple, the elements related by LINK are like queue elements except the mover 12. c3(lc2(merge2)) [likes] (4-_.=d =d v => 3-_:+wh c ,2-3:-wh (2-_.c _M => 0-_:c _M) 13. c(shift) [] 3-5:+wh c ,2-3:-wh (2-_.c _M => 0-_:c _M) The derivation tree in Figure 2 has 17 nodes, 70 lists are always variables, and spans are always un- specified. Clearly, for any grammar, this LINK re- lation is easy to compute. Possible head feature se- quences are non-empty suffixes of lexical features, suffixes that do not begin with -f. The possible left corners of those head sequences are computable from the 7 left corner rules above. This simple LINK relation is our oracle. sponding derivation tree simply by adding tree ar- guments to the syntactic features of any grammar, as in (Pereira and Shieber, 1987, §6.1.2). For ex- ample, we can augment G1 with derivation tree arguments as follows, writing R/L for trees where R is root and L a list of subtrees, where • is merge and ◦is move, and single capital letters are vari- ables: ǫ :: =v(V) c(•/[ǫ::=v c/[],V]) ǫ :: =v(V) c(•/[ǫ::=v c/[],V]) ǫ :: =v(V) +wh c(◦/[•/[ǫ::=v c/[],V]]) knows :: =c(C) =d(D) v(•/[•/[knows::=c =d v/[],C],D]) likes :: =d(E) =d(D) v(•/[•/[likes::=d =d v/[],E],D]) Aca :: d(Aca::d/[]) Bibi :: d(Bibi::d/[]) what :: d(what::d -wh/[]) -wh 6 Conclusions and future work This paper defines left-corner MG parsing. It is non-deterministic, leaving the question of how to search for a parse. As in context free LC pars- ing, when there are empty left corners, backtrack- ing search is not guaranteed to terminate. So we could use memoization or a beam or both. All of these search strategies are improved by discard- ing intermediate results which cannot contribute With these policies there is a 1-1 correspon- dence between parses and derivations. In fact, since all variables are instantiated after all subsi- tutions have applied, we can get the LC parser to construct an explicit representation of the corre- 71 - Stanojevi´c (2017) shows how bottom-up transition-based parsers can be provided for MGs, and those allow LSTMs and other neural systems to be trained as oracles (Lewis et al., 2016). It would be interesting to explore similar oracles for slightly more predictive methods like LC, and trained on recently built MGbank (Torr, 2018). to a completed parse, and so we define a very sim- ple oracle which does this. That oracle suffices to make backtrack LC parsing of G1 and G2 feasible (see footnote 2). For grammars with empty left corners, stronger oracles can also be formulated, e.g. fully specifying all features and testing spans for emptiness. But for empty left corners, prob- ably the left corner parser is not the best choice. Other ways of mixing top-down and bottom-up can be developed too, for the whole range of gen- eralized left corner methods (Demers, 1977), some of which might be more appropriate for models of human parsing than LC (Johnson and Roark, 2000; Hale, 2014). - Stanojevi´c (2017) shows how bottom-up transition-based parsers can be provided for MGs, and those allow LSTMs and other neural systems to be trained as oracles (Lewis et al., 2016). It would be interesting to explore similar oracles for slightly more predictive methods like LC, and trained on recently built MGbank (Torr, 2018). - For her ‘geometric’ neural realizations of MG derivations (Gerth and beim Graben, 2012), Gerth (2015, p.78) says she would have used an LC MG parser in her neural modeling if one had been available, so that kind of project could be revisited. As noted earlier, Hunter (2017) aims to define a parser that appropriately models certain aspects of human sentence parsing. Acknowledgments The first author is supported by ERC H2020 Advanced Fellowship GA 742137 SEMANTAX grant. The authors are grateful to Tim Hunter for sharing the early version of his LC paper and to Mark Steedman for support in developing and pre- senting this work. 6 Conclusions and future work In particular, there is some evidence that, in hearing or reading a sen- tence from beginning to end, humans are inclined to assume that movements are as short as possi- ble – “active gap-filling”. It looks like the present model has a structure which would allow for mod- eling this preference in something like the way Hunter proposes, but we have not tried to capture that or any other human preferences here. Our goal here has been just to design a simple left- corner mechanism that does exactly what an arbi- trary MG requires. Returning to Hunter’s project with this simpler model will hopefully contribute to the project of moving toward more reasonable models of human linguistics performance. We leave these to future work. We leave these to future work. References Steven P. Abney and Mark Johnson. 1991. Memory re- quirements and local ambiguities of parsing strate- gies. Journal of Psycholinguistic Research 20:233– 249. There are many other natural extensions of these ideas: Alfred V. Aho and Jeffrey D. Ullman. 1972. The The- ory of Parsing, Translation, and Compiling. Volume 1: Parsing. Prentice-Hall, Englewood Cliffs, New Jersey. - The proposed definition of LC parsing is de- signed to make correctness transparent, but now that the idea is clear, some simplifica- tions will be possible. In particular, it should be possible to eliminate explicit unification, and to eliminate spans in stack elements. Joan Bresnan, Ronald M. Kaplan, Stanley Peters, and Annie Zaenen. 1982. Cross-serial dependencies in Dutch. Linguistic Inquiry 13(4):613–635. Noam Chomsky. 1995. The Minimalist Program. 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Odontogenic Keratocyst of Coronoid process presenting as an infratemporal mass
Bangladesh journal of otorhinolaryngology
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Specialist, Department of ENT, ESIC Hospital K. K. Nagar, Chennai 600 078, India Address of Correspondence: Dr. G. Raju, 4, Saravana Apartments. 348 T.T.K. Road, Alwarpet, Chennai 600018, India, Telephone: (0091-44) 24981566, E-mail : shobraju@yahoo.com Abstract A pediatric patient presented with facial swelling. CT scans showed a left infratemporal mass with erosion of coronoid process and normal dentition. CT guided FNAB suggested the possibility of odontogenic keratocyst. The mass was excised by a transzygomatic approach. A four year followup has not shown any recurrence. The possibility of odontogenic keratocyst needs to be considered while evaluating infratemporal fossa swellings. Key words : Infratemporal fossa, Odontogenic keratocyst, Coronoid process Odontogenic Keratocyst of Coronoid Process Presenting as an Infratemporal Mass G. Raju1 Bangladesh J Otorhinolaryngol 2014; 20(2): 106-108 Bangladesh J Otorhinolaryngol 2014; 20(2): 106-108 Specialist, Department of ENT, ESIC Hospital K. K. Nagar, Chennai 600 078, India Address of Correspondence: Dr. G. Raju, 4, Saravana Apartments. 348 T.T.K. Road, Alwarpet, Chennai 600018, India, Telephone: (0091-44) 24981566, E-mail : shobraju@yahoo.com Case report diagnosis of an odontogenic keratocyst was made. The cyst was excised by a trans- zygomatic approach. The cyst was completely excised along with surrounding temporalis muscle. Remnant of the coronoid process was curetted. The patient had an uneventful recovery. Histological examination was characteristic of odontogenic keratocyst. In a four year follow up, there has been no recurrence. An eleven year old girl presented with painless progressive Left sided facial swelling since two months. There were no nasal, dental and ophthalmologic complaints. Examination showed an ill defined soft tissue swelling of the left infratemporal region. Nasal, ophthalmic, oral cavity and dental examinations were normal. Plain X-ray of the Para-nasal sinuses showed an ill defined soft tissue mass in the left infratemporal region with normal sinuses. A CT scan showed a soft tissue swelling of the left infratemporal fossa involving the masticator muscles with erosion of the coronoid process of the mandible (Figs 1& 2). Oropharynx, paranasal sinuses, nasopharynx and pterygoid plates were normal. Orthopantogram showed normal dentition with destruction of left coronoid process of the mandible (Fig.3). Fine needle aspiration from the mass was inconclusive. Over a period of one month the swelling increased in size and the patient developed mild trismus. A CT guided aspiration revealed thick creamy pus that was sterile and was negative for AFB. A provisional Fig.-1. Photograph of CT scan (coronal) showing the mass and destruction of left coronoid process of mandible (indicated by arrow) Fig.-1. Photograph of CT scan (coronal) showing the mass and destruction of left coronoid process of mandible (indicated by arrow) Odontogenic Keratocyst of Coronoid Process Presenting as an Infratemporal Mass G. Raju Fig.-2. Case report Photograph of CT scan (Axial) showing the mass and destruction of left coronoid process of mandible (indicated by arrow) cell nevus syndrome (Gorlin-Goltz syndrome).3 These lesions have a peak incidence in second and third decades and occur rarely below ten years of age.2 The clinical behavior in children is similar to the condition in adults.6 and have a high recurrence rate ranging between 10 to 60%.2 Odontogenic keratocysts occurring in the soft tissue of skull are usually caused by erosion of cortical plate of bone by aggressive lesions which extend into the soft tissues, skull base, zygoma, lateral orbital rim and temporalis muscle or recurrences after initial surgery.1,7 Odontogenic keratocysts of the infratemporal fossa usually are from extensions from the maxilla7 and very rarely from the coronoid process of the mandible.1 Primary extra osseous odontogenic keratocysts have only been rarely reported and present as gingival cysts.8 Odontogenic keratocysts located primarily in the coronoid process of the mandible have hardly been reported in the literature. Kru¿yñski et al. seems to be the first who described these atypical case.4 Primary tumors of infratemporal fossa are rare and comprise of Schwanommas, Neurofibromas, Rhabdomyosarcomas etc. Extensions into infratemporal fossa occur from tumors of maxilla and salivary glands. In this case, several of these possibilities were considered as differential diagnosis. The possibility of an odontogenic cyst or tumor was not initially considered of in view of clinically and radio logically normal dentition. Non contributory FNAB added to the problem of diagnosis. Pre operative histological confirmation of the lesion has been advocated by several authors.1,3 Incisional biopsy for confirmation of pathology was not possible in this case due to the location of the swelling in the infratemporal fossa. Odontogenic keratocysts was considered only after a CT guided aspiration suggested the possibility of the condition. Fig.-2. Photograph of CT scan (Axial) showing the mass and destruction of left coronoid process of mandible (indicated by arrow) Fig.-3. Photograph of OPG showing destruction of left coronoid process of mandible (indicated by arrow) Fig.-3. Photograph of OPG showing destruction of left coronoid process of mandible (indicated by arrow) Discussion Odontogenic keratocysts are not uncommon. It was first described by Philipsen in 1956.1,2 WHO reclassified OKC as Keratocystic Odontogenic Tumor (KCOT) in 2005.,2,3,4 Odontogenic keratocysts arise from the remnants of dental lamina, also known as rests of Serres. Odontogenic keratocysts present as slow growing non specific cysts. Symptoms depend on the location of the cyst. Intraosseous cysts may present as a jaw swelling, loosening of teeth and pathological fracture of mandible. Multiple keratocysts are frequently associated with the bifid-rib, basal 107 Vol. 20, No. 2, October 2014 Bangladesh J Otorhinolaryngol 2. Peter R.Larsen in Otolaryngology Head & Neck Surgery, Charles W.Cummins. 4th edition Vol. 2 1511- 43 Because of possible malignant transformation and high recurrence rates, radical en-block resection and close follow-up has been advocated.1 In this case, besides radical excision, cosmetic consideration was also important in view of the age and sex of the patient. 3. Mahadesh J, Kokila, Laxmidevi BL. Odontogenic Keratocyst of Maxilla Involving the Sinus – OKC to be a Cyst or a Tumour? Journal of Dental Sciences & Research 2010:1:2:83-90 Transzygomatic approach was considered as most suitable since the mass was confined to the infratemporal fossa and the coronoid process. Other approaches like trans-antral, trans-parotid and submandibular would not have provided sufficient access. 4. Madras J, Lapointe H, Keratocystic Odontogenic Tumour: Reclassification of the Odontogenic Keratocyst from Cyst to Tumour: J Can Dent Assoc 2008;74(2):165-165h 5. Worral SF Recurrent odontogenic keratocyst within the temporalis muscle. British J Oral and Maxillofacial Surg1992;30:59 – 62 The case is reported for it’s rarity in pediatric age group and for it’s occurrence in the coronoid process of mandible. The possibility of odontogenic keratocyst needs to be kept in mind while evaluating swellings of infratemporal fossa. 6. Preston RD, Narayana N. Peripheral odontogenic keratocyst J Periodontol 2005; 76(12):2312-5. There is no conflict of interest in the manuscript. Ethical approval for this manuscript is not required. 7. Meara JG, Li KK, ShahSS, Cunningham MJ. Odontogenic keratocysts in the pediatric population. Arch Otolaryngol Head Neck Surg1996 ;122(7):725-8. References 8. Brzozowski F, Wanyura H, Stopa Z, Kowalska K Odontogenic keratocysts in the material of the Department of Craniomaxillofacial Surgery, Medical University of Warsaw. Czas. Stomatol 2010; 63(2):69-78 1. Jackson IT, Potparik Z, Fasching M, Schievink WI, Tidstrom K, Hussain K.Penetration of the skull base by dissecting keratocyst Journal of Cranio- Maxillo-Facial Surgery 1993:21:319–25 108
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Perinatal Exposure to a Diet High in Saturated Fat, Refined Sugar and Cholesterol Affects Behaviour, Growth, and Feed Intake in Weaned Piglets
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RESEARCH ARTICLE Perinatal Exposure to a Diet High in Saturated Fat, Refined Sugar and Cholesterol Affects Behaviour, Growth, and Feed Intake in Weaned Piglets Caroline Clouard1*, Walter J. J. Gerrits2, Bas Kemp1, David Val-Laillet3, J. Elizabeth Bolhuis1 1 Adaptation Physiology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands, 2 Animal Nutrition Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands, 3 UR1341 ADNC, INRA, Saint Gilles, France a1111 * caroline.clouard@wur.nl * caroline.clouard@wur.nl OPEN ACCESS The increased consumption of diets high in saturated fats and refined sugars is a major pub- lic health concern in Western human societies. Recent studies suggest that perinatal expo- sure to dietary fat and/or sugar may affect behavioural development. We thus investigated the effects of perinatal exposure to a high-fat high-sugar diet (HFS) on behavioural develop- ment and production performance of piglets. Thirty-two non-obese sows and their piglets were allocated to 1 of 4 treatments in a 2 × 2 factorial design, with 8-week prenatal (gesta- tion) and 8-week postnatal (lactation and post-weaning) exposure to a HFS diet (12% satu- rated fat, 18.5% sucrose, 1% cholesterol) or control low-fat low-sugar high-starch diets as factors. From weaning onwards (4 weeks of age), piglets were housed in group of 3 litter- mates (n = 8 groups/treatment) and fed ad libitum. After the end of the dietary intervention (8 weeks of age), all the piglets were fed a standard commercial diet. Piglet behaviours in the home pens were scored, and skin lesions, growth, feed intake and feed efficiency were measured up to 8 weeks after the end of the dietary treatment, i.e. until 16 weeks of age. At the end of the dietary treatment (8 weeks of age), response to novelty was assessed in a combined open field and novel object test (OFT/NOT). During the weeks following weaning, piglets fed the postnatal HFS diet tended to be less aggressive (p = 0.06), but exhibited more oral manipulation of pen mates (p = 0.05) than controls. Compared to controls, piglets fed the prenatal or postnatal HFS diet walked more in the home pen (p  0.05), and tended to have fewer skin lesions (p < 0.10). Several behavioural effects of the postnatal HFS diet depended on the prenatal diet, with piglets subjected to a switch of diet at birth being more active, and exploring feeding materials, pen mates, and the environment more than piglets that remained on the same diet. Behaviours during the OFT/NOT were not affected by the diet. The intake of the postnatal HFS diet drastically reduced feed intake, but improved feed efficiency up to 8 weeks after the end of the dietary intervention, i.e. 16 weeks of age (p < 0.0001 for both). Introduction In the recent decades, modern human societies have been subjected to a rapid shift in diet com- position, from food items high in complex carbohydrates and fibres to highly palatable and low-cost food, high in saturated fat, refined sugars and cholesterol. The increased availability and consumption of high-fat high-sugar (HFS) diets is a major public health concern, as it is accompanied by adverse health consequences, including an increased incidence of obesity, car- diovascular diseases and type-2 diabetes [1,2]. In addition, several human and animal studies suggest that the consumption of diets or beverages rich in fat and/or refined sugars affects behavioural and emotional processes, including anxiety/depression [3–5] and aggression [4,6,7]. In addition to the impact of dietary fat and refined sugars on behaviours, dietary choles- terol, another major component of the modern Western diet, has been found to affect aggres- sion and social interactions in monkeys [8] and minipigs [9]. Inevitably, the rise in consumption of HFS diets in Western modern societies leads to an increased exposure to these dietary components during the perinatal developmental period, notably via the maternal diet, maternal milk or early life diet. It is now widely accepted that perinatal conditions, and notably prenatal and early life nutrition, can have long-lasting impacts on health and behaviours [10,11]. Accordingly, growing evidence indicates that peri- natal exposure to high levels of dietary fat and/or sugars, often associated with maternal obe- sity, has strong programming effects on health [12,13] and behaviour of offspring in later life, as reviewed by Sullivan et al. [14]. In non-human male primates [15] and rats [16], increased aggressive behaviours have been reported in offspring of mothers fed a high-fat diet. In rats [17] [18,19], mice [20] and non-human primates [15], offspring exposed to a maternal high-fat diet also showed increased anxiety-like behaviours in a variety of tests later in life. On the other hand, some studies have reported reduced anxiety-related behaviours and motor activity, and increased exploration and social behaviours in rats exposed to a cafeteria diet (i.e. high in both refined sugars and saturated fat) via the maternal diet [21] or via the post-weaning diet [22]. Research in animal models has revealed the impact of perinatal nutrition on health and behaviours in later life. There is, however, a large variability in methodologies between studies, resulting in equivocal research findings. OPEN ACCESS Our study highlights the key role of prenatal and postnatal nutritional Citation: Clouard C, Gerrits WJJ, Kemp B, Val-Laillet D, Bolhuis JE (2016) Perinatal Exposure to a Diet High in Saturated Fat, Refined Sugar and Cholesterol Affects Behaviour, Growth, and Feed Intake in Weaned Piglets. PLoS ONE 11(5): e0154698. doi:10.1371/journal.pone.0154698 doi:10.1371/journal.pone.0154698 Editor: Antonio Gonzalez-Bulnes, INIA, SPAIN Received: November 13, 2015 Accepted: April 18, 2016 Published: May 18, 2016 Copyright: © 2016 Clouard 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. Editor: Antonio Gonzalez-Bulnes, INIA, SPAIN Received: November 13, 2015 Accepted: April 18, 2016 Published: May 18, 2016 Copyright: © 2016 Clouard 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. Copyright: © 2016 Clouard 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. Data Availability Statement: All relevant data are available from the Figshare database(http://figshare. com/account/projects/5229). Funding: This research has been supported by a post-doctoral study grant from the Fyssen foundation (http://www.fondationfyssen.fr/en/) awarded to CC. 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. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 1 / 24 Programming Effects of Perinatal Nutrition in Pigs interactions for early behavioural development, and reveals programming effects of early life nutrition on voluntary feed intake of piglets later in life. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Animals and housing A total of 32 multiparous sows and their litters (Tempo × Topigs 20) from the Swine Innova- tion Centre of Wageningen UR (VIC, Sterksel, The Netherlands) were used. The experiment was carried out in 2 successive replicates, with 16 sows per replicate. During gestation, the sows were housed in groups of 4 or 5 sows in pens (12 m2) with individual feeding stalls (230 cm × 72 cm). Room temperature was maintained at 18–20°C. One week before the expected parturition date, sows were housed in individual farrowing pens (240 cm × 180 cm) distributed in 2 rooms, and with partly solid (65%) and partly slatted (35%) floors. Distribution of sows over and within the 2 rooms was balanced for treatment. A jute bag was available in the pen until after parturition to be used as nesting material. During the suckling period, sows were confined in a farrowing crate, and a creep area with plastic flooring and a heating lamp above it was available for the piglets. Room temperature was maintained at a minimum of 23°C. Piglets remained in the sow’s farrowing pen with littermates until weaning. Within 3 days after birth, if needed, piglets were cross-fostered within dietary treatment groups to balance litter sizes. At 4 days of age, piglets were ear-notched for identification, received iron injections and had their tails docked. During gestation and lactation, the sows had ad libitum access to water and rooms had a natural light-dark cycle. At weaning (i.e. 4 weeks of age), 3 female piglets with a birth weight the closest to the aver- age birth weight of the females of the litter were selected per litter. Piglets with a birth weight less than 600 g and with a history of leg problems or long-term medication were excluded from selection. After weaning, the selected piglets were transported to the experimental farm Carus (Wageningen UR, The Netherlands) and housed in groups of 3 littermates in pens (280 cm × 180 cm) distributed in 2 identical and adjacent rooms. Pens were enriched with wood shavings and equipped with a chain with screws attached to it as a toy. Distribution of piglets over and within the 2 rooms was balanced for treatment. Seventy Litres of fresh wood shavings and, at the end of the dietary treatment (i.e. 8 weeks of age), 50 g of straw were added daily in the pens. Introduction First, while the majority of studies have addressed the effects of diets enriched in fat alone, only a few studies have used diets enriched in both fat and refined sugars. Yet, in modern Western societies, excessive consumption of fat is frequently associated with the consumption of excessive amounts of refined sugars [23]. Furthermore, in most published studies, mothers became obese as a result of the long-term intake of a high-fat or high-energy diet, making it hard to disentangle the effects of the diet per se from those of the maternal health status [14,24]. In addition, very little is known on the effects of maintaining the offspring on the high-fat and/or high-sugar diet after weaning, which would be highly rele- vant for human nutrition, since the early diet of children often resembles their parents’ eating habits [25,26]. Finally, as far as we know, no study has investigated the differential impact of prenatal vs. postnatal nutrition on behavioural development. While the large majority of the studies performed on rodents have yielded substantial scien- tific knowledge for future research on perinatal nutrition, the metabolic and physiological dif- ferences between rodents and humans complicate the translation of research findings into PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 2 / 24 Programming Effects of Perinatal Nutrition in Pigs applications in human health and nutrition [27]. The pig is a highly social species that shares several similarities with humans in terms of intestinal and brain anatomy and physiology [28,29]. The pig therefore emerges as a pertinent animal model to study the influence of early nutrition on spontaneous behaviours, e.g. aggression and social interactions, and responses to specific stimuli during behavioural tests, e.g. anxiety- or fear-related behaviours. We investigated the effects of prenatal and/or postnatal exposure to a HFS diet on the beha- vioural development of piglets. To that aim, the effects of prenatal and/or postnatal exposure to a diet enriched in saturated fat, sucrose, and cholesterol was compared with exposure to control diets, low in these components but high in starch. We hypothesized that 8-week prenatal (through the maternal diet during gestation) and/or 8-week postnatal (through maternal milk during the suckling period and piglet feed after weaning) exposure to the HFS diet would have adverse effects on behaviours, skin lesions as an indicator of aggression [30], and emotional reactivity (i.e. anxiety- or fear-related behaviours) of piglets after weaning. Introduction Behavioural record- ings are discussed in relation to measurements of growth, feed intake and feed efficiency. Materials and Methods The Animal Care and Use Committee of Wageningen University has approved this experiment. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Dietary treatments Four experimental diets were formulated (Table 1), with 3 control diets: for the sows, a stan- dard gestation diet and a standard lactation diet; for the piglets, a standard starter diet; and a HFS diet for both sows and piglets, i.e. an “all-in-one” diet high in saturated fat (lard), sucrose, and cholesterol. All the sows and piglets were fed standard commercial diets before the start of the experiment (i.e. before day 59 of gestation) and/or after the end of the dietary treatment (i. e. 8 weeks of age). All diets were provided as pellets. The control diets were formulated to meet or exceed the recommendations for animals’ requirements by CVB [31]. During the last 8 weeks of gestation, half of the sows received the HFS diet and the other half the standard gestation diet. Starting on the day of parturition, half of the sows of each group received the HFS diet and the other half the standard lactation diet during the 4 weeks of lactation. Starting on the day of weaning, the piglets were fed the HFS diet or the standard starter diet for 4 weeks, so that they remained on the same treatment as their mothers during lactation. Consequently, piglets were allocated to one of 4 dietary treatments in a 2 × 2 factorial design, with 8-week prenatal/ 8-week postnatal exposure to the HFS or control diets (CON) as factors: HFS/HFS, CON/HFS HFS/CON, and CON/CON treatment. Allocation to the treat- ments was balanced for sow parity, and treatments were evenly distributed between replicates, as well as within and between the rooms during gestation, lactation and after weaning. During gestation and lactation, the sows were restrictedly fed twice daily to meet the normal energy recommendations for pregnant and lactating sows. As the organoleptic properties of the HFS diet strongly differed from that of the gestation and lactation diets, gradual feed transi- tions over 4 days (i.e. 25%, 50%, 75%, 100% of the HFS diet in the total feed ration and vice versa) were done to prevent neophobic responses of the sows when exposed to a change in diet. Additionally, from 16 days before weaning, piglets also received the HFS or control starter diet (0.12 kg/piglet/day) as a creep feed to facilitate the transition to solid feed after weaning. Piglets were fed ad libitum. Animals and housing Piglets had ad libitum access to a feeder and a drinking nipple. A heating lamp was provided for the first 4 post-weaning weeks. During the first 2 post-weaning weeks, room tem- perature was maintained at a minimum of 25°C. Room temperature was then decreased to PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 3 / 24 Programming Effects of Perinatal Nutrition in Pigs 22°C for the 2 following weeks, and to 20°C for the rest of the experiment. Lights were on from 7:00 h to 19:00 h, and pop radio music was broadcasted live in the rooms during light time. 22°C for the 2 following weeks, and to 20°C for the rest of the experiment. Lights were on from 7:00 h to 19:00 h, and pop radio music was broadcasted live in the rooms during light time. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 doi:10.1371/journal.pone.0154698.t001 Measurements Weighing, feed intake and skin lesions. Piglets were weighed at birth. Piglets and feed refusals were weighed on 3 occasions, i.e. on the day of weaning (4 weeks of age), at the end of the dietary treatment (8 weeks of age), and 8 weeks later (16 weeks of age). Average daily gain (ADG, kg/day), average daily feed intake (ADFI, kg of feed/day) and gain to feed ratio (G:F, i.e. a measure of feed efficiency) were calculated per pen from weaning to the end of the treatment and from the end of the treatment to 8 weeks later. Net energy (NE, MJ) intake and the gain: NE intake ratio were also presented. On the day of weaning, and 7, 14 and 21 days later, the number of skin lesions was counted on the front, middle and rear parts of the body of standing piglets in the home pen, according to the procedure of Turner et al. [30]. Scratches (i.e. superfi- cial lesions) and deep wounds (i.e. haemorrhages) were differentiated. Behavioural observations in the home pen after weaning. On the day of weaning, and 15 and 27 days after weaning, behaviours of weaned piglets were scored live using 2-min instanta- neous scan sampling for 6 h/day during 6 sessions of 1 h (8:00–9:00 h, 9:15–10:15 h, 10:30– 11:30 h, 14:00–15:00 h, 15:15–16:15 h, 16:30–17:30 h). The behaviours (S1 Table) were recorded using a Psion hand-held computer with the Observer 5.0 software package (Noldus Information Technology B.V., Wageningen, The Netherlands). PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 4 / 24 utral detergent fibre; ADF: acid detergent fibre; (f)NSP: (fermentable) non-starch polysaccharides; NE: net energy [31] 1 DM: dry matter; NDF: neutral detergent fibre; ADF: acid detergent fibre; (f)NSP: (fermentable) non-starch polysaccharides; NE: net energy. 2 Based on calculated values [31]. 3 Standardized ileal digestible. ues [31]. ible. after 7 h of access to the feed. If needed, feed was added in the feeders to ensure that no feeder was emptied throughout the night. Feed refusals were weighed again at 9:00 h the next day, i.e. after 24 h of access to the feed. Assign- ment of the diets to the left and right feeders was counterbalanced across pens, dietary treat- ment and testing days to avoid any laterality bias. Novel environment and novel object test. Starting 5 days after the end of the dietary treatment, 2 piglets per pen were individually subjected to a combined open field (OFT) and novel object test (NOT) [32,33]. Before the tests, the piglets were habituated to the experiment- ers in their pens for 7 days. Each day, the experimenters entered each pen in random order, and stayed in each pen for approximately 5 min. First the experimenter sat in the pen (d 1 and 2), squatted (d 2 and 3), stood still in the pen (d 3 to 4), and finally walked in the pen (d 5 to 7). Each day, the experimenter allowed the piglets to approach spontaneously and tried to touch their nose, head, and body. At the end, the experimenter could walk at a normal pace around the pen and touch all piglets without signs of stress. The tests were carried out on 2 consecutive days with half of the pigs being tested on day 1 and the other half on day 2, balanced for treatment. The test arena was 5.27 x 5.25 m with wooden black walls (1.2 m high) and concrete floor. The arena was located in a room adjacent to the piglets’ home pens. The OFT started when the piglet had entered the arena with all 4 hooves and the door was closed. After 5 min, the NOT started by dropping a metal bucket from the ceiling until it touched the floor at the centre of the test arena, resulting in a sudden noise. The bucket was then left on the floor for 5 min. After each test, faeces were removed from the test arena, which was cleaned with water and cleanser, and dried with towels. The order of testing was balanced for treatment and room. During the tests, behaviours and pos- tures (S2 Table) were scored live using Psion hand-held computers with the Observer 5.0 software package (Noldus Information Technology, Wageningen, The Netherlands). Programming Effects of Perinatal Nutrition in Pigs Table 1. Ingredient and nutrient composition of the experimental diets1. Gestation diet Lactation diet Starter diet HFS diet Ingredient composition (%) Barley 34.0 26.1 24.2 15.0 Wheat 19.9 29.0 23.2 16.9 Wheat bran 15.0 10.0 ‒ 5.00 Soybean meal 11.0 14.0 22.6 10.0 Maize 10.0 12.0 25.0 ‒ Dehydrated sugarbeet pulp 5.00 ‒ ‒ ‒ Sugarbeet molasses ‒ 3.00 ‒ ‒ Vegetable fat 2.00 ‒ ‒ ‒ Sucrose ‒ ‒ ‒ 18.5 Animal fat (Lard) ‒ ‒ ‒ 12.0 Cholesterol ‒ ‒ ‒ 1.00 Peas ‒ ‒ ‒ 7.00 Potato protein ‒ ‒ ‒ 5.00 Soybean hulls ‒ ‒ ‒ 5.00 Calcium carbonate 1.20 1.15 1.70 1.50 Dicalcium phosphate 0.85 1.50 ‒ 1.60 Monocalcium phosphate ‒ ‒ 1.35 ‒ Premix 0.50 0.50 0.50 0.50 Sodium chloride 0.45 0.45 0.40 0.60 Acidifying agent 0.10 0.10 0.10 ‒ Phytase 0.01 0.01 0.01 ‒ Sodium bicarbonate ‒ ‒ ‒ 0.40 Soy oil ‒ 2.00 0.45 ‒ L-lysine HCl ‒ 0.20 0.34 ‒ L-threonine ‒ 0.04 0.08 ‒ DL-Methionine ‒ ‒ 0.11 ‒ L-tryptophan ‒ ‒ 0.02 ‒ Nutrient composition (g/kg DM)2 Sugar 46.0 60.0 45.0 225 Crude fat 51.0 50.0 37.0 147 Starch 420 439 466 238 Crude protein 166 178 207 171 Crude fibre 59.0 43.0 35.0 48.0 Crude ash 60.0 64.0 66.0 61.0 NDF 210 167 127 128 ADF 74.0 56.0 46.0 59.0 NSP 266 217 187 169 fNSP 149 120 121 100 Lysine3 6.00 8.20 11.3 8.60 Methionine + cystine3 4.80 5.00 6.90 4.80 Threonine3 4.60 5.40 7.00 5.80 Tryptophan3 1.70 1.80 2.30 1.80 DM (g/kg) 878 873 876 918 NE (MJ/kg DM) 10.7 10.9 11.0 13.2 1 DM: dry matter; NDF: neutral detergent fibre; ADF: acid detergent fibre; (f)NSP: (fermentable) non-starch polysaccharides; NE: net energy. 2 Based on calculated values [31]. 3 S d di d il l di ibl Table 1. Ingredient and nutrient composition of the experimental diets1. Ingredient composition (%) PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 5 / 24 Programming Effects of Perinatal Nutrition in Pigs Feed preference tests. The day after the end of the dietary treatment (i.e. 8 weeks of age) and 8 weeks later, the piglets were subjected to a two-choice feed preference test. The control starter diet and the HFS diet were distributed in excess to estimated intake in two adjacent feed- ers at 9:00 h. Feed refusals were weighed at 16:00 h, i.e. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 The tests were also recorded on video to perform a posteriori analyses of locomotion patterns in the arena using the Ethovision XT 10 video tracking software (Noldus Information Tech- nology B.V., Wageningen, The Netherlands). The variables calculated in Ethovision were: the time spent in the centre, walls, observer, entrance and novel object zones (Fig 1), the latencies (s) to enter the centre and novel object zones, and the total distance (m) covered during the tests. Saliva sampling and cortisol analysis. The day before the end of the dietary treatment, the piglets were habituated to the saliva collection procedure: they were allowed to chew on 2 cotton buds simultaneously for 1 min at least twice during the morning. Saliva samples were then collected at the end of the dietary treatment and 8 weeks later to determine basal cortisol levels. The day of the OFT/NOT, saliva samples were collected from each piglet in the home pen 10 min before (t0), and 15, 30 and 60 min after the piglet entered the test arena. Saliva was systematically sampled in the morning, before feeding. On the days of sampling, saliva was collected by allowing the pigs to chew on 2 cotton buds simultaneously until they were thor- oughly moistened. The cotton buds were placed in plastic tubes (2 buds per tube, Sarstedt, Etten-Leur, The Netherlands) directly after sampling and stored on ice until all samples were taken. Then, samples were centrifuged at 1560 × g for 10 min at 4°C and stored at -20°C until further analyses. Salivary cortisol concentrations (ng/mL) were measured in duplicate using a radioimmunoassay kit (COAT-A-COUNT1, Siemens Healthcare Diagnostics, Los Angeles, USA) modified and validated for pigs [34], with an intra-assay CV of 4% and an inter-assay CV of 5%. 6 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs Fig 1. Zones in the open field and novel object tests. The zones were defined using the Ethovision XT 10 video tracking software to perform a posteriori analyses of locomotion patterns in the arena. doi:10.1371/journal.pone.0154698.g001 Fig 1. Zones in the open field and novel object tests. The zones were defined using the Ethovision XT 10 video tracking software to perform a posteriori analyses of locomotion patterns in the arena. d i 10 1371/j l 0154698 001 doi:10.1371/journal.pone.0154698.g001 doi:10.1371/journal.pone.0154698.g001 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Statistical analyses As preliminary 7 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs analyses showed that the number of skin lesions on the day of arrival to the home pen signifi- cantly differed from the number of lesions 7, 14 or 21 days after weaning, these data were ana- lysed separately. The numbers of skin lesions the day of weaning were analysed using a mixed model that included the fixed effects of prenatal diet, postnatal diet, their interactions and rep- licate. Skin lesions at 7, 14 and 21 days after weaning were analysed using a repeated mixed model with prenatal diet, postnatal diet, day, their interactions and replicate as fixed effects. Piglet nested within pen, prenatal diet, postnatal diet and replicate was the experimental unit. In each treatment group (HFS/HFS, CON/HFS, HFS/CON, CON/CON), intake of the control starter diet during the two-choice feed preference tests was compared with the intake of the HFS diet by paired Student’s t tests. Salivary cortisol levels were averaged per pen and per sam- pling time. A mixed repeated model was used to estimate the fixed effect of prenatal diet, post- natal diet, sampling time, their interactions and replicate on salivary basal cortisol levels (at the end of the treatment and 8 weeks later), or cortisol levels before and after the OFT/NOT (before, and 15, 30 and 60 min after testing). Pen nested within prenatal diet, postnatal diet and replicate was the experimental unit. Principal component analysis. A Principal Component Analysis (PCA) was conducted on the variables from the OFT/ NOT to examine whether variation in behavioural responses of the pigs (n = 63 piglets in total) could be summarized in a limited number of factors. In both the OFT and NOT, ‘jumping’, ‘comfort behaviours’, ‘sitting’, ‘lying’ and ‘barks’ hardly occurred, and were excluded from the analyses. ‘Nosing floor’, ‘rooting floor’, ‘nosing walls’ and ‘rooting walls’ were pooled as ‘exploring arena’. ‘Touching bucket’, ‘exploring bucket’ and ‘chewing bucket’ were pooled as ‘exploring bucket’. ‘Slow approach’ and ‘fast approach’ were pooled as ‘approaching bucket’. ‘Urinating’ and ‘defecating’ were pooled as ‘eliminating’. ‘Squeals’, ‘grunt squeals’ and ‘screams’ were pooled as ‘high-pitched vocalisations’, while ‘long grunts’, and ‘short grunts’ were pooled as ‘low-pitched vocalisations’. All variables were sub- jected to a general linear model with replicate as fixed effect to obtain residuals used for the PCA. Statistical analyses Statistical analyses were conducted using SAS version 9.1.3 (Statistical Analysis Software; SAS Institute, Cary, NC, USA). If the model residuals were not normally distributed, the statistical analyses were performed on (arcsin) square root or logarithmically transformed data. Two pens were excluded from the study because of a methodological error in replicate 2, resulting in n = 8 pens for CON/HFS and HFS/CON treatments, and n = 7 pens for HFS/HFS and CON/CON treatments. Data are presented as (untransformed) means ± SEMs. The upper limit for the statistically significant effect was set at p  0.05, with 0.05 < p  0.10 considered as a trend. Effects of dietary treatment. Litter size at farrowing was analysed using a mixed model with prenatal diet and replicate as fixed effects. BW of piglets was averaged per pen. BW at birth was analysed using a mixed model with prenatal diet and replicate as fixed effects. BW, ADG and ADFI after weaning were analysed using mixed models with prenatal diet, postnatal diet, their interactions and replicate as fixed effects. BW at birth was included as covariate for BW at weaning. BW at weaning was included as covariate for BW after weaning, ADG, G:F and ADFI. Including BW at birth as a covariate for BW at weaning, and BW at weaning as a covariate for BW, ADG, G:F and ADGI after weaning did not change the results. Piglet behav- iours in the home pen after weaning were averaged per pen and per day. Weaning is a major stressor for piglets, and the behaviours on the day after weaning may therefore reflect the response of piglets to this stressor rather than display their normal time budget. Indeed, behav- iours on this day differed profoundly from behaviours 15 and 27 days later, and were therefore analysed separately. Behaviours on the day after weaning were analysed using a mixed model that included the fixed effects of prenatal diet, postnatal diet, their interactions and replicate. Behaviours at 15 and 27 days after weaning were analysed using a repeated mixed model with prenatal diet, postnatal diet, day, their interactions and replicate as fixed effects. Statistical analyses After extraction, principal components were scaled by their standard deviations (square roots of associated Eigenvalues) and subjected to orthogonal rotation (varimax) to obtain inde- pendent factors. The factors retained from the PCA were analysed using a mixed model with prenatal diet, postnatal diet and their interactions as fixed effects, and pig as the experimental unit. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs Table 2. Body weight and average daily feed intake of piglets after weaning. Prenatal diet Control HFS p-values Postnatal diet Control HFS Control HFS Prenatal Postnatal Prenatal × Postnatal Body weight (kg) Birth 1.41 ± 0.06 1.50 ± 0.09 1.49 ± 0.09 1.48 ± 0.07 0.71 ‒ ‒ Weaning (4 weeks of age) 7.94 ± 0.34 8.43 ± 0.16 8.71 ± 0.29 8.60 ± 0.15 0.04 0.50 0.28 End treatment (8 weeks of age) 19.2 ± 1.13 15.9 ± 0.46 19.6 ± 0.91 16.3 ± 0.37 0.67 < 0.0001 0.67 8 weeks later (16 weeks of age) 73.0 ± 1.85 65.6 ± 1.66 73.8 ± 2.35 67.6 ± 1.93 0.94 0.0004 0.56 Average daily gain (kg/day) Weaning-End of treatment 0.36 ± 0.03 0.26 ± 0.02 0.39 ± 0.03 0.27 ± 0.01 0.75 < 0.0001 0.67 End treatment-8 weeks later 0.96 ± 0.03 0.89 ± 0.02 0.97 ± 0.03 0.92 ± 0.03 0.80 0.02 0.62 Average daily feed intake (kg/day) Weaning-End of treatment 0.58 ± 0.04 0.53 ± 0.03 0.62 ± 0.04 0.53 ± 0.03 0.82 0.05 0.75 End treatment-8 weeks later 2.11 ± 0.09 1.65 ± 0.06 2.07 ± 0.13 1.70 ± 0.06 0.49 < 0.0001 0.44 Gain to feed ratio (kg weight/kg feed) Weaning-End of treatment 0.67 ± 0.01 0.50 ± 0.03 0.63 ± 0.03 0.52 ± 0.03 0.52 < 0.0001 0.26 End treatment-8 weeks later 0.43 ± 0.02 0.51 ± 0.01 0.45 ± 0.01 0.51 ± 0.01 0.20 < 0.0001 0.58 Data are averaged per pen and presented as means ± SEMs. Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). Table 2. Body weight and average daily feed intake of piglets after weaning. Data are averaged per pen and presented as means ± SEMs. Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). doi:10.1371/journal.pone.0154698.t002 Eight weeks after the end of the treatment (16 weeks of age), the piglets exposed to postnatal HFS diet weighed significantly less than the control piglets (HFS: 66.54 ± 0.29 kg, CON: 73.42 ± 1.47 kg). Skin lesions Day of weaning. The day of arrival to the post-weaning pen, the piglets exposed to the prenatal HFS diet tended to have fewer skin lesions on the front (Fig 2A) and middle parts (Fig 2B) of the body than the control piglets. The piglets exposed to the prenatal HFS diet also had fewer deep wounds on the whole body than the control piglets (Fig 2F). The postnatal diet did not affect body lesions on the day of weaning. Post-weaning weeks. The weeks following weaning, both the postnatal, and to a lesser extent, prenatal HFS diet decreased the total number of skin lesions on the whole body (Fig 2D), which was mostly due to fewer scratches on the whole body (postnatal diet effect, Fig 2E), and/or fewer lesions on the middle part of the body (postnatal and prenatal diet effect, Fig 2B). The number of skin lesions on the rear part of the body was also affected by a prenatal diet × postnatal diet interaction, with the CON/HFS-piglets having fewer skin lesions on the rear part of the body than the CON/CON-piglets (Fig 2C). From the end of the treatment to 8 weeks later, the piglets exposed to the post- natal HFS diet had a 20% lower ADFI (HFS: 1.68 ± 0.04, CON: 2.09 ± 0.08 kg/day), but only 7% lower ADG (HFS: 0.90 ± 0.02, CON: 0.97 ± 0.02 kg/day), resulting in an increased G:F (HFS: 0.51 ± 0.00, CON: 0.44 ± 0.01) compared to the control piglets. The prenatal diet or its interactions with the postnatal diet did not affect piglet BW, ADG, ADFI or G:F after weaning. Body weight and feed intake Initial litter size was not affected by the prenatal diet (HFS: 15.38 ± 0.64 piglets, CON: 15.73 ± 0.62 piglets; F1, 30 = 0.08, p = 0.78). Data of piglets’ growth, feed intake and feed effi- ciency are presented in Table 2. The prenatal diet did not affect piglet BW at birth (HFS: 1.48 ± 0.05 kg, CON: 1.46 ± 0.06 kg). The day of weaning (i.e. 4 weeks of age), the piglets exposed to the prenatal HFS diet weighed more than the control piglets (HFS: 8.65 ± 0.16 kg, CON: 8.18 ± 0.19 kg). At the end of the treatment (8 weeks of age), the piglets exposed to the postnatal HFS diet weighed significantly less than the control piglets (HFS: 16.06 ± 0.29 kg, CON: 19.38 ± 0.69 kg). From weaning to the end of the treatment, the piglets exposed to the postnatal HFS diet had a lower ADG (-30%, HFS: 0.27 ± 0.01, CON: 0.39 ± 0.02 kg/day), ADFI (-12%, HFS: 0.53 ± 0.02 kg/day, CON: 0.60 ± 0.03 kg/day), and G:F (HFS: 0.51 ± 0.02 kg/kg feed, i.e. ~0.42 kg/10 MJ NE, CON: 0.65 ± 0.02 kg/kg feed, i.e. ~0.68 kg/10 MJ NE) compared to the control piglets. The piglets exposed to the postnatal HFS diet seemed to have higher daily NE intake than the control piglets (HFS: ~6.42 MJ NE/day, Control: ~5.78 MJ NE/day). PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 8 / 24 Programming Effects of Perinatal Nutrition in Pigs Fig 2. Skin lesions of piglets after weaning. (A) Total lesions, (B) total scratches and (C) total deep wounds on the whole body, and total lesions in the (D) front, (E) middle or (F) rear part of the body. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth. Data on the day of weaning (left of the dotted line) were analysed separately from data on 7, 14 and 21 days after weaning (right of the dotted line). Different letters indicate a significant time effect between 7, 14 and 21 days after weaning (p  0.05). doi:10 1371/journal pone 0154698 g002 g g g g. (A) Total lesions, (B) total scratches and (C) total deep wounds on the whole body, and total lesions in the y. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth. Data were analysed separately from data on 7, 14 and 21 days after weaning (right of the dotted line). Different en 7, 14 and 21 days after weaning (p  0.05). Fig 2. Skin lesions of piglets after weaning. (A) Total lesions, (B) total scra (D) front, (E) middle or (F) rear part of the body. Piglets were exposed to a HF h d f i (l f f h d d li ) l d l f d Fig 2. Skin lesions of piglets after weaning. (A) Total lesions, (B) total scratches and (C) total deep wounds on the whole body, and total lesions in the (D) front, (E) middle or (F) rear part of the body. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth. Data on the day of weaning (left of the dotted line) were analysed separately from data on 7, 14 and 21 days after weaning (right of the dotted line). Different letters indicate a significant time effect between 7, 14 and 21 days after weaning (p  0.05). doi:10.1371/journal.pone.0154698.g002 and a tendency for prenatal diet × postnatal diet interaction effects for time spent on mainte- nance behaviours, standing and exploring pen mates. Post hoc tests did not reveal significant pairwise differences. Post-weaning weeks. Behavioural activity in the home pen 15 and 27 days after weaning is presented in Table 4. doi:10.1371/journal.pone.0154698.g002 Behavioural observations Day after weaning. The prenatal diet, postnatal diet and their interactions did not affect piglet behaviours on the day after weaning, with the exception that the piglets exposed to the postnatal HFS diet spent more time mounting pen mates than the control piglets (Table 3), PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 9 / 24 Programming Effects of Perinatal Nutrition in Pigs Table 3. Behavioural activity of piglets in the home pen the day after weaning. Prenatal diet Control HFS p-values Postnatal diet Control HFS Control HFS Prenatal Postnatal Prenatal × Postnatal Inactive behaviours (%) Lying 55.0 ± 3.98 55.0 ± 2.77 59.0 ± 3.55 48.0 ± 2.59 0.66 0.11 0.12 Sitting/kneeling 1.24 ± 0.27 1.00 ± 0.46 0.93 ± 0.19 1.11 ± 0.30 0.76 0.93 0.51 Standing 6.85 ± 0.92 6.16 ± 0.55 5.35 ± 0.47 7.51 ± 1.07 0.92 0.34 0.06 Locomotion behaviours (%) Walking 1.77 ± 0.51 2.41 ± 0.71 1.88 ± 0.46 2.22 ± 0.40 0.92 0.26 0.53 Feed-related behaviours (%) Ingesting feeding materials 6.48 ± 1.10 6.16 ± 1.09 5.49 ± 0.59 7.01 ± 0.91 0.94 0.54 0.33 Exploring feeding materials 1.34 ± 0.27 1.06 ± 0.34 1.11 ± 0.29 1.27 ± 0.30 0.85 0.84 0.35 Exploratory behaviours (%) Exploring environment 21.0 ± 2.41 22.8 ± 1.53 20.9 ± 2.51 26.1 ± 1.24 0.44 0.10 0.40 Social behaviours (%) Aggressing pen mates 1.03 ± 0.38 0.76 ± 0.41 0.65 ± 0.29 1.53 ± 1.13 0.82 0.95 0.35 Manipulating pen mates 0.45 ± 0.10 0.44 ± 0.19 0.69 ± 0.20 0.56 ± 0.08 0.13 0.50 0.63 Exploring pen mates 2.17 ± 0.27 1.39 ± 0.33 1.37 ± 0.34 1.75 ± 0.26 0.48 0.52 0.08 Mounting pen mates 0.05 ± 0.03 0.37 ± 0.19 0.09 ± 0.05 0.19 ± 0.10 0.64 0.05 0.29 Playing behaviours (%) Social, non-social and substrate playing 1.77 ± 0.55 2.04 ± 0.33 1.99 ± 0.60 1.72 ± 0.51 0.79 0.88 0.52 Other (%) Maintenance 0.40 ± 0.15 0.23 ± 0.12 0.25 ± 0.10 0.58 ± 0.24 0.35 0.47 0.07 Eliminating 0.16 ± 0.11 0.07 ± 0.03 0.12 ± 0.07 0.21 ± 0.06 0.50 0.96 0.23 Data are presented as % of observation (means ± SEMs). Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). doi:10 1371/journal pone 0154698 t003 Table 3. Behavioural activity of piglets in the home pen the day after weaning. Data are presented as % of observation (means ± SEMs). Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). doi:10.1371/journal.pone.0154698.t003 interactions. As no interactions between prenatal diet or postnatal diet and time were found, data were averaged over both observation days. The weeks following weaning, the time spent lying and sitting/kneeling inactive was affected by prenatal diet × postnatal diet PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 10 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Feed preference tests Although the CON/CON‒piglets seemed to systematically prefer the control starter diet to the HFS diet, a statistical trend was only found for the 24‒h feed preference tests at the end of the treatment (p = 0.06; Fig 3). The CON/HFS‒piglets seemed to prefer the HFS diet to the control starter diet during both the 7‒h and 24‒h feed preference tests at the end of the treatment, but the preference did not reach the threshold for significance. Eight weeks later, however, the CON/HFS‒piglets tended to prefer the HFS diet to the control starter diet during both the 7‒h and 24‒h feed preference tests (p = 0.05 and p = 0.08, respectively). The HFS/CON‒piglets exhibited no consistent patterns of feed preferences during the tests (p > 0.10). The HFS/ HFS‒piglets tended to prefer the HFS diet to the control starter diet during both the 7‒h and 24‒h tests at the end of the dietary treatment (p = 0.23 and p = 0.10, respectively) and 8 weeks later (p = 0.05 and p = 0.09, respectively). Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). doi:10.1371/journal.pone.0154698.t004 Post hoc comparisons showed that the CON/CON-piglets tended to spend more time lying inactive than the HFS/CON-piglets (p = 0.06), with levels of the CON/HFS- and HFS/HFS-piglets in between. The CON/CON-piglets and HFS/HFS-piglets spent more time sitting/kneeling than the CON/HFS-piglets (p = 0.01 for both), with levels of the HFS/CON- piglets in between. Standing inactive was increased by the postnatal HFS diet. Both the prenatal and postnatal HFS diet increased the time spent walking. The time spent exploring and ingesting feeding materials and exploring the environment was influenced by prenatal diet × postnatal diet interactions. Compared to the CON/HFS -pig- lets, the HFS/HFS-piglets spent less time ingesting feeding materials (p = 0.02). The HFS/HFS- piglets also spent less time exploring feeding materials than the HFS/CON- (p = 0.0004) and CON/CON-piglets (p = 0.02), while the HFS/CON-piglets explored feeding materials (p = 0.01) more than the CON/HFS-piglets. Numerical data suggest a lower time spent explor- ing the environment in the CON/CON- and HFS/HFS-piglets compared to the other groups. The postnatal HFS diet tended to reduce time spent on aggression, but increased oral manipulation of pen mates. Trends were found for an effect of prenatal diet × postnatal diet interaction on the time spent mounting and exploring pen mates. Numerical data suggest less time spent mounting and exploring the pen mates in the CON/CON- and HFS/HFS-piglets compared to the other groups. The prenatal and postnatal diets did not affect the time spent on play behaviour, elimination or maintenance behaviour. 11 / 24 Programming Effects of Perinatal Nutrition in Pigs Table 4. Behavioural activity of piglets in the home pen 15 and 27 days after weaning. Prenatal diet Control HFS p-values Postnatal diet Control HFS Control HFS Prenatal Postnatal Prenatal × Postnatal Inactive behaviours (%) Lying 58.3 ± 3.41 53.0 ± 2.39 52.2 ± 1.77 56.0 ± 1.72 0.51 0.74 0.05 Sitting/kneeling 1.15 ± 0.28 0.43 ± 0.09 0.94 ± 0.25 1.13 ± 0.17 0.21 0.17 0.02 Standing 1.28 ± 0.28 2.54 ± 0.65 1.93 ± 0.47 2.60 ± 0.32 0.34 0.01 0.60 Locomotion behaviours (%) Walking 0.91 ± 0.22 1.20 ± 0.33 1.25 ± 0.45 1.71 ± 0.38 0.03 0.05 0.98 Feed-related behaviours (%) Ingesting feeding materials 11.9 ± 0.67 13.7 ± 1.40 12.7 ± 0.98 11.2 ± 0.82 0.28 0.87 0.02 Exploring feeding materials 0.71 ± 0.11 0.54 ± 0.08 1.00 ± 0.09 0.39 ± 0.10 0.94 0.001 0.04 Exploratory behaviours (%) Exploring environment 18.9 ± 2.07 20.7 ± 1.29 23.1 ± 1.68 19.1 ± 1.42 0.38 0.46 0.07 Social behaviours (%) Aggressing pen mates 0.26 ± 0.12 0.08 ± 0.03 0.22 ± 0.08 0.09 ± 0.07 0.50 0.06 0.72 Manipulating pen mates 1.16 ± 0.23 1.68 ± 0.31 1.44 ± 0.21 2.55 ± 0.91 0.22 0.05 0.76 Exploring pen mates 1.78 ± 0.40 1.91 ± 0.15 2.03 ± 0.22 1.34 ± 0.21 0.50 0.24 0.08 Mounting pen mates 0.08 ± 0.05 0.21 ± 0.06 0.13 ± 0.08 0.04 ± 0.02 0.25 0.44 0.09 Playing behaviours (%) Social, non-social and substrate playing 2.82 ± 0.61 3.20 ± 0.64 2.08 ± 0.20 2.98 ± 0.70 0.68 0.40 0.68 Others (%) Maintenance 0.18 ± 0.06 0.19 ± 0.08 0.19 ± 0.05 0.09 ± 0.03 0.30 0.30 0.12 Eliminating 0.59 ± 0.11 0.56 ± 0.11 0.63 ± 0.06 0.68 ± 0.07 0.37 0.87 0.53 Data are presented as % of observations (means ± SEMs). Within each treatment, data from day 15 and day 27 after weaning are averaged. Significant main effects of prenatal diet, postnatal diet or their interactions are indicated in bold (p  0.05) and trends are indicated in bold italics (0.05 < p  0.10). doi:10 1371/journal pone 0154698 t004 Behavioural activity of piglets in the home pen 15 and 27 days after weaning. Data are presented as % of observations (means ± SEMs). Within each treatment, data from day 15 and day 27 after weaning are averaged. doi:10.1371/journal.pone.0154698.t004 Programming Effects of Perinatal Nutrition in Pigs Fig 3. Feed intake (kg) during the feed preference tests. (A) 7‒h and (B) 24‒h feed preference tests done at the end of the dietary treatment, and (C) 7‒h and (D) 24‒h feed preference tests done 8 weeks later. During the tests, the piglets had the choice between the HFS diet and the control (CON) starter diet distributed in two feeders in the home pen. Percentages above bars indicate the intake of the HFS diet relative to total intake during the test. Symbols indicate significant differences between the absolute intake of the HFS vs. CON diet during the test: * p  0.05; † 0.05 < p  0.10. doi:10 1371/journal pone 0154698 g003 Fig 3. Feed intake (kg) during the feed preference tests. (A) 7‒h and (B) 24‒h feed preference tests done at the end of the dietary treatment, and (C) 7‒h and (D) 24‒h feed preference tests done 8 weeks later. During the tests, the piglets had the choice between the HFS diet and the control (CON) starter diet distributed in two feeders in the home pen. Percentages above bars indicate the intake of the HFS diet relative to total intake during the test. Symbols indicate significant differences between the absolute intake of the HFS vs. CON diet during the test: * p  0.05; † 0.05 < p  0.10. doi:10.1371/journal.pone.0154698.g003 vocalisations in the OFT and NOT, and high negative loadings for time spent exploring the arena and walking in the OFT. The variables time spent in centre and novel object zones during the NOT loaded positively, and time spent in wall and observer zones during the NOT loading negatively on the ‘Location NOT’ factor. The factor ‘Locomotion NOT & Activity’ had high positive loadings for distance covered and time spent walking and exploring the arena during the NOT, and high negative loadings for time spent standing alert in the NOT and OFT. The time spent walking and the distance covered during the OFT loaded positively, and the time spent standing in the OFT loaded negatively in the ‘Locomotion OFT’ factor. The ‘Location OFT’ had high positive loadings for time spent in wall, observer and entrance zones, and a high negative loading for time spent in the centre of the OFT. Principal component analysis The variables (means ± SEMs) of the OFT/ NOT are presented in S3 Table. Seven factors were retained from the PCA (Eigenvalue > 1.2) and were labelled according to the variables loaded on the factor (Table 5). The factors explained 78% of total variance. The factor ‘Alert OFT & Vocalisations’ had high positive loadings for standing alert in OFT, and low- and high-pitched 12 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 The ‘Interactions with novel object’ factor had high positive loadings for the time spent walking, approaching the bucket and with- drawing from the bucket, and a high negative loading for standing in the NOT. Finally, the fre- quency of eliminating behaviours (i.e. defecating and urinating) in the OFT and NOT loaded positively, and the time exploring the novel object loaded negatively in the ‘Eliminating & Avoiding novel object’ factor. No trends or significant effects of prenatal or postnatal diet or their interaction were found on the retained PCA factors (Table 6). 13 / 24 Programming Effects of Perinatal Nutrition in Pigs Table 5. Loadings on the factors extracted by principal component analysis, after orthogonal rotation, of variables recorded on individual piglets Measures Alert OFT & Vocalisations Location NOT Locomotion NOT & Activity Locomotion OFT Location OFT Interactions with novel object Eliminating & Avoiding novel object Open field test Walking (%) -0.48 0.26 0.30 0.69 -0.03 0.11 0.10 Standing alert (%) 0.67 -0.21 -0.48 0.01 -0.11 0.04 -0.22 Standing (%) -0.14 -0.07 0.19 -0.82 0.25 -0.20 0.13 Exploring arena (%) -0.76 0.08 0.38 -0.09 -0.05 0.08 0.24 Low-pitched vocalisations (freq) 0.72 0.16 0.01 0.38 0.14 0.00 0.03 High-pitched vocalisations (freq) 0.64 0.29 0.02 0.34 0.02 -0.12 0.21 Eliminating (freq) 0.19 0.08 0.06 ‒0.01 0.14 ‒0.04 0.47 Distance covered (m) 0.21 0.25 ‒0.01 0.74 0.15 ‒0.12 ‒0.01 Latency to centre zone (s) ‒0.02 0.10 0.08 ‒0.28 0.04 ‒0.03 0.16 Time in the centre zone (%) 0.06 0.05 ‒0.16 0.23 ‒0.65 0.28 0.15 Time in wall zone (%) 0.06 0.12 0.01 ‒0.03 0.76 ‒0.23 ‒0.01 Time in observer zone (%) 0.26 ‒0.16 ‒0.10 0.07 0.73 0.12 0.15 Time in entrance zone (%) -0.03 ‒0.21 ‒0.23 0.02 0.45 0.18 0.28 Novel object test Walking (%) 0.19 ‒0.04 0.72 -0.22 ‒0.08 0.50 ‒0.15 Standing alert (%) ‒0.08 ‒0.10 ‒0.83 0.16 0.01 0.02 ‒0.02 Standing (%) 0.04 0.04 0.07 ‒0.06 0.14 ‒0.67 0.26 Exploring arena (%) ‒0.01 ‒0.18 0.48 ‒0.12 ‒0.35 0.03 0.32 Low-pitched vocalisations (freq) 0.74 0.11 0.20 ‒0.12 0.07 ‒0.03 0.05 High-pitched vocalisations (freq) 0.58 0.24 0.16 ‒0.08 0.06 ‒0.14 0.11 Eliminating (freq) ‒0.07 ‒0.04 0.19 ‒0.21 0.01 ‒0.09 0.51 Distance covered (m) ‒0.02 0.12 0.50 0.37 -0.21 ‒0.06 0.20 Latency to centre zone (s) ‒0.03 0.25 0.16 ‒0.26 ‒0.05 0.12 ‒0.15 Time in the centre zone (%) 0.12 0.89 ‒0.05 0.11 ‒0.13 0.13 0.13 Latency to novel object zone (s) ‒0.18 ‒0.24 ‒0.04 ‒0.13 ‒0.10 0.18 ‒0.14 Time in novel object zone (%) 0.08 0.87 0.02 0.08 ‒0.05 ‒0.03 ‒0.01 Time in wall zone (%) ‒0.13 ‒0.87 0.03 ‒0.03 ‒0.13 0.01 0.04 Time in observer zone (%) 0.01 ‒0.59 0.48 ‒0.04 0.31 0.03 0.22 Time in entrance zone (%) ‒0.17 ‒0.31 0.55 0.05 0.15 ‒0.03 ‒0.01 (Continued by principal component analysis, after orthogonal rotation, of variables recorded on individual piglets. s on the factors extracted by principal component analysis, after orthogonal rotation, of variables recorded o Table 5. Loadings on the factors extracted by principal component analysis, after orthogonal rotation, o Table 5. Loadings on the factors extracted by princ (Continued) (Continued) PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 14 / 24 Programming Effects of Perinatal Nutrition in Pigs Table 5. (Continued) Measures Alert OFT & Vocalisations Location NOT Locomotion NOT & Activity Locomotion OFT Location OFT Interactions with novel object Eliminating & Avoiding novel object Approaching bucket (%) ‒0.08 0.17 0.13 ‒0.02 0.00 0.75 ‒0.03 Withdrawing from bucket (%) ‒0.12 ‒0.06 ‒0.01 0.07 ‒0.04 0.80 0.19 Exploring bucket (%) 0.24 0.11 0.30 ‒0.22 0.34 ‒0.11 ‒0.59 Variance explained (%) 19.02 14.76 12.99 9.74 8.69 7.21 5.60 Variables were recorded in 8-week-old piglets (n = 63) during the combined open field and novel object tests. Proportions of total variation explained by each factor are given. Loadings  0.40 or  ‒0.40 are indicated in bold italics, and loadings  0.50 or  ‒0.50 are indicated in bold. d i 10 1371/j l 0154698 t005 Variables were recorded in 8-week-old piglets (n = 63) during the combined open field and novel object tests. Proportions of total variation explained by each factor are given. Loadings  0.40 or  ‒0.40 are indicated in bold italics, and loadings  0.50 or  ‒0.50 are indicated in bold. Salivary cortisol analyses Compared to the prenatal control diet, the prenatal HFS diet tended to decrease basal salivary cortisol levels measured at the end of the treatment and 8 weeks later (HFS: 2.68 ± 0.20 ng/mL, CON: 2.26 ± 0.19 ng/mL, F1, 27 = 3.75, p = 0.06). No effects of the postnatal diet, time or their interactions were found on basal salivary cortisol levels (p > 0.10). A significant effect of time was found on salivary cortisol levels the day of the OFT/NOT (Fig 4), with a transient increase in concentration 15 min after the test and a return to basal levels 60 min after the test. The day of the OFT/NOT, the piglets exposed to the postnatal HFS diet had higher salivary cortisol lev- els than the control piglets (HFS: 1.92 ± 0.14 ng/mL, CON: 1.61 ± 0.12 ng/mL). Discussion This study showed that late prenatal and/or early postnatal exposure to a diet enriched in satu- rated fat, sucrose, and cholesterol had no evident effects on anxiety- or fear-related behaviours in a novelty test, but impacted locomotion, social and exploratory behaviours, as well as long- term feed intake, growth, and feed efficiency in weaned piglets. Both prenatal and postnatal exposure to the HFS diet affected piglet aggressive behaviour in the home pen after weaning. Piglets exposed to the HFS diet before birth had fewer skin lesions Table 6. Behavioural responses of piglets in the open field and novel object tests expressed as factor scores extracted by principal component analysis. Prenatal diet Control HFS p-values Postnatal diet Control HFS Control HFS Prenatal Postnatal Prenatal × postnatal Alert OFT & Vocalisations 0.29 ± 0.47 -0.01 ± 0.24 -0.31 ± 0.29 0.06 ± 0.31 0.38 0.96 0.32 Location NOT 0.09 ± 0.23 -0.26 ± 0.24 0.07 ± 0.17 0.01 ± 0.26 0.55 0.56 0.56 Locomotion NOT & Activity 0.37 ± 0.22 -0.12 ± 0.41 0.15 ± 0.27 -0.27 ± 0.32 0.67 0.12 0.82 Locomotion OFT -0.15 ± 0.20 -0.18 ± 0.44 0.14 ± 0.19 0.08 ± 0.17 0.49 0.84 0.51 Location OFT 0.19 ± 0.23 -0.51 ± 0.30 0.14 ± 0.20 -0.06 ± 0.22 0.75 0.12 0.43 Interaction with novel object -0.07 ± 0.45 -0.03 ± 0.21 0.30 ± 0.24 -0.12 ± 0.28 0.56 0.67 0.31 Eliminating & exploring novel object 0.13 ± 0.21 -0.03 ± 0.23 0.17 ± 0.23 -0.26 ± 0.25 0.93 0.38 0.58 Data are presented as means ± SEMs. doi:10.1371/journal.pone.0154698.t006 ehavioural responses of piglets in the open field and novel object tests expressed as factor scores extracted n the open field and novel object tests expressed as factor scores extracted by principal component Table 6. Behavioural responses of piglets in the open field and novel object tests expressed as factor sc analysis. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 15 / 24 Programming Effects of Perinatal Nutrition in Pigs Fig 4. Salivary cortisol concentrations the day of the open field and novel object tests. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth. Saliva samples were collected 10 min before (t0), and 15 (t15), 30 (t30) and 60 (t60) min after start of the test. Different letters indicate a significant time effect (p  0.05). Discussion doi:10 1371/journal pone 0154698 g004 Fig 4. Salivary cortisol concentrations the day of the open field and novel object tests. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth Saliva samples were collected 10 min before (t0) and Fig 4. Salivary cortisol concentrations the day of the open field and novel object tests. Piglets were exposed to a HFS diet or a control (CON) diet 8 weeks before and/or 8 weeks after birth. Saliva samples were collected 10 min before (t0), and 15 (t15), 30 (t30) and 60 (t60) min after start of the test. Different letters indicate a significant time effect (p  0.05). doi:10.1371/journal.pone.0154698.g004 doi:10.1371/journal.pone.0154698.g004 on the front and middle body parts, and fewer deep wounds on the whole body on the day of arrival to the post-weaning pen. Lesions on the front part of the body and on the flanks are valid indicators of reciprocal fighting [30], indicating that piglets fed the HFS diet before birth engaged less, and with lower intensity, in reciprocal fights in the farrowing crate and/or during transport in the truck. During the weeks following weaning, piglets exposed to the HFS diet after birth exhibited fewer aggressive behaviours, and had fewer skin lesions on the whole body than control piglets. Notably, compared to piglets not exposed to the HFS diet at all, piglets exposed to the HFS diet only after birth had fewer skin lesions on the rear part of the body, which reflect receiving un-retaliated aggression, i.e. ‘bullying’ behaviours [30]. This suggests that the postnatal HFS diet decreased not only ‘normal’ reciprocal aggression, but also aberrant bullying behaviours during the early post-weaning period. High-fat and high-sugar diets have been found to exert some “comforting effects” in stressful situations, with both animals and humans showing a tendency to consume this so-called “comfort food” following chronic stress [35]. We speculate that chronic exposure to the HFS diet, a palatable “comfort food”, may have alleviated the social tensions, and reduced the agonistic interactions after weaning, a stressful event in pig husbandry. The intake of the HFS diet after birth affected other social interactions, with more mounting directly after weaning, and more manipulative behaviours directed at pen mates during the weeks following weaning. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Discussion Mounting is a complex social behaviour, which has been linked not only with dominance and sexual behaviours [36], but also with motivation to play or explore, and a high state of arousal [37,38]. Manipulative behaviours (e.g. belly nosing, chewing tail or 16 / 24 Programming Effects of Perinatal Nutrition in Pigs ears of pen mates) are known to represent re-directed exploratory or suckling behaviours in weaned piglets [39,40]. Although excessive occurrences of these behaviours may reflect poor adaptation to weaning [41], can cause severe skin injuries, and are not desirable on pig farms [42,43], their frequency remained very low in our study. The increase in mounting and, possi- bly, manipulative behaviours might thus reflect an enhanced motivation for social contact [44] rather than an increase in negative social interactions per se. Prior studies have reported increased agonistic behaviours with a high-fat diet in non- human primates [15] and rats [4,16]. Others found fewer skin lesions, reduced aggression, and increased non-agonistic social interactions in juvenile minipigs fed a diet high in fat and cho- lesterol [9] or in juvenile monkeys fed a high-cholesterol diet [8]. We also reported decreased aggression with a high-cholesterol diet, suggesting that dietary cholesterol may have inhibitory effect on aggressiveness. Alternatively, we cannot rule out the possibility that the decrease in aggression was caused by high levels of sucrose, or the combination of high levels of fat and sugars in the HFS diet. Accordingly, Lalanza et al. [22] found increased social interactions in juvenile rats fed a cafeteria diet high in both fat and refined sugars for 8 weeks after weaning while intake of beverages high in sugars has been found to decrease aggression in adolescent humans [7]. We found no evidence of dietary effects on anxiety-related behaviours in the OFT/NOT, nor on the behavioural activity of piglets on the day directly after weaning. As stated earlier, weaning is a stressful event, and changes in behavioural activity (e.g. increased aggression, abnormal behaviours) are thought to reflect the piglet’s ability to cope with this stressful chal- lenge. Taken together, our behavioural data do not support the postulate that a HFS diet would increase stress or anxiety-related behaviours, thus contradicting prior research in rodents and non-human primates [15,17–20]. Prior studies have confirmed that standing alert, high- pitched vocalisations, and defecations in novelty tests are related to negative emotional states in pigs [32,45]. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Discussion This, together with the transient increased in salivary cortisol concentrations after the test, suggests that the combined OFT/NOT is a significant stressful event, and a rele- vant test to assess emotional reactivity in piglets. Discrepancies in results between studies may be related to differences in diet composition. While increased anxiety levels have been found in offspring from obese mothers fed high-fat diets [17–19], some studies have reported reduced anxiety-related behaviours in rats exposed to a maternal high-fat high-sugar cafeteria diet [21] or fed a cafeteria diet after weaning [22], suggesting that high-fat diets and diets combining high levels of fat and refined sugars may have contrasted effects on anxiety-related behaviours. It is worth noting that, although the diet did not affect behaviours during the OFT/NOT, piglets exposed to the HFS diet after birth had higher salivary cortisol levels than control piglets on the day of testing. This difference in cortisol levels, however, was already observed at t0, i.e. basal level before testing, indicating that the high cortisol levels were likely not caused by an enhanced physiological response to acute stress, but rather by a chronic difference in basal cor- tisol levels. How the postnatal HFS diet affected cortisol levels and whether this was related to the presence of cholesterol, a cortisol precursor, in this diet, is unclear. On the other hand, pig- lets exposed to the HFS diet before birth tended to have reduced basal salivary cortisol levels after weaning compared to control piglets. Lower basal serum corticosterone levels have been found in rat offspring exposed to a maternal high-fat diet [17], while increased basal plasma corticosterone levels have been reported in female rats fed a post-weaning high-fat diet [46], and in male rats fed a post-weaning ‘junk food fatty diet’ [47]. These findings indicate that the programming effects of a prenatal high-fat diet on the hypothalamic-pituitary-adrenal axis responsivity may be different from that of a postnatal diet. Both prenatal and postnatal exposure to the HFS diet increased the time spent walking in the home pen during the weeks following weaning, which contradicts prior findings in rats PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 17 / 24 Programming Effects of Perinatal Nutrition in Pigs [17,20–22]. It is worth noting that, while we found increasedlocomotion in the familiar home pen, the aforementioned studies measured locomotion during novelty tests, in which locomo- tion may have been affected by stress [48]. Discussion Alternatively, it is possible that high-fat and high- fat/sugar diets exert differential effects on locomotion, as supported by prior studies showing that high-fat diets and diets enriched in both fat and refined sugars had, respectively, no effect [17,20] and inhibitory effects [21,22] on locomotion. In addition, while in prior studies the diets often resulted in increased BW or adipose mass in the offspring, piglets fed the HFS diet were not overweight in our study, indicating that the increase in BW induced by elevated levels of dietary fat may be the critical parameter required to observe decreased locomotion [22]. In addition to the independent effects of the prenatal or postnatal HFS diet, we found that several effects of the postnatal diet on behaviours depended on the prenatal diet. Piglets sub- jected to a switch of diet at birth spent less time inactive, and more time exploring and/or ingesting feeding materials than piglets maintained on the same treatment. Numerical data also suggest that piglets subjected to a switch of diet at birth spent more time exploring the environment, mounting and exploring pen mates than piglets maintained on the same diet. Mammals have the ability to perceive in utero the flavour of the maternal feed, which reaches the foetus through the amniotic fluid [49]. This ability enables the individual to identify, after birth, the organoleptic properties of their early postnatal diet that were already present (or not) in the maternal diet during gestation, which influences the development of food preferences [50,51]. We speculate that the disruption of this “in utero-early life sensory continuum” in pig- lets subjected to a dietary change at birth might have influenced their exploratory and social behaviour. Indeed, the switch of feed may have stimulated exploratory behaviours (to seek for the familiar prenatal diet), and social interactions (partly as re-directed exploratory behav- iours). On the other hand, piglets that remained on the same diet may have been less motivated to seek for an alternative feed, and spent more time inactive. Although further studies would be needed to confirm this postulate, our findings emphasise the importance of the interactions between foetal and early life nutritional factors for the development of (eating) behaviours. In our study, piglets exposed to the HFS diet before birth were heavier at weaning than con- trol piglets, but this effect was not sustained after weaning. PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Discussion In addition, piglets fed the HFS diet after birth ate significantly less than the control pigs from weaning (4 weeks of age) to 8 weeks of age, which resulted in a lower AA intake relative to net energy (e.g. lysine: 4.3 vs. 6.2 g/day). The decrease in growth and feed efficiency found in piglets fed the HFS diet after birth was thus likely caused by a lower intake and deposition of AA during the early post-weaning period, which the pigs apparently did not compensate for by increasing their feed intake. Another hypothesis to explain the reduced growth of piglets fed the HFS diet would be that pig- lets had difficulties to digest the high levels of animal fat contained in the HFS diet. However, although fat digestion has been reported to be limited in weaned piglets [64–66], the calculated NE intake was 11% higher in the piglets fed the HFS diet than in control piglets, indicating that a reduction in the intake of essential AA, such as lysine, rather than energy limited the growth rate of these piglets, and thus decreased feed efficiency. We cannot exclude the possibility that some of the behavioural changes observed in piglets fed the postnatal HFS diet were caused by the reduction in BW gain, as a relationship between BW gain and agonistic behaviour around weaning and regrouping in piglets has been reported [67]. In our study, however, some behaviours were also affected by the interaction between pre- natal and postnatal diet, suggesting that reduction in BW (gain) is likely not the only factor underlying the effects of the HFS diet on behavioural activity, as the prenatal diet did not affect BW (gain). Further research using pair-feeding groups of piglets of similar BW (gain) and fed HFS or control diets would enable to disentangle the respective role of diet composition and growth on behavioural activity. A remarkable finding is the long-lasting effects of the postnatal HFS diet on piglet perfor- mance. During the 8 weeks following the dietary intervention, compared to control piglets, pig- lets fed the HFS diet after birth had a 20% decrease in ADFI, paired with a slight reduction in ADG, resulting in a higher G:F. The improved feed efficiency, associated with the attenuation of the effects on growth (7% vs. Discussion Despite the higher caloric intake, piglets exposed to the HFS diet after birth weighed less at the end of the treatment than control piglets, which was caused by a 30% reduction in ADG from weaning onwards. Interestingly, G:F from weaning to the end of the dietary intervention was also lower in piglets fed the HFS diet after birth compared to control pigs. Crude protein [62] and amino acid (AA) levels, e.g. lysine [63], are known to be critical factors for (muscle) growth and feed efficiency in pigs. According to recommendations for weaned piglets by CVB [31], the HFS diet was deficient in essential AA, particularly lysine. In addition, piglets fed the HFS diet after birth ate significantly less than the control pigs from weaning (4 weeks of age) to 8 weeks of age, which resulted in a lower AA intake relative to net energy (e.g. lysine: 4.3 vs. 6.2 g/day). The decrease in growth and feed efficiency found in piglets fed the HFS diet after birth was thus likely caused by a lower intake and deposition of AA during the early post-weaning period, which the pigs apparently did not compensate for by increasing their feed intake. Another hypothesis to explain the reduced growth of piglets fed the HFS diet would be that pig- lets had difficulties to digest the high levels of animal fat contained in the HFS diet. However, although fat digestion has been reported to be limited in weaned piglets [64–66], the calculated NE intake was 11% higher in the piglets fed the HFS diet than in control piglets, indicating that a reduction in the intake of essential AA, such as lysine, rather than energy limited the growth rate of these piglets, and thus decreased feed efficiency. Despite the higher caloric intake, piglets exposed to the HFS diet after birth weighed less at the end of the treatment than control piglets, which was caused by a 30% reduction in ADG from weaning onwards. Interestingly, G:F from weaning to the end of the dietary intervention was also lower in piglets fed the HFS diet after birth compared to control pigs. Crude protein [62] and amino acid (AA) levels, e.g. lysine [63], are known to be critical factors for (muscle) growth and feed efficiency in pigs. According to recommendations for weaned piglets by CVB [31], the HFS diet was deficient in essential AA, particularly lysine. Discussion This confirms prior findings in rodents that a maternal high-fat diet increases offspring BW during the pre-weaning period, but not necessarily later [17]. Supplementing sow diets with fat during gestation has been found to affect both milk yield and composition [52,53], two limiting factors of piglet growth [54,55]. We therefore assume that the increase in piglet BW at weaning was induced by an increased milk production (and intake) and/or by changes in milk nutrient composition, e.g. elevated levels of fat [56]. Further research should include milk analyses to disentangle the respective role of milk composition and quantity on piglet BW at weaning. The intake of the HFS diet after birth resulted in a 12% reduction in ADFI from weaning to the end of the treatment. The feed preference tests revealed consistent long- and short-term preferences for the HFS diet in piglets exposed to this diet after birth. Since piglets fed the con- trol diet after birth did not show significant preferences for the control diet, we assume that the preferences for the HFS diet were not only due to habituation processes, but also to a high per- ceived palatability. Therefore, rather than from low palatability, the reduced ADFI in these pig- lets likely resulted from high satiating effects of the HFS diet, as confirmed by behavioural data showing that piglets fed the HFS diet after birth explored feed materials after weaning less than control pigs, i.e. showed fewer appetitive ingestive behaviours, indicating a lower motivation for feed [57], which may result from higher satiety. Accordingly, Besson et al. [58] found that minipigs were more motivated to obtain a HFS diet than a control diet at the very beginning of a progressive ratio task (i.e. higher palatability), but obtained fewer rewards in total at the end of the task (i.e. quicker satiating effect). In our study, piglets fed the HFS diet after birth had a PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 18 / 24 Programming Effects of Perinatal Nutrition in Pigs lower intake of fibres and proteins, two nutrients known to enhance satiety [59,60], than con- trol piglets, suggesting that other factors contributed to the dietary effects on ADFI. Energy intake appears to be a major determinant of feed intake in pigs [61], indicating that the lower ADFI found in piglets fed the HFS diet may simply result from a higher total energy intake (6.42 vs. 5.78 MJ NE/day). PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs diet remained unchanged from the early post-weaning period to the 8-week period following the dietary intervention. This may indicate that piglets fed the HFS diet directly after birth compensate for myofibre size and hypertrophy when exposed to a commercial diet with ade- quate levels of AA, leading to an improved G:F ratio in these pigs. Alternatively, it is possible that the intake of high levels of fat in the HFS diet during early life altered early life gut development and long-term gut functioning in the HFS piglets, thus complicating the transition to a standard diet later in life. Accordingly, de Souza et al. [65] reported that the intake of high dietary levels of fat after weaning increased and decreased lipase and amylase activity, respectively. They posited that these changes in the activity of enzymes involved in lipids and starch break down may impair the piglets’ ability to cope with a standard (high-starch low-fat) diet later in life, i.e. during the recovery period needed for enzyme levels to rebound. Further research should consider investigating the impact of the HFS diet on digestive enzyme activity in weaned piglets, and its potential role for long-term performance and behavioural development. While partial compensation for growth and feed efficiency occurred, piglets fed the HFS diet after birth showed a large decrease in ADFI during the 8 weeks following the dietary inter- vention. One postulate to explain the drastic and long-lasting reduction of feed intake would be that 8-week early life exposure to the HFS diet resulted in long-lasting alterations of the sati- ety/appetite regulation system of the piglets. These effects might be mediated by long-lasting changes of circulating blood levels of appetite-regulating metabolites, such as leptin, ghrelin, insulin or glucose. Accordingly, we reported a significant decrease in fasting blood insulin lev- els during the 8-week period following the dietary intervention in piglets fed the postnatal HFS diet compared to control piglets [71]. Further analyses, however, should be done to support the postulate of altered appetite regulation. Conclusions In conclusion, the present study provides evidence that foetal or early life exposure to a diet enriched in saturated fat, sucrose and cholesterol has subtle effects on behaviour of (non- obese) piglets, with reduced aggression and increased locomotion, without having apparent adverse effects on anxiety-related behaviours after weaning. The exposure to the HFS diet after birth also induced long-lasting changes in voluntary feed intake, growth and feed efficiency in piglets, which may have resulted from early post-weaning AA restriction. Our study also emphasises the importance of the interactions between in utero and early postnatal nutrition for the behavioural development of the offspring, as some behavioural effects of postnatal exposure to the HFS diet depended on the prenatal dietary history. Further studies are needed to determine which factors, such as maternal and offspring metabolic status, diet composition or digestive enzymatic activity, underlie the equivocal results found between our study and prior research in rodents. Considering the current socio-economic context characterised by the widespread availability of diet high in fat and refined sugars, the characterisation of dietary or metabolic factors underlying the effects of a perinatal high-fat high-sugar high-cholesterol diet on behaviour in pigs could have interesting applications in terms of dietary recommendations for perinatal nutrition in humans. S1 Table. Behaviours of piglets in the home pen after weaning. (PDF) Discussion 30% reduction during the early post-weaning period), suggests that, when fed a commercial diet that meets their needs for nutrients, the piglets fed the HFS diet after birth were able to partially compensate for the growth reduction caused by AA restriction in early life, as previously reported [68,69]. The 8-week period, however, may not have been long enough to fully compensate. As BW mainly depends on muscle weight, one hypothesis to explain the long-term retardation of growth would be that the postnatal HFS diet affected myogenesis. Muscle weight depends on both myofibre number and myofibre size. While the number of myofibres is determined mainly before birth, postnatal myofibre develop- ment consists mainly of increase in fibre size, i.e. myofibre hypertrophy [70]. It is possible that low AA intake in piglets fed the HFS diet during the 4 first post-weaning weeks delayed hyper- trophic muscle growth, resulting in long-lasting changes in body composition, with reduced muscle tissue and increased adipose tissue, contributing to the long-lasting reduction of BW. Additionally, in contrast to the control group, feed efficiency of piglets fed the postnatal HFS PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 19 / 24 Acknowledgments The authors are very grateful to Fleur Bartels, Monique Ooms, Jan Wijnen, Anouschka Mid- delkoop and Welmoed Wehkamp for all the help in conducting this experiment. We would like to thank Rudie Koopmanschap for his assistance with the cortisol analyses, Sietse-Jan Koopmans for his valuable advice on the study and the personnel from the experimental farms of Carus (Wageningen) and VIC (Sterksel) for taking care of the animals and their technical assistance. We are also very thankful to Dr. Claudia Kalbe for her invaluable help in interpret- ing data on piglet performance. This research has been supported by a post-doctoral study grant from the Fyssen Foundation awarded to Dr. C. Clouard. Scientific interactions with the INRA DID’IT Metaprogramme made possible to share insights on the methodology and results interpretation. Author Contributions Conceived and designed the experiments: CC WJJG BK DVL JEB. Performed the experiments: CC. Analyzed the data: CC JEB. Wrote the paper: CC WJJG JEB DVL. Formulated the experi- mental diets: WJJG. Supporting Information S1 Table. Behaviours of piglets in the home pen after weaning. (PDF) 20 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 References Maternal high fat diet consumption during the perinatal period programs offspring behavior. Physiology & Behavior. 2014; 123: 236–242. 15. Sullivan EL, Grayson B, Takahashi D, Robertson N, Maier A, Bethea CL, et al. Chronic Consumption of a High-Fat Diet during Pregnancy Causes Perturbations in the Serotonergic System and Increased Anxiety-Like Behavior in Nonhuman Primate Offspring. Journal of Neuroscience. 2010; 30: 3826– 3830. doi: 10.1523/JNEUROSCI.5560-09.2010 PMID: 20220017 16. Raygada M, Cho E, Hilakivi-Clarke L. High maternal intake of polyunsaturated fatty acids during preg- nancy in mice alters offsprings' aggressive behavior, immobility in the swim test, locomotor activity and brain protein kinase C activity. Journal of Nutrition. 1998; 128: 2505–2511. PMID: 9868200 17. Sasaki A, de Vega WC, St-Cyr S, Pan P, McGowan PO. Perinatal high fat diet alters glucocorticoid sig- naling and anxiety behavior in adulthood. Neuroscience. 2013; 240: 1–12. doi: 10.1016/j. neuroscience.2013.02.044 PMID: 23454542 18. Rodriguez JS, Rodriguez-Gonzalez GL, Reyes-Castro LA, Ibanez C, Ramirez A, Chavira R, et al. Maternal obesity in the rat programs male offspring exploratory, learning and motivation behavior: pre- vention by dietary intervention pre-gestation or in gestation. International Journal of Developmental Neuroscience. 2012; 30: 75–81. doi: 10.1016/j.ijdevneu.2011.12.012 PMID: 22239918 19. Bilbo SD, Tsang V. Enduring consequences of maternal obesity for brain inflammation and behavior of offspring. The FASEB Journal. 2010; 24: 2104–2115. doi: 10.1096/fj.09-144014 PMID: 20124437 20. Peleg-Raibstein D, Luca E, Wolfrum C. Maternal high-fat diet in mice programs emotional behavior in adulthood. Behavioural Brain Research. 2012; 233: 398–404. doi: 10.1016/j.bbr.2012.05.027 PMID: 22633920 21. Wright TM, Fone KC, Langley-Evans SC, Voigt JP. Exposure to maternal consumption of cafeteria diet during the lactation period programmes feeding behaviour in the rat. International Journal of Develop- mental Neuroscience. 2011; 29: 785–793. doi: 10.1016/j.ijdevneu.2011.09.007 PMID: 22004940 22. Lalanza JF, Caimari A, del Bas JM, Torregrosa D, Cigarroa I, Pallas M, et al. Effects of a Post-Weaning Cafeteria Diet in Young Rats: Metabolic Syndrome, Reduced Activity and Low Anxiety-Like Behaviour. Plos One. 2014; 9. 23. Horgan GW, Whybrow S. Associations between fat, sugar and other macronutrient intakes in the National Diet and Nutrition Survey. Nutrition Bulletin. 2012; 37: 213–223. 24. Francis HM, Stevenson RJ. Higher Reported Saturated Fat and Refined Sugar Intake Is Associated With Reduced Hippocampal-Dependent Memory and Sensitivity to Interoceptive Signals. Behavioral Neuroscience. 2011; 125: 943–955. doi: 10.1037/a0025998 PMID: 22023100 25. Birch LL, Doub AE. Learning to eat: birth to age 2 y. American Journal of Clinical Nutrition. References 1. Wardle J. Eating behaviour and obesity. Obesity Reviews. 2007; 8: 73–75. PMID: 17316306 2. 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The 'Twinkie Defense': the relationship between carbonated non-diet soft drinks and violence perpetration among Boston high school students. Injury Prevention. 2012; 18: 259–263. doi: 10.1136/injuryprev-2011-040117 PMID: 22025524 7. DeWall CN, Deckman T, Gailliot MT, Bushman BJ. Sweetened blood cools hot tempers: physiological self-control and aggression. Aggressive Behavior. 2011; 37: 73–80. doi: 10.1002/ab.20366 PMID: 21064166 8. Kaplan JR, Shively CA, Fontenot MB, Morgan TM, Howell SM, Manuck SB, et al. Demonstration of an Association among Dietary-Cholesterol, Central Serotonergic Activity, and Social-Behavior in Mon- keys. Psychosomatic Medicine. 1994; 56: 479–484. PMID: 7532867 9. Haagensen AMJ, Sorensen DB, Sandoe P, Matthews LR, Birck MM, Fels JJ, et al. High Fat, Low Car- bohydrate Diet Limit Fear and Aggression in Gottingen Minipigs. Plos One. 2014; 9. 10. Barker DJP (1992) Fetal and infant origins of adult disease. London: BMJ Publishing Group. 11. 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CVB TP (2007) Chemical composition and nutritional value of feedstuffs and feeding standards. The Hague, The Netherlands: CVB Series no 36. 32. Ursinus WW, Bolhuis JE, Zonderland JJ, Rodenburg TB, de Souza AS, Koopmanschap RE, et al. Rela- tions between peripheral and brain serotonin measures and behavioural responses in a novelty test in pigs. Physiology & Behavior. 2013; 118: 88–96. 33. Reimert I, Rodenburg TB, Ursinus WW, Kemp B, Bolhuis JE. Responses to novel situations of female and castrated male pigs with divergent social breeding values and different backtest classifications in barren and straw-enriched housing. Applied Animal Behaviour Science. 2014; 151: 24–35. 22 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs 34. Ruis MA, Te Brake JH, Engel B, Ekkel ED, Buist WG, Blokhuis HJ, et al. The circadian rhythm of sali- vary cortisol in growing pigs: effects of age, gender, and stress. Physiology & Behavior. 1997; 62: 623– 630. 35. Torres SJ, Nowson CA. Relationship between stress, eating behavior, and obesity. Nutrition. 2007; 23: 887–894. PMID: 17869482 36. Fredriksen B, Lium BM, Marka CH, Mosveen B, Nafstad O. Entire male pigs in farrow-to-finish pens— Effects on animal welfare. Applied Animal Behaviour Science. 2008; 110: 258–268. 37. Hintze S, Scott D, Turner S, Meddle SL, D'Eath RB. Mounting behaviour in finishing pigs: Stable individ- ual differences are not due to dominance or stage of sexual development. Applied Animal Behaviour Science. 2013; 147: 69–80. 38. References Clark CCA, D'Eath RB. Age over experience: Consistency of aggression and mounting behaviour in male and female pigs. Applied Animal Behaviour Science. 2013; 147: 81–93. 39. Colson V, Martin E, Orgeur P, Prunier A. Influence of housing and social changes on growth, behaviour and cortisol in piglets at weaning. Physiology & Behavior. 2012; 107: 59–64. 40. 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The effects of weaning at 7, 14 and 28 days on piglet behav- iour. Applied Animal Behaviour Science. 1999; 62: 173–182. 45. Reimert I, Rodenburg TB, Ursinus WW, Duijvesteijn N, Camerlink I, Kemp B, et al. Backtest and novelty behavior of female and castrated male piglets, with diverging social breeding values for growth. Journal of Animal Science. 2013; 91: 4589–4597. doi: 10.2527/jas.2013-6673 PMID: 23942705 46. Boukouvalas G, Antoniou K, Papalexi E, Kitraki E. Post weaning high fat feeding affects rats' behavior and hypothalamic pituitary adrenal axis at the onset of puberty in a sexually dimorphic manner. Neuro- science. 2008; 153: 373–382. doi: 10.1016/j.neuroscience.2008.02.023 PMID: 18378403 47. Mitra A, Crump EM, Alvers KM, Robertson KL, Rowland NE. Effect of high-fat diet on stress responsive- ness in borderline hypertensive rats. Stress. 2011; 14: 42–52. doi: 10.3109/10253890.2010.494746 PMID: 20666663 48. Rutherford KMD, Donald RD, Lawrence AB, Wemelsfelder F. 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The Effect of Source of Supplemental Dietary Energy on Sow Milk- Yield, Milk-Composition and Litter Performance. Journal of Animal Science. 1982; 55: 1388–1394. PMID: 7161211 54. Harrell RJ, Thomas MJ, Boyd RD (1993) Limitations of sow milk yield on baby pig growth. Cornell Nutri- tion Conference for Feed Manufacturers. Rochester, NY, USA: Cornell University. pp. 156–164. 55. Williams IH (1995) Sow’s milk as a major nutrient source before weaning. In: Hennessy V, Cranwell P, editors. Manipulating pig production. Werribee, Victoria, Australia: Australasian Pig Science Association. pp. 107–113. 56. Besson M, Blat S, Guérin S, Randuineau G, Nogret I, Quesnel H, et al. High-fat high-sugar maternal diet has consequences on milk composition and offspring's microbiota activity, metabolism and 23 / 24 PLOS ONE | DOI:10.1371/journal.pone.0154698 May 18, 2016 Programming Effects of Perinatal Nutrition in Pigs behavioural responses in Yucatan pigs. Journal of Developmental Origins of Health and Disease. 2015; 6 Suppl 1: S40. behavioural responses in Yucatan pigs. Journal of Developmental Origins of Health and Disease. 2015; 6 Suppl 1: S40. 57. Keen-Rhinehart E, Ondek K, Schneider JE. Neuroendocrine regulation of appetitive ingestive behavior. Frontiers in Neuroscience. 2013; 7: 213. doi: 10.3389/fnins.2013.00213 PMID: 24298235 58. Besson M, Génissel M, Georges J, Janvier R, Val-Laillet D. Impact d'une exposition périnatale au sucre et au gras via le régime maternel sur les capacités cognitives, les préférences et la motivation alimen- taires de porcelets Yucatan. Nutrition Clinique et Métabolisme. 2014; 28 Suppl S1: S59–S60. 59. Souza da Silva C, Bolhuis JE, Gerrits WJ, Kemp B, van den Borne JJ. Effects of dietary fibers with dif- ferent fermentation characteristics on feeding motivation in adult female pigs. Physiology & Behavior. 2013; 110–111: 148–157. 60. 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Myocardial perfusion MRI with SW-CG-HYPR: a comparison to conventional SR-Turbo-FLASH and x-ray angiography in patients with suspected coronary artery disease
Journal of cardiovascular magnetic resonance
2,012
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© 2012 Ma et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background A sliding-window (SW) conjugate-gradient (CG) highly constrained back-projection reconstruction (HYPR) (SW-CG-HYPR) technique has been developed for time- resolved myocardial perfusion imaging. Using this method, the acquisition time per cardiac cycle can be reduced dramatically while maintaining the temporal resolution of one frame per heartbeat in myocardial per- fusion MRI, allowing increased spatial coverage (whole left ventricular coverage), improved temporal and spatial resolution and SNR, and reduced motion artifacts com- pared with the conventional SR-Turbo-FLASH sequence. However, the diagnostic accuracy of myocar- dial perfusion MRI with SW-CG-HYPR for detecting coronary artery disease (CAD) has not been directly compared to that with conventional SR-Turbo-FLASH. The purpose of this study was to prospectively compare the diagnostic value of SW-CG-HYPR and conventional Summary h In the current study, we prospectively compared the diagnostic value of SW-CG-HYPR and conventional SR- Turbo-FLASH for myocardial perfusion MRI in patients with suspected CAD. Compared with conventional SR- Turbo-FLASH, SW-CG-HYPR allows increased spatial coverage (whole left ventricular coverage), improved temporal and spatial resolution and SNR, reduced motion artifacts and has higher diagnostic accuracy in patients with suspected CAD. Ma et al. Journal of Cardiovascular Magnetic Resonance 2012, 14(Suppl 1):P303 http://www.jcmr-online.com/content/14/S1/P303 Ma et al. Journal of Cardiovascular Magnetic Resonance 2012, 14(Suppl 1):P303 http://www.jcmr-online.com/content/14/S1/P303 Ma et al. Journal of Cardiovascular Magnetic Resonance 2012, 14(Suppl 1):P303 http://www.jcmr-online.com/content/14/S1/P303 Myocardial perfusion MRI with SW-CG-HYPR: a comparison to conventional SR-Turbo-FLASH and x-ray angiography in patients with suspected coronary artery disease SR-Turbo-FLASH for myocardial perfusion MRI in patients with suspected CAD. Methods Thirty consecutive patients (17 men, 13 women; age range, 39-74 years; mean age, 55 years ± 19) with sus- pected CAD who were scheduled for coronary angiogra- phy underwent myocardial perfusion MRI with both SW-CG-HYPR and SR-Turbo-FLASH at 3.0T. Perfusion defects were interpreted visually by 2 blinded observers and were correlated to x-ray angiographic stenoses ≥ 50%. Receiver-operating characteristic (ROC) curve ana- lysis was used to compare the diagnostic performance of the two imaging techniques. Results The prevalence of CAD was 60%. Compared with SR- Turbo-FLASH, SW-CG-HYPR produced better left ven- tricular (LV) coverage (whole LV vs. only 3 slices). In the per-patient analysis, SW-CG-HYPR provided a higher sensitivity (94% vs. 89%), specificity (83% vs. 75%) and diagnostic accuracy (90% vs. 83%) for the detection of CAD than SR-Turbo-FLASH. In the per-vessel analy- sis, the diagnostic performance of SW-CG-HYPR was significantly greater than that of SR-Turbo-FLASH for the overall detection of CAD (area under ROC curve: 0.96 ± 0.02 vs. 0.90 ± 0.03, respectively; p < 0.05). 1Radiology, Yuhuangding Hospital, Yantai, China Full list of author information is available at the end of the article Conclusions High-resolution, whole left ventricle myocardial perfu- sion MRI with SW-CG-HYPR allows higher diagnostic accuracy than conventional SR-Turbo-FLASH in patients with suspected CAD. 1Radiology, Yuhuangding Hospital, Yantai, China Full list of author information is available at the end of the article Page 2 of 2 Page 2 of 2 Ma et al. Journal of Cardiovascular Magnetic Resonance 2012, 14(Suppl 1):P303 http://www.jcmr-online.com/content/14/S1/P303 Funding This work was supported by National Institute of Health (NIBIB EB002623) and National Natural Science Foun- dation of China (30828009). Author details 1 1Radiology, Yuhuangding Hospital, Yantai, China. 2Xuanwu Hospital, Capital Medical University, Beijing, China. 3University of California, Los Angeles, CA, USA. 4Siemens Mindit Magnetic Resonance, Shenzhen, China. 5Siemens Limited China, Shanghai, China. Published: 1 February 2012 Published: 1 February 2012 doi:10.1186/1532-429X-14-S1-P303 Cite this article as: Ma et al.: Myocardial perfusion MRI with SW-CG- HYPR: a comparison to conventional SR-Turbo-FLASH and x-ray angiography in patients with suspected coronary artery disease. Journal of Cardiovascular Magnetic Resonance 2012 14(Suppl 1):P303. doi:10.1186/1532-429X-14-S1-P303 Cite this article as: Ma et al.: Myocardial perfusion MRI with SW-CG- HYPR: a comparison to conventional SR-Turbo-FLASH and x-ray angiography in patients with suspected coronary artery disease. Journal of Cardiovascular Magnetic Resonance 2012 14(Suppl 1):P303. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit
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Some Properties of Cut Locus of a Flat Torus
Zenodo (CERN European Organization for Nuclear Research)
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World Academy of Science, Engineering and Technology International Journal of Mathematical and Computational Sciences Vol:8, No:12, 2014 World Academy of Science, Engineering and Technology International Journal of Mathematical and Computational Sciences Vol:8, No:12, 2014 International Scholarly and Scientific Research & Innovation 8(12) 2014 Some Properties of Cut Locus of a Flat Torus Authors : Pakkinee Chitsakul Abstract : In this article, we would like to show that there is no cut point of any point in a plane, but there exists the cut locus of a point in a flat torus. By the results, we would like to determine the structure of cut locus of a flat torus. Keywords : cut locus, flat torus, geodesics Authors : Pakkinee Chitsakul Abstract : In this article, we would like to show that there is no cut point of any point in a plane, but there exists the cut locus of a point in a flat torus. By the results, we would like to determine the structure of cut locus of a flat torus. Keywords : cut locus, flat torus, geodesics Conference Title : ICMCSSE 2014 : International Conference on Mathematical, Computational and Statistical Sciences and Engineering C f L ti B k k Th il d Authors : Pakkinee Chitsakul Abstract : In this article, we would like to show that there is no cut point of any point in a plane, but there exists the cut locus of a point in a flat torus. By the results, we would like to determine the structure of cut locus of a flat torus. Keywords : cut locus, flat torus, geodesics Conference Title : ICMCSSE 2014 : International Conference on Mathematical, Computational and Statistical Sciences and Engineering Conference Location : Bangkok, Thailand Conference Dates : December 24-25, 2014 g SE 2014 : International Conference on Mathematical, Computational and Statistical Sciences and y g Conference Title : ICMCSSE 2014 : International Conference on Mathematical, Computational and Statistical Sciences and Engineering Conference Location : Bangkok, Thailand Conference Dates : December 24-25, 2014 International Scholarly and Scientific Research & Innovation 8(12) 2014 ISNI:0000000091950263
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https://repositorio.uam.es/bitstream/10486/691820/1/recomendations_kort_KNEE_2020.pdf
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Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members
Knee surgery, sports traumatology, arthroscopy
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Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS‑CoV‑2 pandemic: the European Hip Society and European Knee Associates Survey of Members N. P. Kort1 · E. Gómez Barrena2 · M. Bédard3 · S. Donell4   · J.‑A. Epinette5 · B. Gomberg6 · M. T. Hirschmann7,8 · P. Indelli9,10 · Ismail Khosravi11 · T. Karachalios12 · M. C. Liebensteiner11 · B. Stuyts13 · R. Tandogan14 · B. Violante15 · L. Zagra16 · M. Thaler11 N. P. Kort1 · E. Gómez Barrena2 · M. Bédard3 · S. Donell4   · J.‑A. Epinette5 · B. Gomberg6 · M. T. Hirschmann7,8 · P. Indelli9,10 · Ismail Khosravi11 · T. Karachalios12 · M. C. Liebensteiner11 · B. Stuyts13 · R. Tandogan14 · B. Violante15 · L. Zagra16 · M. Thaler11 Received: 11 July 2020 / Accepted: 6 August 2020 / Published online: 18 August 2020 © The Author(s) 2020 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 https://doi.org/10.1007/s00167-020-06212-0 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 https://doi.org/10.1007/s00167-020-06212-0 KNEE KNEE Abstract Purpose  The COVID-19 pandemic has disrupted the health care system around the entire globe. A consensus is needed about resuming total hip and knee procedures. The European Hip Society (EHS) and the European Knee Association (EKA) formed a panel of experts that have produced a consensus statement on how the safe re-introduction of elective hip and knee arthroplasty should be undertaken. Methods  A prospective online survey was done among members of EHS and EKA. The survey consisted of 27 questions. It includes basic information on demographics and details the participant’s agreement with each recommendation. The participant could choose among three options (agree, disagree, abstain). Recommendations focussed on pre-operative, peri- operative, and post-operative handling of patients and precautions. Results  A total of 681 arthroplasty surgeons participated in the survey, with 479 fully completing the survey. The partici- pants were from 44 countries and 6 continents. Apart from adhering to National and Local Guidelines, the recommendations concerned how to make elective arthroplasty safe for patients and staff. p y pf Conclusion  The survey has shown good-to-excellent agreement of the participants with regards to the statements made in the recommendations for the safe return to elective arthroplasty following the first wave of the COVID-19 pandemic. Keywords  COVID-19 · Primary arthroplasty · Hip · Knee · Recommendations · Survey * S. Abstract Donell s.donell@uea.ac.uk 1 CortoClinics, Schijndel, The Netherlands 2 Dept of Orthopaedic Surgery and Traumatology, Hospital La Paz, Universidad Autónoma de Madrid, Madrid, Spain 3 Département de Chirurgie Orthopédique, CHU de Québec-Université Laval, Quebec City, QC, Canada 4 Norwich Medical School, University of East Anglia, Norwich, UK 5 Center for Research and Documentation in Arthroplasty, Lille, France 6 OA Centers for Orthopaedics, Portland, ME, USA 7 Department of Orthopaedic Surgery and Traumatology, Kantonsspital Baselland, (Bruderholz, Liestal, Laufen), 4101 Bruderholz, Switzerland 8 University of Basel, Basel, Switzerland 9 Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA, USA 10 International Committee American Academy Hip and Knee Surgeons (AAHKS), Rosemont, IL, USA 11 Department of Orthopaedic Surgery, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria 12 Orthopaedic Department, School of Health Sciences, Faculty of Medicine, University General Hospital of Larissa, University of Thessalia, Thessalia, Greece 13 Department of Orthopedic Surgery and Traumatology, GZA Hospitals, Antwerp, Belgium 14 Ortoklinik and Cankaya Orthopedics, Ankara, Turkey 15 Orthopaedic Department, Istituto Clinico Sant’Ambrogio IRCCS Galeazzi, Milan, Italy 16 Hip Department IRCCS Istituto Ortopedico Galeazzi, Milan, Italy * S. Donell s.donell@uea.ac.uk 1 CortoClinics, Schijndel, The Netherlands 2 Dept of Orthopaedic Surgery and Traumatology, Hospital La Paz, Universidad Autónoma de Madrid, Madrid, Spain 3 Département de Chirurgie Orthopédique, CHU de Québec-Université Laval, Quebec City, QC, Canada 4 Norwich Medical School, University of East Anglia, Norwich, UK 5 Center for Research and Documentation in Arthroplasty, Lille, France 6 OA Centers for Orthopaedics, Portland, ME, USA 7 Department of Orthopaedic Surgery and Traumatology, Kantonsspital Baselland, (Bruderholz, Liestal, Laufen), 4101 Bruderholz, Switzerland 8 University of Basel, Basel, Switzerland 9 Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA, USA 10 International Committee American Academy Hip and Knee Surgeons (AAHKS), Rosemont, IL, USA 11 Department of Orthopaedic Surgery, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria 12 Orthopaedic Department, School of Health Sciences, Faculty of Medicine, University General Hospital of Larissa, University of Thessalia, Thessalia, Greece 13 Department of Orthopedic Surgery and Traumatology, GZA Hospitals, Antwerp, Belgium 14 Ortoklinik and Cankaya Orthopedics, Ankara, Turkey 15 Orthopaedic Department, Istituto Clinico Sant’Ambrogio IRCCS Galeazzi, Milan, Italy 7 Department of Orthopaedic Surgery and Traumatology, Kantonsspital Baselland, (Bruderholz, Liestal, Laufen), 4101 Bruderholz, Switzerland 16 Hip Department IRCCS Istituto Ortopedico Galeazzi, Milan, Italy (0123 1 3456789) 3 2724 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 Introduction In recent months, the SARS-CoV-2 pandemic (COVID-19) has evolved rapidly in Europe, disrupting the personal, social, economic and professional lives of health profes- sionals on a large scale. The overall goal of most govern- ments in Europe has been to flatten the curve of infected SARS-CoV-2 patients and prevent a collapse of national health systems. The April 2020 SARS-CoV-2 survey com- pleted by EHS and EKA members in Europe has confirmed the impact of SARS-CoV-2: this pandemic has resulted in a tremendous reduction in primary hip and knee arthro- plasty procedures as shown in the survey. A broad con- sensus is needed about the factors that need to be in place before restarting such procedures. A prospective online survey was done online using Sur- veyMonkey (Portland, USA: https​://www.surve​ymonk​ ey.com) among members of European Hip Society (EHS) and European Knee Associates (EKA). A link to the sur- vey was sent by email to all members of the EHS and the EKA and affiliated arthroplasty surgeons. The online survey was launched on 23rd May 2020 and concluded on 6th June 2020. The survey consisted of 27 questions. It includes basic information on demographics and details the participant’s agreement with each recommendation. The participant could choose among three options (agree, disagree, abstain). The recommendations focus on three time periods; pre-operative, per-operative, and post-operative (Table 1). Delaying hip and knee arthroplasty in patients with severe osteoarthritis (OA) may lead to increased opi- oid use. It is associated with lower clinical results and increased readmission rates after the index procedure. Moreover, when access to hip and knee arthroplasty is limited, as it is now in the wake of the COVID-19 sanitary measures, the direct and indirect costs for our health care and social systems are enormous. Many patients suffering from OA have to prolong their absence from work, request temporary unemployment benefits, and burden the public welfare system. This survey did not require formal ethical approval with a practice dedicated to adult reconstruction. Results A total of 681 arthroplasty surgeons participated in the survey, with 479 fully completing the survey. The geographical spread of this survey included surgeons from 44 different countries in 6 continents (Fig. 1). The EHS and EKA had a 22.1% and 20.9% response rate, respectively. The mean time in practice for all participants was 20 years (min 1 year–max 46 years). We are now entering a new phase in most European countries, where we can consider restarting elective hip and knee arthroplasty in a “post-pandemic” period. To date, the scientific basis for the existing guidelines is not robust; there is much room for an exchange of ideas between surgeons. The current concern is to map out the optimal trajectory for starting up elective hip and knee arthroplasties. As a result, the European Hip Society (EHS) and the European Knee Association (EKA) formed a panel of experts that have produced a consensus on how the safe re-introduction of elective arthroplasty should be undertaken. They have provided recommendations based on the available evidence [1]. This survey aimed to vali- date the recommendations by involving arthroplasty sur- geons from a wide geographical area to promote then the recommendations for a safe return to elective joint arthro- plasty across Europe and elsewhere. The detailed results are shown in Table 2. Discussion The survey has shown good-to-excellent agreement by the participants to the Statements made in the Recommenda- tions for the safe return to elective arthroplasty following the COVID-19 pandemic. Although the response rate from both the EHS and EKA membership was low, at around 20%, it is notable that the mean time in elective arthroplasty of the participants was 20 years. This means that very experienced surgeons gave their opinions. Coupled with the global cover- age of the survey, the mean time in elective arthroplasty is a proper validation for the recommendations. 1 3 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 2725 Questions Statements Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic 1. When should elective hip and knee arthroplasty be resumed? Elective hip and knee arthroplasty can be resumed when appropriate prerequisites concerning facilities, workforce, testing, supplies are met, and approval of local health authorities are obtained. Facilities in areas with low, or relatively low and stable incidence of SARS-CoV-2, can be allowed to provide care for patients needing non- emergent, non-SARS-CoV-2 healthcare 2. Are new triage/patient selection criteria needed for hip and knee arthroplasty patients once elective surgery is resumed? Increased demand for hip and knee arthroplasty, coupled with limited hospital resources, will force surgeons to select which patients will receive hip and knee arthroplasties sooner than others. This will entail employing objective, transparent criteria in prior- itizing patient selection to identify the patients most in need who also have lower risk factors for disease transmission and post-operative complications 3. What are the priority indications for elective adult hip and knee reconstruction? There is universal agreement regarding the indications for urgent hip and knee arthro- plasty procedures, such as femoral neck fractures, periprosthetic fractures, dislocations and acute infection, even in the setting of the SARS-CoV-2 pandemic. However, prior- ity indications for non-emergency procedures in primary and revision hip and knee arthroplasty are lacking and should be clarified 4. What is the role of outpatient hip and knee arthro- plasty/enhanced recovery protocols in light of the SARS-CoV-2 pandemic? It is universally accepted that shorter hospital stays and treatment in a SARS-CoV-2-free environment decrease the risk of SARS-CoV-2 infection in patients undergoing elec- tive surgery. Discussion Performing hip and knee arthroplasty with enhanced recovery protocols that decrease the length of stay in a facility or can be used in ambulatory care centres to allow for day surgery might be beneficial for reducing the risk of viral transmission. Transitioning to enhanced recovery systems requires full support, adoption of all the subspecialties involved and the possible approval of health care payers, which may not be possible in the pandemic setting 5. What is the impact of delaying hip and knee arthro- plasty for the patients themselves and for society? Delaying elective hip and knee arthroplasty has negative consequences on the quality of life of patients and negatively impacts society as a whole. The benefits of hip and knee arthroplasty should be carefully weighed against the risks of viral transmission and infection, complications and mortality in the mostly elderly population requiring joint arthroplasty Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: pre-operative phase 1. What is the appropriate pre-operative clinical and laboratory screening and timeline for patients? All patients undergoing surgery should have their temperature and oxygen saturation measured. A thorough medical history should be acquired and patients asked about any symptoms they may have, such as cough, fever, loss of smell or taste, headache or gastrointestinal disorders. Additionally, they should be questioned about recent travels and their occupation to stratify them into possible high-risk groups. Regarding the laboratory testing, it would be ideal for all patients to undergo RT-PCR testing for SARS-CoV-2 before the operation. However, local guidelines and the efficacy of tests must also be taken into consideration. If there is a paucity of available tests, then only high-risk patients should be tested. There is no indication for additional chest CT scans in the pre-operative screening. Time allowing, all surgical patients should apply social distancing principles for two full weeks prior to testing and the surgical procedure and self-quarantine in their home for the period between test acquisition and day of surgery 2. Is pre-operative tracking of patients, staff and rela- tives necessary? All patients and staff will need to be screened for potential symptoms of SARS-CoV-2 prior to entering a hospital facility. In particular, staff must be routinely screened for potential symptoms. Isolation prior to surgery can be guided. Discussion What is the role of outpatient hip and knee arthro- plasty/enhanced recovery protocols in light of the SARS-CoV-2 pandemic? i It is universally accepted that shorter hospital stays and treatment in a SARS-CoV-2-free environment decrease the risk of SARS-CoV-2 infection in patients undergoing elec- tive surgery. Performing hip and knee arthroplasty with enhanced recovery protocols that decrease the length of stay in a facility or can be used in ambulatory care centres to allow for day surgery might be beneficial for reducing the risk of viral transmission. Transitioning to enhanced recovery systems requires full support, adoption of all the subspecialties involved and the possible approval of health care payers, which may not be possible in the pandemic setting Delaying elective hip and knee arthroplasty has negative consequences on the quality of life of patients and negatively impacts society as a whole. The benefits of hip and knee arthroplasty should be carefully weighed against the risks of viral transmission and infection, complications and mortality in the mostly elderly population requiring joint arthroplasty All patients undergoing surgery should have their temperature and oxygen saturation measured. A thorough medical history should be acquired and patients asked about any symptoms they may have, such as cough, fever, loss of smell or taste, headache or gastrointestinal disorders. Additionally, they should be questioned about recent travels and their occupation to stratify them into possible high-risk groups. Regarding the laboratory testing, it would be ideal for all patients to undergo RT-PCR testing for SARS-CoV-2 before the operation. However, local guidelines and the efficacy of tests must also be taken into consideration. If there is a paucity of available tests, then only high-risk patients should be tested. There is no indication for additional chest CT scans in the pre-operative screening. Time allowing, all surgical patients should apply social distancing principles for two full weeks prior to testing and the surgical procedure and self-quarantine in their home for the period between test acquisition and day of surgeryf 2. Is pre-operative tracking of patients, staff and rela- tives necessary? All patients and staff will need to be screened for potential symptoms of SARS-CoV-2 prior to entering a hospital facility. In particular, staff must be routinely screened for potential symptoms. Isolation prior to surgery can be guided. 4. What is the role of outpatient hip and knee arthro- plasty/enhanced recovery protocols in light of the SARS-CoV-2 pandemic? Discussion All patients, staff and relatives, especially those with patient contact, need to be investigated for previous symptoms, travels abroad and possible contacts with populations at high-risk for SARS-CoV-2 3. Should spinal anaesthesia be routine? Spinal anaesthesia can be considered safer for every negatively screened patient (with or without a SARS-CoV-2 test) than general anaesthesia, since the latter requires airway manipulation and endotracheal intubation, procedures that can more easily transmit SARS-CoV-2  – Should we only select patients as candidates who also consent to regional/spinal anaesthesia? It cannot be made mandatory that patients consent to regional/spinal anaesthesia. Nev- ertheless, the benefits of regional anaesthesia should be thoroughly explained to the patients, and whenever possible, this should be strongly considered as the preferred means of anaesthesia  – If spinal anaesthesia does not occur, should we cancel the operation? If general anaesthesia cannot be avoided, every precaution should be taken to avoid con- tamination. If a SARS-CoV-2-negative environment has been achieved that is as secure as possible, then general anaesthesia with informed consent can be considered Elective hip and knee arthroplasty can be resumed when appropriate prerequisites concerning facilities, workforce, testing, supplies are met, and approval of local health authorities are obtained. Facilities in areas with low, or relatively low and stable incidence of SARS-CoV-2, can be allowed to provide care for patients needing non- emergent, non-SARS-CoV-2 healthcare 2. Are new triage/patient selection criteria needed for hip and knee arthroplasty patients once elective surgery is resumed? 2. Are new triage/patient selection criteria needed for hip and knee arthroplasty patients once elective surgery is resumed? Increased demand for hip and knee arthroplasty, coupled with limited hospital resources, will force surgeons to select which patients will receive hip and knee arthroplasties sooner than others. This will entail employing objective, transparent criteria in prior- itizing patient selection to identify the patients most in need who also have lower risk factors for disease transmission and post-operative complications 3. What are the priority indications for elective adult hip and knee reconstruction? There is universal agreement regarding the indications for urgent hip and knee arthro- plasty procedures, such as femoral neck fractures, periprosthetic fractures, dislocations and acute infection, even in the setting of the SARS-CoV-2 pandemic. However, prior- ity indications for non-emergency procedures in primary and revision hip and knee arthroplasty are lacking and should be clarified 4. Discussion Patient numbers in the clinical areas (wards, waiting areas, outpatient clinics) should be halved, with the patients spaced at least 2 m apart – Separation of elective and trauma orthopaedic surgery (with regard to the general orthopaedic departments)? – Separation of elective and trauma orthopaedic surgery (with regard to the general orthopaedic departments)? SARS-CoV-2 screening practices should ensure the health and safety of patients and staff. SARS-CoV-2-negative elective hip and knee arthroplasty must be separated from the SARS-COV-2-positive trauma unit. Since all patients undergoing elective proce- dures are screened before administration and have tested negative for SARS-COV-2, they may be reluctant to go into certain settings for fear of viral transmission. There should be a physical separation of SARS-COV-2-positive and SARS-COV-2-negative patients and specific wards should be exclusively dedicated to treating patients with SARS-CoV-2 to reduce the risk of contaminating other patients 2. Should relatives/visitors or other supportive per- sonnel be allowed onto the orthopaedic wards and operating suite? Until normality returns, the number of visitors should be minimized as much as possible to reduce potential transmission of SARS-CoV-2 among patients, their family members and medical staff. This includes vendor representatives who travel to facilities to undergo, perform and support procedures. Limiting interactions between individuals and social distancing are part of the mainstream management against the spread of SARS-CoV-2. The number of visitors should be limited to those who are essential for a patient’s care. Although it is recognized that these rules create considerable anxiety for the patient, keeping all patients, relatives and staff safe from SARS-CoV-2 is the priority 3. Is there a need for extra disinfecting environmental procedures in between surgeries? Standard protocols for cleaning and sterilizing instruments need to be meticulously applied Moreover, once the patient has departed from the operating room, this should be left empty for a specific period of time and all high-touch surfaces, including the anaes- thetic machine and the anaesthetic work area, should be cleaned and disinfected with an Environmental Protection Agency (EPA)-approved hospital disinfectant. The length of time in between patients depends on the number of air exchanges per hour in the room or space in question Elective orthopaedic theatres and operative procedures, including personal protective equipment, are designed to reduce the risk of surgical site infection. Discussion It should be assumed that, after the resumption of normal functions at hospitals and in society in general, there will still be a risk of another outbreak of the disease. In such a situation, hospitals should be prepared to return to a “safe mode” with reorganization of the wards and personnel. Every hospital should have in place a plan for emergency distribution of the personnel and wards before elective surgery resumes Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: perioperative phase 1 Is there a need for: Statements It is reasonable to assume that patients who test positive for SARS-CoV-2 should not be operated on and should be discharged from the hospital. These patients should remain in quarantine at least 14 days and until a subsequent test turns out negative (two con- firmed negative PCR swab tests with a 24 h interval) and they are free of fever, cough or other symptoms 5. What kind of back-up plan is needed to guarantee quality care and patient safety in this pandemic situation? The treatment of SARS-CoV-2 patients is placing a huge strain on the resources of many hospitals, to the detriment of treatment of other health problems. Safety of hip and knee arthroplasty patients remains of paramount importance. Complications of cardiac and respiratory origin are the most common problems needing acute care. As elective operations begin, every hospital should have ICU capacity available to accept and accommodate patients with cardiopulmonary or other significant complications. It should be assumed that, after the resumption of normal functions at hospitals and in society in general, there will still be a risk of another outbreak of the disease. In such a situation, hospitals should be prepared to return to a “safe mode” with reorganization of the wards and personnel. Every hospital should have in place a plan for emergency distribution of the personnel and wards before elective surgery resumes Resuming elective hip and knee arthroplasty in the se 1. Is there a need for: – Modification or reorganization of hospital wards (patient density, bed density, medical and nursing staff density, etc.)? In most orthopaedic departments, the workforces have been adjusted to accommodate fewer cases, due to the reduction in trauma cases and cancellation of elective proce- dures. As elective operations restart, the standard social distancing guidelines should be sufficient. Discussion All patients, staff and relatives, especially those with patient contact, need to be investigated for previous symptoms, travels abroad and possible contacts with populations at high-risk for SARS-CoV-2 3. Should spinal anaesthesia be routine? Spinal anaesthesia can be considered safer for every negatively screened patient (with or without a SARS-CoV-2 test) than general anaesthesia, since the latter requires airway manipulation and endotracheal intubation, procedures that can more easily transmit SARS-CoV-2 – Should we only select patients as candidates who also consent to regional/spinal anaesthesia? It cannot be made mandatory that patients consent to regional/spinal anaesthesia. Nev- ertheless, the benefits of regional anaesthesia should be thoroughly explained to the patients, and whenever possible, this should be strongly considered as the preferred means of anaesthesia It cannot be made mandatory that patients consent to regional/spinal anaesthesia. Nev- ertheless, the benefits of regional anaesthesia should be thoroughly explained to the patients, and whenever possible, this should be strongly considered as the preferred means of anaesthesia – If spinal anaesthesia does not occur, should we cancel the operation? If general anaesthesia cannot be avoided, every precaution should be taken to avoid con- tamination. If a SARS-CoV-2-negative environment has been achieved that is as secure as possible, then general anaesthesia with informed consent can be considered 1 3 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 2726 Table 1   (continued) Questions Statements 4. If the SARS-CoV-2 tests are positive, how long should the hip or knee arthroplasty surgery be postponed? It is reasonable to assume that patients who test positive for SARS-CoV-2 should not be operated on and should be discharged from the hospital. These patients should remain in quarantine at least 14 days and until a subsequent test turns out negative (two con- firmed negative PCR swab tests with a 24 h interval) and they are free of fever, cough or other symptoms 5. What kind of back-up plan is needed to guarantee quality care and patient safety in this pandemic situation? The treatment of SARS-CoV-2 patients is placing a huge strain on the resources of many hospitals, to the detriment of treatment of other health problems. Safety of hip and knee arthroplasty patients remains of paramount importance. Complications of cardiac and respiratory origin are the most common problems needing acute care. As elective operations begin, every hospital should have ICU capacity available to accept and accommodate patients with cardiopulmonary or other significant complications. 4. What role do ultra-clean operating theatres, ortho- paedic exhaust suits and ultraviolet light systems play in both the wards/beds and the theatre? 3. Is there a need for extra disinfecting environmental procedures in between surgeries? Discussion Since the impact on mind and body during joint arthroplasty is significant, our patients may have lower immunity and be more vulnerable to SARS- CoV-2 infection As SARS-CoV-2-positive is an absolute contra-indication for elective surgery, the stand- ard enhanced recovery protocol for reducing complications is imperative 2.Organization of a shelter-in-place post-operative period, home care, community nurses or informal care Ideally, patients should be discharged home with the standard SARS-CoV-2 precautions being taken and only transferred to a nursing home in cases where that is not possible, since higher rates of SARS-CoV-2 may exist in those facilities 3. Avoid face-to-face contact for the orthopaedic follow-up and physical therapy guidance  – Consider telemedicine Web-based tools and telemedicine are preferred during this SARS-CoV-2 pandemic and may become the standard in the post-pandemic era  – Consider a new approach in wound closure tech- nique in the setting of the SARS-CoV-2 pandemic Post-operative in-office visits should be minimized, and digital health programmes allowing health care providers to closely monitor patients remotely should be sup- ported. Self-administered wound management should become the standard of care for patients in the post-pandemic era 4. What is the advice for patients who develop SARS- CoV-2 symptoms? In the event a patient develops SARS-CoV-2 symptoms or comes into contact with a SARS-CoV-2-positive person, they should seek health care advice. The patient should use the system in place in their country to seek the relevant advice. This may be through their primary care physician or an online or telephone advice service. Their orthopaedic surgeon and hospital should also be notified 5. Are special adjustments needed for post-op SARS- CoV-2 prophylaxis? Since SARS-CoV-2-positive is an absolute contraindication or elective surgery, the standard enhanced f recovery protocol and SARS-CoV-2 preventive measures are imperative. Time allowing, all surgical patients should apply social distancing princi- ples for the first two weeks after the operation and self-quarantine in their home During hip and knee arthroplasty, the use of power tools, burrs or electrocautery gener- ates potentially infective aerosol. The major aim should be to avoid transmission of SARS-CoV-2 by aerosolization of blood or other body fluids. Hence, adequate personal protective equipment should be available and used during surgery. First and foremost, all patients undergoing elective surgery should wear a mask. Discussion Surgeons and the entire surgical team who scrub during procedures should ideally wear an exhaust suit, including a mask (preferably N95, filtering face piece [FFP2, or P3] and a face shield). In the absence of a face shield, protective eyewear may be used, but this is a compromise. In addition, scrubs should be frequently changed during the surgical day. Single-use gowns, single-use gloves and hair and shoe covers can also, theoretically, reduce the transmission of the virus Resuming elective hip and knee arthroplasty in the sett Resuming elective hip and knee arthroplasty in the setti g elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase As SARS-CoV-2-positive is an absolute contra-indication for elective surgery, the stand- ard enhanced recovery protocol for reducing complications is imperative As SARS-CoV-2-positive is an absolute contra-indication for elective surgery, the stand- ard enhanced recovery protocol for reducing complications is imperative 1. Since the impact on mind and body during joint arthroplasty is significant, our patients may have lower immunity and be more vulnerable to SARS- CoV-2 infection Ideally, patients should be discharged home with the standard SARS-CoV-2 precautions being taken and only transferred to a nursing home in cases where that is not possible, since higher rates of SARS-CoV-2 may exist in those facilities 2.Organization of a shelter-in-place post-operative period, home care, community nurses or informal care Web-based tools and telemedicine are preferred during this SARS-CoV-2 pandemic and may become the standard in the post-pandemic era 3. Avoid face-to-face contact for the orthopaedic follow-up and physical therapy guidance  – Consider telemedicine Post-operative in-office visits should be minimized, and digital health programmes allowing health care providers to closely monitor patients remotely should be sup- ported. Self-administered wound management should become the standard of care for patients in the post-pandemic era – Consider a new approach in wound closure tech- nique in the setting of the SARS-CoV-2 pandemic 4. What is the advice for patients who develop SARS- CoV-2 symptoms? In the event a patient develops SARS-CoV-2 symptoms or comes into contact with a SARS-CoV-2-positive person, they should seek health care advice. The patient should use the system in place in their country to seek the relevant advice. This may be through their primary care physician or an online or telephone advice service. Discussion Their orthopaedic surgeon and hospital should also be notified i Since SARS-CoV-2-positive is an absolute contraindication or elective surgery, the standard enhanced f recovery protocol and SARS-CoV-2 preventive measures are imperative. Time allowing, all surgical patients should apply social distancing princi- ples for the first two weeks after the operation and self-quarantine in their home Discussion There are no guidelines or protocols published for managing elective hip and knee arthroplasty procedures with respect to laminar flow in the presence of SARS-CoV-2. It is recom- mended that surgical helmets not be used as primary protection against aerosol and airborne disease. The surgeon should consider wearing an N95 mask as an added precaution when using a surgical helmet in patients considered to be SARS-CoV- 2-negative in the pre-operative work-up Elective orthopaedic theatres and operative procedures, including personal protective equipment, are designed to reduce the risk of surgical site infection. There are no guidelines or protocols published for managing elective hip and knee arthroplasty procedures with respect to laminar flow in the presence of SARS-CoV-2. It is recom- mended that surgical helmets not be used as primary protection against aerosol and airborne disease. The surgeon should consider wearing an N95 mask as an added precaution when using a surgical helmet in patients considered to be SARS-CoV- 2-negative in the pre-operative work-up Ultraviolet light has no evidence to support its routine use and poses a hazard to operat- ing staff 1 3 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 2727 Table 1   (continued) Questions Statements 5. What are the guidelines for personal protective equipment (PPE), in terms of availability and instructions regarding its use and what to wear in relation to the patient’s position in the perioperative chain? During hip and knee arthroplasty, the use of power tools, burrs or electrocautery gener- ates potentially infective aerosol. The major aim should be to avoid transmission of SARS-CoV-2 by aerosolization of blood or other body fluids. Hence, adequate personal protective equipment should be available and used during surgery. First and foremost, all patients undergoing elective surgery should wear a mask. Surgeons and the entire surgical team who scrub during procedures should ideally wear an exhaust suit, including a mask (preferably N95, filtering face piece [FFP2, or P3] and a face shield). In the absence of a face shield, protective eyewear may be used, but this is a compromise. In addition, scrubs should be frequently changed during the surgical day. Single-use gowns, single-use gloves and hair and shoe covers can also, theoretically, reduce the transmission of the virus Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase 1. Conclusion What role do ultra-clean operating theatres, orthopaedic exhaust suits and ultraviolet light sys- tems play in both the wards/beds and the theatre? 320 (65) 96 (20) 76 (16) 492 (72) 5. What are the guidelines for personal protective equipment (PPE), in terms of availability and instructions regarding its use and what to wear in relation to the patient’s position in the periop- erative chain? 359 (74) 83 (17) 4 (9) 446 (65) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phasei 1. Since the impact on mind and body during joint arthroplasty is significant, our patients may have lower immunity and be more vulnerable to SARS-CoV-2 infection 427 (88) 2.Organization of a shelter-in-place post-operative period, home care, community nurses or infor- mal care 419 (87) 36 (8) 26 (5) 481 (71) – Consider a new approach in wound closure technique in the setting of the SARS-CoV-2 pan- demic 299 (62) 141 (29) 39 (8) 4. What is the advice for patients who develop SARS-CoV-2 symptoms? 5. Are special adjustments needed for post-op SARS-CoV-2 prophylaxis? Conclusion Fig. 1   Geographical distribution of survey participants The survey has shown good-to-excellent agreement of the participants with regards to the statements made in the rec- ommendations for the safe return to elective arthroplasty following the first wave of the COVID-19 pandemic. Fig. 1   Geographical distribution of survey participants 1 3 1 3 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 2728 Table 2   Results of the survey Time periods and questions Agree n (%) Disagree n (%) Abstain n (%) Response n (%) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic 1. When should elective hip and knee arthroplasty be resumed? 653 (96) 18 (3) 10 (2) 681 (100) 2. Are new triage/patient selection criteria needed for hip and knee arthroplasty patients once elec- tive surgery is resumes? 515 (82) 94 (15) 21 (3) 630 (93) 3. What are the priority indications for elective adult hip and knee reconstruction? 510 (83) 82 (13) 25 (4) 623 (92) 4. What is the role of outpatient hip and knee arthroplasty/enhanced recovery protocols in light of the SARS-CoV-2 pandemic? 450 (77) 76 (13) 59 (10) 585 (86) 5. What is the impact of delaying hip and knee arthroplasty for the patients themselves and for society? 530 (92) 27 (5) 19 (3) 576 (85) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: preoperative phase 1. What is the appropriate preoperative clinical and laboratory screening and timeline for patients? 435 (80) 80 (15) 31 (6) 546 (80) 2. Is preoperative tracking of patients, staff and relatives necessary? 379 (71) 121 (23) 36 (7) 536 (79) 3. Should spinal anaesthesia be routine? 420 (79) 74 (14) 40 (8) 534 (78)  – Should we only select patients as candidates who also consent to regional/spinal anaesthesia? 383 (72) 111 (21) 36 (7) 530 (78)  – If spinal anaesthesia does not occur, should we cancel the operation? 384 (73) 108 (20) 37 (7) 539 (78) 4. If the SARS-CoV-2 tests are positive, how long should the hip or knee arthroplasty surgery be postponed? 474 (90) 29 (6) 24 (5) 527 (77) 5. What kind of back-up plan is needed to guarantee quality care and patient safety in this pandemic situation? 476 (92) 19 (4) 24 (5) 519 (76) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: perioperative phase 1. Conclusion 515 (82) 94 (15) 21 (3) 630 (93) 3. What are the priority indications for elective adult hip and knee reconstruction? 510 (83) 82 (13) 25 (4) 623 (92) 4. What is the role of outpatient hip and knee arthroplasty/enhanced recovery protocols in light of the SARS-CoV-2 pandemic? 450 (77) 76 (13) 59 (10) 585 (86) 5. What is the impact of delaying hip and knee arthroplasty for the patients themselves and for society? 530 (92) 27 (5) 19 (3) 576 (85) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: preoperative phase 1. What is the appropriate preoperative clinical and laboratory screening and timeline for patients? 435 (80) 80 (15) 31 (6) 546 (80) 2. Is preoperative tracking of patients, staff and relatives necessary? 379 (71) 121 (23) 36 (7) 536 (79) 3. Should spinal anaesthesia be routine? 420 (79) 74 (14) 40 (8) 534 (78)  – Should we only select patients as candidates who also consent to regional/spinal anaesthesia? 383 (72) 111 (21) 36 (7) 530 (78)  – If spinal anaesthesia does not occur, should we cancel the operation? 384 (73) 108 (20) 37 (7) 539 (78) 4. If the SARS-CoV-2 tests are positive, how long should the hip or knee arthroplasty surgery be postponed? 474 (90) 29 (6) 24 (5) 527 (77) 5. What kind of back-up plan is needed to guarantee quality care and patient safety in this pandemic situation? 476 (92) 19 (4) 24 (5) 519 (76) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: perioperative phase 1. Is there a need for  – Modification or reorganization of hospital wards (patient density, bed density, medical and nurs-f 417 (81) 70 (14) 25 (5) 512 (75) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: perioperative phase 1. Is there a need for – Modification or reorganization of hospital wards (patient density, bed density, medical and nurs- ing stuff density, etc.)? 417 (81) 70 (14) 25 (5) 512 (75) f  – Separation of elective and trauma orthopaedic surgery (with regard to the general orthopaedic departments)? 449 (89) 36 (7) 20 (4) 505 (74) 2. Should relatives/visitors or other supportive personnel be allowed onto the orthopaedic wards and operating suite? 458 (91) 32 (6) 13 (2) 503 (74) 4. Conclusion Is there a need for  – Modification or reorganization of hospital wards (patient density, bed density, medical and nurs- ing stuff density, etc.)? 417 (81) 70 (14) 25 (5) 512 (75)  – Separation of elective and trauma orthopaedic surgery (with regard to the general orthopaedic departments)? 449 (89) 36 (7) 20 (4) 505 (74) 2. Should relatives/visitors or other supportive personnel be allowed onto the orthopaedic wards and operating suite? 458 (91) 32 (6) 13 (2) 503 (74) 3. Is there a need for extra disinfecting environmental procedures in between surgeries? 341 (69) 107 (22) 48 (10) 496 (73) 4. What role do ultra-clean operating theatres, orthopaedic exhaust suits and ultraviolet light sys- tems play in both the wards/beds and the theatre? 320 (65) 96 (20) 76 (16) 492 (72) 5. What are the guidelines for personal protective equipment (PPE), in terms of availability and instructions regarding its use and what to wear in relation to the patient’s position in the periop- erative chain? 359 (74) 83 (17) 4 (9) 446 (65) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase 1. Since the impact on mind and body during joint arthroplasty is significant, our patients may have lower immunity and be more vulnerable to SARS-CoV-2 infection 427 (88) 32 (7) 24 (5) 483 (71) 2.Organization of a shelter-in-place post-operative period, home care, community nurses or infor- mal care 419 (87) 36 (8) 26 (5) 481 (71) 3. Avoid face-to-face contact for the orthopaedic follow-up and physical therapy guidance  – Consider telemedicine 310 (65) 130 (27) 40 (8) 480 (70)  – Consider a new approach in wound closure technique in the setting of the SARS-CoV-2 pan- demic 299 (62) 141 (29) 39 (8) 479 (70) 4. What is the advice for patients who develop SARS-CoV-2 symptoms? 455 (95) 11 (2) 13 (3) 479 (70) 5. Are special adjustments needed for post-op SARS-CoV-2 prophylaxis? 362 (76) 86 (18) 31 (7) 479 (70) Table 2   Results of the survey Time periods and questions Agree n (%) Disagree n (%) Abstain n (%) Response n (%) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic 1. When should elective hip and knee arthroplasty be resumed? 653 (96) 18 (3) 10 (2) 681 (100) 2. Are new triage/patient selection criteria needed for hip and knee arthroplasty patients once elec- tive surgery is resumes? Compliance with ethical standards Conflict of interest  NC has provided consultancy services to Stryker Netherlands (amsterdam), Zimmer-Biomet (Warsaw Indiana) and 1 3 2729 Knee Surgery, Sports Traumatology, Arthroscopy (2020) 28:2723–2729 in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates recommendations. Knee Surg Sports Traumatol Arthrosc Open Access  This article is licensed under a Creative Commons Attri- bution 4.0 International License, which permits use, sharing, adapta- tion, 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/. Publisher’s Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References Kort NP, Gómez Barrena E, Bédar M, Donell S, Epinette JA, Gomb- erg B et al (2020) Resuming elective hip and knee arthroplasty 1 3
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Regulation of SIVmac239 Basal Long Terminal Repeat Activity and Viral Replication in Macrophages
Journal of biological chemistry/˜The œJournal of biological chemistry
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cc-by
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THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 285, NO. 4, pp. 2258 –2273, January 22, 2010 © 2010 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A. Regulation of SIVmac239 Basal Long Terminal Repeat Activity and Viral Replication in Macrophages FUNCTIONAL ROLES OF TWO CCAAT/ENHANCER-BINDING PROTEIN ␤ SITES IN ACTIVATION AND INTERFERON ␤-MEDIATED SUPPRESSION *□ S Received for publication, October 19, 2009, and in revised form, November 20, 2009 Published, JBC Papers in Press, November 20, 2009, DOI 10.1074/jbc.M109.075929 Shruthi Ravimohan‡§, Lucio Gama§, Sheila A. Barber§, and Janice E. Clements§¶储1 From the ‡McKusick-Nathans Institute of Genetic Medicine and Departments of §Molecular and Comparative Pathobiology, ¶ Neurology, and 储Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 CCAAT/enhancer-binding protein (C/EBP) ␤ and C/EBP sites in the HIV-1 long terminal repeat (LTR) are crucial for HIV-1 replication in monocyte/macrophages and for the ability of interferon ␤ (IFN␤) to inhibit ongoing active HIV replication in these cells. This IFN␤-mediated down-regulation involves induction of the truncated, dominant-negative isoform of C/EBP␤ referred to as liver-enriched transcriptional inhibitory protein (LIP). Although binding of the C/EBP␤ isoform to C/EBP sites in the simian immunodeficiency virus (SIV) LTR has previously been examined, the importance of these sites in core promoter-mediated transcription, virus replication, IFN␤mediated regulation, and the relative binding of the two isoforms (C/EBP␤ and LIP) has not been investigated. Here, we specifically examine two C/EBP sites, JC1 (ⴚ100 bp) and DS1 (ⴙ134 bp), located within the minimal region of the SIV LTR, required for core promoter-mediated transcription and virus replication in macrophages. Our studies revealed that the JC1 but not DS1 C/EBP site is important for basal level transcription, whereas the DS1 C/EBP site is imperative for productive virus replication in primary macrophages. In contrast, either JC1 or DS1 C/EBP site is sufficient to mediate IFN␤-induced down-regulation of SIV LTR activity and virus replication in these cells. We also characterized the differential binding properties of C/EBP␤ and LIP to the JC1 and DS1 sites. In conjunction with previous studies from our laboratory, we demonstrate the importance of these sites in virus gene expression, and we propose a model for their role in establishing latency and persistence in macrophages in the brain. During acute infection, human immunodeficiency virus(HIV)2 and simian immunodeficiency virus (SIV)-infected cells * This work was supported, in whole or in part, by National Institutes of Health Grants NS047984, MH070306, and HL75840. The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S5. 1 To whom correspondence should be addressed: Dept. of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, 733 North Broadway, BRB831, Baltimore, MD 21205. Tel.: 410-9559770; Fax: 410-955-9823; E-mail: jclement@jhmi.edu. 2 The abbreviations used are: HIV, human immunodeficiency virus; HIV-1, HIV type 1; C/EBP, CCAAT/enhancer-binding protein; LTR, long terminal repeat; IFN␤, interferon ␤; SIV, simian immunodeficiency virus; LIP, liver inhibitory protein; LAP, liver-enriched transcriptional activation protein; ChIP, chromatin immunoprecipitation; EMSA, electrophoretic mobility shift assays; siRNA, small interfering RNA; m.o.i., multiplicity of infection; □ S 2258 JOURNAL OF BIOLOGICAL CHEMISTRY invade the central nervous system (1, 2). However, HIV-associated neurocognitive disorders do not usually develop until late in the disease process. Using an accelerated and consistent SIV/ macaque model for HIV/AIDS and central nervous system disease, we have demonstrated that SIV RNA is detected in the brain as early as 7 days postinoculation (p.i.) and peaks by 10 days p.i. (3). Between 14 and 21 days p.i., SIV RNA expression in the brain is down-regulated, at least in part, at a transcriptional level because SIV DNA levels remain constant during this time (3, 4). Previous reports in our model have implicated IFN␤ in the suppression of acute SIV replication in the brain (4, 5). IFN␤, the predominant type I IFN induced as part of the innate immune response to viral pathogens in the central nervous system (6), has been shown to inhibit HIV/SIV replication in macrophages (7, 8), a major source of productive HIV/SIV replication in the brain (5, 9). Transcriptional suppression of the HIV/SIV long terminal repeat (LTR) by IFN␤ involves the induction of a truncated, dominant-negative isoform of the transcription factor CCAAT/enhancer-binding protein ␤ (C/EBP␤), LIP (7, 10). There are three known isoforms of C/EBP␤ also referred to as NF-IL6 (nuclear factor-IL6) and LAP (liver-enriched transcriptional activation protein), which are alternatively translated from the same mRNA (11, 12). We use the term C/EBP␤ and LIP in this study to refer to the second and third in-frame AUG start site translated products, respectively. C/EBP␤ and LIP belong to the C/EBP family of transcription factors characterized by their basic leucine zipper and highly conserved DNA binding domain (13). LIP is the truncated isoform that retains the DNA binding domain but lacks the transactivation domain (14). As a result, LIP competes with C/EBP␤ for the same DNAbinding sites, and because of its inability to associate with histone acetyltransferases, it antagonizes C/EBP␤-mediated transcriptional activation (14 –17). C/EBP␤ has been demonstrated as an important regulator of the HIV LTR in macrophages and promonocytic cell lines in vitro (18). In these cells, but not CD4⫹ lymphocytes, at least one functional C/EBP␤ site in the HIV LTR is necessary and sufficient for maintaining basal level activity (19, 20). Similar to the HIV-1 LTR, the SIV LTR (Fig. 1) has C/EBP sites that bind C/EBP␤ (21). Nonnemacher et al. (21) demonstrated C/EBP␤ p.i., postinfection; mLTR, mid-LTR; qPCR, quantitative PCR; ELISA, enzymelinked immunosorbent assay; TAR, transactivation response. VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR FIGURE 1. Schematic of SIV LTR. 390-bp fragment (⫺236 to ⫹154 bp) of full-length SIV LTR representing mid-LTR (mLTR) was cloned into pGL4.11 luciferase vector. The relative position and nucleotide sequence of the JC1 (⫺100) and DS1 (⫹134) sites are indicated, with the underlined sequence indicating the C/EBP site. binding to four out of five putative C/EBP sites; however, the functional roles of these sites remain to be elucidated. Reports from our laboratory demonstrated that nucleotide sequences spanning from ⫺225 to ⫹18 bp of SIV LTR relative to the transcription start are sufficient for basal level activity in U937 promonocytic cells (22, 23), and the addition of ⫹19 to ⫹149 bp established the minimal region for Tat-mediated transactivation (22, 24). There are two distinct C/EBP sites in the ⫺225 to ⫹149-bp region. The first site, JC1, is located at ⫺100 bp from the SIV LTR transcriptional start site. JC1 contains overlapping NF-␬B and C/EBP-binding sequences based on in silico analysis and is protected in DNase I footprint assays (21, 23). The second site, DS1, is located at ⫹134 bp and binds C/EBP␤ (21). We have previously demonstrated that C/EBP␤ activates transcription of the ⫺225 to ⫹149-bp region of the SIV LTR, whereas LIP suppresses C/EBP␤-mediated transcriptional activation in a dose-dependent manner (4). Using a chromatin immunoprecipitation assay (ChIP), we have demonstrated that C/EBP␤ binds the ⫺225 to ⫹149-bp core promoter region of the SIV LTR in U937 monocytic cells as well as the SIV LTR in brains of infected macaques examined at 7, 10, and 21 days p.i. In addition, ChIP results demonstrated decreased histone H4 acetylation at the SIV LTR upon co-transfection with LIP into the U937 cells, consistent with the lack of histone acetyltransferase recruitment by LIP (4). In vivo, ChIP demonstrated a similar decrease in acetylated histone H4 at the SIV LTR in brains of animals during the transition from active SIV replication at 7–10 days p.i. to suppression of SIV RNA expression at 21 days p.i. These observations collectively suggested that LIP also binds to the ⫺225 to ⫹149-bp region and is crucial in the suppression of SIV transcription and virus replication (4). However, we could not specifically assay binding of LIP to the SIV LTR because there are no antibodies that distinguish C/EBP␤ and truncated (LIP) isoforms. Additionally, the contribution of the JC1 and/or DS1 C/EBP sites to transcriptional regulation remained unclear because the two sites are only 200 bp apart, and binding of C/EBP␤ and LIP to these sites could not be resolved using standard ChIP assays. To address these issues in the current studies, FLAG-tagged LIP and Myc-tagged C/EBP␤ were used to examine binding to JC1 and DS1 C/EBP sites in transient ChIP assays. JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 In this study, transcriptional activity assays of the SIV LTR in primary macrophages demonstrate that the JC1 but not the DS1 C/EBP site is crucial for basal transcription by the core promoter. In the context of the whole virus, however, virus replication assays demonstrate that the DS1 C/EBP site is necessary for productive virus replication. In contrast, either site can mediate IFN␤-induced suppression of promoter (basal)mediated SIV LTR activity and virus replication, independently. We also demonstrate binding of C/EBP␤ and, for the first time, binding of LIP to the JC1 and DS1 C/EBP sites. Finally, we show that the two isoforms have differential binding affinities for JC1 and DS1, which, together with the functional activities of these sites, enable us to propose a molecular model to describe C/EBP␤/LIP regulation of the SIV LTR and their role in establishing viral latency in macrophages in the brain. EXPERIMENTAL PROCEDURES Cell Culture—HEK-293T cells were maintained in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (Invitrogen), 2 mM L-glutamine, and 0.5 mg/ml gentamicin (Invitrogen) and cultured as described previously (25). CEMx174 cells were cultured as described previously (24). Blood-derived primary macrophages were prepared from healthy human blood, obtained in compliance to Institutional Review Board protocols, or adult rhesus macaques and cultured as described previously (26). Briefly, peripheral blood mononuclear cells were isolated by the FicollPaque method. Ten million (107) cells were seeded into each well of a 6-well plate and cultured for 7 days in macrophage differentiation media containing RPMI 1640 medium (Invitrogen) supplemented with human AB serum, 10 mM HEPES, 2 mM L-glutamine, 0.5 mg/ml gentamicin, and 100 units/ml macrophage colony-stimulating factor. Under these culture conditions, lymphocytes do not proliferate, and ⬎ 95% of the cells are macrophages (26). Plasmids—A 390-bp (⫺236 to ⫹154 bp) and a 271-bp fragment (⫺117 to ⫹154 bp) of the SIVmac239 LTR was inserted into the pGL4.11 firefly luciferase vector (Promega Corp.) to generate the mid-LTR (mLTR) and mLTRII construct, respectively. The JC1mC/EBP and DS1mC/EBP constructs were generated from the mLTR and mLTRII constructs by site-directed mutagenesis using the following primers: JC1mC/EBP (forward primer, 5⬘-AACAGCAGGGACTGTCCAACCGGGGAT-3⬘; reverse primer, 5⬘-ATCCCCGGTTGGACAGTCCCTGCTGTT-3⬘) and DS1mC/EBP (forward primer, 5⬘-GCTTGCCCGCTTCAAGCCCTCTTCAATAA-3⬘; reverse primer, 5⬘-TTATTGAAGAGGGCTTGAAGCGGGCAAGC-3⬘). The JC1/DS1mC/EBP construct was generated from the JC1mC/ EBP construct using the DS1mC/EBP primer set for site-directed mutagenesis. The mLTR and the derivative constructs were used for luciferase assay, whereas the mLTRII and the derivative constructs were used for chromatin immunoprecipitation assay (ChIP). SIV/17EFr full-length 5⬘- and 3⬘LTR mutant viruses were generated by stepwise cloning. 5⬘LTR mutations were introduced by digesting pEGFP-N1 (Clontech) and the SIV/17EFr-pUC19 plasmid with BsrGI and inserting the 1108 –3291-bp fragment of the 5⬘LTR into pEGFP-N1 plasmid, followed by site-directed mutagenesis using the aforemenJOURNAL OF BIOLOGICAL CHEMISTRY 2259 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR tioned primer pairs. The mutated 5⬘LTRs were cloned back into the SIV/17EFr-pUC19 plasmid after BsrGI digestion. Next, SIV/17EFr-pUC19 and the pEGFP-N1 plasmid were digested with EcoR/NheI, thereby inserting the 10,233–13,940-bp fragment of the 3⬘LTR into the pEGFP-N1 plasmid. This construct was then used as template to introduce mutations in the 3⬘LTR JC1 and/or DS1 C/EBP sites. The mutated 3⬘LTR-pEGFP-N1 constructs were digested with NheI/BlpI, thereby inserting the 10,233-11,771-bp fragment of the 3⬘LTR into the respective SIV/17EFr 5⬘LTR-pUC19 mutant plasmids digested with the same enzymes. This generated JC1mC/EBP, DS1mC/EBP, and JC1/DS1mC/CEBP 5⬘–3⬘LTR mutant virus plasmids. The QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA) was used to generate all of the above plasmids. The Renilla luciferase reporter plasmid pGL4.74 (hRluc/TK) used for cotransfection in luciferase assays to control for transfection efficiency was obtained from Promega Corp. Expression vectors for C/EBP, pCMV-C/EBP␤ (LAP), and LIP, pCMV-LIP, have been described elsewhere (4). Two FLAG tags were added to the N terminus of LIP (pCMV-LIP was used as template) by inverse mutagenesis using forward primer 5⬘-GACTACAAAGACGATGATGACAAGGCGGCCGGCTTCCCGTTCGCC-3⬘ and reverse primer 5⬘-CTTGTCATCATCGTCTTTGTAGTCCATGGTGGCGCGAATTCGAAG-3⬘ (27). A Myc tag was added to the N terminus of the C/EBP␤(LAP) where C/EBP␤ from the pCMV-C/EBP␤(LAP) construct was inserted into the pCMV-Myc vector (Clontech). All plasmid constructs were sequenced to confirm mutations and the correct insertion of fragments. Transient Transfection—HEK-293T cells were transfected with Lipofectamine-2000 according to manufacturer’s instructions (Invitrogen). Nuclear lysates for EMSAs were extracted from 1.2 ⫻ 106 cells transfected with 4 ␮g of DNA (pCMV-C/ EBP␤(LAP), -LIP, or -FLAG-LIP). Nuclear extracts were prepared according to manufacturer’s protocol (Marligen Biosciences, Inc.). For ChIP assays, 2 ⫻ 107 HEK-293T cells were seeded in 100-mm culture dishes with 15 ml of Dulbecco’s modified Eagle’s media and transfected with 12 ␮g of mLTRII or one of the mLTRII mutant constructs and co-transfected with either 12 ␮g of pCMV-Myc-C/EBP␤(LAP) or -FLAG-LIP constructs. Blood-derived primary macrophages were plated in macrophage differentiation media as described above. Cells were cotransfected with 3 ␮g of the indicated luciferase reporter construct pGL4.11 and 1 ␮g of the pGL4.74-Renilla-luciferase vector (Promega Corp.). Cells were treated with or without 100 units/ml recombinant human IFN␤-1a (PBL Biomedical Laboratories) 5 h post-transfection. IFN␤ treatment was carried out for 24 h, after which cells were harvested, and luciferase activity was measured. Luciferase Assay—Blood-derived primary macrophages cotransfected as described above were used to measure firefly and Renilla activity with the Dual-Luciferase reporter assay kit (Promega Corp.) and Fluoroskan Ascent FL luminometer according to the manufacturer’s instructions. Primary human macrophages were used instead of rhesus macrophages because the transfection efficiency in rhesus macrophages was too low 2260 JOURNAL OF BIOLOGICAL CHEMISTRY to assess the effects of mutations. The relative luciferase activity of the constructs was consistent between human blood donors. SIV Viral Stock Production, Infection of Rhesus Macaque Macrophages, and p27 ELISA—CEMx174 cells were transfected with 12 ␮g of viral DNA as described previously (28), specifically, SIV/17EFr (a macrophage-tropic recombinant chimeric clone of SIVmac239 that shares 100% sequence homology in the LTR within the region of interest) and the 5⬘–3⬘LTR mutant virus constructs generated above. The TCID50 assay was performed as described elsewhere (29). SIV RNA from every virus stock was sequenced to verify the presence of the mutations. Rhesus monocyte-derived macrophages were infected with wild-type and mutant viruses at a multiplicity of infection (m.o.i.) of 0.01. After 6 h of infection, cells were washed extensively and cultured in media (1 ml) with or without 100 units/ml IFN␤. Supernatants were collected (1 ml) daily from 1 to 5 days postinfection and replaced with the appropriate media. The level of SIV capsid protein, p27, in supernatants was analyzed by ELISA (SIV p27 ELISA kit, Zeptomatrix) to assess virus replication. EMSA—Double-stranded oligonucleotide probes used in EMSA were as follows: canonical C/EBP (5⬘-TGCAGATTGCGCAATCTGCA-3⬘); JC1 C/EBP (5⬘-AACAGCAGGGACTTTCCACAAGGGGATG-3⬘); JC1-mutated C/EBP (JC1mC/ EBP, 5⬘-AACAGCAGGGACTGTCCAACCGGGGAT-3⬘); DS1 C/EBP (5⬘-GCTTGCTTGCTTAAAGCCCT-3⬘); and DS1-mutated C/EBP (DS1mC/EBP, 5⬘-GCTTGCCCGCTTCAAGCCCTCTTCAATAA-3⬘). Nuclear extracts (8 ␮g) from HEK-293T cells transfected with pCMV-C/EBP␤(LAP) or pCMV-FLAG-LIP were incubated with 5 ⫻ 104 cpm of [␥-32P]ATP-labeled oligonucleotides as described previously (30). Incubation was carried out in binding reaction buffer containing 1 mM MgCl2, 60 mM KCl, 0.1 mM EDTA, 20 mM HEPES (pH 8.0), 15% glycerol, and 1 ␮g of poly(dI-dC) as nonspecific competitor. Antibodies used in supershift assays were anti-C/ EBP␤ antibody (sc-150X; Santa Cruz Biotechnology), antiFLAG M2 monoclonal antibody (Sigma), or anti-p50 antibody (sc-7178X; Santa Cruz Biotechnology). For competition assays, unlabeled JC1, DS1, canonical C/EBP oligonucleotides (5⬘TGCAGATTGCGCAATCTGCA-3⬘ (31)), or oligonucleotides with a mutated canonical C/EBP site (5⬘-TGCAGAGACTAGTCTCTGCA-3⬘) were added to the binding reaction at the concentrations indicated in each figure. Samples were incubated for 30 min at room temperature and 15 min at 4 °C prior to electrophoresis at 4 °C in 5% nondenaturing TBE gels at 155 V for 2 h; in this way free probe was run off the gel to resolve protein complexes. Chromatin Immunoprecipitation Assay (ChIP)—Transient ChIP assays were performed as published previously (32, 33) with modifications using the Magna ChIP kit (Millipore). Briefly, cells were treated with 1% formaldehyde for 10 min at room temperature and neutralized with 1⫻ glycine. Nuclei were isolated and sonicated to obtain 200 –500-bp DNA fragments using the Branson sonicator for 15 12-s pulses at 50% amplitude with 1 min of incubation on ice between pulses. One million (106) cells were used per immunoprecipitation in a 50-␮l volume and pre-cleared with protein A/G-PLUS-agarose beads (Santa Cruz Biotechnology) for 3 h followed by a 16-h VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR pre-clear with Dynabeads protein G (Invitrogen) at 4 °C. Input was determined from 1% of the cell lysate. For immunoprecipitation, pre-cleared cell lysates were incubated with no antibody, 1– 4 ␮g of mouse IgG (12-371, Millipore) as control, anti-Myc (sc-9E10X, Santa Cruz Biotechnology), or FLAG M2 monoclonal antibody (Sigma) antibody at 4 °C for 4 h. Reverse crosslinked and eluted samples were then used for real time quantitative PCR by SYBR-Green (Qiagen) and PCR using the following primers: JC1F, 5⬘-AAGCTTCGCTGAAACAGCAG3⬘, and DS1R, 5⬘-TTTGGCATCTTCCATGGTG-3⬘. To verify that the no antibody and mouse IgG controls were negative, PCR was carried out on the same samples used in the qPCR assay and analyzed by agarose gel (supplemental Fig. S4). Western Blot—Nuclear extracts from HEK-293T cells were prepared as described above. Protein lysates were resolved on 12.5% gradient Tris-HCl polyacrylamide gel (Bio-Rad) and transferred onto polyvinylidene difluoride membranes (Millipore). Blots were blocked at room temperature with 5% milk diluted in Tris-buffered saline/Tween 20 (TBST) and probed with anti-C/EBP␤ polyclonal antibody (sc-150, Santa Cruz Biotechnology) and anti-lamin A/C antibody (sc-7292; Santa Cruz Biotechnology) as a loading control at appropriate dilutions. Membranes were washed with TBST and incubated with appropriate horseradish peroxidase-conjugated secondary antibodies (Dako) for 1 h at room temperature. Membranes were washed with TBST and analyzed with Super Signal West Dura extended duration substrate (Pierce). Data and Statistical Analysis—Luciferase and ChIP assay figures depict mean signal from triplicate samples ⫾ S.E., whereas p27 ELISA graphs depict mean signal from duplicate samples ⫾ S.E. from three or more independent experiments as indicated in the figures. ChIP data was analyzed by the ⌬⌬Ct method, where all signals are initially normalized to corresponding input followed by normalization to C/EBP␤ or LIP binding to wild-type, mLTRII, construct as indicated. Statistical significance (p ⬍ 0.05) was evaluated using a Student’s two-sided t test. Densitometric analysis of EMSA complexes was carried out using Kodak MI software. In competition experiments, the intensity of the complexes incubated with labeled oligonucleotide alone was set to 100%, and the intensities of complexes in all other lanes were normalized to this. Standard calculations were performed to determine binding affinities. Unlabeled oligonucleotide concentration (in nanomolar) used in the competition EMSA, expressed as ⫺log[nM], was plotted against band intensity represented as percentage (%) of protein bound to labeled oligonucleotide. Data were fit using nonlinear regression, sigmoidal dose-response curve described by the following equation: Y ⫽ min ⫹ (max ⫺ min)/(1 ⫹ 10∧((logEC50 ⫺ X)䡠n), where max is maximum protein binding at lowest competitor concentration (unlabeled oligonucleotide); min is minimum protein binding at highest competitor concentration (unlabeled oligonucleotide); EC50 is half-maximal protein binding; X is logarithm of unlabeled oligonucleotide concentration, and n is the Hill coefficient (GraphPad Prism version 4.0a software). The following Reaction 1 was used to estimate the KD value of C/EBP␤ and FLAG-LIP to the canonical, JC1, and DS1 C/EBP JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 sites, where C is protein complex; DH is labeled oligonucleotide, and DC is unlabeled oligonucleotide. 关 CD H 兴 ⫹ 关 D C 兴 7 关 CD C 兴 ⫹ D H共runs off兲 REACTION 1 Therefore, KD ⫽ [CDH] ⫻ [DC]/[CDC]. The above is a modification of the reaction derived by Sun and Baltimore (34). Because siRNA could not be used to selectively knock down endogenous C/EBP␤ or LIP, we assumed that ectopically expressed C/EBP␤/C/EBP␤ or FLAG-LIP/ FLAG-LIP homodimers predominate in the complexes bound to the labeled oligonucleotide especially considering that pCMV-C/EBP␤(LAP)-transfected 293T cells express undetectable levels of LIP and that pCMV-FLAG-LIP- transfected cells express undetectable levels of C/EBP␤(LAP) (Fig. 3A). With the addition of excess unlabeled oligonucleotides, complexes bound to labeled oligonucleotide were increasingly competed away, shifting the binding of complexes from labeled to unlabeled oligonucleotides, with unbound labeled oligonucleotides running off the gel. At the unlabeled oligonucleotide concentration DC (1/2), where 50% of complexes bound to labeled oligonucleotide (DH) are competed away (i.e. EC50 from the graph), the concentration of CDH is equal to CDC. Therefore, the KD value is equal to the concentration of unlabeled oligonucleotide at 50% competition, i.e. [DC(1/2)] to the closest approximation (14, 34). RESULTS Promoter-mediated Transcriptional Activation of the SIV LTR Requires the JC1 but Not the DS1 C/EBP␤ Site, although the DS1 C/EBP Site Is Crucial for Productive Virus Replication in Primary Macrophages—ChIP assays previously demonstrated that C/EBP␤ binds to the ⫺225 to ⫹149-bp region of the SIVLTR in vitro and in vivo (4). The JC1 C/EBP site resides at ⫺100 bp within the ⫺225 to ⫹18-bp region required for basal SIV LTR activity, whereas the DS1 C/EBP site resides at ⫹134 bp within the ⫹19 to ⫹149-bp region required for Tat transactivation and apparently dispensable for basal SIV LTR activity (22–24). However, no study has examined the specific contribution of either site in regulating SIV LTR transcriptional activity. To this end, we transfected primary human macrophages with firefly luciferase constructs (Fig. 2A) containing ⫺236 to ⫹154 bp of the SIV LTR, referred to as mid-sized LTR (mLTR); the mLTR construct with mutations in the JC1 C/EBP site (JC1mC/E), DS1 C/EBP site (DS1mC/E), or both JC1 and DS1 C/EBP sites (JC1/DS1mC/E) along with a Renilla luciferase vector to normalize transfection. Mutation of the JC1 C/EBP site (JC1mC/E) reduced LTR activity by 70.4% (p ⬍ 0.001), whereas mutation of the DS1 C/EBP site (DS1mC/E) did not significantly alter LTR activity, consistent with the lack of requirement for the ⫹19 to ⫹149-bp region for basal activity (Fig. 2A). Mutation of both the JC1 and DS1 C/EBP sites (JC1/DS1mC/E) decreased LTR activity by 73% (p ⬍ 0.001) further confirming that the JC1 C/EBP site is important for transcriptional activation of the SIV LTR in macrophages, whereas the DS1 C/EBP site is largely dispensable. JOURNAL OF BIOLOGICAL CHEMISTRY 2261 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR FIGURE 2. JC1 C/EBP site is crucial for basal transcriptional activation of the SIV LTR, whereas DS1 C/EBP site is critical for virus replication. A, functional analysis of mLTR (wild type), JC1, DS1, and JC1/DS1 mutant C/EBP (mC/E) constructs in primary human macrophages were carried out by luciferase assay. Primary human macrophages were transfected with pGL4-firefly luciferase construct DNA containing mLTR (wild type) insert or mLTR constructs with mutations in the indicated C/EBP sites. Co-transfection with pGL4.74 Renilla luciferase vector was used for normalizing transfection efficiency. The activity of mutant constructs is normalized to wild-type mLTR construct, set to 100%. Results are expressed as the mean ⫾ S.E. (n ⱖ 4). *, p ⬍ 0.001, Student’s two-sided paired t test. B, p27 ELISA was carried out to measure virus replication. Primary rhesus macaque macrophages were infected with SIV/17EFr (wild type; open squares), JC1mC/E (closed triangles), DS1mC/E (gray circles), or JC1/DS1mC/E (open diamonds) 5⬘–3⬘LTR mutant viruses at m.o.i. of 0.01. Supernatants (1 ml) were collected at 24, 48, and 72 h p.i. and were used for p27 analysis. C, JC1mC/E mutant virus replication measured by p27 ELISA normalized to SIV/17EFr (wild type)-infected cells set at 100% after 24 h of infection. DS1mC/E and JC1/DS1mC/E mutant virus replication were below the limit of detection at this time point. D, indicated mutant virus replication measured by p27 ELISA normalized to SIV/17EFr set at 100% after 48 h of infection, when SIV/17EFr peak virus replication was observed. Mock-infected (⫻) p27 values were below the limit of detection. Results are expressed as the mean ⫾ S.E. from three independent experiments carried out in duplicate; p values calculated by Student’s two-sided paired t test. To better understand the functions of these sites in the context of the whole virus and productive virus replication in primary rhesus macrophages by endogenous C/EBP␤, the same mutations were introduced into the 5⬘- and 3⬘LTR JC1 and/or DS1 C/EBP sites of the infectious molecular clone of the SIV/ 17EFr virus. SIV/17EFr is a macrophage-tropic, recombinant clone of SIVmac239 that shares 100% LTR sequence homology (26). Primary rhesus macrophages were infected with SIV/ 17E-Fr (wild type) and individual SIV/17EFr viruses with mutations in the JC1, DS1 and JC1/DS1 C/EBP sites. Virus replication was measured from 1 to 5 days p.i. using an SIV capsid protein, p27 ELISA. SIV/17EFr (wild type) and JC1mC/E virus 2262 JOURNAL OF BIOLOGICAL CHEMISTRY replication was detected at 24 h p.i., peaked at 48 h p.i., and decreased consistently thereafter (Fig. 2B; data for 4 and 5 days p.i. not shown). In contrast, replication of DS1mC/E and JC1/ DS1mC/E viruses was not detectable until 48 h p.i. (Fig. 2B). Replication of the mutant viruses was compared with wild type, SIV/17EFr, set to 100% at 24 and 48 h p.i. (Fig. 2, C and D, respectively). Mutation of the JC1 C/EBP site (JC1mC/E) decreased virus replication consistently, particularly at 24 h p.i. when replication was significantly lower than wild-type virus by 56% (p ⫽ 0.033; Fig. 2C). Although there was a 31% decrease in virus replication of the JC1mC/E mutant compared with the wild type at 48 h p.i. (Fig. 2D), this decrease was not significant, VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR suggesting that the JC1 C/EBP site may be important for initial cycles of infection within a cell and the initial round of transcription. Of note, Muesing et al. (35) have also demonstrated that upstream LTR regulatory elements are not essential for transactivation in their HIV-1 LTR studies in keeping with our observations here. The SIV/17E-Fr viruses with mutations in the DS1 (DS1mC/E) and JC1/DS1 C/EBP (JC1/DS1mC/E) sites had dramatically lowered virus replication and were below the limit of detection until 48 h p.i., when replication was 95% (p ⫽ 0.013) and 97% (p ⬍ 0.001) lower than wild-type virus, respectively (Fig. 2D). These observations indicate that in the context of the whole virus, the DS1 C/EBP site is crucial for productive virus replication. These functional data again corroborate previous observations that the ⫹19- to ⫹149-bp region is necessary for Tat transactivation (22, 24). The DS1 C/EBP site is 9 bp downstream of the 3⬘ end of the transactivation-response element (TAR), spanning ⫹1 to ⫹126 bp (36, 37). This region forms a secondary RNA structure upon transcription (35, 38). Tat binds this element in association with transcription elongation factor (p-TEFb), TAR-RNA-binding protein, as well as several other DNA binding transcription factors and functions to enhance RNA polymerase II processivity (39 – 41). Using the Mfold software that analyzes secondary RNA structure, we verified that the DS1 C/EBP site mutation did not alter the RNA structure of the TAR element (data not shown). C/EBP␤ Binds to JC1 and DS1 C/EBP Sites—In the studies above, we have demonstrated that the JC1 C/EBP site is important for basal transcription, and the DS1 C/EBP site is critical for productive virus replication in primary human and rhesus macrophages; therefore, we next characterized binding of C/EBP␤ to these sites individually. To be consistent with previous studies by several groups, including those studies of C/EBP␤-mediated regulation of the HIV LTR (15, 20), we used the rat homologs of C/EBP␤ (LAP) and LIP (42– 46). We carried out EMSAs with these proteins after confirming (supplemental Fig. S1) that the binding characteristics of the rat homologs are very similar to the human homologs, hC/EBP␤ (NF-IL6) and hLIP, and recognize the same C/EBP consensus sequence as described by Osada et al. (31). EMSAs were conducted using nuclear extracts enriched in the respective proteins of interest from HEK-293T cells. The levels of endogenous C/EBP␤ and LIP in HEK-293T cells are undetectable as reported previously (42), and we confirmed this by Western blot (Fig. 3A). We first examined the binding of C/EBP␤ to the JC1 and DS1 C/EBP sites. Complexes formed using the canonical C/EBP, JC1 and DS1 probes (Fig. 3, B and D, lanes 1 and 3; see arrows), and the complexes were supershifted or abrogated by the addition of anti-C/EBP antibody (Fig. 3, B and D, lanes 2 and 4), demonstrating the binding of C/EBP␤ to each site. Importantly, no complexes were formed with JC1 and DS1 probes containing point mutations in the core C/EBPbinding site (Fig. 3, B and D, lanes 5 and 6; see arrows). It should be noted as well that the JC1 probe with the mutation in the JC1 site but not the NF-␬B site retains the ability to bind NF-␬B (top complex; supplemental Fig. S2), indicating that C/EBP␤ binding to JC1 occurs independently of NF-␬B binding. JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 Specificity of C/EBP␤ binding to JC1 and DS1 probes was confirmed by competition EMSAs, where the C/EBP␤-containing complexes were competed with excess unlabeled canonical C/EBP probe (Fig. 3, C and E, lanes 1 and 2; see arrows) but not canonical C/EBP probe containing mutations in the core C/EBP-binding site (Fig. 3, C and E, lane 3). There were no C/EBP␤ complexes formed on mutated JC1 and DS1 probes (Fig. 3, C and E, lane 4), and no competition could be detected with wild-type or mutated canonical C/EBP probes (Fig. 3, C and E, lanes 5 and 6). To substantiate the above findings, i.e. binding of C/EBP␤ to these sites, in a more biologically relevant in vivo setting, we performed ChIP assays. With standard ChIP, characterization of binding sites at high resolution is difficult to achieve as shearing DNA yields fragments between 200 and 500 bp, and fragments smaller than this makes the assay inefficient. To resolve C/EBP␤ binding to the JC1 and DS1 C/EBP sites, which are only 200 bp apart, we modified the standard ChIP assay. We initially tried using restriction enzymes to resolve the two sites prior to carrying out immunoprecipitation; however, contamination with incomplete digestion fragments interfered with the assay and could not be overcome (data not shown). Modifying previously published methods (32, 33), we transiently transfected HEK-293T cells with a 271-bp fragment of the LTR, mLTRII (wild type), that encompassed just the JC1 and DS1 C/EBP sites with and without the mutations in the JC1, DS1, or both JC1/ DS1 C/EBP sites. In addition, we co-transfected the pCMVMyc-C/EBP␤ vector, where the Myc tag was used to aid in efficient and clean immunoprecipitation. We carried out standard immunoprecipitation followed by quantitative PCR (qPCR; Fig. 3F). The data are presented as the percentage binding of C/EBP␤ to the indicated constructs normalized to mLTRII binding, set at 100%. Individually mutating the JC1 or DS1 C/EBP sites led to a significant decrease in binding by 63 (p ⫽ 0.009) and 66% (p ⫽ 0.016), respectively. Furthermore, mutating both sites led to 85% decrease in binding of C/EBP␤ (p ⫽ 0.002), confirming that C/EBP␤ binds to both the JC1 and DS1 sites. qPCR signals for no antibody and mouse IgG controls were less than 0.1% relative to input. We further verified that the no antibody and mouse IgG controls were negative by carrying out PCR on the above samples and analyzing them on agarose gel (supplemental Fig. S4A). To ensure there was the same amount of protein in each immunoprecipitation, we measured myc-C/EBP␤ expression by Western blot and observed no significant differences (supplemental Fig. S5). Collectively, the EMSA and ChIP data demonstrate not only that C/EBP␤ binds to both JC1 and DS1 but also that binding requires an intact C/EBP site. IFN␤-induced Suppression of SIV LTR Transcriptional Activity and Virus Replication in Primary Macrophages Is Mediated by Either JC1 or DS1 C/EBP Sites—We have previously demonstrated that IFN␤-mediated suppression of SIV LTR activity correlates with increased expression of LIP relative to C/EBP␤ in monocytic cell lines and in the brain of SIV-infected macaques (4, 5). Having demonstrated that C/EBP␤ regulates LTR activity through the JC1 and DS1 C/EBP sites, we next examined the functions of these sites in IFN␤-mediated suppression of SIV LTR activity. Primary human macrophages JOURNAL OF BIOLOGICAL CHEMISTRY 2263 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR were transfected with mLTR, JC1mC/E, DS1mC/E, and JC1/ DS1mC/E firefly luciferase constructs (Fig. 4A), and each construct was co-transfected with a Renilla luciferase construct, to use as an internal transfection control. Cells were then treated with or without 100 units/ml recombinant human IFN␤ for 24 h post-transfection. Each sample was initially normalized for transfection efficiency (firefly/Renilla), and then to assess the effect of IFN␤, the normalized luciferase activity of the IFN␤-treated cells was compared with the normalized luciferase activity of untreated control cells transfected with the same firefly constructs. Treatment of wild-type mLTRtransfected cells with 100 units/ml IFN␤ for 24 h significantly decreased LTR activity by 59% (p ⫽ 0.0035). A similar decrease in LTR activity was observed in cells transfected with the JC1mC/E or DS1mC/E construct treated with 100 units/ml IFN␤, where the decrease in LTR activity was 51 (p ⫽ 0.025) and 48% (p ⫽ 0.0091), respectively. However, a lack of IFN␤-mediated suppression was observed with mutation of both the JC1 and DS1 C/EBP sites (JC1/DS1mC/E). These data demonstrate that JC1 and DS1 C/EBP sites are individually important and that at least one of these sites is required for the suppressive effect of IFN␤ on SIV LTR transcriptional activity in macrophages. Initial studies from our laboratory have demonstrated that IFN␤ induces LIP expression at 24 h posttreatment and suppresses SIV replication (4, 47). More recent studies from our laboratory have demonstrated that inhibition of IFN␤-induced LIP expression also inhibits IFN␤-mediated suppression of SIV replication (47). Therefore, we investigated the contribution of these C/EBP sites in the IFN␤-induced, LIP-mediated down-regulation of SIV virus replication (Fig. 4, B and C). Primary rhesus macaque macrophages were infected with SIV/17EFr and SIV/17EFr viruses 2264 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR FIGURE 4. JC1 and DS1 C/EBP sites are important for IFN␤-mediated down-regulation SIV LTR activity in primary macrophages. A, functional role of JC1 and DS1 C/EBP sites in IFN␤-mediated suppression of SIV (mLTR) activity was studied by transfecting primary human macrophages with the indicated constructs. Cells were treated with or without 100 units/ml IFN␤ 4 h post-transfection and lysed 24 h post-IFN␤ treatment, when luciferase activity was measured. The luciferase activity of IFN␤ treated cells was normalized to untreated cells transfected with the same firefly luciferase construct (⫺IFN␤), with activity of untreated controls set to 100%. Results expressed as the mean ⫾ S.E. (n ⱖ 4); p values calculated by Student’s two-sided paired t test. IFN␤mediated suppression of virus replication was assayed by p27 ELISA (B and C). Primary rhesus macaque macrophages were infected with SIV/17EFr (wild type), JC1mC/E, DS1mC/E, or JC1/DS1mC/E 5⬘–3⬘LTR mutant viruses at m.o.i. of 0.01 and treated with or without 100 units/ml IFN␤. p27 analysis on supernatants collected at 24 (B) and 48 h postinfection (C), when peak virus replication was observed, is plotted. Mock-infected p27 values were below the limit of detection. Results are expressed as the mean ⫾ S.E. from three independent experiments carried out in duplicate; p values calculated by Student’s two-sided paired t test. containing mutations in the JC1, DS1, or JC1/DS1 C/EBP sites at an m.o.i. of 0.01 followed by 100 units/ml IFN␤ treatment (or not) 6 h post-infection. The supernatants (1–5 days p.i.) were used to monitor virus replication by quantitating the SIV viral capsid protein, p27. At 24 h p.i. (Fig. 4B), there was a significant decrease in SIV/17EFr (83.5%; p ⫽ 0.015) and JC1mC/E (93%; p ⫽ 0.0016) virus replication upon treatment with IFN␤, which was maintained at 48 h p.i. (Fig. 4C), when compared with virus replication in the infected untreated controls. In the case of the SIV/17EFr-DS1mC/E and JC1/ DS1mC/E mutated viruses, replication in the infected untreated controls was not detected until 48 h p.i. At this point IFN␤ treatment decreased virus replication significantly, down-regulating it to levels below the limit of detection. We also carried out infections at an m.o.i. of 0.05 followed by 1000 units/ml IFN␤ treatment and observed similar suppressive effects regardless of the mutations (data not shown). These findings were surprising in light of our previous experiments demonstrating that siRNA-mediated knockdown of CUGBP1 (CUG-repeat RNA-binding protein 1), the RNA-binding protein required for IFN␤-induced LIP expression, not only inhibited LIP expression but also the ability of IFN␤ to suppress SIV replication (47). Thus, we suspected that the ability of IFN␤ to suppress replication of SIV/17EFr-JC1mC/E, DS1mC/E, and JC1/DS1mC/E mutant viruses may be due to the FIGURE 3. C/EBP␤ binds JC1 and DS1 C/EBP sites. A, Western blot analysis of nuclear extract from untransfected HEK-293T and 293T cells transfected with C/EBP␤(LAP) or dominant-negative, FLAG-LIP, expression vector. The blot was probed with anti-C/EBP␤ and lamin A/C antibody as loading control. Expression of C/EBP␤ (37 kDa) and LIP (20 kDa) in untransfected HEK-293T cells is undetectable. EMSA was conducted using nuclear extracts from C/EBP␤ expressing HEK-293T cells in all lanes of B–E. B, nuclear extract incubated with canonical (can) C/EBP, JC1, or JC1mC/EBP-P32 radiolabeled probes alone (lanes 1, 3, and 5) or with anti-C/EBP␤ antibody (lanes 2, 4, and 6). C, nuclear extract incubated with JC1 or JC1mC/EBP-P32 radiolabeled probes alone (lanes 1 and 4); competed with excess unlabeled canonical C/EBP (lanes 2 and 5) or mutated canonical C/EBP probes (lanes 3 and 6). D, nuclear extract incubated with canonical C/EBP, DS1, or DS1mC/EBP32P-radiolabeled probes alone (lanes 1, 3, and 5) or with anti-C/EBP␤ antibody (lanes 2, 4, and 6). E, nuclear extract incubated with DS1 or DS1mC/EBP32P-radiolabeled probes alone (lanes 1 and 4), competed with excess unlabeled canonical C/EBP (lanes 2 and 5), or mutated canonical C/EBP probes (lanes 3 and 6). Unlabeled canonical and mutated canonical C/EBP probes were in 1000- or 500-fold molar excess of labeled JC1 and DS1 probes, respectively. These concentrations were chosen as they were in excess of that necessary for complete competition of C/EBP␤-containing complex bound to labeled probes as shown in Fig. 6. Free probe was run off the gel to resolve bands. F, C/EBP␤ binding to the JC1 and DS1 C/EBP sites was assessed by ChIP assays. HEK-293T cells were transfected with mLTRII (⫺117 to ⫹154 bp; wild type), JC1mC/E, DS1mC/E, or JC1/Ds1mC/E constructs and co-transfected with myc-C/EBP␤ expression vector. Standard ChIP-qPCR was carried out on these cells as described under “Experimental Procedures.” Data are presented as the percentage of C/EBP␤ binding to mutant constructs compared with wild type, mLTRII construct. qPCR signal for no antibody and mouse IgG controls were less than 0.1% of the input. Results are expressed as the mean ⫾ S.E. (n ⫽ 3); p values were calculated by Student’s two-sided paired t test. JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 JOURNAL OF BIOLOGICAL CHEMISTRY 2265 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR ability of LIP to bind JC1 and DS1 C/EBP sites despite the mutations. Dominant-negative C/EBP␤ Isoform, LIP, Binds to JC1 and DS1 C/EBP Sites—Based on our previous reports described above (47) and the fact that LIP has been shown to bind the albumin D element C/EBP site with higher affinity than C/EBP␤ (14), we investigated whether LIP would bind to the mutated JC1 and DS1 sites, perhaps accounting for the ability of IFN␤ to suppress JC1 and DS1 mutant virus replication. Our previous studies have shown by ChIP that C/EBP␤ binds to ⫺225 to ⫹149-bp region of the SIV LTR in vitro and in vivo, and at that time, however, we were unable to demonstrate the specific binding of LIP to the LTR because there is no commercially available anti-C/EBP␤ antibody that distinguishes the fulllength C/EBP␤ and the truncated, dominant-negative isoform of C/EBP␤, LIP. Furthermore, we could not use siRNA directed toward C/EBP␤ mRNA because LIP is expressed from the same mRNA as wild-type C/EBP␤ using an alternative translation start site such that an siRNA approach would down-regulate expression of both isoforms; hence, the logic behind our previous strategy to knock down expression of the CUGBP1 protein that is required for the alternative translation of LIP (47). Therefore, in this study we generated a FLAG-tagged LIP expression vector (FLAG-LIP) as a novel tool to examine the direct and specific binding of LIP to JC1 and DS1 C/EBP sites. EMSAs performed with nuclear extracts prepared from HEK-293T cells that were transfected with the FLAG-LIP expression vector revealed that LIP complexes formed on canonical C/EBP, JC1, and DS1 probes (Fig. 5, A and C, lanes 1 and 3; see arrows) and were supershifted or abrogated by the addition of anti-FLAG antibody (Fig. 5, A and C, lanes 2 and 4), demonstrating the presence of LIP on each probe. (Binding of the FLAG-LIP protein to labeled canonical and JC1 C/EBP probe was also demonstrated with C/EBP␤ antibody (supplemental Fig. S3, A and B)). We also verified that the addition of the FLAG epitope did not interfere with the activity of LIP in the 293T cells (supplemental Fig. S3C). Importantly, no complexes formed with JC1 and DS1 probes containing point mutations in the core C/EBP-binding site (Fig. 5, A and C, lanes 5 and 6; see arrows). Competition EMSAs were carried out to examine the specificity of LIP binding to JC1 and DS1 probes. LIP-containing complexes on JC1 and DS1 probes (Fig. 5, B and D, lane 1, see arrows) were competed away with excess unlabeled canonical C/EBP probe (Fig. 5, B and D, lane 2) but not with canonical C/EBP probe containing mutations in the core C/EBP-binding site (Fig. 5, B and D, lane 3). As no LIP complexes formed on mutated JC1 and DS1 probes (Fig. 5, B and D, lane 4), competition was not detected with wild-type or mutated canonical C/EBP probes (Fig. 5 B and D, lanes 5 and 6). Together, these data demonstrate that LIP binds to both the JC1 and DS1 C/EBP sites. To confirm binding of LIP to the JC1 and DS1 C/EBP sites, we performed ChIP assays (Fig. 5E). HEK-293T cells were transfected with mLTRII (wild type) or the C/EBP site mutant constructs as indicated and co-transfected with the pCMVFLAG-LIP construct before carrying out qPCR. Mutating either the JC1 or DS1 C/EBP site did not significantly hinder 2266 JOURNAL OF BIOLOGICAL CHEMISTRY LIP binding to this region, which was surprising considering the EMSA data, where mutating the sites clearly abolished LIP binding thus underscoring the sensitivity of quantitative PCR. However, mutating both the JC1/DS1 C/EBP sites decreased binding by 45.5% (p ⫽ 0.009), indicating that at least one intact site is necessary for maximum binding of LIP to this region. These results implicate residual LIP binding even in the presence of mutations when taking the ⫺117 to ⫹154-bp region into consideration as opposed to just the individual JC1 and DS1 C/EBP sites as in the EMSAs. Importantly, the ability of LIP to associate with these sites, despite mutations, explains in part the IFN␤-mediated suppression of virus replication unaffected by the JC1, DS1, and JC1/DS1mC/EBP mutations. The no antibody and IgG negative controls in the qPCR results confirmed insignificant background, as the qPCR signal for these samples was less than 0.1% of the input. This result was further verified by carrying out PCR on the same samples followed by analysis on agarose gel (supplemental Fig. S4B). We also confirmed that the FLAG-LIP expression levels were consistent in each immunoprecipitation by Western blot and saw no significant differences (supplemental Fig. S5). Collectively, the EMSA and ChIP data presented here demonstrate LIP binding to both JC1 and DS1 C/EBP sites; however, in contrast to C/EBP␤ binding, LIP was observed to have residual binding to the ⫺117 to ⫹154-bp region despite mutation in both the sites. C/EBP␤ Has a Higher Affinity for the JC1 C/EBP Site than the DS1 C/EBP Site—The functional analyses, luciferase assay and virus replication assay (p27 ELISA assay), support the conclusions that the JC1 and DS1 C/EBP sites differentially regulate not only basal SIV LTR activity and productive virus replication but also differentially down-regulate SIV LTR activity in response to IFN␤ by endogenous C/EBP␤ proteins in primary macrophages. Therefore, we hypothesized that this may be the result of the two C/EBP␤ isoforms having different affinities for the site, and to this end we determined the binding affinities of C/EBP␤ and the dominant-negative FLAG-LIP isoform for the JC1 and DS1 C/EBP sites using gradient competition EMSA. To examine this hypothesis and validate the binding approaches used, we first conducted competition EMSA to determine the binding affinity of C/EBP␤ and FLAG-LIP for the canonical C/EBP site, and we compared it with previously published data by Descombes and Schibler (14). To this end, we incubated nuclear extracts containing either C/EBP␤ or FLAGLIP isoform from HEK-293T cells with labeled JC1 oligonucleotides and increasing concentrations of unlabeled canonical C/EBP oligonucleotides (Fig. 6), the sequence of which was based on PCR-mediated random site selection (31). C/EBP␤containing complexes bound to labeled JC1 oligonucleotides and required ⬃28-fold molar excess unlabeled canonical C/EBP oligonucleotide for complete competition (Fig. 6A, lane 10). FLAG-LIP-containing complexes also bound to labeled JC1 oligonucleotides but required only 10-fold molar excess unlabeled canonical C/EBP oligonucleotide for complete competition (Fig. 6B, lane 11). Quantitation of the band intensities in the EMSAs was carried out and plotted with unlabeled oligonucleotide concentration, expressed as ⫺log[nM], against percentage of protein complex bound to labeled oligonucleotide (Fig. 6C). Based on the calculations described under VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR FIGURE 5. Dominant-negative isoform, LIP, binds JC1 and DS1 C/EBP sites in the SIV LTR. Nuclear extracts (8 ␮g) from FLAG-LIP-expressing 293T cells were used in all lanes. A, nuclear extract was incubated with canonical (can) C/EBP, JC1, or JC1mC/EBP32P-radiolabeled probes alone (lanes 1, 3, and 5) or with anti-FLAG antibody (lanes 2, 4, and 6). B, nuclear extract was incubated with JC1 or JC1mC/EBP32P-radiolabeled probes alone (lanes 1 and 4), competed with excess unlabeled canonical (can) C/EBP (lanes 2 and 5), or mutated canonical C/EBP probes (lanes 3 and 6). C, nuclear extract was incubated with canonical C/EBP, DS1, or DS1mC/EBP32P-radiolabeled probes alone (lanes 1, 3, and 5) or with anti-FLAG antibody (lanes 2, 4, and 6). D, nuclear extract was incubated with DS1 or DS1mC/EBP32P-radiolabeled probes alone (lanes 1 and 4), competed with excess unlabeled canonical C/EBP probes (lanes 2 and 5), or mutated canonical C/EBP probes (lanes 3 and 6). Unlabeled canonical and mutated canonical C/EBP probes were in 1000- or 500-fold molar excess of labeled JC1 and DS1 probes, respectively. These concentrations were chosen, as they were in excess of that necessary for complete competition of FLAG-LIP containing complex bound to labeled probes as shown in Fig. 6. Free probe was run off the gel to resolve bands. E, LIP binding to the JC1 and DS1 C/EBP sites was assessed by ChIP assays. HEK-293T cells were transfected with mLTRII (⫺117 to ⫹154 bp; wild type), JC1mC/E, DS1mC/E, or JC1/Ds1mC/E constructs and co-transfected with FLAG-LIP expression vector. Standard ChIP-qPCR was carried out on these cells as described under “Experimental Procedures.” Data are presented as percentage of LIP binding to mutant constructs compared with mLTRII (wild type) construct. qPCR signals for no antibody and mouse IgG controls were less than 0.1% of the input. Results are expressed as the mean ⫾ S.E. (n ⫽ 3); p values were calculated by Student’s two-sided paired t test. JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 JOURNAL OF BIOLOGICAL CHEMISTRY 2267 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR C/EBP␤ for the canonical C/EBP site were calculated to be 1.30 ⫻ 10⫺7 and 4.12 ⫻ 10⫺7 M, respectively (Table 1). Although the absolute KD values differ, our results are similar to previous reports by Descombes and Schibler (14) where bacterially expressed recombinant LIP was demonstrated to bind the C/EBP site from the albumin promoter element D and had a 2.5-fold higher affinity than recombinant C/EBP␤ (LAP) for this site. It must be noted that the small difference in our results compared with those of Descombes and Schibler (14) may be due to the fact that we used the consensus C/EBP site identified by Osada et al. (31), which is slightly different in sequence from the C/EBP site in the albumin promoter element D and also because we used nuclear extracts from HEK-293T cells expressing these proteins. We used this validated technique for competition EMSAs using C/EBP␤ containing nuclear extract from HEK-293T cells incubated with either labeled JC1 or DS1 C/EBP oligonucleotides and increasing concentrations of unlabeled DS1 or JC1 C/EBP oligonucleotides, respectively (Fig. 7, A and B). The C/EBP␤-containing complexes bound to the labeled JC1 C/EBP oligonucleotide required 1000-fold molar excess of unlabeled DS1 C/EBP oligonucleotide for complete competition (Fig. 7A, lane 11), whereas complete competition of C/EBP␤-containing complexes bound to labeled DS1 C/EBP oligoFIGURE 6. Dominant-negative isoform, LIP, binds canonical C/EBP site with 3-fold higher affinity than nucleotides required only 400-fold C/EBP␤. A, competition EMSA was conducted using nuclear extracts from C/EBP␤ expressing HEK-293T cells, incubated with 5 ⫻ 104 cpm JC1 C/EBP32P-radiolabeled oligonucleotide and 0 –35-fold molar excess unlabeled molar excess unlabeled JC1 C/EBP canonical (can) C/EBP oligonucleotide. B, competition EMSA was conducted using nuclear extract from FLAG- oligonucleotide (Fig. 7B, lane 9). LIP expressing HEK-293T and incubated with 5 ⫻ 104 cpm JC1 C/EBP32P-radiolabeled oligonucleotide and 0 –15-fold molar excess unlabeled canonical C/EBP oligonucleotide. Representative EMSAs are shown. Free Quantitation of the band intensities probe was run off the gel to resolve bands. C, densitometric analysis of the C/EBP␤-containing complexes in the in the EMSAs were carried out and EMSAs was carried out using Kodak MI software. The intensity of the C/EBP␤-containing complex incubated plotted with unlabeled oligonucleowith labeled oligonucleotide alone was set to 100%, and the intensity of complexes in all other lanes was normalized to this. Unlabeled canonical C/EBP oligonucleotide concentration, expressed as ⫺log[nM], was tide concentration, expressed as plotted against percentage (%) of protein bound to labeled oligonucleotide (JC1 C/EBP32P). A nonlinear regres- ⫺log[nM], against the percentage of sion, sigmoidal dose-response curve was fit to the data to determine EC50. Reaction 1 described under “Experprotein complex bound to labeled imental Procedures” was used to calculate KD. KD values from the graph were calculated to be 4.12 ⫻ 10⫺7 M for C/EBP␤- and 1.30 ⫻ 10⫺7 M for dominant-negative FLAG-LIP-containing complex for the canonical C/EBP site. oligonucleotide (Fig. 7C). Based on the calculations described under “Experimental Procedures,” the canonical C/EBP site has ⬃3.2- “Experimental Procedures,” the KD values of C/EBP␤ were fold higher binding affinity for FLAG-LIP than C/EBP␤-con- determined to be 2.38 ⫻ 10⫺6 and 4.97 ⫻ 10⫺6 M for JC1 and taining complexes as the KD values of the FLAG-LIP and DS1 C/EBP sites, respectively (Table. 1). Therefore, C/EBP␤ 2268 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR DISCUSSION TABLE 1 KDa C/EBP site C/EBP␤ Canonical JC1 DS1 4.1 23.8 ⫾ 1.9 49.7 ⫾ 1.3 Truncated FLAG-LIP Affinity ratiob (C/EBP␤:FLAG-LIP) 10⫺7 M 1.3 14.9 ⫾ 1.3 16.4 ⫾ 1.6 3.2 1.6 3.0 KD calculations are based on competition EMSA graphs (Figs. 6 – 8). KD ⫽ EC50, i.e. concentration of unlabeled oligonucleotide at which 50% competition is observed. Details of calculation are described under “Experimental Procedures.” KD calculations are represented as mean ⫾ S.D. b Affinity ratio reflects increased fold affinity of truncated FLAG-LIP over C/EBP␤ for the indicated C/EBP site calculated by dividing C/EBP␤-KD by FLAG-LIP-KD. a has approximately 2-fold higher affinity for the JC1 C/EBP site than the DS1 C/EBP site. Dominant-negative Isoform, LIP, Binds with Equal Affinity to JC1 and DS1 C/EBP Sites but Has Higher Affinity than C/EBP␤ for These Sites—Virus replication was significantly suppressed by IFN␤ treatment despite mutations in the JC1 and DS1 sites (Fig. 4B). Additionally, the ChIP data for LIP binding suggested that LIP binds these sites (albeit at 45% lower levels) even in the presence of mutations in contrast to the binding of C/EBP␤ isoform being significantly hindered by JC1 and/or DS1 mutations. Therefore, we examined whether the affinity of LIP to the JC1 and DS1 sites varied and how it compared with the affinity of C/EBP␤ to these sites. Labeled JC1 or DS1 oligonucleotides were incubated with FLAG-LIP-containing nuclear extracts prepared from HEK-293T cells and increasing concentrations of unlabeled DS1 or JC1 oligonucleotides, respectively (Fig. 8, A and B). Complete competition of FLAG-LIP-containing complexes bound either to JC1 or DS1 C/EBP oligonucleotide required 400-fold molar excess unlabeled DS1 or JC1 oligonucleotide, respectively (Fig. 8, A and B, lane 9). Quantitation of the band intensities in the EMSAs were carried out and plotted with unlabeled oligonucleotide concentration, expressed as ⫺log[nM], against percentage of protein complex bound to labeled oligonucleotide (Fig. 8C). The KD value of FLAG-LIP was 1.49 ⫻ 10⫺6 and 1.64 ⫻ 10⫺6 M for JC1 and DS1 C/EBP sites, respectively (Table. 1), demonstrating that both C/EBP sites have similar affinities for FLAG-LIP. However, it was observed that LIP has a higher affinity for the JC1 and DS1 C/EBP sites compared with the C/EBP␤ isoform by 1.6- and 3-fold, respectively. These results are consistent with our observations of IFN␤ mediating suppression of virus replication despite the presence of mutations, possibly due to the higher affinity of LIP for these sites. However, further investigation is necessary to confirm the role of the increased affinity of LIP and also whether other multiprotein complexes containing LIP are present at these sites unimpeded by the C/EBP site mutation. Nevertheless, these results are consistent with the previously published observation where ratios of LIP:C/EBP␤ greater than 0.2 are sufficient to suppress C/EBP␤-mediated transactivation when LIP affinities for C/EBP sites exceed that of C/EBP␤ (14) and our previous studies, in vitro and in vivo, where LIP:C/EBP␤ ratios being greater than 0.2 correlate with SIV LTR suppression (4, 14). JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 HIV and SIV infection and disease progression are the result of a complex interplay between viral and host cell factors. One such interplay involves specific transcription factor-binding sites found in the LTRs of HIV and SIV, to which cellular transcription factors such as Sp1, NF-␬B, and C/EBP␤ have been demonstrated to bind and regulate viral gene expression (48 – 51). These interactions are cell type-specific. C/EBP sites in the HIV-1 LTR have been demonstrated to be crucial for LTR regulation in monocyte/macrophages but not in lymphocytes (20). In this study we characterized regulatory functions of SIV LTR C/EBP sites in primary macrophages, the major cells associated with productive HIV/SIV replication in brain, lung, and spleen, and the major reservoirs of long term viral persistence in tissues, particularly the brain (52, 53). We demonstrate that the two C/EBP sites have different functions in basal transcription and virus replication; however, both sites play a role in the IFN␤-induced down-regulation of basal SIV LTR activity and virus replication in macrophages. Furthermore, we provide specific demonstration of C/EBP␤ and LIP binding to the JC1 and DS1 sites by ChIP and show that the two proteins have different affinities for the two sites consistent with their observed function in the context of both LTR luciferase assays as well as in virus replication. Previous studies of the HIV-LTR demonstrated that C/EBP sites (C/EBP site I and II) function independently and that only one C/EBP site is necessary for basal LTR activation and virus replication (18, 19). In contrast, we found that the SIV JC1 and DS1 C/EBP sites have different regulatory functions in basal LTR activation and productive virus replication; the JC1 site is crucial for basal LTR activation, whereas the DS1 site is dispensable. Additionally, we found that C/EBP␤ binds with higher affinity to JC1 than DS1 site, possibly contributing to the crucial function of the JC1 site in positively regulating basal LTR activity. An intact DS1 site, however, is imperative for productive virus replication, whereas the JC1 site does not seem to play as significant a role after the initial rounds of transcription and infection. The dramatic impairment in productive virus replication upon mutating the DS1 site in the single (DS1mC/E) and double (JC1/DS1mC/E) mutants was an unexpected result. Even though the DS1 site is 9 bp downstream of the TAR element (⫹1 to ⫹125 bp) and several base pair downstream of the critical 5⬘ stem-loop 1 necessary for Tat binding (54), we verified that these mutations did not alter the predicted secondary RNA structure formed by TAR using in silico-assisted RNA secondary structure prediction program Mfold. It is tempting to speculate that the DS1 site may be involved in mediating Tat transactivation and productive virus replication perhaps by tethering and stabilizing Tat binding to the TAR element. Tat has been shown to increase expression of the C/EBP␤ protein and binding of C/EBP␤ to DNA in vitro (55), in addition to physically and functionally interacting (in vitro and in vivo) with C/EBP␤ to induce interleukin 6 and MCP-1 (monocyte chemoattractant protein 1 or CCL2 (55–58)). Moreover, Mameli et al. (58) demonstrated that the Tat-C/EBP␤ functional and physical association is mediated through cyclin T1/cdk9 in U-87MG astrocytic cells and possibly influences JOURNAL OF BIOLOGICAL CHEMISTRY 2269 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR SIV C/EBP sites are not equivalent in function, suggesting the following: 1) they may play differential roles in mediating Tat transactivation, and 2) the proximity of a functional C/EBP-binding site to TAR is important for virus replication. We have previously demonstrated that acute SIV replication is suppressed in the brain without the decrease in viral DNA levels, supporting the conclusion that transcriptional suppression occurs in the brain (3, 4). The innate immune response to virus infection, particularly IFN␤ and the induction of LIP mediated by CUGBP1, is crucial for suppression of SIV transcription (4, 47), thereby providing a mechanism for HIV/SIV latency in macrophages in the central nervous system. Although we have previously demonstrated that knockdown of CUGBP1 leads to inhibition of LIP expression and SIV replication, the specific contributions of the JC1 and DS1 C/EBP sites in LIPmediated suppression of basal transcription and virus replication remained unknown. Thus, in this study we have demonstrated that either the JC1 or the DS1 site can independently function to downregulate basal LTR activity, although at least one intact C/EBP site is necessary. In contrast, we found that in the context of the infectious virus and virus replication, IFN␤ significantly suppressed virus replication despite mutations in the JC1 and/or DS1 sites. These results, combined with FIGURE 7. C/EBP␤ has 2-fold higher affinity for JC1 C/EBP site than the DS1 C/EBP site. Competition EMSA was conducted using nuclear extracts from HEK-293T cells transfected with C/EBP␤ (LAP) expression vector in studies demonstrating that LIP has all lanes. A, nuclear extract was incubated with 5 ⫻ 104 cpm JC1 C/EBP32P-radiolabeled oligonucleotide and a higher binding affinity for C/EBP 0 –1000-fold molar excess unlabeled DS1 C/EBP oligonucleotide (lanes 1–11). Addition of anti-C/EBP␤ antibody led to supershift of C/EBP␤-containing complexes (lane 12). B, nuclear extract was incubated with 5 ⫻ 104 cpm sites, prompted examination of the DS1 C/EBP32P-radiolabeled oligonucleotide and 0 –1000-fold molar excess unlabeled JC1 C/EBP oligonucleo- ability of LIP to bind the mutated tide (lanes 1–11). The complex was supershifted with the addition of anti-C/EBP␤ antibody (lane 12). Free probe C/EBP sites. Indeed, ChIP assays was run off the gel to resolve bands. C, densitometric measurements and KD calculations of C/EBP␤-containing complexes (indicated by arrows) in the EMSAs was carried out as described under “Experimental Procedures.” confirmed that LIP continued to Unlabeled oligonucleotide concentration, expressed as ⫺log[nM], was plotted against percentage (%) of pro- bind the mutated JC1 and DS1 sites tein bound to labeled oligonucleotide (JC1 or DS1 C/EBP). A nonlinear regression, sigmoidal dose-response in SIV LTR, including the mutant curve was fit to the data and used to determine EC50. C/EBP␤-containing complex has a KD of 4.97 ⫻ 10⫺6 M for the DS1 C/EBP site and 2.38 ⫻ 10⫺6 M the JC1 C/EBP site. KD calculations are represented as mean ⫾ S.D. in Table JC1/DS1 C/EBP construct com1. Shown are representative EMSAs (n ⫽ 2). pared with wild type. Additionally, albeit speculative, the binding affinHIV-1 transcription. Thus, it will be interesting to characterize ity of LIP to the C/EBP sites suggests that the equal affinity of and identify the specific HIV C/EBP sites involved in facilitating LIP for the JC1 and DS1 sites allows it to bind to these sites the functional outcome of this Tat-C/EBP interaction, espe- either directly or indirectly through its association with other cially taking into consideration our findings which indicate that proteins in a multiprotein complex that might also bind to 2270 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 285 • NUMBER 4 • JANUARY 22, 2010 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR FIGURE 8. Dominant-negative isoform, LIP, has similar affinity for both the JC1 C/EBP site and DS1 C/EBP sites. Competition EMSA was conducted using nuclear extracts from HEK-293T cells overexpressing FLAG-LIP in all lanes. A, nuclear extract was incubated with 5 ⫻ 104 cpm JC1 C/EBP32P-radiolabeled oligonucleotide and 0 –1000-fold molar excess unlabeled DS1 C/EBP oligonucleotide (lanes 1–11). Addition of anti-FLAG antibody led to supershift of complex (lane 12). B, nuclear extract was incubated with 5 ⫻ 104 cpm DS1 C/EBP32Pradiolabeled oligonucleotide and 0 –1000-fold molar excess unlabeled JC1 C/EBP oligonucleotide (lanes 1–11). The complex was supershifted with the addition of anti-FLAG antibody (lane 12). Free probe was run off the gel to resolve bands. C, densitometric analysis and KD calculations of the dominant-negative C/EBP␤ isoform (FLAG-LIP)-containing complexes in the EMSAs were carried out as described previously. Unlabeled oligonucleotide concentration, expressed as ⫺log[nM], was plotted against percentage (%) of protein bound to labeled oligonucleotide (JC1 or DS1 C/EBP). A nonlinear regression, sigmoidal dose-response curve was fit to the data and used to determine EC50. FLAG-LIP-containing complex has a KD of 1.49 ⫻ 10⫺6 M for the DS1 C/EBP site and 1.64 ⫻ 10⫺6 M for the JC1 C/EBP site. KD calculations are represented as mean ⫾ S.D. in Table 1. Shown are representative EMSA (n ⫽ 2). nearby sites without being significantly impeded by the C/EBP site mutation. Finally, in lieu of the abundant literature exploring other IFN␤-mediated antiviral mechanisms, we cannot ignore the potential contributions of APOBEC3G and the recently identified TRIM22 activities (59 – 62), including the JANUARY 22, 2010 • VOLUME 285 • NUMBER 4 expression of myxovirus resistance GTPase, the oligoadenylate synthetase/RNaseLpathway,andtheRNAdependent protein kinase pathway, further underscoring the potency of this antiviral mechanism (63). The higher binding affinity of LIP for the JC1 and DS1 sites compared with C/EBP␤ (1.6- and 3.0-fold, respectively) provides a mechanistic link between IFN␤-mediated suppression of SIV transcription in macrophages and the establishment of SIV latency in brain (3–5, 47). We postulate that having two functional C/EBP sites that mediate transcriptional suppression (as compared with one for basal transcription) accelerates the transition from active to suppressed transcription. Thus, IFN␤-mediated suppression of SIV LTR activity may require not only substoichiometric protein levels of LIP relative to C/EBP␤ (4, 5) but also higher affinities of LIP relative to C/EBP␤ for JC1 and DS1. Our studies of the relative affinities of C/EBP␤ and LIP, derived from nuclear extracts, for the C/EBP sites corroborate previous observations that used bacterially expressed recombinant proteins binding to the canonical C/EBP site (14). The higher affinity of LIP relative to C/EBP␤ was found not only for binding to the canonical C/EBP site but also to the JC1 and DS1 sites. Interestingly, the affinities of LIP binding to JC1 and DS1 were equivalent, although the affinity of C/EBP␤ binding differed between the sites. The SIV LTR has multiple C/EBP sites like several other viral (Rous and avian sarcoma virusLTR) and cellular promoters (albumin gene and interleukin 5 promoter (64 – 68)), and the redundancy in C/EBP sites may be important not only for maintaining active virus transcription despite random mutations in HIV/SIV viral genomes but also for efficient regulation of LTR activity in multiple cellular environments. We propose the following molecular model for the regulation of acute SIV replication in the brain based on this study and our previous reports (3–5, 47). SIV enters the brain during acute infection in infected lymphocytes and monocytes, repliJOURNAL OF BIOLOGICAL CHEMISTRY 2271 C/EBP␤ Sites and Isoforms Differentially Regulate SIV LTR cates in perivascular macrophages, and spreads to resident macrophages (1, 2, 8, 69). At this early time point there is an abundance of the C/EBP␤ isoform in macrophages (5, 69) that bind the JC1 and DS1 sites of the SIV-LTR. C/EBP␤ recruits histone acetyltransferases such as CBP/p300 and PCAF (15, 16, 70), leading to chromatin remodeling events. Such events, as demonstrated previously in vitro and in vivo in our SIV/macaque model (4), mediate transcriptional activation of the LTR, most likely through the JC1 site. Once Tat is expressed, it binds to the TAR element, assisted by C/EBP␤ bound to the DS1 site and thus contributes, in part, to the surge of SIV RNA production and virus replication during acute infection (peaking at 10 days p.i.) in the brain (3, 69). Virus replication in macrophages in the brain triggers the innate immune responses and production of IFN␤ (8, 69), which activates CUGBP-1 required for IFN␤-induced translation of the dominant-negative LIP isoform (47). Between 10 and 21 days p.i., LIP expression predominates in the brain (5), which effectively competes with the C/EBP␤ for occupancy of JC1 and DS1 sites due to the higher affinity of LIP compared with C/EBP␤ for both sites. LIP lacks the transactivating domain (71) and does not interact with histone acetyltransferases leading to repression of LTR activity (4, 15). As a result, chromatin remodeling events subside, evidenced by the decrease in acetylated histone H4 both in vitro and in vivo (4), and expression of SIV RNA decreases (3). This mechanism accounts for the suppression of acute SIV replication observed by 21 days p.i. (3) and the establishment of transcriptional latency in macrophages in brain (4). It also appears that SIV and likely HIV have evolved to utilize the classical host type I IFN response providing a mechanism for the establishment of transcriptional latency and hence the persistent viral reservoirs in macrophages. 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مقاصد البلاء في ضوء القرآن الكريم: دراسة موضوعية/The Purposes of Allah's Trials from a Quranic Perspective: A Thematic Study
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األستاذ املشارك بقسم القرآن الكريم وعلومه، كلية ماليزيا- العلوم اإلسالمية، جامعة املدينة العاملية حصل على درجة الماجستير من كلية معارف الوحي والعلوم اإلنسانية، قسم القرآن والسُّ نة، . ماليزيا- الجامعة اإلسالمية العالمية حصل على درجة الدكتوراه من كلية معارف الوحي والعلوم اإلنسانية، قسم القرآن والسُّ نة، ال ز ا ال ا ة اإل ال َّة ال ال ة :قDدم للن‚شDر فــDي قبDل للن‚شDر فـــDي: نــــــ‚شــــDر فـــــــــDي: 1441/7/19 1441/12/22 1443/7/1 َاإ ُي النتاج العلمي: «دور توظيف تدبُّر القرآن الكريم يف تعزيز أخالق البحث العلمي من وجهة نظر محاضري كلية العلوم اإلسالمية بجامعة المدينة العالمية ماليزيا»، (بحث محكَّم منشور)، «القلب بين القرآن الكريم والعلم الحديث»، (بحث محكَّم منشور)، «من خصائص الخطاب اإلصالحي يف تفسير اإلمام عبد الحميد بن باديس»، (بحث محكَّم منشور)، «وجوه الخطاب اإلصالحي يف تفسير اإلمام عبد الحميد بن باديس»، (بحث محكَّم منشور)، «مصطلح المال يف القرآن الكريم ووسائل الحفاظ عليه يف الشريعة اإلسالمية»، (بحث محكَّم منشور)، «الطُّرق المنحرفة يف التفسير وأثرها يف تفريق األُمَّة اإلسالمية»، (بحث محكَّم منشور)، «هدايات تشريعيّة ألحكام األطعمة يف ظالل سورة المائدة: دراسة تفسيرية موضوعية»، (بحث محكَّم منشور) «مقوّمات تدبّر القرآن الكريم ومعوّقاته»، (بحث محكَّم منشور)، مصطلح العقل يف القرآن الكريم ووسائل الحفاظ عليه: دراسة قرآنية مقاصدية (بحث محكَّم منشور) وغير ذلك. ور) و ير مَ ص ي (ب ر ي ر ي ل وو bey.zekkoub@mediu.edu.my/ beyzekoub@yahoo.fr : البريد الشبكي يُعنَى هذا البحث بدراسة: (مقاصد البالء يف ضوء القرآن الكريم: دراسة موضوعية)، وقد هدف إلى بيان مقاصد البالء المنصوص عليها يف القرآن الكريم، أو المبثوثة يف ثنايا سياقاته؛ لِمَا له من أثر عقائديٍّ ، وتربويٍّ ، وأخالقيٍّ ، يف حياة المسلم. موظِّفًا المنهج االستقرائي التحليلي، ثم المنهج االستنباطي. وقد توصَّ ل البحث إلى أنَّ المقصد الرئيس من البالء؛ استخراج ما عند المبتَلَى من معاين العبوديَّة هلل وحده، والتعرُّ ف على حاله يف الطَّاعة والمعصية؛ بتحميله الضِّ يق، والمشقَّة، واأللم. كما توصَّ ل إلى استنباط أهمِّ مقاصد البالء من خالل القرآن الكريم، وتحليلها ودراستها، التي أوصلها الباحث إلى اثني عشر مقصدًا قرآنيًّا؛ ليكون ذلك طريقًا هاديًا يف الحفاظ على النِّعم وإربائها، ويف دفع ما يستجدُّ من أنواع المصائب ودرئها؛ ذلك أنَّ البالء يُظهرُ حالَ المبتَلِين، ومدى تطبيقهم للتَّكاليف والنَّواهي، وتتجلَّى به نيَّاهتم يف سرعة االستجابة هلل، وللرسول |، ويختلف ذلك من شخص آلخر، حسب قوة اإليمان يف القلب، وحسب إدراك المعاين، والحِكم، للبالء يف الخير، والشَّ رِّ . ِ الكلمات المفتاحية: مقاصد، البالء واالبتالء، القرآن الكريم، الخير والشَّ رُّ ، ِ الكلمات المفتاحية: مقاصد، البالء واالبتالء، القرآن الكريم، الخير والشَّ رُّ ، المفسِّ رون. المفسِّ رون. The purposes of Allah’s Trials from a Quranic perspective: A Thematic Study The Rationales behind Tribulations from a Quranic Perspective (An Objective Study) Prepared by: Dr. Bey Zekkoub Abdelali Associate Professor, the Department of Qur’an and its Sciences, the Faculty of Islamic Sciences at Al-Madinah International University, Malaysia Dr. Bey Zekkoub Abdelali Associate Professor, the Department of Qur’an and its Sciences, the Faculty of Islamic Sciences at Al-Madinah International University, Malaysia states of those in trouble as well as the extent of their compliance with religious obligations and prohibitions and their responsiveness to Allâh and the Prophet (may Allâh's blessings and peace be upon him). All of this varies from one person to another according to the strength of his faith, sensemaking and the rationales behind tribula- tions and trials. Keywords: Rationales- tribulation and trial- the Noble Quran- good and evil-exegetes Abstract This research examines the rationales behind tribulations from a Quranic perspective. It aims to shed light on the objectives of trib- ulations as reflected in the Noble Quran because of their doctrinal, educational, and moral impacts on the Muslim's life. It also employs the inductive analytical and the deductive approaches. The research found that the main rationale behind tribulation is to elicit the mean- ings of servitude to Allâh alone from the afflicted person's psyche and find out about the extent of his religiousness by burdening him with distress, hardship and agony. The research concluded the main rationales behind tribulation in accordance with the Noble Quran, analyzed and explored them, which reached twelve Quranic purpos- es according to the researcher. This is designed to be a guiding way of preserving and maximizing divine blessings and warding off new types of misfortunes. This is because tribulation shows the spiritual الحمد هلل الذي كتب الرَّ حمة على نفسه، وحرَّ م الظلم على ذاته، وابتلى عباده بالخير والشَّ رِّ بمقتضى رحمته وعدله، فمنهم من شكر اهلل على نِعَمه؛ فسخَّرها يف مرضاته؛ فوفَّقهم لطاعته، وزادهم من خيره، ومنهم من جحد نِعمة اهلل عليه؛ فوظَّفها يف سخطه؛ فخذلهم عن طاعته، وحرمهم من خيره، والصَّ الة والسَّ الم األتمَّان األكمالن على نبيِّنا محمد، أكثر من ابتُليَ ؛ فشكر وصرب؛ ولذلك وصفه اهلل تعالى يف أشرف المقامات بالعبوديَّة: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡﭢ ﭣ ﭤ ﭥ ﭦ﴾ ]، ورضي اهلل تعالى عن آله الطيِّبين الطَّاهرين، وأصحابه الغُرِّ 1:[سورة اإلسراء الميامين، الذين قاموا بالدَّعوة إلى اهلل، والجهاد يف سبيله أحسن قيام: ﴿ﯕ ﯖ ]؛ فنالوا 146 :ﯗ ﯘ ﯙ ﯚ ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ﴾ [آل عمران بذلك شرف الصُّ حبة، والثَّناء، والرِّ ضى من ربِّهم، ومَنِ اقتفى أثره، ودان بدينه إلى يوم الدِّين. Abstract أمَّا بعد؛ فقد أنزل اهلل القرآن الكريم؛ ليكون منهج حياة للنَّاس جميعًا، فأمرنا بتدبُّره؛ لفهم معانيه، واستنباط أحكامه، وكشف وجوه إعجازه، واستخراج سُ ننه، وسرب أغواره، والولوج يف أعماق أسراره وحِكَمِه، فقال تعالى ذكره: ﴿ﭲ ﭳ ﭴ ]، ومن المعلوم أنَّ اهلل لَمَّا خلق 29 :ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ﴾ [ص هذا الكون جعل له سننًا يسير وَفقها؛ حتى ينتظم أمر الخلق، وخرق هذه السُّ نن يقود إلى ظهور الفساد يف برِّ األرض وبحرها، ومن هذه السُّ نن اإللهيَّة: سُ نَّة البالء بالخير والشَّ رِّ المنصوص عليها يف القرآن الكريم، وهي سُ نَّة من سنن اهلل تعالى يف األوَّلين واآلخرين، من األنبياء والمرسلين، وأتباعهم، التي تجري باطِّراد يف حياة ]، 43 :البشر، يقول تعالى ذكره: ﭐ﴿ﯰ ﯱ ﯲ ﯳ ﯴﯵ ﯶ ﯷ ﯸ ﯹ ﯺ﴾ [فاطر (، ويف الصَّ حيح عن ((»والمعنى: «لن يغيِّر ذلك وال يبدِّله؛ ألنَّه ال مردَّ لقضائه عياض بن حِمار الْمُجَاشِ عِيِّ أنَّ رسول اهلل |، روى عن ربِّه × أنَّه قال: «إنَّما (. ((»بعثتك ألبتليك وأبتلي بك األوَّلين واآلخرين، من األنبياء والمرسلين، وأتباعهم، التي تجري باطِّراد يف حياة ]، 43 :البشر، يقول تعالى ذكره: ﭐ﴿ﯰ ﯱ ﯲ ﯳ ﯴﯵ ﯶ ﯷ ﯸ ﯹ ﯺ﴾ [فاطر (، ويف الصَّ حيح عن ((»والمعنى: «لن يغيِّر ذلك وال يبدِّله؛ ألنَّه ال مردَّ لقضائه عياض بن حِمار الْمُجَاشِ عِيِّ أنَّ رسول اهلل |، روى عن ربِّه × أنَّه قال: «إنَّما (. ((»بعثتك ألبتليك وأبتلي بك بيد أنَّ إخالل بعض النَّاس هبذه السُّ نَّة الكونيَّة؛ أدَّى إلى فقدان الرَّ خاء يف العيش، والصِّ حَّة يف البدن، وحلول الشَّ ظف يف العيش، واالعتالل يف البدن، وال شكَّ أنَّ هذا ناتج عن قلَّة الوعي لدى الناس بشأن مقاصد البالء المذكورة يف القرآن الكريم. : جماالت الن‚شر تصبُّ هذه الدِّراسة يف مجال االستنباط من القرآن الكريم، وقد تناوَلتُ فيها استخراج مقاصد البالء المنصوص عليها يف القرآن الكريم؛ مستعينًا يف ذلك بآراء العلماء المفسِّ رين، أصيلها ومعاصرها، مع دراستها وتحليلها؛ ألجل الوصول إلى أهمِّ مقاصد البالء، التي من الممكن أن تكون طريقًا هاديًا يف حسن التَّعامل مع البالء يف الخير والشَّ رِّ . Abstract لذا، بات من األهمِّية بمكان التعرُّ ف على مقاصد البالء، وإدراك حِكَمِه؛ حتى يحسن تعامل الناس معه، وال يتأتَّى لنا هذا إلَّ بعد تتبُّع مواضع ذكر البالء، ونظائره يف القرآن الكريم، ثم االطِّالع على أقوال المفسِّ رين القدامى والمعاصرين لتلك المواضع، وما يتعلَّق هبا من سُ نَّة رسول اهلل |؛ ألنَّها بمنزلة القرآن يف التشريع، ثم تحليلها ودراستها؛ حتى هنتدي يف األخير إلى بعض مقاصد البالء، التي قد تخفى على بعض عباد اهلل، وتظهر آلخرين، ونحن إذ نقوم باستخراج هذه المقاصد، ال ندَّعي أنَّها تقتصر على ما ذكرناه يف هذا البحث فحسب؛ ذلك ألنَّ هذه المقاصد لها ارتباط بواقع النَّاس، وبما أنَّ الواقع يتجدّد، فإنَّ المقاصد والحِكَم والغايات تتجدَّد معه، وقد يظهر لنا يف هذا الزَّ مان ما لم يظهر لغيرنا يف األزمنة الماضية، وقد يظهر لألجيال القادمة ما ال يظهر لنا يف الوقت الحالي؛ ألنَّ القرآن الكريم له عالقة وطيدة .)484/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه مسلم يف صحيحه: كتاب الجنة وصفة نعيمها وأهلها، باب الصفات التي يعرف هبا يف الدنيا(( .)2865( أهل الجنة وأهل النار، برقم بواقع الناس، ومنه يقوم العلماء باستخراج هداياته، وأحكامه، وحِكَمِه، كلٌّ حسب ]، قال إبراهيم 269 :توفيق اهلل له: ﴿ﯩ ﯪ ﯫ ﯬ ﯭ ﯮ ﯯﯰ﴾ [البقرة (.((»النَّخعي &: «الحكمة معرفة معاين األشياء وفهمها بواقع الناس، ومنه يقوم العلماء باستخراج هداياته، وأحكامه، وحِكَمِه، كلٌّ حسب ]، قال إبراهيم 269 :توفيق اهلل له: ﴿ﯩ ﯪ ﯫ ﯬ ﯭ ﯮ ﯯﯰ﴾ [البقرة (.((»النَّخعي &: «الحكمة معرفة معاين األشياء وفهمها : حدود الدِّرا7سة تدور الحدود الموضوعية لهذه الدِّراسة حولَ اآليات ذات الصّ لة بمقاصد البالء يف القرآن الكريم، مع الرُّ جوع يف فَهْمها واستخراج مقاصدها إلى كُتب تفسير القرآن الكريم، واألخْ ذ بعين االعتبار بما أتانا به | يف سنَّته؛ ألنَّه بمنزلة القرآن يف التَّشريع. : �أهداف الدِّرا7سة . التَّعريف بمقاصد البالء يف القرآن الكريم-1 استنباط أهمِّ مقاصد البالء المنصوص عليها يف القرآن الكريم، أو المبثوثة-2 .يف ثنايا سياقاته بيان معاين مقاصد البالء المستنبطة من القرآن الكريم، وذلك من وجهات -3 .نظر عدَّةٍ للمفسِّ رين .)373/1( ،( معالم التنزيل يف تفسير القرآن، للبغوي(( : �أهداف الدِّرا7سة . التَّعريف بمقاصد البالء يف القرآن الكريم-1 استنباط أهمِّ مقاصد البالء المنصوص عليها يف القرآن الكريم، أو المبثوثة-2 .يف ثنايا سياقاته بيان معاين مقاصد البالء المستنبطة من القرآن الكريم، وذلك من وجهات -3 .نظر عدَّةٍ للمفسِّ رين .)373/1( ،( معالم التنزيل يف تفسير القرآن، للبغوي(( : �هداف الدِرا7سة . التَّعريف بمقاصد البالء يف القرآن الكريم-1 استنباط أهمِّ مقاصد البالء المنصوص عليها يف القرآن الكريم، أو المبثوثة-2 .يف ثنايا سياقاته .)373/1( ،( معالم التنزيل يف تفسير القرآن، للبغوي(( لفت انتباه القرَّ اء إلى كيفيَّة التَّعامل مع البالء يف الخير والشَّ رِّ بمشيئة اهلل-4 .تعالى لفت انتباه القرَّ اء إلى كيفيَّة التَّعامل مع البالء يف الخير والشَّ رِّ بمشيئة اهلل-4 .تعالى : منهج الدِّرا7سة استخدمت الدِّراسة المنهجَ االستقرائيَّ التحليليَّ ؛ حيثُ يقومُ الباحث باستقراء اآليات التي تحدَّثت عن موضوع مقاصد البالء يف القرآن الكريم، ثمَّ باستقراء آراء العلماء المفسِّ رين حولَ تلك اآليات، وما يتعلَّق هبا من سُ نَّة رسول اهلل |، ثمَّ تُحلَّل وتُصنَّف حسَ ب الخطَّة البحثيَّة للموضوع، كما استفادت الدِّراسة من المنهج االستنباطيِّ يف استخراج أهمِّ مقاصد البالء بناءً على ما تمَّ استقراؤه. ِ : الدِّرا7سات السَّ ابقة ِ : الدِّرا7سات السَّ ابقة ) دراسة بعنوان «االبتالء1988( أجرى الباحث محمد عبدالعزيز الرحالي-1 يف القرآن الكريم»، وهي رسالة مقدَّمة لنيل درجة الدكتوراه يف الكتاب والسُّ نَّة، بجامعة أم القرى، يف المملكة العربية السُّ عودية، هدفت إلى الكشف عن معنى االبتالء يف القرآن الكريم، وأنواعه وصوره، وموقف اإلنسان منه، ومن أهم ما توصَّ لت إليه هذه الدِّراسة: أنَّ االبتالء يكون يف ميدان الخير بالصَّ رب على الطاعة، من حيث امتثال أمر اهلل واجتناب هنيه، ويف ميدان الشَّ رِّ بالصَّ رب على ما يلقى اإلنسان من مكاره ومصاعب، وأنَّ االبتالء طريق إلظهار موقف المكلَّف من األوامر والنَّواهي التي تعبَّدنا اهلل هبا على وجه االختيار، فكان الخلق لالبتالء وسيلة إلظهار نتيجة الخلق للعبادة؛ فكلٌّ من الخلق لالبتالء والخلق للعبادة الزم لآلخر ومكمِّل له، (.((وقد استخدمت الدِّراسة المنهج االستقرائي التحليلي .) وما بعدها419 ( االبتالء يف القرآن الكريم، لمحمد عبدالعزيز الرحالي، (ص(( :) دراسة بعنوان1988( وتناول الباحث محمد يوسف أحمد دوفش-2 «االبتالء يف القرآن الكريم»، وهي رسالة ماجستير يف التفسير من قسم أصول الدين، بالجامعة األردنية، والبحث عبارة عن دراسة قرآنية لسنة البالء، وقد هدفت إلى تجلية هذه السنة وتحديد موقف اإلنسان تجاهها، محاولةً الكشف عن مزايا األسلوب القرآين يف تناولها، ومعالِـجة لبعض التصوُّرات الخاطئة العالقة يف أذهان الناس، وقد ضمَّنها الباحث تمهيدًا، وأربعة فصول، وخاتمة، وخصص يف الفصل الثاين مبحثًا مختصرً ا عن حكم البالء، أورد فيه الباحث األهداف والغايات التي يحقِّقها االبتالء، وقد توصَّ لت الدراسة إلى أهم ما ينبغي أن يتزوَّد به اإلنسان لمواجهة البالء، (. ِ : الدِّرا7سات السَّ ابقة ((وتخفيف شدَّته، وقد استخدمت الدِّراسة المنهج االستقرائي التحليلي )، فقد أجرى دراسةً 2007( وأما الباحث رجب نصر موسى األنس-3 بعنوان: «سُ نة االبتالء يف القرآن الكريم»، وهي رسالة مقدَّمة الستكمال متطلبات درجة الماجستير يف أصول الدِّين، بكلية الدراسات العليا يف جامعة النجاح الوطنية، يف نابلس، فلسطين، هدفت إلى الكشف عن ظواهر المحن واالبتالء يف القرآن الكريم، وضروبه، وموقف اإلنسان منه، وقد توصَّ لت الدِّراسة إلى أهمية التشبُّت بالصَّ رب وضرورته، والعقيدة (.((مهما تكن الظُّروف واألحوال، موظَّفة المنهج االستقرائي التحليلي )، قد تناول دراسةً بعنوان: 2009( بينما الباحث حمدي سلمان معمر-4 «الرتبية باالبتالء: دراسة تربوية آليات االبتالء يف القرآن الكريم»، وهو اايبحث نشرته مجلَّة جامعة األقصى، يف غزَّ ة، فلسطين، هدفت إلى بيان :) دراسة بعنوان1988( وتناول الباحث محمد يوسف أحمد دوفش-2 «االبتالء يف القرآن الكريم»، وهي رسالة ماجستير يف التفسير من قسم أصول الدين، بالجامعة األردنية، والبحث عبارة عن دراسة قرآنية لسنة البالء، وقد هدفت إلى تجلية هذه السنة وتحديد موقف اإلنسان تجاهها، محاولةً الكشف عن مزايا األسلوب القرآين يف تناولها، ومعالِـجة لبعض التصوُّرات الخاطئة العالقة يف أذهان الناس، وقد ضمَّنها الباحث تمهيدًا، وأربعة فصول، وخاتمة، وخصص يف الفصل الثاين مبحثًا مختصرً ا عن حكم البالء، أورد فيه الباحث األهداف والغايات التي يحقِّقها االبتالء، وقد توصَّ لت الدراسة إلى أهم ما ينبغي أن يتزوَّد به اإلنسان لمواجهة البالء، (. ِ : الدِّرا7سات السَّ ابقة ((وتخفيف شدَّته، وقد استخدمت الدِّراسة المنهج االستقرائي التحليلي )، فقد أجرى دراسةً 2007( وأما الباحث رجب نصر موسى األنس-3 بعنوان: «سُ نة االبتالء يف القرآن الكريم»، وهي رسالة مقدَّمة الستكمال متطلبات درجة الماجستير يف أصول الدِّين، بكلية الدراسات العليا يف جامعة النجاح الوطنية، يف نابلس، فلسطين، هدفت إلى الكشف عن ظواهر المحن واالبتالء يف القرآن الكريم، وضروبه، وموقف اإلنسان منه، وقد توصَّ لت الدِّراسة إلى أهمية التشبُّت بالصَّ رب وضرورته، والعقيدة (.((مهما تكن الظُّروف واألحوال، موظَّفة المنهج االستقرائي التحليلي )، قد تناول دراسةً بعنوان: 2009( بينما الباحث حمدي سلمان معمر-4 «الرتبية باالبتالء: دراسة تربوية آليات االبتالء يف القرآن الكريم»، وهو بحث نشرته مجلَّة جامعة األقصى، يف غزَّ ة، فلسطين، هدفت إلى بيان .) وما بعدها337 و3 ( االبتالء يف القرآن الكريم، لمحمد يوسف أحمد دوفش، (ص(( .) وما بعدها176 وص3 ( سنة االبتالء يف القرآن الكريم، لرجب نصر موسى األنس، (ص(( الغرض من إصابة المسلمين بأنواع المصائب، مستخدمًا المنهج الفلسفي التحليليَّ ، وخرج البحث بعدَّة نتائج، من أهمِّها: أنَّ االبتالء سُ نَّة دائمة هلل (.((يف خلقه، وهو للمؤمنين تطهير، وللكافرين تذكير وعقاب الغرض من إصابة المسلمين بأنواع المصائب، مستخدمًا المنهج الفلسفي التحليليَّ ، وخرج البحث بعدَّة نتائج، من أهمِّها: أنَّ االبتالء سُ نَّة دائمة هلل (.((يف خلقه، وهو للمؤمنين تطهير، وللكافرين تذكير وعقاب : التَّعليق على الدِّرا7سات السَّ ابقة تناولت الدِّراسة الحاليَّة تحديد أهم مقاصد البالء واستنباطها من خالل القرآن الكريم؛ حيثُ قام الباحث باستقراء لفظتي البالء واالبتالء يف القرآن الكريم، وتتبع معانيهما دراسةً وتحليلً يف كتب التفسير، ثم باستنباط أهم مقاصد البالء بناء على ما تم استقراؤه ودراسته، موظِّفًا المنهج االستقرائي التَّحليليَّ ، والمنهج االستنباطيَّ ، وهذا ما لم تفعله الدِّراسات السَّ ابقة، باستثناء تطرُّ قها إلى مفهوم البالء يف اللُّغة واالصطالح، وبعض الحِكَم العامة للبالء، واقتصارها على المنهج االستقرائي والفلسفي التحليلي، وقد لوحظ أنَّ دراسة )، ودراسة رجب نصر موسى األنس 1988( محمد يوسف أحمد دوفش ) يف بعض أجزاء 1988( )، مماثلة لرسالة محمد عبدالعزيز الرحالي2007( ،)1988( موضوعاهتا وتقسيماهتا، إلَّ أنَّ دراسة محمد عبدالعزيز الرحالي اتَّسمت باألصالة والعمق والمنهجية العلمية؛ ذلك ويالحظ أنَّ الدِّراسة الحاليَّة تختلف عن الدِّراسات السَّ ابقة من حيث هدفها ومنهجها المستخدم، ومن حيث موضوعها وتقسيماهتا، وطريقة تناولها لمقاصد البالء القرآنية؛ حيث يتناول هذا البحث استخراج مقاصد البالء يف القرآن الكريم، من خالل نظرة تفسيريَّة موضوعيَّة، وهذا يؤكِّد أنَّ موضوع الدِّراسة الحاليَّة جدير بالتناول؛ ألنَّه يركِّز على مقاصد البالء التفصيليَّة من خالل القرآن الكريم. ِ : الدِّرا7سات السَّ ابقة .)94 ( الرتبية باالبتالء: دراسة تربوية آليات االبتالء يف القرآن الكريم، (ص(( : خطَّ ة البحث :وتشتمل على مقدِّمة، ومبحثَيْن، ثم الخاتمة، هذا هو بياهنا المقدِّ مة: موضوع البحث، مجاله، حدوده، أهدافه، منهجه، الدِّراسات السَّ ابقة وخطة البحث. املبحث األوَّ ل: تعريف املقاصد القرآنية، وتعريف البالء ومواطن وروده يف القرآن الكريم. المطلب األوَّل: تعريف المقاصد القرآنية. المطلب الثاين: تعريف البالء يف القرآن الكريم. المطلب الثَّالث: مفهوم مقاصد البالء يف القرآن الكريم. المطلب الرَّ ابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم. المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة. المطلب السَّ ادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم. المطلب السابع: رسومات بيانية تبيِّن الصيغ التصريفية لمادة «بال» يف القرآن الكريم. المطلب الثامن: تحليل نتائج الرُّ سومات البيانية. املبحث الثاين: مقاصد البالء يف القرآن الكريم. للها أل َّ هِ المقدِّ مة: موضوع البحث، مجاله، حدوده، أهدافه، منهجه، الدِّراسات السَّ ابقة وخطة البحث. املبحث األوَّ ل: تعريف املقاصد القرآنية، وتعريف البالء ومواطن وروده يف القرآن الكريم. المطلب األوَّل: تعريف المقاصد القرآنية. المطلب الثاين: تعريف البالء يف القرآن الكريم. المطلب الثَّالث: مفهوم مقاصد البالء يف القرآن الكريم. المطلب الرَّ ابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم. المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة. المطلب السَّ ادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم. المطلب السابع: رسومات بيانية تبيِّن الصيغ التصريفية لمادة «بال» يف القرآن الكريم. المطلب الثامن: تحليل نتائج الرُّ سومات البيانية. املبحث الثاين: مقاصد البالء يف القرآن الكريم. المطلب األوَّل: البالء بمقصد تحقيق العبادة هلل وحده. المطلب الثاين: البالء بمقصد استخراج التوكل. المطلب الثَّالث: البالء بمقصد استخراج الدُّعاء. املبحث األوَّ ل: تعريف املقاصد القرآنية، وتعريف البالء ومواطن وروده يف القرآن الكريم. المطلب األوَّل: تعريف المقاصد القرآنية. المطلب الثاين: تعريف البالء يف القرآن الكريم. المطلب الثَّالث: مفهوم مقاصد البالء يف القرآن الكريم. المطلب الرَّ ابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم. المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة. المطلب السَّ ادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم. المطلب السابع: رسومات بيانية تبيِّن الصيغ التصريفية لمادة «بال» يف القرآن لك المطلب األوَّل: تعريف المقاصد القرآنية. المطلب الثاين: تعريف البالء يف القرآن الكريم. المطلب الثَّالث: مفهوم مقاصد البالء يف القرآن الكريم. المطلب الرَّ ابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم. المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة. المطلب السَّ ادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم. المطلب السابع: رسومات بيانية تبيِّن الصيغ التصريفية لمادة «بال» يف القرآن الكريم. ِ : الدِّرا7سات السَّ ابقة .المطلب الرَّ ابع: البالء بمقصد استخراج الصَّ رب المطلب الخامس: البالء بمقصد استخراج الرِّ ضا. المطلب السَّ ادس: البالء بمقصد استخراج الشُّ كر. المطلب السَّ ابع: البالء بمقصد استخراج التَّوبة. المطلب الثَّامن: البالء بمقصد الرَّ حمة. المطلب التَّاسع: البالء بمقصد التَّمحيص. المطلب العاشر: البالء بمقصد االستدراج. المطلب الحادي عشر: البالء بمقصد التَّخويف. المطلب الثَّاين عشر: البالء بمقصد العقوبة. ثم الخاتمة. و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا :المبحث األوَّ ل تعريف املقاصد القرآنية، وتعريف البالء ومواطن وروده يف القرآن الكريم سيتطرَّ ق هذا المبحث إلى تعريف المصطلحات األساسية للبحث، والوقوف مع معاين البالء واالبتالء يف اللُّغة ويف اصطالح المفسِّ رين، ثم محاولة استخراج الفرق بينهما، وتتبع األلفاظ ذات الصلة هبما؛ ذلك وقد تم تتبُّع مفرديت البالء واالبتالء يف القرآن الكريم وتحديد مواطن ورودهما، ثم دارستهما وتحليلهما، ويتضمَّن هذا المبحث ثمانية مطالب، هي: المطلب األوَّل: تعريف المقاصد القرآنية. المطلب الثاين: تعريف البالء يف القرآن الكريم. المطلب الثَّالث: مفهوم مقاصد البالء يف القرآن الكريم. المطلب الرَّ ابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم. المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة. المطلب السَّ ادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم. المطلب السَّ ابع: رسومات بيانية تبيِّن الصيغ التصريفية لمادة «بال» يف القرآن الكريم. المطلب الثامن: تحليل نتائج الرُّ سومات البيانية. لأ .)351/6( ( تفسير القرآن العظيم، البن كثير(( .)473/4( ( النكت والعيون، الماوردي(( .)271/14( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)192/3( ( معاين القرآن، للزجاج(( .)146/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)308/8( ( تأويالت أهل السنة، ألبي منصور الماتريدي(( .)10/3( ( قواعد األحكام يف مصالح األنام، للعز بن عبدالسالم(( :المطلب األول أ تعريف المقاصد القرآنية المقاصد يف اللُّغة مصدر الفعل الثالثي لمادَّة: قصد، يقصد، قصدًا، ومقصدًا، فهو قاصد، والمفعول مقصود، والقصد لغة هو: التوجه واالعتزام والنهوض والهدف، قال ابن جنّيّ : «أصل (ق ص د) ومواقعها يف كالم العرب االعتزام، (، ((»والتَّوجُّ ه، والنُّهود، والنُّهوض نحو الشَّ يء، على اعتدال كان ذلك أو جَ وْر ويأيت يف اللُّغة لمعانٍ متنوِّعة، هي: استقامة الطَّريق، وطريق سهل، والعدل، (، وجاء يف ((واالعتماد واألَمُّ، وإتيان الشيء، والتوسُّ ط، والكسر، واللَّحم اليابس (، وقد ورد لفظ القصد يف ستَّة مواضع يف القرآن ((»المعجم: «القصد: «الهدف الكريم، تحمل معاين: االعتدال، والسهولة، والتبيين، والتواضع، كما سيأيت: . التوسُّ ط يف قوله تعالى: ﴿ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ 1 .]66 :ﭨ ﭩ ﭪ ﭫ ﭬ ﭭﭮ ﭯ ﭰ ﭱﭲ﴾ [المائدة (، ((»ويعني بـ: ﴿ﭱﭲ﴾؛ أي: «عادلة غير غالية، وال مقصرة جافية وقوله: ﴿ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ]. روي عن ابن زيد ﴿ﮟ﴾ قال: «هو 32 :ﮝ ﮞ ﮟﮠ﴾ [لقمان .)187/6( ( المحكم والمحيط األعظم، للمرسي أبي الحسن(( .)356-353/3( ( انظر: لسان العرب، البن منظور(( .)1820/3( ( معجم اللغة العربية المعاصرة، ألحمد مختار(( .)68/2( ( معالم التنزيل يف تفسير القرآن، للبغوي(( و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا (، وقوله: ﴿ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩﭪ((»المتوسط يف العمل ]. 32 :ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ﴾ [فاطر (. ((»ويعني بـ ﴿ﭯ﴾؛ أي: «متوسط يف الطَّاعات . السُّ هولة يف قوله تعالى: ﭐ﴿ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ﴾2 .(((» ً]. وقوله: ﴿ﭧ﴾ فمعناه: «قريبًا سهل42 :[التوبة ]. 9 :. التبيين يف قوله تعالى: ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ ﭱﭲ﴾ [النحل3 وقوله: ﭐ﴿ﭬ ﭭ ﭮ ﭯ﴾ فإنه يعني: «تبيين الطريق المستقيم إليه (.((»بالحُجج والرباهين ]. 9 :. التبيين يف قوله تعالى: ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ ﭱﭲ﴾ [النحل3 وقوله: ﭐ﴿ﭬ ﭭ ﭮ ﭯ﴾ فإنه يعني: «تبيين الطريق المستقيم إليه (.((»بالحُجج والرباهين ]. 9 :. التبيين يف قوله تعالى: ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ ﭱﭲ﴾ [النحل3 وقوله: ﭐ﴿ﭬ ﭭ ﭮ ﭯ﴾ فإنه يعني: «تبيين الطريق المستقيم إليه (.((»بالحُجج والرباهين ]. رُوي عن مجاهد 19 :. :المطلب األول التواضع يف قوله تعالى: ﭐ﴿ﰉ ﰊ ﰋ﴾ [لقمان4 (، وعن الماتريدي قال: «اقصد يف((»﴿ﰉ ﰊ ﰋ﴾ قال: «التواضع (.((»المشي يف الناس، وال تمشِ متكربًا مستخفًّا هبم؛ لتؤذيهم وقد عُرِّ فت المقاصد اصطالحً ا، مضافةً إلى علم مقاصد القرآن الكريم، بأهنا: (، ((»«األمر باكتساب المصالح وأسباهبا، والزجر عن اكتساب المفاسد وأسباهبا وهذا التعريف قريب من تعريفات علماء مقاصد الشريعة، وعرَّ فها آخر بأنَّها: ]. رُوي عن مجاهد 19 :. التواضع يف قوله تعالى: ﭐ﴿ﰉ ﰊ ﰋ﴾ [لقمان4 (، وعن الماتريدي قال: «اقصد يف((»﴿ﰉ ﰊ ﰋ﴾ قال: «التواضع (.((»المشي يف الناس، وال تمشِ متكربًا مستخفًّا هبم؛ لتؤذيهم وقد عُرِّ فت المقاصد اصطالحً ا، مضافةً إلى علم مقاصد القرآن الكريم، بأهنا: (، ((»«األمر باكتساب المصالح وأسباهبا، والزجر عن اكتساب المفاسد وأسباهبا وهذا التعريف قريب من تعريفات علماء مقاصد الشريعة، وعرَّ فها آخر بأنَّها: .)351/6( ( تفسير القرآن العظيم، البن كثير(( ا .)473/4( ( النكت والعيون، الماوردي(( .)271/14( ( جامع البيان عن تأويل آي القرآن، للطربي(( «الكشف عن المعاين المعقولة، والغايات المتنوِّعة التي يدور حولها القرآن الكريم (، ومن هنا ((»كليًّا أو جزئيًّا، مع بيان كيفية اإلفادة منها يف تحقيق مصلحة العباد يمكننا تعريف علم مقاصد القرآن الكريم بأنَّه: الغايات واألهداف التي أُنزل القرآن الكريم من أجلها؛ تحقيقًا لجلب مصالح العباد يف المعاش والمعاد من جهة، وتحقيقًا لدرء مفاسد العباد يف المعاش والمعاد من جهة أخرى. «الكشف عن المعاين المعقولة، والغايات المتنوِّعة التي يدور حولها القرآن الكريم (، ومن هنا ((»كليًّا أو جزئيًّا، مع بيان كيفية اإلفادة منها يف تحقيق مصلحة العباد يمكننا تعريف علم مقاصد القرآن الكريم بأنَّه: الغايات واألهداف التي أُنزل القرآن الكريم من أجلها؛ تحقيقًا لجلب مصالح العباد يف المعاش والمعاد من جهة، وتحقيقًا لدرء مفاسد العباد يف المعاش والمعاد من جهة أخرى. «الكشف عن المعاين المعقولة، والغايات المتنوِّعة التي يدور حولها القرآن الكريم (، ومن هنا ((»كليًّا أو جزئيًّا، مع بيان كيفية اإلفادة منها يف تحقيق مصلحة العباد يمكننا تعريف علم مقاصد القرآن الكريم بأنَّه: الغايات واألهداف التي أُنزل القرآن الكريم من أجلها؛ تحقيقًا لجلب مصالح العباد يف المعاش والمعاد من جهة، وتحقيقًا لدرء مفاسد العباد يف المعاش والمعاد من جهة أخرى. و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا .)340/8( ( كتاب العين، للفراهيدي(( .)293/1( ( معجم مقاييس اللغة، البن فارس(( .)84/14( ( لسان العرب، البن منظور(( .)493/1( ( التحرير والتنوير، البن عاشور(( :المطلب الثاني تعريف البالء في القرآن الكريم ا البالء مصدر الفعل الثالثي على وزن فعل، وتصريفه: بَلَ ، يبلو، ابْلُ ، بلوًا وبالءً، فهو بال، والمفعول مبلوٌّ، واالبتالء مصدر الفعل الثالثي المزيد بحرفَيْن، أصله من بال، فزيد فيه األلف يف أوله، والتاء بين الفاء والعين على وزن افتعل، وتصريفه: ابتلى، يبتلي، ابتلِ، ابتالء، فهو مُبتلٍ، والمفعول مبتلًى. (، ويف ((»(، و«االمتحان واالختبار((»البالء واالبتالء لغة هو: «التجربة اللِّسان: «البالء: االختبار، يكون بالخير والشَّ رِّ ، يقال: ابتليته بالءً حسنًا وبالءً سيِّئًا، واهلل تعالى يُبْلي العبد بالءً حسنًا ويُبْلِيه بالء سيِّئًا، والمعروف أنَّ االبتالء يكون (. وأمَّا اصطالحً ا فهو: «االختبار بالخير والشرِّ ، قال تعالى: ((»يف الخير والشَّ رِّ معًا ] وهو مجاز مشهور 168 :﴿ﮧ ﮨ ﮩ ﮪ ﮫ﴾ [األعراف حقيقته بالء الثواب، وهو تخلُّقه، وترهُّله، ولَمَّا كان االختبار يوجب الضَّ جر، والتَّعب؛ سُ مي بالءً، كأنه يَخلُق النَّفس، ثم شاع يف اختبار الشَّ رِّ ؛ ألنَّه أكثر إعناتًا للنَّفس، وأشهر استعماله إذا أطلق أن يكون للشَّ رِّ ، فإذا أرادوا به الخير احتاجوا إلى قرينة أو تصريح، فيُطلق غالبًا على المصيبة التي تحلُّ بالعبد؛ ألنَّ هبا يُخترب (. وأمَّا االبتالء فهو: «استخراج ما عند المبتَلَى، وتَعَرُّ ف ((»مقدار الصَّ رب، واألناة البالء مصدر الفعل الثالثي على وزن فعل، وتصريفه: بَلَ ، يبلو، ابْلُ ، بلوًا وبالءً، فهو بال، والمفعول مبلوٌّ، واالبتالء مصدر الفعل الثالثي المزيد بحرفَيْن، أصله من بال، فزيد فيه األلف يف أوله، والتاء بين الفاء والعين على وزن افتعل، وتصريفه: ابتلى، يبتلي، ابتلِ، ابتالء، فهو مُبتلٍ، والمفعول مبتلًى. ٍا ِ (، ويف ((»(، و«االمتحان واالختبار((»البالء واالبتالء لغة هو: «التجربة اللِّسان: «البالء: االختبار، يكون بالخير والشَّ رِّ ، يقال: ابتليته بالءً حسنًا وبالءً سيِّئًا، واهلل تعالى يُبْلي العبد بالءً حسنًا ويُبْلِيه بالء سيِّئًا، والمعروف أنَّ االبتالء يكون (. وأمَّا اصطالحً ا فهو: «االختبار بالخير والشرِّ ، قال تعالى: ((»يف الخير والشَّ رِّ معًا ] وهو مجاز مشهور 168 :﴿ﮧ ﮨ ﮩ ﮪ ﮫ﴾ [األعراف حقيقته بالء الثواب، وهو تخلُّقه، وترهُّله، ولَمَّا كان االختبار يوجب الضَّ جر، والتَّعب؛ سُ مي بالءً، كأنه يَخلُق النَّفس، ثم شاع يف اختبار الشَّ رِّ ؛ ألنَّه أكثر إعناتًا للنَّفس، وأشهر استعماله إذا أطلق أن يكون للشَّ رِّ ، فإذا أرادوا به الخير احتاجوا إلى قرينة أو تصريح، فيُطلق غالبًا على المصيبة التي تحلُّ بالعبد؛ ألنَّ هبا يُخترب (. وأمَّا االبتالء فهو: «استخراج ما عند المبتَلَى، وتَعَرُّ ف ((»مقدار الصَّ رب، واألناة .)340/8( ( كتاب العين، للفراهيدي(( .)293/1( ( معجم مقاييس اللغة، البن فارس(( .)84/14( ( لسان العرب، البن منظور(( .)493/1( ( التحرير والتنوير، البن عاشور(( (. :المطلب الثاني تعريف البالء في القرآن الكريم ويبدو لي بعد عرض المعنى((»حاله يف الطَّاعة، والمعصية؛ بتحميله المشقَّة اللُّغوي واالصطالحي للبالء واالبتالء، أنَّ البالء أعمُّ من االبتالء، واالبتالء فيه معنى المشقَّة، واالختبار أكثر، فزيادة المبنى تدلُّ على الزِّ يادة يف المعنى، وهما يشرتكان يف أهنما يحمالن معنى االختبار، وكالهما يكون يف الخير والشَّ رِّ معًا من غير فرق بين فعليهما. :المطلب الثالث مفهوم مقاصد البالء في ضوء القرآن الكريم مما سبق من تعريفات لمقاصد البالء؛ يتبين لنا أنَّه يدور حول الكشف عن الغايات، واختبار أحوال النَّاس، وذلك يف مجال القرآن الكريم. ومن هنا يمكننا تعريف مقاصد البالء يف القرآن الكريم على أنَّها: الحِكَم التي يدور حولها اختبار أحوال الناس يف تلقِّي التَّكاليف، وأنواع النِّعم، والنِّقم، من منظور القرآن الكريم. (. ويبدو لي بعد عرض المعنى((»حاله يف الطَّاعة، والمعصية؛ بتحميله المشقَّة اللُّغوي واالصطالحي للبالء واالبتالء، أنَّ البالء أعمُّ من االبتالء، واالبتالء فيه معنى المشقَّة، واالختبار أكثر، فزيادة المبنى تدلُّ على الزِّ يادة يف المعنى، وهما يشرتكان يف أهنما يحمالن معنى االختبار، وكالهما يكون يف الخير والشَّ رِّ معًا من غير فرق بين فعليهما. (. ويبدو لي بعد عرض المعنى((»حاله يف الطَّاعة، والمعصية؛ بتحميله المشقَّة اللُّغوي واالصطالحي للبالء واالبتالء، أنَّ البالء أعمُّ من االبتالء، واالبتالء فيه معنى المشقَّة، واالختبار أكثر، فزيادة المبنى تدلُّ على الزِّ يادة يف المعنى، وهما يشرتكان يف أهنما يحمالن معنى االختبار، وكالهما يكون يف الخير والشَّ رِّ معًا من غير فرق بين فعليهما. :المطلب الثالث مفهوم مقاصد البالء في ضوء القرآن الكريم مما سبق من تعريفات لمقاصد البالء؛ يتبين لنا أنَّه يدور حول الكشف عن الغايات، واختبار أحوال النَّاس، وذلك يف مجال القرآن الكريم. مما سبق من تعريفات لمقاصد البالء؛ يتبين لنا أنَّه يدور حول الكشف عن الغايات، واختبار أحوال النَّاس، وذلك يف مجال القرآن الكريم. ومن هنا يمكننا تعريف مقاصد البالء يف القرآن الكريم على أنَّها: الحِكَم التي ِّ ِّ َّ ِّي مما سبق من تعريفات لمقاصد البالء؛ يتبين لنا أنَّه يدور حول الكشف عن الغايات، واختبار أحوال النَّاس، وذلك يف مجال القرآن الكريم. ومن هنا يمكننا تعريف مقاصد البالء يف القرآن الكريم على أنَّها: الحِكَم التي يدور حولها اختبار أحوال الناس يف تلقِّي التَّكاليف، وأنواع النِّعم، والنِّقم، من منظور القرآن الكريم. ومن هنا يمكننا تعريف مقاصد البالء يف القرآن الكريم على أنَّها: الحِكَم التي يدور حولها اختبار أحوال الناس يف تلقِّي التَّكاليف، وأنواع النِّعم، والنِّقم، من منظور القرآن الكريم. .)216/1( ( الوجوه والنظائر، ألبي هالل العسكري(( و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا األلفاظ ذات الصِّ لة بالبالء في القرآن الكريم لقد أخرب اهلل يف كتابه أنَّه يبتلي عباده تارةً بالخير، وتارةً بالشَّ رِّ ، فقال: ﴿ﯿ ]، ومن أهمِّ األلفاظ ذات الصِّ لة بالبالء 35 :ﰀ ﰁ ﰂﰃ ﰄ ﰅ﴾ [األنبياء يف الخير والشَّ رِّ ، كما سيأيت: لقد أخرب اهلل يف كتابه أنَّه يبتلي عباده تارةً بالخير، وتارةً بالشَّ رِّ ، فقال: ﴿ﯿ ]، ومن أهمِّ األلفاظ ذات الصِّ لة بالبالء 35 :ﰀ ﰁ ﰂﰃ ﰄ ﰅ﴾ [األنبياء يف الخير والشَّ رِّ ، كما سيأيت: : �أوَّلً : البالء باخلري : اإلمالء-1 : اإلمالء-1 وقد جاءت الحسنة بمعنى البالء ((»]، قال: «الحسنة: الخير95 :ﰁ﴾ [األعراف ]؛ 131 :بالخيرات، كما يف قوله تعالى: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖﭗ﴾ [األعراف (، وكما يف قوله: ﭐ﴿ﯦ ﯧ ﯨ ﯩ ﯪ ﯫ ﯬ ﯭﯮ﴾ ((»أي: «العافية والرَّ خاء (، ونحو ذلك من اآليات.((»]، ويعني بـ ﭐ﴿ﯨ﴾: «رخاء وظفر78 :[النِّساء النِّعمة:-3 تعود لفظة النِّعمة إلى جذرها اللُّغوي (نَعِمَ)، وقد بلغ عدد الكلمات الكلي (، ومعناها يف اللُّغة: «التَّنعُّمُ ((»لهذا الجذر يف القرآن الكريم؛ «مائة وأربعًا وأربعين (، وقد جاءت النِّعمة بمعنى البالء بالنِّعم، كما يف قوله تعالى: ((»وطِيبُ العَيش ]، قال المفسِّ رون: «وهذا 83 :﴿ﯔ ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ﴾ [اإلسراء (، وكما يف قوله بشأن فرعون: ﭐ﴿ﮈ ﮉ ((»اإلِنعام: سَ عة الرزق، وكشف البالء .)205-202 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)116/13( ( لسان العرب، البن منظور(( .)574/12( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)47/13( ( المصدر السابق(( .)555/8( (المصدر السابق(( .)709-707 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)446/5( ( معجم مقاييس اللغة، البن فارس(( .)49/3( ( زاد المسير يف علم التفسير، البن الجوزي(( : اإلمالء-1 اإ تعود لفظة اإلمالء إلى جذرها اللُّغوي (مَلِيَ )، وقد بلغ عدد الكلمات الكلِّي (، واإلمالء يف اللُّغة: «اإلمهال، والتَّأخير، ((»لهذا الجذر يف القرآن الكريم؛ «سبعًا (، وقد جاء اإلمالء بمعنى البالء بالتأخير، والتَّمتيع، كما يف قوله ((»وإطالة العمر تعالى: ﭐ﴿ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝﮞ ﮟ ﮠ ﮡ ﮢ ﮣ﴾ ]، 48 :]، وقوله: ﴿ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ﴾ [الحج178 :[آل عمران (، ((»وعلَّق ابن عجيبة & على اآلية فقال: «واإلمالء هو اإلمهال مع إرادة المعاقبة (، مع استمرار الظَّالمين على ((»ويتضمَّن اإلمالء: «التمتيعَ بطيبات الدُّنيا وزينتِها ظلمهم؛ حتى يزدادوا إثمًا بذلك التَّأخير، ونحو ذلك من اآليات التي دلَّت على .)676 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)290/15( ( لسان العرب، البن منظور(( .)542/3( ( البحر المديد يف تفسير القرآن المجيد، البن عجيبة(( )118/2( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)676 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)290/15( ( لسان العرب، البن منظور(( .)542/3( ( البحر المديد يف تفسير القرآن المجيد، البن عجيبة(( .)118/2( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)676 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)290/15( ( لسان العرب، البن منظور(( تعود لفظة الحسنة إلى جذرها اللُّغوي (حَ سُ نَ)، وقد بلغ عدد الكلمات (، ومعناها يف ((»الكلِّي لهذا الجذر يف القرآن الكريم؛ «مائة وأربعًا وتسعين (، وعن مجاهد &: ﭐ﴿ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ((»اللُّغة: «النِّعمة (. وقد جاءت الحسنة بمعنى البالء ((»]، قال: «الحسنة: الخير95 :ﰁ﴾ [األعراف ]؛ 131 :بالخيرات، كما يف قوله تعالى: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖﭗ﴾ [األعراف (، وكما يف قوله: ﭐ﴿ﯦ ﯧ ﯨ ﯩ ﯪ ﯫ ﯬ ﯭﯮ﴾ ((»أي: «العافية والرَّ خاء (، ونحو ذلك من اآليات.((»]، ويعني بـ ﭐ﴿ﯨ﴾: «رخاء وظفر78 :[النِّساء 4 ﯾ نُِ (. الرَّ حمة:-4 َ تعود لفظة الرَّ حمة إلى جذرها اللُّغوي (رَحِمَ)، وقد بلغ عدد الكلمات الكلي (، ومعناها يف اللُّغة: ((»لهذا الجذر يف القرآن الكريم؛ «ثالثمائة وتسعًا وثالثين ]؛ أي: 9 :(، وعن ابن جرير &: ﭐ﴿ﮝ ﮞ ﮟ ﮠ ﮡ﴾ [هود((»«الرَّ أفة (، وقد جاءت الرَّ حمة هبذا المعنى، كما يف قوله ((»«رخاء وسعةً يف الرِّ زق والعيش ]، ويعني بـ: ﭐ﴿ﭺ﴾:«خصب، 36 :تعالى: ﭐ﴿ﭷ ﭸ ﭹ ﭺ ﭻ ﭼﭽ﴾ [الروم (، ونحو ذلك من اآليات.((»ورخاء، وعافية يف األبدان، واألموال :ِّ ثانيًا: البالء بال‚شَّ ر النِّعمة:-3 تعود لفظة النِّعمة إلى جذرها اللُّغوي (نَعِمَ)، وقد بلغ عدد الكلمات الكلي (، ومعناها يف اللُّغة: «التَّنعُّمُ ((»لهذا الجذر يف القرآن الكريم؛ «مائة وأربعًا وأربعين (، وقد جاءت النِّعمة بمعنى البالء بالنِّعم، كما يف قوله تعالى: ((»وطِيبُ العَيش ]، قال المفسِّ رون: «وهذا 83 :﴿ﯔ ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ﴾ [اإلسراء (، وكما يف قوله بشأن فرعون: ﭐ﴿ﮈ ﮉ ((»اإلِنعام: سَ عة الرزق، وكشف البالء .)205-202 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص((ا 42 و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا :& (، قال قتادة((»]، ويعني بالنِّعمة: «متعة، وعيشً ا ليِّنًا27 :ﮊ ﮋ﴾ [الدخان (، ((»«أخرجه اهلل [أي: فرعون] من جنَّاته، وعيونه، وزروعه؛ حتى ورَّطه يف البحر ونحو ذلك من اآليات. و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا :& (، قال قتادة((»]، ويعني بالنِّعمة: «متعة، وعيشً ا ليِّنًا27 :ﮊ ﮋ﴾ [الدخان (، ((»«أخرجه اهلل [أي: فرعون] من جنَّاته، وعيونه، وزروعه؛ حتى ورَّطه يف البحر ونحو ذلك من اآليات. و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا : الفتنة-1 تعود لفظة الفتنة إلى جذرها اللُّغوي (فَتَنَ)، وقد بلغ عدد الكلمات الكلي (، ومعناها يف اللُّغة: «االبتالء، واالمتحان، ((»لهذا الجذر يف القرآن الكريم؛ «ستين .)177/4( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)32/22( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)309-304 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)446/5( ( معجم مقاييس اللغة، البن فارس(( .)574/12( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)102/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)420-419 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)177/4( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)32/22( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)309-304 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)446/5( ( معجم مقاييس اللغة، البن فارس(( .)574/12( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)102/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)420-419 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)177/4( ( معالم التنزيل يف تفسير القرآن، للبغوي(( (، وقد جاءت الفتنة بمعنى البالء، كما يف قوله تعالى: ﴿ﮣ((»واالختبار ]، عن مجاهد & يف 2 :ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ﴾ [العنكبوت (، وكما ((»قول اهلل: ﴿ﮩ ﮪ ﮫ ﮬ﴾ قال: «يُبْتَلَوْنَ يف أنفسهم، وأموالهم ]، 15 :يف قوله: ﴿ﮝ ﮞ ﮟ ﮠﮡ ﮢ ﮣ ﮤ ﮥ﴾ [التغابن (، ونحو ((»عن قتادة &، قوله: ﴿ﮝ ﮞ ﮟ ﮠﮡ﴾ يقول: «بالء ذلك من اآليات. : ُّ الضُّ ر-3 : ُّ الضُّ ر-3 ُ تعود لفظة الضُّ رِّ إلى جذرها اللُّغوي (ضَ رَ رَ)، وقد بلغ عدد الكلمات الكلي (، ومعناها يف اللُّغة: «الهزال، وسوء ((»لهذا الجذر يف القرآن الكريم؛ «أربعًا وسبعين (، وقد جاء الضُّ رُّ بمعنى الشدَّة والبالء ((»(، ويقول آخر: «الشدَّة، والبالء((»الحال ] 42 :كما يف قوله تعالى: ﴿ﯣ ﯤ ﯥ ﯦ ﯧ﴾ [األنعام (، وقال ابن جرير: «والضَّ رَّ اء هي األسقام، ((»قال ابن قتيبة: «والضَّ رَّ اء: البالء (، وكما يف قوله سبحانه: ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ((»والعلل العارضة يف األجسام ]، عن قتادة & يف قول اهلل: ﭐ﴿ﮠ ﮡ ﮢ ﮣ﴾ قال: «الوجع، 8 :ﮦ ﮧ﴾ [الزمر (، ونحو ذلك من اآليات.((»والبالء، والشدَّة البؤس:-2 تعود لفظة البؤس إلى جذرها اللُّغوي (بَأَسَ )، وقد بلغ عدد الكلمات الكلي (، والبؤس يف اللُّغة: «الشدَّة، ((»لهذا الجذر يف القرآن الكريم؛ «ثالثًا وسبعين (، وقد جاء البؤس بمعنى شدَّة الفقر والبالء، كما يف (( »والفقر، والبائس: المبتَلَى قوله تعالى: ﴿ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ﴾ (، ((»]، وقوله: ﴿ﯤ﴾ معناه: «شدَّة الفقر، والضِّ يق يف المعيشة42 :[األنعام ]، 28 :وكما يف قوله سبحانه: ﭐ﴿ﮦ ﮧ ﮨ ﮩ ﮪ﴾ [الحج (، ونحو ((»ومعنى قوله: ﴿ﮩ﴾ هو: «الذي به ضرُّ الجوع، والزَّ مانة والحاجة ذلك من اآليات. .)317/13( ( لسان العرب، البن منظور(( 4 .)317/13( ( لسان العرب، البن منظور(( .)7/19( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)426/23( ( المرجع السابق(( .)114-113 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)21-20/6( ( لسان العرب، البن منظور(( .)354/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)611/18( ( المرجع السابق(( و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا المصيبة:-4 المصيبة:-4 تعود لفظة المصيبة إلى جذرها اللُّغوي (صَ وَبَ )، وقد بلغ عدد الكلمات (، والمصيبة يف اللُّغة: «األمر ((»الكلي لهذا الجذر يف القرآن الكريم؛ «سبعًا وسبعين (، وقد جاءت المصيبة بمعنى الشدَّة والبالء كما يف قول ((»المكروه ينزل باإلنسان ]، 30 :اهلل تعالى: ﴿ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ﴾ [الشورى .)512-511 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)720/2( ( الصحاح تاج اللغة وصحاح العربية، للجوهري(( .)403/1( ( نزهة األعين النواظر يف علم الوجوه والنظائر، البن الجوزي(( .)134/1( ( غريب القرآن، البن قتيبة(( ا .)355/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( ا .)355/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)416-415 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)535/1( ( لسان العرب، البن منظور(( (، وكقوله تعالى: ﭐ﴿ﮯ ﮰ((»وقوله: ﴿ﯽ ﯾ ﯿ ﰀ﴾ فمعناه: «بليَّة، وشدَّة ]، والمصيبة يف األرض هي: «قحط 22 :ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ﯘ﴾ [الحديد (، والمصيبة ((»المطر، وقلة النَّبات، ونقص الثِّمار، وغالء األسعار، وتتابع الجوع (، ((»يف األنفس هي: «األمراض، والفقر، وذهاب األوالد، وإقامة الحدود عليها ونحو ذلك من اآليات. (، وكقوله تعالى: ﭐ﴿ﮯ ﮰ((»وقوله: ﴿ﯽ ﯾ ﯿ ﰀ﴾ فمعناه: «بليَّة، وشدَّة ]، والمصيبة يف األرض هي: «قحط 22 :ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ﯘ﴾ [الحديد (، والمصيبة ((»المطر، وقلة النَّبات، ونقص الثِّمار، وغالء األسعار، وتتابع الجوع (، ((»يف األنفس هي: «األمراض، والفقر، وذهاب األوالد، وإقامة الحدود عليها ونحو ذلك من اآليات. السُّ وء:-5 ُ تعود لفظة السُّ وء إلى جذرها اللُّغوي (سَ وُءَ)، وقد بلغ عدد الكلمات الكلي (، والسُّ وء يف اللُّغة: «اسم ((»لهذا الجذر يف القرآن الكريم؛ «مائة وسبعًا وستين (، وعن مجاهد &: ﭐ﴿ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ((»للضُّ رِّ ، وسوء الحال (. وقد جاء السُّ وء بمعنى الضرِّ والبالء، ((» ُّ]، قال:«السَّ يِّئة: الشَّ ر95 :ﰁ﴾ [األعراف كما يف قوله تعالى: ﭐ﴿ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦﭧ﴾ (، ((»]، وقوله: ﭐ﴿ﭤ ﭥ ﭦﭧ﴾ أي: «الضرُّ ، والفقر، والجوع188 :[األعراف ]، عن ابن جُ رَ يج 62 :وكقوله: ﴿ﯘ ﯙ ﯚ ﯛ ﯜ ﯝ ﯞ﴾ [النمل (، كما وردت لفظة السُّ وء يف كثير ((» ُّ&، قوله: ﴿ﯝ ﯞ﴾ قال: «الضر و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا ﴾من المواضع بمعنى السيِّئة، وذلك مثل قوله تعالى: ﴿ﯣ ﯤ ﯥ ﯦ ﯧﯨ (، وكقوله أيضً ا: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ((»]؛ أي: «مصيبة ومكروه120 :[آل عمران (، وقوله: ﴿ﭾ ﭿ ((»] ؛ أي: «بالء، وعقوبة131 :ﭜ ﭝ ﭞﭟ﴾ [األعراف ]، ويعني بـ ﭐ ﴿ﮀ﴾: «شدَّة من جدب، 36 :ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ﴾ [الروم (، ونحو ذلك من اآليات.((»وقحط، وبالء يف األموال واألبدان و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا ﴾من المواضع بمعنى السيِّئة، وذلك مثل قوله تعالى: ﴿ﯣ ﯤ ﯥ ﯦ ﯧﯨ (، وكقوله أيضً ا: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ((»]؛ أي: «مصيبة ومكروه120 :[آل عمران (، وقوله: ﴿ﭾ ﭿ ((»] ؛ أي: «بالء، وعقوبة131 :ﭜ ﭝ ﭞﭟ﴾ [األعراف ]، ويعني بـ ﭐ ﴿ﮀ﴾: «شدَّة من جدب، 36 :ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ﴾ [الروم (، ونحو ذلك من اآليات.((»وقحط، وبالء يف األموال واألبدان و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا ﴾من المواضع بمعنى السيِّئة، وذلك مثل قوله تعالى: ﴿ﯣ ﯤ ﯥ ﯦ ﯧﯨ (، وكقوله أيضً ا: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ((»]؛ أي: «مصيبة ومكروه120 :[آل عمران (، وقوله: ﴿ﭾ ﭿ ((»] ؛ أي: «بالء، وعقوبة131 :ﭜ ﭝ ﭞﭟ﴾ [األعراف ]، ويعني بـ ﭐ ﴿ﮀ﴾: «شدَّة من جدب، 36 :ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ﴾ [الروم (، ونحو ذلك من اآليات.((»وقحط، وبالء يف األموال واألبدان :المطلب الخامس 102 :ﮗ ﮘ ﮙ﴾ [هود و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا :المطلب الخامس َ ال شكَّ أنَّ البالء يختلف بين كونه رحمةً للنَّاس، وكونه عقوبةً لهم. فيكون رحمةً للنَّاس بثالثة معانٍ: يُنعم على جميع خلقه بنعمه I فاألوَّل: اإلنعام واإلفضال، والمقصود أنَّ اهلل : ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ + الظَّاهرة والباطنة، قال تعالى على لسان رسوله سليمان ].40 :ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل اّ يُنعم على جميع خلقه بنعمه I فاألوَّل: اإلنعام واإلفضال، والمقصود أنَّ اهلل : ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ + الظَّاهرة والباطنة، قال تعالى على لسان رسوله سليمان ].40 :ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل يطهِّر المسلمين خصوصً ا I والثاين: التَّطهير والتكفير، والمقصود أنَّ اهلل بما كسبت أيديهم من اآلثام والمعاصي، قال تعالى: ﭐ﴿ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ]. 30 :ﰃ ﰄ ﰅ ﰆ﴾ [الشورى يمهل النَّاس عمومًا، I والثالث: التَّأخير واإلمهال، والمقصود أنَّ اهلل وال يعجِّل لهم العقوبة على اقرتافهم المعاصي، مِن كفر ألنعم اهلل، ومن فساد يف برِّ األرض وبحرها، ومن ظلم وطغيان؛ حتى يتوبوا على ما صدر منهم من ، يقول تعالى ذكره: H تفريط يف جنب اهلل، وتقصير يف األعمال التي تُرضي اهلل ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ].45 :ﭠ ﭡﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ﴾ [فاطر ٍا ّس ب وب ي و شرع عقوبات رادعة مغلَّظة من حدود I فاألوَّل: الرَّ دع، والمقصود أنَّ اهلل وقصاص وتعازير شرعيَّة على مرتكبي المعاصي، والجرائم والسَّ اعين يف األرض يف حدِّ - فسادًا؛ ألجل ضبط سلوكاهتم، وردعهم عن اقرتاف الجرائم، قال تعالى : ﭐ﴿ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢﭣ ﭤ ﭥ ﭦ ﭧ ﭨ -الزِّ نى تمثيلً ، ال حصرً ا ].2 :ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰﭱ ﭲ ﭳ ﭴ ﭵ ﭶ﴾ [النور يُرغِد عيش العاصين من I والثاين: االستدراج واإلمالء، والمقصود أنَّ اهلل الكَفَرة والفسقة والجهلة لمدَّة طويلة؛ حتى يغرتُّوا بما هم فيه، ويعتقدون أنَّهم على خير، قال تعالى: ﭐ﴿ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ].183-182 :ﮙ ﮚ﴾ [األعراف والثالث: األخذ، والتي تأيت بعد مرحلة االستدراج واإلمالء، والمقصود أنَّ يوقع عقوبة األخذ على الكافرين بأحكامه، والمستحلِّين لمحرَّ ماته، I اهلل والصَّ ادِّين عن دينه، والمؤذين ألوليائه، والسَّ اعين يف األرض ظلمًا، وطغيانًا، وفسقًا، وجهلً ، وفسادًا، قال تعالى: ﴿ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔﮕ ﮖ ]. :المطلب السادس :المطلب السادس اشتقاقات مادة «بال» وتصريفاتها في القرآن الكريم لقد ورد فعل «بال» باشتقاقاته، وتصريفاته المختلفة يف سبعة وثالثين موضعًا، من خالل أربع وثالثين آية من آي الذِّكر الحكيم، منها ستَّ عشرةَ آية مكِّية، وثماينَ (.((عشرةَ آية مدنيَّة، وذلك يف مجموع أربع وعشرين سورة )، 4( ٌ)، بَلَ ء1( ٰوالصيغ التي ورد هبا فعل «بال» يف القرآن الكريم هي: ابْتَلَى )، وَلِيَبْتَلِيَ 4( ْ)، لِيَبْلُوَكُم1( ْ)، لِيَبْتَلِيَكُم2( ْ)، وَلَنَبْلُوَنَّكُم1( ْ)، مُبْتَلِيكُم1( ًبَلَ ء )، ابْتُلِيَ 1( ْ)، نَبْلُوهُم1( َ)، لَمُبْتَلِين1( )، وَابْتَلُوا1( َّ)، لَتُبْلَوُن1( ُ)، لَيَبْلُوَنَّكُم1( ،)1( ُ)، يَبْلُوكُم1( )، تَبْلُو2( ُ)، ابْتَلَ ه1( َ)، وَلِيُبْلِي1( ِ)، نَبْتَلِيه2( ْ)، بَلَوْنَاهُم1( )، بَلَوْنَا1( َ)، وَنَبْلُو1( َ)، لِيَبْلُو1( ُ)، الْبَلَ ء1( )، لِيَبْلُوَنِي1( ْ)، وَنَبْلُوكُم1( ْلِنَبْلُوَهُم ).1( )، تُبْلَى1( :المطلب السادس :المطلب السادس اشتقاقات مادة «بال» وتصريفاتها في القرآن الكريم لقد ورد فعل «بال» باشتقاقاته، وتصريفاته المختلفة يف سبعة وثالثين موضعًا، من خالل أربع وثالثين آية من آي الذِّكر الحكيم، منها ستَّ عشرةَ آية مكِّية، وثماينَ (.((عشرةَ آية مدنيَّة، وذلك يف مجموع أربع وعشرين سورة )، 4( ٌ)، بَلَ ء1( ٰوالصيغ التي ورد هبا فعل «بال» يف القرآن الكريم هي: ابْتَلَى )، وَلِيَبْتَلِيَ 4( ْ)، لِيَبْلُوَكُم1( ْ)، لِيَبْتَلِيَكُم2( ْ)، وَلَنَبْلُوَنَّكُم1( ْ)، مُبْتَلِيكُم1( ًبَلَ ء )، ابْتُلِيَ 1( ْ)، نَبْلُوهُم1( َ)، لَمُبْتَلِين1( )، وَابْتَلُوا1( َّ)، لَتُبْلَوُن1( ُ)، لَيَبْلُوَنَّكُم1( ،)1( ُ)، يَبْلُوكُم1( )، تَبْلُو2( ُ)، ابْتَلَ ه1( َ)، وَلِيُبْلِي1( ِ)، نَبْتَلِيه2( ْ)، بَلَوْنَاهُم1( )، بَلَوْنَا1( َ)، وَنَبْلُو1( َ)، لِيَبْلُو1( ُ)، الْبَلَ ء1( )، لِيَبْلُوَنِي1( ْ)، وَنَبْلُوكُم1( ْلِنَبْلُوَهُم ).1( )، تُبْلَى1( الفعل المبني للمعلوم الرسم البياين الثالث: يبيِّن نسبة اآليات التي تحدَّثت عن البالء واالبتالء القرآن الكريم نستنتج أنَّ فعل «بال» باشتقاقاته المختلفة، ذُكر يف القرآن الكريم سبعًا 1 وثالثين مرة، منها إحدى وعشرين مرة يف النصف األول، وستَّ عشرة مرة يف النصف الثاين. القرآن الكريم لقد ورد فعل «بال» باشتقاقاته، وتصريفاته المختلفة يف سبعة وثالثين موضعًا، من خالل أربع وثالثين آية من آي الذِّكر الحكيم، منها ستَّ عشرةَ آية مكِّية، وثماينَ (.((عشرةَ آية مدنيَّة، وذلك يف مجموع أربع وعشرين سورة َ )، 4( ٌ)، بَلَ ء1( ٰوالصيغ التي ورد هبا فعل «بال» يف القرآن الكريم هي: ابْتَلَى )، وَلِيَبْتَلِيَ 4( ْ)، لِيَبْلُوَكُم1( ْ)، لِيَبْتَلِيَكُم2( ْ)، وَلَنَبْلُوَنَّكُم1( ْ)، مُبْتَلِيكُم1( ًبَلَ ء )، ابْتُلِيَ 1( ْ)، نَبْلُوهُم1( َ)، لَمُبْتَلِين1( )، وَابْتَلُوا1( َّ)، لَتُبْلَوُن1( ُ)، لَيَبْلُوَنَّكُم1( ،)1( ُ)، يَبْلُوكُم1( )، تَبْلُو2( ُ)، ابْتَلَ ه1( َ)، وَلِيُبْلِي1( ِ)، نَبْتَلِيه2( ْ)، بَلَوْنَاهُم1( )، بَلَوْنَا1( َ)، وَنَبْلُو1( َ)، لِيَبْلُو1( ُ)، الْبَلَ ء1( )، لِيَبْلُوَنِي1( ْ)، وَنَبْلُوكُم1( ْلِنَبْلُوَهُم ).1( )، تُبْلَى1( .)311/5( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( المطلب السابع: رسومات بيانية تبيِّن الصِّ يغ التصريفية لمادة «بال» في سور القرآن الكريم الرَّ سم البياين األوَّل: يبيِّن عدد تكرار تصريفات فعل «بال» يف سور القرآن الكريم على حدة: صيغ الترصيف عدد الصيغ التَّكرار النسبة 1اسم فاعل ): ﴿ﭮ ﭯ ﭰ﴾ 1( َلَمُبْتَلِين ]30 :[المؤمنون ): ﴿ﭖ ﭗ ﭘ 1( ْمُبْتَلِيكُم ]249 :ﭙ﴾ [البقرة 2 % 6 2 الفعل المبني للمجهول ): ﴿ﮖ ﮗ ﮘ﴾ 1( َابْتُلِي ]11 :[األحزاب ): ﴿ﭸ ﭹ ﭺ﴾ 1( تُبْلَى ]9 :[الطارق ): ﴿ﯛ ﯜ 1( َّلَتُبْلَوُن ﯝ ﯞ﴾ ]186 :[آل عمران 3 % 8 ): ﴿ﮥ ﮦ ﮧ ﮨ1( ابْتَلَى المطلب السابع: رسومات بيانية تبيِّن الصِّ يغ التصريفية لمادة «بال» في سور القرآن الكريم الرَّ سم البياين األوَّل: يبيِّن عدد تكرار تصريفات فعل «بال» يف سور القرآن الكريم على حدة: صيغ الترصيف عدد الصيغ التَّكرار النسبة 1اسم فاعل ): ﴿ﭮ ﭯ ﭰ﴾ 1( َلَمُبْتَلِين ]30 :[المؤمنون ): ﴿ﭖ ﭗ ﭘ 1( ْمُبْتَلِيكُم ]249 :ﭙ﴾ [البقرة 2 % 6 2 الفعل المبني للمجهول ): ﴿ﮖ ﮗ ﮘ﴾ 1( َابْتُلِي ]11 :[األحزاب ): ﴿ﭸ ﭹ ﭺ﴾ 1( تُبْلَى ]9 :[الطارق ): ﴿ﯛ ﯜ 1( َّلَتُبْلَوُن ﯝ ﯞ﴾ ]186 :[آل عمران 3 % 8 ): ﴿ﮥ ﮦ ﮧ ﮨ1( ابْتَلَى ]124 :ﮩ ﮪﮫ﴾ [البقرة ): ﴿ﭕ ﭖ ﴾ 2( ْبَلَوْنَاهُم المطلب السابع: رسومات بيانية تبيِّن الصِّ يغ التصريفية لمادة «بال» في سور القرآن الكريم المطلب السابع: رسومات بيانية تبيِّن الصِّ يغ التصريفية لمادة «بال» في سور القرآن الكريم الرَّ سم البياين األوَّل: يبيِّن عدد تكرار تصريفات فعل «بال» يف سور القرآن الكريم على حدة: صيغ الترصيف عدد الصيغ التَّكرار النسبة 1اسم فاعل ): ﴿ﭮ ﭯ ﭰ﴾ 1( َلَمُبْتَلِين ]30 :[المؤمنون ): ﴿ﭖ ﭗ ﭘ 1( ْمُبْتَلِيكُم ]249 :ﭙ﴾ [البقرة 2 % 6 2 الفعل المبني للمجهول ): ﴿ﮖ ﮗ ﮘ﴾ 1( َابْتُلِي ]11 :[األحزاب ): ﴿ﭸ ﭹ ﭺ﴾ 1( تُبْلَى ]9 :[الطارق ): ﴿ﯛ ﯜ 1( َّلَتُبْلَوُن ﯝ ﯞ﴾ ]186 :[آل عمران 3 % 8 ): ﴿ﮥ ﮦ ﮧ ﮨ1( ابْتَلَى ]124 :ﮩ ﮪﮫ﴾ [البقرة ): ﴿ﭕ ﭖ ﴾ 2( ْبَلَوْنَاهُم ]17 :[القلم ): ﴿ﮖ ﮗ ﮘ﴾1( َابْتُلِي الفعل المبني للمجهولَ و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا صيغ الترصيف عدد الصيغ التَّكرار النسبة 3 الفعل المبني للمعلوم ): ﴿ﮓ ﮔ ﮕ ﮖ ﮗ 2( ُابْتَلَ ه ]15 :ﮘ ﮙ ﮚ﴾ [الفجر ﴿ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ﴾ ]16 :[الفجر ): ﴿ﭗ ﭘ ﭙ ﭚ﴾ 1( بَلَوْنَا ]17 :[القلم ): ﴿ﭠ 2( ْلَنَبْلُوَنَّكُم ]155 :ﭡ﴾ [البقرة ﴿ﭠ ﭡ ﭢ ﭣ ]31 :ﭤ ﭥ﴾ [محمد ]6 :): ﴿ﯥ ﯦ﴾ [النساء1( ابْتَلُوا ): ﴿ﮛ ﮜ ﮝ 1( ْلِيَبْتَلِيَكُم ]152 :ﮞﮟ﴾ [آل عمران ): ﴿ﮦ ﮧ ﮨ 4( ْلِيَبْلُوَكُم ]48 :ﮩ ﮪﮫ﴾ [المائدة ]165 :﴿ﰒ ﰓ ﰔ ﰕﰖ﴾ [األنعام ﴿ﭰ ﭱ ﭲ ﭳﭴ﴾ ]7 :[هود ]2 :﴿ﭟ ﭠ ﭡ ﭢﭣ﴾ [الملك 26 % 70 رعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا ف عدد الصيغ التَّكرار النسبة ي ): ﴿ﮓ ﮔ ﮕ ﮖ ﮗ 2( ُابْتَلَ ه ]15 :ﮘ ﮙ ﮚ﴾ [الفجر ﴿ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ﴾ ]16 :[الفجر ): ﴿ﭗ ﭘ ﭙ ﭚ﴾ 1( بَلَوْنَا ]17 :[القلم ): ﴿ﭠ 2( ْلَنَبْلُوَنَّكُم ]155 :ﭡ﴾ [البقرة ﴿ﭠ ﭡ ﭢ ﭣ ]31 :ﭤ ﭥ﴾ [محمد ]6 :): ﴿ﯥ ﯦ﴾ [النساء1( ابْتَلُوا ): ﴿ﮛ ﮜ ﮝ 1( ْلِيَبْتَلِيَكُم ]152 :ﮞﮟ﴾ [آل عمران ): ﴿ﮦ ﮧ ﮨ 4( ْلِيَبْلُوَكُم ]48 :ﮩ ﮪﮫ﴾ [المائدة ]165 :﴿ﰒ ﰓ ﰔ ﰕﰖ﴾ [األنعام ﴿ﭰ ﭱ ﭲ ﭳﭴ﴾ ]7 :[هود ]2 :﴿ﭟ ﭠ ﭡ ﭢﭣ﴾ [الملك ): ﴿ﮖ ﮗ ﮘ ﮙ 1( َوَلِيَبْتَلِي 26 % 70 ]17 :[القلم ]7 :[هود 51 صيغ الترصيف عدد الصيغ التَّكرار النسبة ): ﴿ﮣ ﮤ 1( ُلَيَبْلُوَنَّكُم ]94 :ﮥ ﮦ ﮧ﴾ [المائدة ): ﴿ﯤ﴾ 1( ْنَبْلُوهُم ]163 :[األعراف ): ﴿ﯨ ﯩ ﯪ ﯫ ﯬ 1( ِنَبْتَلِيه ]2 :ﯭ ﯮ﴾ [االنسان ): ﴿ﭟ ﭠ﴾ 1( َوَلِيُبْلِي ]17 :[األنفال ): ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ 1( لِيَبْلُوَنِي ]40 :ﮥ ﮦ ﮧ ﮨﮩ﴾ [النمل ): ﴿ﲍ ﲎ ﲏ 1( َلِيَبْلُو ]4 :ﲐﲑ﴾ [محمد ): ﴿ﭦ ﭧ﴾ 1( َوَنَبْلُو ].31 :[محمد ): ﭐ﴿ﭷ ﭸ ﭹ 1( ْلِنَبْلُوَهُم ].7 :ﭺ﴾ [الكهف ): ﴿ﯿ ﰀ 1( ْوَنَبْلُوكُم ] ﰁﰂﰃ﴾ [ أل ا عدد الصيغ التَّكرار النسبة ): ﴿ﮣ ﮤ 1( ُلَيَبْلُوَنَّكُم ]94 :ﮥ ﮦ ﮧ﴾ [المائدة ): ﴿ﯤ﴾ 1( ْنَبْلُوهُم ]163 :[األعراف ): ﴿ﯨ ﯩ ﯪ ﯫ ﯬ 1( ِنَبْتَلِيه ]2 :ﯭ ﯮ﴾ [االنسان ): ﴿ﭟ ﭠ﴾ 1( َوَلِيُبْلِي ]17 :[األنفال ): ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ 1( لِيَبْلُوَنِي ]40 :ﮥ ﮦ ﮧ ﮨﮩ﴾ [النمل ): ﴿ﲍ ﲎ ﲏ 1( َلِيَبْلُو ]4 :ﲐﲑ﴾ [محمد ): ﴿ﭦ ﭧ﴾ 1( َوَنَبْلُو ].31 :[محمد ): ﭐ﴿ﭷ ﭸ ﭹ 1( ْلِنَبْلُوَهُم ].7 :ﭺ﴾ [الكهف ): ﴿ﯿ ﰀ 1( ْوَنَبْلُوكُم ]35 :ﰁ ﰂﰃ﴾ [األنبياء ): ﴿ﯙ ﯚ ﯛ 1( ُيَبْلُوكُم ]92 :ﯜﯝ﴾ [النحل َعدد الصيغ ): ﴿ﮣ ﮤ 1( ُلَيَبْلُوَنَّكُم ]94 :ﮥ ﮦ ﮧ﴾ [المائدة ): ﴿ﯤ﴾ 1( ْنَبْلُوهُم ]163 :[األعراف ): ﴿ﯨ ﯩ ﯪ ﯫ ﯬ 1( ِنَبْتَلِيه ]2 :ﯭ ﯮ﴾ [االنسان ): ﴿ﭟ ﭠ﴾ 1( َوَلِيُبْلِي ]17 :[األنفال ): ﭐ﴿ﮠ ﮡ ﮢ ﮣ ﮤ 1( لِيَبْلُوَنِي ]40 :ﮥ ﮦ ﮧ ﮨﮩ﴾ [النمل ): ﴿ﲍ ﲎ ﲏ 1( َلِيَبْلُو ]4 :ﲐﲑ﴾ [محمد ): ﴿ﭦ ﭧ﴾ 1( َوَنَبْلُو ].31 :[محمد ): ﭐ﴿ﭷ ﭸ ﭹ 1( ْلِنَبْلُوَهُم ].7 :ﭺ﴾ [الكهف ): ﴿ﯿ ﰀ 1( ْوَنَبْلُوكُم ]35 :ﰁ ﰂﰃ﴾ [األنبياء ): ﴿ﯙ ﯚ ﯛ 1( ُيَبْلُوكُم ]92 :ﯜﯝ﴾ [النحل 52 و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا صيغ الترصيف عدد الصيغ التَّكرار النسبة ): ﴿ﮦ ﮧ ﮨ ﮩ 1( تَبْلُوا ]30 :ﮪ ﮫﮬ﴾ [يونس 4االسم ): ﴿ﭢ ﭣ﴾ 1( ًبَلَ ء ]17 :[األنفال ): ﴿ﮎ ﮏ ﮐ ﮑ 4( ٌبَلَ ء / األعراف: 6 :ﮒ ﮓ﴾ [البقرة ]6 :/ إبراهيم141 ﭐ ﴿ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ ]33 :ﯛ﴾ [الدخان ): ﴿ﭣ ﭤ ﭥ ﭦ 1( ُالْبَلَ ء ]106 :ﭧ﴾ [الصافات 6 %16 املجموع صيغ4 مرة37 %100 الرسم البياين الثاين: يبين نسبة تكرار صيغ التصريف لفعل «بال» يف القرآن الكريم رَ ): ﴿ﮦ ﮧ ﮨ ﮩ 1( تَبْلُوا ]30 :ﮪ ﮫﮬ﴾ [يونس 4االسم ): ﴿ﭢ ﭣ﴾ 1( ًبَلَ ء ]17 :[األنفال ): ﴿ﮎ ﮏ ﮐ ﮑ 4( ٌبَلَ ء / األعراف: 6 :ﮒ ﮓ﴾ [البقرة ]6 :/ إبراهيم141 ﭐ ﴿ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ ]33 :ﯛ﴾ [الدخان ): ﴿ﭣ ﭤ ﭥ ﭦ 1( ُالْبَلَ ء ]106 :ﭧ﴾ [الصافات 6 %16 املجموع صيغ4 مرة37 %100 الرسم البياين الثاين: يبين نسبة تكرار صيغ التصريف لفعل «بال» يف القرآن الكريم 53 الرَّ سم البياين الرابع: يوضِّ ح نسب الصيغ التصريفية التي ذكر هبا فعل بال يف القرآن الكريم الرّ سم البياين الخامس: يوضِّ ح نسبة ذكر تصريفات فعل «بال» يف اآليات المكيَّة والمدنيَّة الرّ سم البياين الخامس: يوضِّ ح نسبة ذكر تصريفات فعل «بال» يف اآليات المكيَّة والمدنيَّة َ 54 و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: . :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: ُ . نستنتج أنَّ فعل «بال» باشتقاقاته المختلفة، ذُكر يف القرآن الكريم سبعًا 1 وثالثين مرة، منها إحدى وعشرين مرة يف النصف األول، وستَّ عشرة مرة يف النصف الثاين. . نستنتج أنَّ فعل «بال» باشتقاقاته المختلفة، ذكر يف القرآن الكريم سبع 2 ،)3( )، المبني للمجهول2( وثالثين مرَّ ة من خالل أربع صيغ، وهي: اسم الفاعل ). 6( )، واالسم26( المبني للمعلوم . نستنتج تكرار فعل «بال» بصيغه المختلفة يف مختلف السور على النَّحو اآليت:3 اسم فاعل: تكرَّ ر ذكره مرتَيْن يف سورتَيْن هما: البقرة، والمؤمنون، وهذا .%6 :بنسبة مئوية قدِّرت بـ صيغة الفعل المبني للمجهول: تكرَّ ر ذكرها ثالث مرات يف ثالث سور قرآنية،  .%8 :هي: آل عمران، األحزاب، والطالق، وهذا بنسبة مئوية قدِّرت بـ صيغة الفعل المبني للمعلوم: تكرَّ ر ذكرها ستًّا وعشرين مرة يف ثماينَ عشرةَ  ،سور قرآنية، هي: البقرة، آل عمران، النساء، المائدة، األنعام، األعراف األنفال، هود، يونس، النحل، الكهف، األنبياء، النمل، محمد، الملك، .%70 :القلم، اإلنسان، الفجر، وهذا بنسبة مئوية قدِّرت بـ صيغة االسم: تكرَّ ر ذكرها ست مرات يف ست سور قرآنية، هي: البقرة، األعراف،  .%16 :األنفال، إبراهيم، الصافات، والدخان، وهذا بنسبة مئوية قدِّرت بـ . نالحظ أنَّ عدد السور التي ورد فيها فعل «بال» باشتقاقاته المختلفة أربع4 ،وعشرون سورة، وهي: البقرة، آل عمران، النساء، المائدة، األنعام، األعراف األنفال، يونس، هود، إبراهيم، النحل، الكهف، األنبياء، المؤمنون، النمل، األحزاب، الصافات، الدخان، محمد، الملك، القلم، اإلنسان الطارق، الفجر. . يالحظ يف مجموع السور التي ورد فيها فعل «بال» باشتقاقاته المختلفة، 5 ،سبع عشرة سورة مكية، وسبع سور مدنية، ، فالمكية: األنعام، األعراف، يونس هود، إبراهيم، النحل، الكهف، األنبياء، المؤمنون، النمل، الصافات، الدخان، الملك، القلم، اإلنسان، الطارق والفجر، والمدنية هي: البقرة، آل عمران، النساء، المائدة، األنفال، األحزاب ومحمد |. . نالحظ أنَّ عدد السور التي ورد فيها فعل «بال» باشتقاقاته المختلفة أربع4 ،وعشرون سورة، وهي: البقرة، آل عمران، النساء، المائدة، األنعام، األعراف األنفال، يونس، هود، إبراهيم، النحل، الكهف، األنبياء، المؤمنون، النمل، األحزاب، الصافات، الدخان، محمد، الملك، القلم، اإلنسان الطارق، الفجر. . يالحظ يف مجموع السور التي ورد فيها فعل «بال» باشتقاقاته المختلفة، 5 ،سبع عشرة سورة مكية، وسبع سور مدنية، ، فالمكية: األنعام، األعراف، يونس هود، إبراهيم، النحل، الكهف، األنبياء، المؤمنون، النمل، الصافات، الدخان، الملك، القلم، اإلنسان، الطارق والفجر، والمدنية هي: البقرة، آل عمران، النساء، المائدة، األنفال، األحزاب ومحمد |. . يالحظ أنَّ اآليات المدنيَّة التي ورد فيها لفظ «بال» باشتقاقاته المختلفة 6 . بالمائة47 بالمائة، بينما المكيَّة بلغت نسبتها53 بلغت نسبتها بالمائة، بينما 70 . :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: يالحظ أنَّ نسبة اآليات التي تحدثت عن البالء بلغت7 بالمائة، وهذا يؤيِّد ما تمَّ التوصُّ ل30 نسبة اآليات التي تحدثت عن االبتالء بلغت إليه سابقًا؛ أنَّ بين البالء واالبتالء عمومًا وخصوصً ا، فكل بالء ابتالء، وليس كلُّ ابتالء بالء. . يالحظ تكرار آيات البالء واالبتالء يف السور المدنية، وأنَّها عُنيت بالتكاليف 8 ،والنهي والضِّ يق، وهذا يؤيِّد قاعدة أنَّ القرآن المدين اهتمَّ اهتمامًا بارزًا بالعبادات والتَّكاليف بما يُطاق، والحرص على تطهير القلوب من األمراض القلبية، وميز خبيثها عن طيِّبها؛ ألجل هتيئتها يف آخر المطاف إلى حمل أعباء رسالة اإلسالم، ، والجهاد يف سبيله.I والدَّعوة إلى اهلل . ويالحظ تكرار آيات البالء واالبتالء يف السور المكية، وأنَّها عُنيت بتبليغ 9 و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا الدعوة، واالتعاظ بقصص األولين، ويوم الحساب، والمصائب، والنعم، والوفاء بالعهد، وعدم الغدر، وهذا يؤيد قاعدة أنَّ القرآن المكي اهتم اهتمامًا بارزًا بتزكية النفوس، ودعوهتا إلى اإليمان باهلل، واليوم اآلخر، والقدر خيره، وشره، وااللتزام بالعهود، والمواثيق، وعدم نقضها. . يستفاد من خالل ورود تصريفات «بال» يف اآليات المكية والمدنية؛ 10 .ضرورة الشُّ كر على المسارِّ، والصَّ رب على المضارِّ، وتحمُّل التكاليف والنواهي . ونالحظ أن مصدر «البالء» باشتقاقاته المختلفة ضُ مِّن يف ثمانية عشر 11 :محورًا رئيسً ا يف القرآن، هي . :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: ونالحظ أن مصدر «البالء» باشتقاقاته المختلفة ضُ مِّن يف ثمانية عشر 11 :محورًا رئيسً ا يف القرآن، هي :محورًا رئيسً ا يف القرآن، هي بتكليفه ذبح ولده إسماعيل، فسارع إلى ذلك + • اختبار اهلل تعالى إبراهيم ].106 :ممتثلً ألمر اهلل تعالى، قال تعالى: ﭐ﴿ﭣ ﭤ ﭥ ﭦ ﭧ﴾ [الصافات بإحضار العرش إليه؛ ليرى منه أيشكر أم + • اختبار اهلل تعالى سليمان أيكفر، وما كان منه إلَّ أن اعرتف بفضل ربه عليه وشكر نِعَمَه، قال تعالى: ﴿ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ].40 :ﯖ﴾ [النمل بتكليفه ذبح ولده إسماعيل، فسارع إلى ذلك + • اختبار اهلل تعالى إبراهيم ].106 :ممتثلً ألمر اهلل تعالى، قال تعالى: ﭐ﴿ﭣ ﭤ ﭥ ﭦ ﭧ﴾ [الصافات بتكليفه ذبح ولده إسماعيل، فسارع إلى ذلك + • اختبار اهلل تعالى إبراهيم ].106 :ممتثلً ألمر اهلل تعالى، قال تعالى: ﭐ﴿ﭣ ﭤ ﭥ ﭦ ﭧ﴾ [الصافات بإحضار العرش إليه؛ ليرى منه أيشكر أم + • اختبار اهلل تعالى سليمان أيكفر، وما كان منه إلَّ أن اعرتف بفضل ربه عليه وشكر نِعَمَه، قال تعالى: ﴿ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ].40 :ﯖ﴾ [النمل • اختبار اهلل تعالى عباده بالمال والقوة والجاه وجودة النفوس واألذهان وغير ذلك؛ ليرى المحسن من المسيء، وضدَّه، قال تعالى: ﭐ﴿ﰍ ﰎ ].165 :ﰏ ﰐ ﰑ ﰒ ﰓ ﰔ ﰕﰖ﴾ [األنعام • اختبار اهلل تعالى عباده بالمصائب تارةً، وبالنِّعَم أُخرى؛ لينظر من يشكر، ومن يكفر، ومن يصرب، ومن يقنط، قال تعالى: ﭐ﴿ﯺ ﯻ ﯼ ﯽﯾ ].35 :ﯿ ﰀ ﰁ ﰂﰃ ﰄ ﰅ﴾ [األنبياء • اختبار اهلل تعالى عباده بإيجاد الموت والحياة؛ ليرى منهم أيهم أكثر استعدادًا • اختبار اهلل تعالى عباده بالمصائب تارةً، وبالنِّعَم أُخرى؛ لينظر من يشكر، ومن يكفر، ومن يصرب، ومن يقنط، قال تعالى: ﭐ﴿ﯺ ﯻ ﯼ ﯽﯾ ].35 :ﯿ ﰀ ﰁ ﰂﰃ ﰄ ﰅ﴾ [األنبياء للموت، وأسرع إلى طاعة ربه، قال تعالى: ﭐ﴿ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ].2 :ﭡ ﭢﭣ ﭤ ﭥ ﭦ﴾ [الملك للموت، وأسرع إلى طاعة ربه، قال تعالى: ﭐ﴿ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ].2 :ﭡ ﭢﭣ ﭤ ﭥ ﭦ﴾ [الملك • اختبار اهلل تعالى كل نفس مؤمنة أو كافرة يف موقف الحساب يوم القيامة على ما عملت من خير أو شر، وترى الجزاء المناسب عن كل عمل؛ ليقضى اهلل بينهم بقضائه العادل، قال تعالى: ﴿ﮦ ﮧ ﮨ ﮩ ﮪ ﮫﮬ ﮭ ﮮ ﮯ ﮰ ﮱﯓ ]. :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: 9 :]، وقوله: ﴿ﭸ ﭹ ﭺ﴾ [الطارق30 :ﯔ ﯕ ﯖ ﯗ ﯘ﴾ [يونس • اختبار اهلل تعالى عباده عن طريق خلق السموات واألرض، وكسوهتما بالزينة، وترتيبه فيهما جميع ما يحتاجون إليه من أسباب المعاش؛ ليتميز المطيع من العاصي، فيثيب المطيعين، ويعاقب العاصين، قال تعالى: ﭐ﴿ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ]، وقوله: ﭐ﴿ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ 7 :ﭲ ﭳﭴ﴾ [هود ].7 :ﭹ ﭺ﴾ [الكهف • اختبار اهلل تعالى بني اسرائيل بنعمة اإلنجاء من آل فرعون بعدما كانوا فيه من العذاب؛ ألجل استخراج الشُّ كر على المسارِّ، قال تعالى: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜﭝ ﭞ ﭟ ]. :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: 6 :]، [إبراهيم141 :]، [األعراف49 :ﭠ ﭡ ﭢ ﭣ﴾ [البقرة • اختبار اهلل تعالى بني إسرائيل بظهور السَّ مك يف اليوم المحرم عليهم صيده؛ ليرتتب الجزاء على عملهم بسبب فسقهم المستمر عن أمر رهبم، وتعديهم حدود شرعه، قال تعالى: ﭐ﴿ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ ﯛ ﯜ ﯝ ﯞ ﯟﯠ ﯡ ].163 :ﯢﯣ ﯤ ﯥ ﯦ ﯧ ﯨ﴾ [األعراف و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا • اختبار اهلل تعالى بني إسرائيل بالنِّعَم والنِّقَم؛ رجاء أن يرجع العصاة منهم إلى طاعة رهبم، ويرتكوا ما نُهوا عنه من المعاصي والسيئات حين يرون حسن حال الصالحين، وسوء حال من هم دون ذلك، قال تعالى: ﭐ﴿ﮧ ].168 :ﮨ ﮩ ﮪ ﮫ﴾ [األعراف • اختبار اهلل تعالى بني إسرائيل بالحُجج والرباهين وخوارق العادات الدالة على صدق رسلهم؛ ليتميز الخبيث من الطيب، والكافر من المؤمن، قال ].33 :تعالى: ﭐ﴿ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ ﯛ﴾ [الدخان • اختبار اهلل تعالى عباده المؤمنين بنعمة النصر والغنيمة يوم بدر؛ إلظهار الشُّ كر منهم، قال تعالى: ﴿ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝﭞ ﭟ ﭠ ].17 :ﭡ ﭢ ﭣﭤ ﭥ ﭦ ﭧ ﭨ﴾ [األنفال • اختبار اهلل تعالى عباده المؤمنين بنعمة النصر والغنيمة يوم بدر؛ إلظهار الشُّ كر منهم، قال تعالى: ﴿ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝﭞ ﭟ ﭠ ].17 :ﭡ ﭢ ﭣﭤ ﭥ ﭦ ﭧ ﭨ﴾ [األنفال • اختبار اهلل تعالى عباده المؤمنين بأمره إياهم بالوفاء والعهد، وأال يغدروا لكثرهتم، وقلة أعدائهم، ﴿ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗﯘ ﯙ ﯚ ﯛ ﯜﯝ﴾ ].92 :[النحل • اختبار اهلل تعالى عباده المؤمنين بأمره إياهم بالوفاء والعهد، وأال يغدروا لكثرهتم، وقلة أعدائهم، ﴿ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗﯘ ﯙ ﯚ ﯛ ﯜﯝ﴾ ]. :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: 92 :[النحل • اختبار اهلل تعالى عباده المسلمين بقليل من الضَّ رَّ اء؛ ألجل استخراج الصَّ رب على المضارِّ، قال تعالى: ﴿ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ].155 :ﭨ ﭩﭪ ﭫ ﭬ﴾ [البقرة • اختبار اهلل تعالى عباده المسلمين بقليل من الضَّ رَّ اء؛ ألجل استخراج الصَّ رب على المضارِّ، قال تعالى: ﴿ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ].155 :ﭨ ﭩﭪ ﭫ ﭬ﴾ [البقرة • اختبار اهلل تعالى عباده فيما آتاهم من الشرائع مختلفة؛ ليثيبهم على طاعته أو يعاقبهم على معصيته، قال تعالى: ﴿ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ].48 :ﮧ ﮨ ﮩ ﮪﮫ﴾ [المائدة • اختبار اهلل تعالى عباده فيما آتاهم من الشرائع مختلفة؛ ليثيبهم على طاعته أو يعاقبهم على معصيته، قال تعالى: ﴿ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ].48 :ﮧ ﮨ ﮩ ﮪﮫ﴾ [المائدة • اختبار اهلل تعالى عباده المسلمين بإرسال شيء كثير من الصيد يف الوقت • اختبار اهلل تعالى عباده المسلمين باألمر بالجهاد ونحوه من التكاليف الشَّ اقة؛ حتى يتميز قويُّ اإليمان من ضعيفه، والصادق من المنافق، والمجاهد من المتخلف، قال تعالى: وقوله: ﭐ﴿ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ]، وقوله: ﭐ﴿ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ 4 :ﮠ﴾ [محمد ].31 :ﭦ ﭧ﴾ [محمد • اختبار اهلل تعالى مشركي قريش بالقحط والجوع بعد جحودهم لنعمة الخير، وتكذيبهم لرسول |، كما اخترب من قبلهم أصحاب الجنة، بأن دمَّرها تدميرً ا، قال تعالى: ﭐ﴿ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ﴾ ].17 :[القلم . :ايالمبحث الثاني مقاصد البالء يف القرآن الكريم ليس من شكٍّ أنَّ البالء بالخير والشَّ رِّ الذي ينزل على النَّاس ال يخلو من مقاصد وغايات وحِكَم وأغراض، عَلِمَها من عَلِم، وجَ هِلَها من جَ هِل، فما علمناه سيأيت الحديث عنه يف هذا المبحث، وأمَّا ما جهلناه فكثير جدًّا وَفقًا التِّساع معلومات اهلل × وحِكَمِه، وإهنا غير متناهية، ولذا قال اهلل تعالى: ﴿ﯷ ﯸ ﯹ ]، وقد ضرب اهلل مثلً على اتِّساع علمه وحكمته بأنَّه لو 85 :ﯺ ﯻ ﯼ﴾ [اإلسراء كُتِبَ علم اهلل بمداد البحر الندثر البحر ولم يندثر علم اهلل، فقال تعالى ذكره: ﴿ﯱ ] 109 :ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ﴾ [الكهف (، ونظيره قوله تعالى: ﴿ﯳ ((»والمراد بكلمات ربي: «كالم اهلل، وعِلْمه، وحِكْمته ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃﰄ ﰅ ]. ويهدف هذا المبحث إلى تبصير النَّاس بمقاصد 27 :ﰆ ﰇ ﰈ﴾ [لقمان البالء الواردة يف القرآن الكريم؛ حتى يحسن تعاملهم مع هذه السُّ نَّة الكونيَّة، وذلك باستحضار قول اهلل تعالى: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞﭟ ﭠ ﭡ ﭢ ﭣ ]. 216 :ﭤ ﭥ ﭦﭧ ﭨ ﭩ ﭪ ﭫ ﭬ﴾ [البقرة ويتضمَّن هذا المبحث اثني عشر مطلبًا، هي: المطلب األوَّل: البالء بمقصد تحقيق العبادة هلل وحده. .)251/5( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( ليس من شكٍّ أنَّ البالء بالخير والشَّ رِّ الذي ينزل على النَّاس ال يخلو من مقاصد وغايات وحِكَم وأغراض، عَلِمَها من عَلِم، وجَ هِلَها من جَ هِل، فما علمناه سيأيت الحديث عنه يف هذا المبحث، وأمَّا ما جهلناه فكثير جدًّا وَفقًا التِّساع معلومات اهلل × وحِكَمِه، وإهنا غير متناهية، ولذا قال اهلل تعالى: ﴿ﯷ ﯸ ﯹ ]، وقد ضرب اهلل مثلً على اتِّساع علمه وحكمته بأنَّه لو 85 :ﯺ ﯻ ﯼ﴾ [اإلسراء كُتِبَ علم اهلل بمداد البحر الندثر البحر ولم يندثر علم اهلل، فقال تعالى ذكره: ﴿ﯱ ] 109 :ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ﴾ [الكهف (، ونظيره قوله تعالى: ﴿ﯳ ((»والمراد بكلمات ربي: «كالم اهلل، وعِلْمه، وحِكْمته ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃﰄ ﰅ ]. ويهدف هذا المبحث إلى تبصير النَّاس بمقاصد 27 :ﰆ ﰇ ﰈ﴾ [لقمان البالء الواردة يف القرآن الكريم؛ حتى يحسن تعاملهم مع هذه السُّ نَّة الكونيَّة، وذلك باستحضار قول اهلل تعالى: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞﭟ ﭠ ﭡ ﭢ ﭣ ]. :المطلب الثامن تحليل نتائج الرُّ سومات البيانية: ونالحظ أيضا أن مصدر «االبتالء» باشتقاقاته المختلفة ضُ مِّن يف تسعة 12 :محاور رئيسة يف القرآن، هي بما كلفه به من األوامر والنواهي، فقام هبا كلها، + • اختبار اهلل تعالى إبراهيم ].124 :قال تعالى: ﭐ﴿ﮥ ﮦ ﮧ ﮨ ﮩ ﮪﮫ﴾ [البقرة بما كلفه به من األوامر والنواهي، فقام هبا كلها، + • اختبار اهلل تعالى إبراهيم ].124 :قال تعالى: ﭐ﴿ﮥ ﮦ ﮧ ﮨ ﮩ ﮪﮫ﴾ [البقرة • اختبار اهلل تعالى جنود طالوت قبل مالقاهتم جالوت وجنوده؛ حتى يتميز من يصرب على الحرب ممن ال يصرب، قال تعالى: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ].249 :ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨﭩ﴾ [البقرة و نطاومو ءالبلا ف يرعتو ةينآرقلا دصاقملا فيرعت :لوألا ثحبملا • اختبار اهلل تعالى المسلمين بنزول األحزاب حول المدينة وهم محصورون يف غاية الجهد والضيق؛ ليظهر المخلص من المنافق، والراسخ من المتزلزل، قال تعالى: ﭐ﴿ﱼ ﱽ ﱾ ﱿ ﲀ ﲁ ﲂ ﲃ ﲄ ].11-10 :ﲅ ﲆ ﲇ ﲈ ﲉ ﲊ ﲋ﴾ [األحزاب • اختبار اهلل تعالى المسلمين بألوان المصائب؛ ليتميز الصادق من المنافق، والصابر من المضطرب، والثابت من الخائف، قال تعالى: ﭐ﴿ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ].186 :ﯧ ﯨ ﯩ ﯪﯫ﴾ [آل عمران • اختبار اهلل لألوصياء حول اليتامى المقاربين للرشد بدفع شيء من أموالهم؛ حتى يتبين بذلك رشدهم من سفههم، قال تعالى: ﴿ﯥ ﯦ ﯧ ﯨ ﯩ ].6 :ﯪ ﯫ ﯬ ﯭ ﯮ ﯯ ﯰ ﯱ﴾ [النساء بتكذيب قومه وأذاهم إياه والمؤمنين معه؛ ليميز + • اختبار اهلل تعالى نوحً ا اهلل للناس الخبيث من الطيب، قال تعالى: ﴿ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ].30-29 :ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ﴾ [المؤمنون • اختبار اهلل اإلنسان بالتكاليف، بعد إرشاده إلى طريق الحق وتزويده بالعقل؛ للتفكر يف آيات اهلل الدالة على وحدانيته، قال تعالى: ﭐ﴿ﯨ ﯩ ﯪ ﯫ ﯬ ].2 :ﯭ ﯮ ﯯ ﯰ ﯱ﴾ [االنسان ،• اختبار اهلل تعالى اإلنسان بالسعة والضِّ يق؛ ليستخرج منه الشُّ كر والصَّ رب والكفر والجزع، قال تعالى: ﴿ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ].16-15 :ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ﴾ [الفجر ،• اختبار اهلل تعالى اإلنسان بالسعة والضِّ يق؛ ليستخرج منه الشُّ كر والصَّ رب والكفر والجزع، قال تعالى: ﴿ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ].16-15 :ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ﴾ [الفجر ،• اختبار اهلل تعالى اإلنسان بالسعة والضِّ يق؛ ليستخرج منه الشُّ كر والصَّ رب والكفر والجزع، قال تعالى: ﴿ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ].16-15 :ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ﴾ [الفجر ،• اختبار اهلل تعالى اإلنسان بالسعة والضِّ يق؛ ليستخرج منه الشُّ كر والصَّ رب والكفر والجزع، قال تعالى: ﴿ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ].16-15 :ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ﴾ [الفجر ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف :المطلب األوَّ ل َ البالء بمقصد تحقيق العبادة لله وحده :ايالمبحث الثاني 216 :ﭤ ﭥ ﭦﭧ ﭨ ﭩ ﭪ ﭫ ﭬ﴾ [البقرة .)251/5( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .المطلب الثاين: البالء بمقصد استخراج التوكُّل المطلب الثَّالث: البالء بمقصد استخراج الدُّعاء. المطلب الرَّ ابع: البالء بمقصد استخراج الصَّ رب. المطلب الخامس: البالء بمقصد استخراج الرِّ ضا. المطلب السَّ ادس: البالء بمقصد استخراج الشُّ كر. المطلب السَّ ابع: البالء بمقصد استخراج التَّوبة. المطلب الثَّامن: البالء بمقصد الرَّ حمة. المطلب التَّاسع: البالء بمقصد التَّمحيص. المطلب العاشر: البالء بمقصد االستدراج. المطلب الحادي عشر: البالء بمقصد التَّخويف. المطلب الثَّاين عشر: البالء بمقصد العقوبة. .المطلب الثاين: البالء بمقصد استخراج التوكُّل المطلب الثَّالث: البالء بمقصد استخراج الدُّعاء. المطلب الرَّ ابع: البالء بمقصد استخراج الصَّ رب. المطلب الخامس: البالء بمقصد استخراج الرِّ ضا. المطلب السَّ ادس: البالء بمقصد استخراج الشُّ كر. المطلب السَّ ابع: البالء بمقصد استخراج التَّوبة. المطلب الثَّامن: البالء بمقصد الرَّ حمة. المطلب التَّاسع: البالء بمقصد التَّمحيص. المطلب العاشر: البالء بمقصد االستدراج. المطلب الحادي عشر: البالء بمقصد التَّخويف. المطلب الثَّاين عشر: البالء بمقصد العقوبة. البالء بمقصد تحقيق العبادة لله وحده وردت مادة «عبد» يف مائتين وخمسة وسبعين موضعًا من آي الذِّكر الحكيم، (. ((بصياغات واشتقاقات مختلفة «العبادة» مصدر الفعل الثالثي: عَبَدَ، يَعبُد، عِبادةً، وعُبُوديَّةً، فهو عابِد، والمفعول مَعْبود، ويف معاين القرآن: «العبادة يف اللغة: الطاعة مع الخضوع، ومنه ]، أي: 5 :طريق مُعَبَّدٌ، إذا كان مذلَّلً بكثرة الوطءِ، فمعنى: ﭐ﴿ﭢ ﭣ﴾ [الفاتحة ]، أي: «أطاع 60 :نطيعُ الطَّاعة التي نخضع معها، وقوله: ﴿ﮇ ﮈﮉ﴾ [المائدة (، ويف الصِّ حاح: «وأصل العبودية الخضوع ((»الشَّ يطان فيما سوَّل له وأغراه به والذل، والتعبيد: التذليل، يقال: طريق مُعَبَّد، والبعير المعبد: المهنوء بالقطران (، وجاء يف اللِّسان أنَّ: «أصل العبوديَّة الخضوع ((»المذلل، والتعبد: التنسك (، ومعنى ((»والتذلُّل، فالن عابد، وهو الخاضع لربِّه المستسلم المُنقاد ألمره العبادة يف اصطالح المفسِّ رين هي: «الخضوعُ هلل بالطاعة، والتذلل له باالستكانة، (، وعرَّ فها آخر بأهنا: «اسم جامع لكل ما يحبُّه ((»واإلقرار له بالربوبية، ال لغيره (، ويقول غيره: هي: ((»اهلل تعالى ويرضاه من األقوال واألعمال الباطنة والظاهرة .)445-441 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)187/2( ،)48/1( ( معاين القرآن وإعرابه، للزجاج(( .)503-502/2( ( الصحاح تاج اللغة وصحاح العربية، للجوهري(( .)12-10/9( ( لسان العرب، البن منظور(( .)362 و155/1( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)20 ( العبودية، البن تيمية (ص(( .)445-441 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)187/2( ،)48/1( ( معاين القرآن وإعرابه، للزجاج(( .)503-502/2( ( الصحاح تاج اللغة وصحاح العربية، للجوهري(( .)12-10/9( ( لسان العرب، البن منظور(( .)362 و155/1( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)20 ( العبودية، البن تيمية (ص(( ،(، ويقول آخر: هي: «إفراد اهلل بالعبادة((»«التعظيم ألمر اهلل والشَّ فقة على خلق اهلل (، هذا وإنَّ المعنى الذي تدلُّ عليه العبادة يف اللُّغة هو ((»أي االعرتاف بوحدانيته الطاعة، مع الخضوع، والتذلُّل، واالنقياد، واالستسالم طوعًا، أو كرهًا، غير أنَّ العبادة يف االصطالح ال تقتصر على هذه المعاين فحسب، وإنَّما تشتمل على معنى الحبِّ أيضً ا، فهي تتضمَّن غاية الذُّلِّ هلل، وغاية المحبَّة له، وغاية االتِّباع له، وغاية التديُّن له، وغاية االنقياد لشرعه، وغاية الخضوع لمشيئته، فيجب أن يكون اهلل أحبَّ إلى العبد من كلِّ شيء، وأن تكون شريعة اهلل أحبَّ إلى العبد من كلِّ الشَّ رائع. البالء بمقصد تحقيق العبادة لله وحده لذا يقول شيخ اإلسالم ابن تيمية &: «العبادة المأمور هبا تتضمَّن معنى الذُّلِّ ومعنى الحبِّ ، فهي تتضمَّن غاية الذُّلِّ هلل بغاية المحبَّة له، ومَن خضع إلنسان مع بغضه له ال يكون عابدًا له، ولو أحبَّ شيئًا ولم يخضع له لم يكن عابدًا له، كما قد يحبُّ ولده وصديقه، ولهذا ال يكفي أحدهما يف عبادة اهلل تعالى، بل يجب أن يكون اهلل أحبَّ إلى العبد من كلِّ شيء، وأن يكون اهلل عنده أعظم من كلِّ شيء، بل اليستحقُّ (، ومن هنا يمكننا تعريف العبادة على أهنا: إفرادُ ((المحبَّة والخضوع التَّامَّ إال اهلل من بيده األمر سبحانه بالطَّاعة، قولً وفعلً واعتقادًا، مع غاية الخضوع والمحبَّة له، وال يُشرَ كُ معه يف الطَّاعة غيره؛ ألنَّ غيره ليس بيده األمر، وامتثالُ جميع تكاليفه التشريعية من األوامر، والنَّواهي، وإرضاؤه. البالء بمقصد تحقيق العبادة لله وحده َأ لقد بيَّن اهلل تعالى المقصد األسنى من العبادة فقال: ﴿ﮜ ﮝ ﮞ ﮟ ]، وجملة قوله: ﴿ﮥ ﮦ﴾ 21 :ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ﴾ [البقرة تعليل لألمر بـ ﴿ﮞ﴾، والمعنى: «لتتقوا سَ خَطه وغضَ به أن يَحلَّ عليكم، ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، وهذا دليل على أنَّ ترك الخضوع((»وتكونُوا من المتقين الذين رضي عنهم رهبم هلل بالطاعة واإلقرار له بالوحدانية موجب للقوارع والجوائح والمصائب التي تصيب بعض بني البشر، ويؤيِّد هذا ما أخرب اهلل تعالى به يف مواضع من كتابه عن سُ نته يف األمم المستنكفة عن طاعته والمكذبة برسله كيف أنه أبادهم بأنواع من المصائب، يقول تعالى: ﭐ﴿ﭠ ﭡ ﭢﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴﭵ ﭶ ﭷ ﭸ ]، وقوله: ﭐ﴿ﭤ ﭥ ﭦ 40 :ﭹ ﭺ ﭻ ﭼ ﭽ﴾ [العنكبوت (، وقوله: ﭐ﴿ﭩ ﭪ ﭫ ﭬ﴾ ((»ﭧ ﭨ﴾ أي: «وهم قوم لوط (، وقوله: ﭐ﴿ﭭ ﭮ ﭯ ﭰ ﭱ﴾ أي: ((»أي: «وهم قوم ثمود، ومدين (، وقوله: ﭐ﴿ﭲ ﭳ ﭴﭵ﴾ أي: «قوم نوح وفرعون ((»«وهم قارون وأصحابه (، وقد دلَّت آيات كثيرة يف القرآن الكريم على النتائج السيِّئة، والعواقب ((»وقومه الوخيمة النَّاشئة عن اإلعراض عن طاعة اهلل جل وعزَّ ، أو الشَّ كِّ فيها، أو اإلشراك فيها، فمنها اإلنذار بالصَّ اعقة، كما قال تعالى: ﴿ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ]، ومنها الوعيد 14-13 :ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ﴾ [فصلت بالمعيشة الضيِّقة المليئة بالهموم، والغموم، واألحزان، وسوء العاقبة كما قال ] 124 :تعالى: ﴿ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ﴾ [طه .)364/1( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)169/4( ،( معاين القرآن وإعرابه، للزجاج(( .)169/4( ( معاين القرآن وإعرابه، للزجاج(( .)169/4( ( المرجع السَّ ابق(( .)37/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( ي .)169/4( ( المرجع السَّ ابق(( َ .)37/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( ومنها هتيئة القرناء من الشياطين، كما قال تعالى: ﴿ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ]، ومنها الطَّبع، والختم، والوقر، والغشاوة، واألكنَّة 36 :ﭭ ﭮ ﭯ ﭰ﴾ [الزخرف المانعة من فهم ما ينفع، كما قال تعالى: ﭐ﴿ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠﮡ ﮢ ﮣ ]، ومنها الخسران يف الدُّنيا، واآلخرة، 57 :ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ﴾ [الكهف لقوله تعالى: ﴿ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜﮝ ﮞ ﮟ ﮠ ﮡ ﮢﮣ ﮤ ﮥ ﮦ ]، وقوله: ﴿ﮞ 11 :ﮧ ﮨ ﮩ ﮪ ﮫ ﮬﮭ ﮮ ﮯ ﮰ ﮱ﴾ [الحج (، وقوله: ﴿ﮤ ﮥ ((»ﮟ ﮠ﴾ فمعناه: «صحَّة يف جسمه وسعة يف معيشته (، قال المفسرون: «نزلت ((»ﮦ﴾، فمعناه: «شرٌّ وبالء يف جسده وضيق يف معيشته يف أعراب كانوا يقدمون على رسول اهلل | المدينة مهاجرين من باديتهم، وكان أحدهم إذا قدم المدينة، فإن صحَّ هبا جسمه، ونتجت فرسه مُهرً ا حسنًا، وولدت امرأته غالمًا، وكثر ماله وماشيته، رضي عنه واطمأنَّ، وقال: ما أصبت منذ دخلت يف ديني هذا إلَّ خيرً ا، وإن أصابه وجع المدينة، وولدت امرأته جارية، وأجهضت رِمَاكُهُ، وذهب ماله، وتأخَّ رت عنه الصَّ دقة، أتاه الشَّ يطان فقال: واهلل ما أصبت منذ كنت على دينك هذا إال شرًّ ا، فينقلب على دينه، فأنزل اهلل تعالى: ﴿ﮖ ﮗ ﮘ ﮙ (. البالء بمقصد تحقيق العبادة لله وحده واآليات بمثل ذلك كثيرة جدًّا. ((»﴾ﮚ ﮛ ﮜﮝ ًآ وأمَّا التَّائبون إلى اهلل، والخاضعون لطاعته؛ فينجيهم بذلك من مصائب الدُّنيا، .)430/2( ( مدارك التنزيل وحقائق التأويل، للنسفي(( .)430/2( ( المرجع السابق(( )، وأخرج معناه البخاري: كتاب تفسير القرآن، باب ﴿ﮖ307/1( ( أسباب نزول القرآن، للواحدي(( ] شك، ﴿ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜﮝ ﮞ ﮟ ﮠ ﮡ ﮢﮣ11 :ﮗ ﮘ ﮙ ﮚ ﮛ ﮜﮝ﴾ [الحج ). 4742( ]، برقم11 :ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ﴾ [الحج .)430/2( ( مدارك التنزيل وحقائق التأويل، للنسفي(( .)430/2( ( المرجع السابق(( )، وأخرج معناه البخاري: كتاب تفسير القرآن، باب ﴿ﮖ307/1( ( أسباب نزول القرآن، للواحدي(( ] شك، ﴿ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜﮝ ﮞ ﮟ ﮠ ﮡ ﮢﮣ11 :ﮗ ﮘ ﮙ ﮚ ﮛ ﮜﮝ﴾ [الحج ). 4742( ]، برقم11 :ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ﴾ [الحج ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف الذين آمنوا قبل نزول+ ويرفع عنهم شدائدها، كما أخرب تعالى عن قوم يونس العذاب، فنفعهم إيماهنم، كما قال تعالى: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ]، 98 :ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ﴾ [يونس وقال ابن تيمية &: «ومن تدبَّر أحوال العالم، وجد كلَّ صالح يف األرض؛ فسببه توحيد اهلل، وعبادته، وطاعة رسوله |، وكلَّ شرٍّ يف العالم، وفتنة، وبالء، وقحط، وتسليط عدوٍّ، وغير ذلك؛ فسببه مخالفة الرَّ سول |، والدَّعوة إلى غير (. ومن المواقف العمليَّة التي كان يستعين هبا رسول اهلل | على مواجهة ((»اهلل ، قال: «كان # األحداث المفاجئة، اإلسراع إلى عبادة الصَّ الة، فرُ وي عن حذيفة (، ورُوي أيضً ا عن أبي الدَّرداء وأبي ذرٍّ ^، عن ((»النبي | إذا حزبه أمر، صلى أنه قال: «ابن آدم، اركع لي أربع ركعات من أول النهار، I رسول اهلل |، عن اهلل (. ((»أكفِكَ آخره .)25/15( ( الفتاوى الكربى، البن تيمية(( ( أخرجه أبو داود يف سننه: كتاب الصالة، أبواب قيام الليل، باب وقت قيام النبي | من الليل برقم(( )، كما أخرجه: أحمد يف مسنده: أحاديث رجال من أصحاب النبي |، حديث حذيفة بن1319( .)1319( ). البالء بمقصد تحقيق العبادة لله وحده وحسَّ نه األلباين يف صحيح وضعيف سنن أبي داود برقم23297( اليمان عن النبي | برقم ( أخرجه الرتمذي يف سننه: أبواب الوتر، باب ما جاء يف صالة الضحى، كما أخرجه الطرباين يف (( معجمه: باب الصاد، القاسم بن عبد الرحمن بن يزيد الشامي مولى معاوية، عن أبي أمامة، برقم ).475( :)، وصحَّ حه األلباين يف صحيح وضعيف سنن الرتمذي برقم7746( :المطلب الثَّاني البالء بمقصد استخراج التوكُّ ل لقد ورد لفظ «التوكُّل» يف سبعين موضعًا من آي الذِّكر الحكيم بصياغات (. ((واشتقاقات مختلفة «التوكُّل» مصدر الفعل الثالثي وَكَلَ ، ولكن زِيد فيه تاء يف أوَّله، وضُ عِّفَت عينُه يف وسطه؛ ليصير على وزن تفعَّل، وهي صيغة الفعل الثالثي المزيد بحرف: توكَّلَ ، يتوكَّل، توكُّلً ، فهو متوكِّل، والمفعول مُتوكَّل عليه، وأصل التوكل يف اللُّغة مركَّب من: «(وَكَلَ ) الواو والكاف والالم: أصل صحيح يدلُّ على إظهار العجز يف األمر (، والتوكُّل يف اصطالح المفسِّ رين هو: «التعويل على من ((»واالعتماد على غيرك يدبِّر أمره، وفيه مالحظة عظمة اهلل وقدرته، واعتقاد الحاجة إليه، وعدم االستغناء (. والحاصل أنَّ التوكُّل هو: عمل قلبيٌّ ، يستشعر العبد من خالله شدَّة حاجته ((»عنه إلى اهلل يف تدبير جميع أموره، وذلك باالعتماد عليه وحده، وقد يصاحب هذا االفتقار القول باللِّسان (حسبنا اهلل ونعم والوكيل)، كما قد يصاحبه دعاء التوكُّل المعروف بصالة االستخارة. البالء بمقصد تحقيق العبادة لله وحده اا إنَّ القرآن الكريم مملوء بالحديث عن موضوع التوكُّل، وحثِّ العباد على التحلِّي به، ومن مقاصد البالء؛ هو إظهار المبتَلَى عجزه يف دفع البالء الذي ألَمَّ I به من جهة، ومن جهة ثانية إظهار المبتَلَى اعتماده وحاجته وافتقاره إلى اهلل ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف َّل وحده ألن ذا قال ت الى: ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف َأ َّوحده لتدبير أمره، ومن جهة أخرى اإلخالص يف إسناد األمور إلى اهلل وحده ألن تفويضها إلى غير اهلل ليس من الهدى، وال يليق مع مقام التوحيد، ولهذا قال تعالى: ]، ومعنى الوكيل هو: «من يتوكل عليه، 2 :﴿ﭯ ﭰ ﭱ ﭲ ﭳ﴾ [اإلسراء ، F فتفوَّض األمور إليه، ليأيت بالخير، ويدفع الشر، وهذا ال يصح إال هلل وحده ، F ولهذا حذَّر من اتخاذ وكيل دونه، ألنه ال نافع وال ضارَّ، وال كايف إلَّ هو وحده (.((»عليه توكَّلنا، وهو حسبنا ونعم الوكيل ]، 80 :: ﭐ﴿ﯰ ﯱ ﯲ ﯳ﴾ [الشعراء+ كان من دعاء إبراهيم الخليل (، ويالحظ يف اآلية خُ لُق ((»والمعنى: «وإذا سقم جسمي واعتلَّ ، فهو يُربئه ويعافيه نسب المرض إلى نفسه، ولم ينسبه + األدب يف التخاطب مع اهلل؛ حيث إنَّ إبراهيم ، هذا ووجه الداللة يف اآلية أنَّ اهلل يبتلي عباده بالمرض، والجراحة، واأللم F إلى ربِّه يف الجسد؛ ألجل أن يتوكَّلوا عليه وحده يف دفعها؛ لذا ينبغي للمريض أن يتوكَّل على اهلل خالق األسباب، وألَّ يتعلَّق قلبه باألسباب، كالمستشفيات واألطباء، والواجب أن يكون تعلُّق القلب بالذي أنزل الدَّاء والدَّواء، فالذي أنزل المرض قادر على أن يرفعه، لذا قال اهلل تعالى: ﭐ﴿ﯯ ﯰ ﯱ ﯲ ﯳ ﯴ ﯵ ﯶ ﯷﯸ ﯹ ﯺ ﯻ ]. 17 :ﯼ ﯽ ﯾ ﯿ ﰀ﴾ [األنعام هذا وإنَّ التوكُّل على اهلل تبارك أعلى مقامات التوحيد؛ لِمَا فيه من بَوْء العبد بعجزه يف مدافعة المضارِّ إال بإذن اهلل تعالى، قال سعيد بن جبير: «التوكُّل على اهلل (، ولهذا عُدَّ التوكل عملً قلبيًّا، فهو ليس بقول اللِّسان، وال بعمل ((»جِماع اإليمان (. وال يكون التوكُّل كاملً، إلَّ بعد((الجوارح، كما عبَّر بذلك ابن القيم يف المدارج بذل الجهد المادِّي، والجهد المعنوي يف دفع المضارِّ، أو تدبير األمور، والجهد المادِّي يعبَّر عنه باتخاذ األسباب الماديَّة، مثل طلب العالج لمن ابتُلِي بالمرض، أو طلب الرزق لمن ابتُلِي بالفقر، وغير ذلك، أما الجهد المعنوي فيعبَّر عنه باتِّخاذ األسباب المعنوية المكمِّلة للتوكُّل، مثل: الدُّعاء، والتضرُّ ع إلى اهلل، وحسن الظنِّ به، واالستغاثة به، وصدق االفتقار، واللَّجء، والرَّ غبة، والرَّ هبة إليه، وغير ذلك. البالء بمقصد تحقيق العبادة لله وحده ومن أجمل معاين التوكُّل على اهلل، واالستعانة به وحده وقت الشِّ دَّة؛ موقف النبي |، وصحابته رضوان اهلل عليهم يف غزوة حمراء األسد؛ حيث يخربنا القرآن الكريم أن المشركين توعَّدوا النبي محمدًا |، وصحبه رضوان اهلل عليهم؛ بالقتل واألسر واألذى، وخوَّفوهم بكثرة العدد، وشدَّة البطش، فلم يكرتثوا لذلك، بل توكَّلوا على اهلل، واستعانوا به، يقول اهلل تعالى: ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ]، وقد صحَّ عن ابن 173 :ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ﴾ [آل عمران حين أُلقي يف النَّار، وقالها + عباس ^: حَ سْ بُنَا اهَّللُ وَنِعْمَ الْوَكِيلُ ، «قالها إبراهيم محمد |» حين قالوا: ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ (، وكذلك موقف النبي |، وصحابته (( ]173 :ﰄ ﰅ ﰆ﴾ [آل عمران رضوان اهلل عليهم، يف غزوة األحزاب، حيث يصوِّر لنا القرآن الكريم تلك السَّ اعات العصيبة التي عاشها المسلمون وقتذاك، يقول اهلل تعالى: ﭐ﴿ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ]، وقوله: ﭐ﴿ﮗ ﮘ ﮙ 11 - 10 :ﮗ ﮘ ﮙ ﮚ ﮛ﴾ [األحزاب .)114/2( ( مدارج السالكين بين منازل إياك نعبد وإياك نستعين، البن القيم(( ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب ﭐ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ﴾ اآلية(( .)4563( ]، برقم173 :[آل عمران 72 ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،(((»وفُتِنوا ،(((»ﮚ ﮛ﴾ فمعناه: «مُحِّصوا، وحُ رِّ كوا بالفتنة تحريكًا شديدًا، وابتُلوا وفُتِنوا ويف هذا الجوِّ العصيب، يخربنا اهلل تعالى أنَّ المؤمنين الصَّ ادقين بوعد اهلل، وبنصر رسالته، توكَّلوا على اهلل حقَّ توكُّله، فبذلوا النّفس والنّفيس يف سبيل نصرة الدِّين فقال: ﭐ﴿ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍﰎ ﰏ ]، وعن ابن رومان قوله: ﭐ﴿ﰏ ﰐ ﰑ 22 :ﰐ ﰑ ﰒ ﰓ﴾ [األحزاب ﰒ ﰓ﴾ قال: «صربًا على البالء، وتسليمًا للقضاء، وتصديقًا بتحقيق ما (، وقد صحَّ عن عبد اهلل بن أبي أوىف ^ قوله: دعا ((»كان اهلل وعدهم ورسوله رسول اهلل | يوم األحزاب على المشركين، فقال: «اللهم منزل الكتاب، سريع (. البالء بمقصد تحقيق العبادة لله وحده ومن التَّطبيقات ((»الحساب، اللهم اهزم األحزاب، اللهم اهزمهم وزلزلهم العمليَّة للتوكُّل ما سنَّه النبيُّ | ألمَّته يف دعاء التوكُّل المعروف بصالة االستخارة، وهما ركعتان يصلِّيهما المسلم إذا احتار بين أمرَ يْن أيَّهما يختار، داعيًا اهلل بدعاء مخصوص أن يوفِّقه إلى خير األمرين، وصالة االستخارة هي بمثابة التوكُّل العملي ، قال: كان النَّبيُّ | يعلِّمنا االستخارة يف األمور كلِّها، # على اهلل، فعن جابر كالسُّ ورة من القرآن: «إذا همَّ باألمر فليركع ركعتَيْن ثم يقول: اللَّهمَّ إين أستخيرك بعلمك، وأستقدرك بقدرتك، وأسألك من فضلك العظيم، فإنَّك تقدر وال أقدر، وتعلم وال أعلم، وأنت علَّ م الغيوب، اللَّهمَّ إن كنت تعلم أنَّ هذا األمر خير لي فاقدره لي، وإن -أو قال: يف عاجل أمري وآجله- يف ديني ومعاشي وعاقبة أمري أو قال: يف عاجل - كنت تعلم أن هذا األمر شرٌّ لي يف ديني ومعاشي وعاقبة أمري .)222/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)236/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه البخاري يف صحيحه: كتاب الجهاد والسير، باب الدعاء على المشركين بالهزيمة(( .)2933( والزلزلة، برقم فاصرفه عنِّي واصرفني عنه، واقدر لي الخير حيث كان، ثم رضِّ ني-أمري وآجله (. ومن وصايا رسول اهلل | يف أدعية الصَّ باح والمساء، ما ((»به. ويسمِّي حاجته يقول: قال # رواه عثمان بن عبداهلل بن مَوْهَب & قال: سمعت أنس بن مالك رسول اهلل | لفاطمة: «ما يمنعك أن تسمعي ما أوصيك به: أن تقولي إذا أصبحت، وإذا أمسيت: يا حي يا قيوم برحمتك أستغيث، أصلح لي شأين كله، وال تكلني إلى نفسي طرفة عين»، وقال الحاكم: هذا حديث صحيح على شرط الشيخين، ولم (.((يخرجاه فاصرفه عنِّي واصرفني عنه، واقدر لي الخير حيث كان، ثم رضِّ ني-أمري وآجله (. ومن وصايا رسول اهلل | يف أدعية الصَّ باح والمساء، ما ((»به. ويسمِّي حاجته يقول: قال # رواه عثمان بن عبداهلل بن مَوْهَب & قال: سمعت أنس بن مالك رسول اهلل | لفاطمة: «ما يمنعك أن تسمعي ما أوصيك به: أن تقولي إذا أصبحت، وإذا أمسيت: يا حي يا قيوم برحمتك أستغيث، أصلح لي شأين كله، وال تكلني إلى نفسي طرفة عين»، وقال الحاكم: هذا حديث صحيح على شرط الشيخين، ولم (.((يخرجاه :المطلب الثَّالث البالء بمقصد استخراج الدُّ عاء 7 جا لقد ورد لفظ «الدُّعاء» يف مائتين واثني عشر موضعًا من آي الذِّكر الحكيم (. البالء بمقصد تحقيق العبادة لله وحده ((بصياغات واشتقاقات مختلفة و«الدُّعاء» يف اللُّغة مصدر الفعل الثالثي المعتلِّ النَّاقص: دعا، يَدعُو، ادْعُ، دُعَاءً، ودَعْوَةً، ودَعْوَى، فهو داعٍ، والمفعول مَدْعُوٌّ، وأصل الدُّعاء يف اللُّغة مركب من: «(دَعَوَ) الدَّال والعين والحرف المعتل أصل واحد، وهو أن تُميل الشيءَ إليك (، ويف اللِّسان: «الدُّعاء: ((»بصوت وكالم يكون منك، تقول: دعوت أدعو دعاء .)6382( ( أخرجه البخاري يف صحيحه: كتاب الدعوات، باب الدعاء عند االستخارة برقم(( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، وأما حديث(( )، كما أخرجه الطرباين يف معجمه: باب الخاء، من اسمه خالد، برقم2000( رافع بن خديج، برقم ). 227( )، وقد صححه األلباين يف سلسلة األحاديث الصحيحة برقم444( .)260-257 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)136/6( ( معجم مقاييس اللغة، البن فارس(( لقد ورد لفظ «الدُّعاء» يف مائتين واثني عشر موضعًا من آي الذِّكر الحكيم (. ((بصياغات واشتقاقات مختلفة و«الدُّعاء» يف اللُّغة مصدر الفعل الثالثي المعتلِّ النَّاقص: دعا، يَدعُو، ادْعُ، دُعَاءً، ودَعْوَةً، ودَعْوَى، فهو داعٍ، والمفعول مَدْعُوٌّ، وأصل الدُّعاء يف اللُّغة مركب من: «(دَعَوَ) الدَّال والعين والحرف المعتل أصل واحد، وهو أن تُميل الشيءَ إليك (، ويف اللِّسان: «الدُّعاء: ((»بصوت وكالم يكون منك، تقول: دعوت أدعو دعاء .)6382( ( أخرجه البخاري يف صحيحه: كتاب الدعوات، باب الدعاء عند االستخارة برقم(( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، وأما حديث(( )، كما أخرجه الطرباين يف معجمه: باب الخاء، من اسمه خالد، برقم2000( رافع بن خديج، برقم ). 227( )، وقد صححه األلباين يف سلسلة األحاديث الصحيحة برقم444( .)6382( ( أخرجه البخاري يف صحيحه: كتاب الدعوات، باب الدعاء عند االستخارة برقم(( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، وأما حديث(( )، كما أخرجه الطرباين يف معجمه: باب الخاء، من اسمه خالد، برقم2000( رافع بن خديج، برقم ). البالء بمقصد تحقيق العبادة لله وحده 227( )، وقد صححه األلباين يف سلسلة األحاديث الصحيحة برقم444( .)260-257 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)136/6( ( معجم مقاييس اللغة، البن فارس(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف بشر، ومنه الرَّ غبة إلى اهلل ×، دعاه دعاء ودعوى؛ ويقال: دعوت اهلل له بخير وعليه بشر، ومنه (، أي: تحوطهم وتكنفهم وتحفظهم، ((»الحديث: «فإنَّ دعوهتم تحيط من ورائهم ومعنى الدُّعاء هلل على ثالثة أوجه: فضرب منها توحيده والثَّناء عليه، كقولك: يا اهلل، ال إله إال أنت، وكقولك: ربَّنا لك الحمد، إذا قلته فقد دعوته بقولك ربَّنا، ثم أتيت بالثَّناء والتَّوحيد، ومثله قوله: ﴿ﭝ ﭞ ﭟ ﭠ ﭡﭢ ﭣ ﭤ ]؛ فهذا ضرب من الدُّعاء، 60 :ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ﴾ [غافر والضَّ رب الثاين مسألة اهلل العفو والرَّ حمة وما يقرِّ ب منه تعالى، كقولك: اللهمَّ اغفر لنا، والضَّ رب الثالث مسألة الحظِّ من الدُّنيا، كقولك: اللَّهمَّ ارزقني مالً وولدًا، وإنَّما سمِّي هذا جميعه دعاءً ألنَّ اإلنسان يُصَ دِّر يف هذه األشياء بقوله يا اهلل، يا ربِّ ، يا (، أمَّا الدُّعاء يف اصطالح المفسِّ رين فهو: «النِّداء لطلب ((»ًرحمن؛ فلذلك سمِّي دعاء مهمٍّ، واستُعمل مجازًا يف العبادة؛ الشتمالها على الدُّعاء، والطَّلب بالقول، أو بلسان (، ويرى آخر أنَّ الدُّعاء: «يطلق على سؤال العبد ((»الحال، كما يف الرُّ كوع والسُّ جود من اهلل حاجته، وهو ظاهر معناه يف اللُّغة، ويطلق على عبادة اهلل على طريق الكناية؛ ألنَّ العبادة ال تخلو من دعاء المعبود بنداء تعظيمه، والتضرُّ ع إليه، وهذا إطالق أقلُّ ( الحديثه بطوله عن عبدالرحمن بن عبداهلل بن مسعود عن أبيه عن النبي | قال: «نضَّ ر اهلل امرأ(( سمع مقالتي فوعاها وحفظها وبلغها؛ فرُبَّ حامل فقه إلى من هو أفقه منه، ثالث ال يغل عليهن قلب مسلم: إخالص العمل هلل، ومناصحة أئمة المسلمين، ولزوم جماعتهم؛ فإن الدعوة تحيط من ورائهم»، أخرجه الرتمذي يف سننه: أبواب العلم، باب ما جاء يف الحث على تبليغ السماع، برقم )، 3056( )، كما أخرجه ابن ماجه يف سننه: كتاب المناسك، باب الخطبة، يوم النحر برقم2658( .قال األلباين يف صحيح وضعيف الرتمذي: وهذا سند صحيح رجاله كلهم ثقات ).261-257/14( ( لسان العرب، البن منظور(( )182/8(( التحرير والتنوير، البن عاشور(( 75 (، مما سبق من تعريفات للدُّعاء يف اللُّغة واالصطالح يتبيَّن لنا أنَّه((»شيوعًا من األوَّل يدور حول النِّداء لطلب مُهمٍّ، وسؤال العبد من اهلل تعالى حاجته. البالء بمقصد تحقيق العبادة لله وحده ومن حاالت الدُّعاء الت تَظه على الدَّاع يف حال الدُّعاء، مُصَ دَّرًا بع ارات (، مما سبق من تعريفات للدُّعاء يف اللُّغة واالصطالح يتبيَّن لنا أنَّه((»شيوعًا من األوَّل يدور حول النِّداء لطلب مُهمٍّ، وسؤال العبد من اهلل تعالى حاجته. هلومن حاالت الدُّعاء التي تَظهر على الدَّاعي يف حال الدُّعاء، مُصَ دَّرًا بعبارات َّ (، مما سبق من تعريفات للدُّعاء يف اللُّغة واالصطالح يتبيَّن لنا أنَّه((»شيوعًا من األوَّل يدور حول النِّداء لطلب مُهمٍّ، وسؤال العبد من اهلل تعالى حاجته. لهٍِ ومن حاالت الدُّعاء التي تَظهر على الدَّاعي يف حال الدُّعاء، مُصَ دَّرًا بعبارات الثَّناء على اهلل تعالى: لهٍِ ومن حاالت الدُّعاء التي تَظهر على الدَّاعي يف حال الدُّعاء، مُصَ دَّرًا بعبارات الثَّناء على اهلل تعالى: ( بعد الرَّ فع ((»• توحيد اهلل، والثَّناء عليه، كقولك: «اللهمَّ ربَّنا لك الحمد من الرُّ كوع. • سؤال اهلل العفو، والرَّ حمة، والرِّ زق، وما يقرب منه تعالى، كقولك: «اللَّهمَّ ( بين السَّ جدتَيْن.((»َاغفر لي، وارحمني، واهدين، وعافني وارزقني ( بعد الرَّ فع ((»• توحيد اهلل، والثَّناء عليه، كقولك: «اللهمَّ ربَّنا لك الحمد من الرُّ كوع. البالء بمقصد تحقيق العبادة لله وحده • سؤال اهلل العفو، والرَّ حمة، والرِّ زق، وما يقرب منه تعالى، كقولك: «اللَّهمَّ ( بين السَّ جدتَيْن.((»اغفر لي، وارحمني، واهدين، وعافني وارزقني ُ • سؤال اهلل العفو، والرَّ حمة، والرِّ زق، وما يقرب منه تعالى، كقولك: «اللَّهمَّ ( بين السَّ جدتَيْن.((»اغفر لي، وارحمني، واهدين، وعافني وارزقني َ • التضرُّ ع إلى اهلل، واالستغاثة به، وصدق االفتقار، واللَّجوء، والرَّ غبة والرَّ هبة إليه؛ عند النَّوازل العظام، وذلك على هيئة استقبال القبلة، ومدِّ اليدَيْن، ورفع الصوت؛ إظهارًا للمسكنة، والحاجة إلى اهلل، كقول نبيِّ اهلل محمَّد | لَمَّا كان يوم بدر، مادًّا يديه، وصوته، مستقبل القبلة، حتى سقط رداؤه عن منكبيه: «اللَّهمَّ أنجز لي ما وعدتني، اللَّهمَّ آتِ ما وعدتني، اللَّهمَّ إنْ تهلك (.((»هذه العصابة من أهل اإلسالم ال تُعبَدْ يف األرض • تذكُّر اهلل، ومناجاته يف جميع األحوال، والهيئات، كدعاء رسول اهلل | يوم .»هذه العصابة من أهل اإلسالم ال تعبد يف األرض • تذكُّر اهلل، ومناجاته يف جميع األحوال، والهيئات، كدعاء رسول اهلل | يوم .)182/24( ( تفسير القرآن الحكيم (تفسير المنار)، لرشيد رضا(( .)796( ( أخرجه البخاري يف صحيحه: كتاب األذان، باب: فضل اللهم ربنا لك الحمد، برقم(( ( أخرجه مسلم يف صحيحه: كتاب الذكر والدعاء والتوبة واالستغفار، باب فضل التهليل والتسبيح(( .)2697( والدعاء، برقم .)182/24( ( تفسير القرآن الحكيم (تفسير المنار)، لرشيد رضا(( .)796( ( أخرجه البخاري يف صحيحه: كتاب األذان، باب: فضل اللهم ربنا لك الحمد، برقم(( ( أخرجه مسلم يف صحيحه: كتاب الذكر والدعاء والتوبة واالستغفار، باب فضل التهليل والتسبيح(( .)2697( والدعاء، برقم ( أخرجه مسلم يف صحيحه: كتاب الجهاد والسير، باب اإلمداد بالمالئكة يف غزوة بدر، وإباحة (( .)1763( الغنائم، برقم ( أخرجه مسلم يف صحيحه: كتاب الجهاد والسير، باب اإلمداد بالمالئكة يف غزوة بدر، وإباحة (( .)1763( الغنائم، برقم هو على كل ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف عرفة: «ال إله إال اهلل وحده ال شريك له، له الملك وله الحمد، وهو على كل (.((»شيء قدير والحاصل أنَّ الدُّ عاء هو: توجُّ ه العبد إلى اهلل تعالى بتوحيده، والثَّناء عليه بما هو أهله، وسؤاله العفو والرَّ حمة، واالستعانة به يف قضاء الحوائج، والتضرُّ ع إليه لكشف الباليا، والظَّفر على األعداء، وتذكُّره يف جميع األحوال، بذكره ومناجاته، وقراءة القرآن الكريم، والفزع إلى الصَّ الة. هو أهله، وسؤاله العفو والرَحمة، واالستعانة به يف قضاء الحوائج، والتضرُع إليه لكشف الباليا، والظَّفر على األعداء، وتذكُّره يف جميع األحوال، بذكره ومناجاته، وقراءة القرآن الكريم، والفزع إلى الصَّ الة. البالء بمقصد تحقيق العبادة لله وحده والقرآن الكريم مملوء بالحديث عن أنواع الدُّعاء، ومن ذلك قوله تعالى : ﭐ﴿ﮨ ﮩ -آمرً ا عباده بدعائه جهرً ا وسرًّ ا وخوفًا من عقابه وطمعًا يف ثوابه- ]، والتضرُّ ع: «إظهار التذلُّل هبيئة55 :ﮪ ﮫﮬ ﮭ ﮮ ﮯ ﮰ﴾ [األعراف خاصَّ ة، ويطلق التضرَّ ع على الجهر بالدُّعاء؛ ألنَّ الجهر من هيئة التضرُّ ع، ألنَّه ]، بيان ألغراض 56 :(، ويف قوله: ﴿ﯙ ﯚ ﯛﯜ﴾ [األعراف((» ٌّتذلُّل جهري الدُّعاء، وأنَّه على نوعَيْن، هما: الخوف من غضب اهلل وعقابه، والطّمع يف رضاه وثوابه، يقول ابن عاشور: «والدُّعاء ألجل الخوف نحو الدُّعاء بالمغفرة، والدُّعاء (، وقال لرسوله |: ﭐ﴿ﯩ ﯪ ((»ألجل الطمَّع نحو الدُّعاء بالتَّوفيق وبالرَّ حمة ﯫ ﯬ ﯭ ﯮﯯ ﯰ ﯱ ﯲ ﯳ ﯴﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ]، وقال ألوليائه: ﴿ﭝ ﭞ ﭟ ﭠ ﭡﭢ ﭣ 186 :ﯻ﴾ [البقرة ] وعن النُّعمان بن 60 :ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ﴾ [غافر )، كما أخرجه مالك يف3585( ( أخرجه الرتمذي يف سننه: أبواب الدعوات، لم يسم بابه، برقم(( ). وحسَّ نه األلباين يف صحيح وضعيف726( موطَّ ئه: كتاب الصالة، باب: ما جاء يف الدعاء، برقم ).3585( سنن الرتمذي، برقم ).171/8( ( التحرير والتنوير، البن عاشور(( .)176/8( ،( المرجع السَّ ابق(( َ والقرآن الكريم مملوء بالحديث عن أنواع الدُّعاء، ومن ذلك قوله تعالى : ﭐ﴿ﮨ ﮩ -آمرً ا عباده بدعائه جهرً ا وسرًّ ا وخوفًا من عقابه وطمعًا يف ثوابه- ]، والتضرُّ ع: «إظهار التذلُّل هبيئة55 :ﮪ ﮫﮬ ﮭ ﮮ ﮯ ﮰ﴾ [األعراف خاصَّ ة، ويطلق التضرَّ ع على الجهر بالدُّعاء؛ ألنَّ الجهر من هيئة التضرُّ ع، ألنَّه ]، بيان ألغراض 56 :(، ويف قوله: ﴿ﯙ ﯚ ﯛﯜ﴾ [األعراف((» ٌّتذلُّل جهري الدُّعاء، وأنَّه على نوعَيْن، هما: الخوف من غضب اهلل وعقابه، والطّمع يف رضاه وثوابه، يقول ابن عاشور: «والدُّعاء ألجل الخوف نحو الدُّعاء بالمغفرة، والدُّعاء (، وقال لرسوله |: ﭐ﴿ﯩ ﯪ ((»ألجل الطمَّع نحو الدُّعاء بالتَّوفيق وبالرَّ حمة ﯫ ﯬ ﯭ ﯮﯯ ﯰ ﯱ ﯲ ﯳ ﯴﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ]، وقال ألوليائه: ﴿ﭝ ﭞ ﭟ ﭠ ﭡﭢ ﭣ 186 :ﯻ﴾ [البقرة ] وعن النُّعمان بن 60 :ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ﴾ [غافر )، كما أخرجه مالك يف3585( ( أخرجه الرتمذي يف سننه: أبواب الدعوات، لم يسم بابه، برقم(( ). البالء بمقصد تحقيق العبادة لله وحده وحسَّ نه األلباين يف صحيح وضعيف726( موطَّ ئه: كتاب الصالة، باب: ما جاء يف الدعاء، برقم ).3585( سنن الرتمذي، برقم I (، وقد ابتلى اهلل(( عن النَّبيِّ | أنه قال: «الدُّعاء هو العبادة»، وقرأ اآلية# بشير عددًا من أنبيائه ورسله؛ حتى يستخرج منهم الدُّعاء، والتضرُّ ع وااللتجاء إليه وحده ، نجده يتضرَّ ع إلى ربه؛ طالبًا منه العون، + يف قضاء الحوائج، فهذا نبي اهلل نوح والغلبة على قومه، بعد أن دعاهم زمنًا طويلً إلى التَّوحيد الخالص، مع صربه على ]، وقال عن مناجاة 10 :إيذائهم وبطشهم، فقال: ﴿ﭯ ﭰ ﭱ ﭲ ﭳ﴾ [القمر الذي اشتدَّ بالؤه مدَّة طويلة؛ فتوسَّ ل إلى اهلل بالشَّ كوى عن حاله: + نبيِّ اهلل أيوب ]، وقد 83 :﴿ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ﴾ [األنبياء ، لَمَّا ابتُلِي بالتقام الحوت له، فقال: ﭐ﴿ﮎ ﮏ + بيَّن اهلل تعالى ما كان يردِّده يونس ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ]، وهذا نبي اهلل موسى \، نجده يف وقت 87 :ﮡ ﮢ ﮣ ﮤ﴾ [األنبياء المحنة يلجأ إلى ربِّه؛ طالبًا منه النُّصرة من جربوت فرعون، وشيعته، فقال: ﭐ﴿ﭩ ]، وقد حكى سبحانه عن أصحاب الكهف 22 :ﭪ ﭫ ﭬ ﭭ ﭮ﴾ [الدُّخان حين التجؤوا إلى الكهف؛ فرارًا بدينهم، سائلين اهلل تعالى أن يتغمَّدهم برحمته؛ ليؤمِّنهم من األعداء: ﭐ﴿ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ]. هذا ووجه الدِّاللة يف اآليات؛ أنَّ اهلل يبتلي عباده 10 :ﮚ ﮛ ﮜ ﮝ﴾ [الكهف بصنوف االبتالءات والمصائب؛ ليظهر منهم التوجُّ ه إلى اهلل وحده بالدُّعاء يف قضاء حوائجهم، وكفايتهم شرور األعداء، وشدَّة بطشهم. ولهذا فقد بيَّن اهلل تعالى أنَّ الغاية من أخذ العباد بالبأساء والضرَّ اء؛ حتى يرجوه ويتضرعوا إليه بالدُّعاء فقال: ( أخرجه الرتمذي يف سننه: أبواب تفسير القرآن عن رسول اهلل |، باب: ومن سورة البقرة، برقم(( ). البالء بمقصد تحقيق العبادة لله وحده كما أخرجه ابن2969( :)، وصحَّ حه األلباين يف صحيح وضعيف سنن الرتمذي برقم2969( )، وصحَّ حه األلباين يف صحيح وضعيف3828( ماجه يف سننه: كتاب الزهد، باب ذكر التوبة، برقم ).3828( سنن ابن ماجه برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،]42:﴿ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ﴾ [األنعام قال ابن جرير &: «فعلنا ذلك هبم ليتضرَّ عوا إليَّ ، ويخلصوا لي العبادة، ويُفْردوا (، ((»رغبتهم إليَّ دون غيري، بالتذلُّل منهم لي بالطَّاعة، واالستكانة منهم إليَّ باإلنابة كما بيَّن سبحانه، أنَّ بعض الناس يتضرعون إليه بالدُّعاء؛ ليكشف عنهم البالء، ثم إذا رفع عنهم البالء عادوا إلى ما كانوا عليه من المعاصي، فقال: ﭐ﴿ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ]، 23 - 22:ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ﴾ [يونس ونظيره: ﭐ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ]، ونظيره: ﭐ﴿ﭑ ﭒ ﭓ ﭔ 54 - 53 :ﰌ ﰍ ﰎ ﰏ ﰐ ﰑ﴾ [النحل ].33 :ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ﴾ [الروم ويفهم من مجموع هذه اآليات أنَّ الغايات والحِكَم من أخذ الناس بالفقر والضِّ يق يف العيش، وباألمراض واألسقام واآلالم يف البدن؛ ألجل استخراج الصَّ رب يف تدبير األمور، I هلل وحده على المضارِّ، وإظهار غاية التوجُّ ه واالفتقار إلى اهلل وقضاء الحوائج، وكشف الكربات، واالعرتاف بقدرته وقهره وسلطانه، وأنَّه ال مدبِّر ألمر اهلل إال هو سبحانه، وأنَّه ال أحد يستطيع أن يدفع هذا الشَّ رَّ إال اهلل؛ إذ ال مُعطِي لما منع، وأنَّ الغايات والحِكَم من التفضُّ ل على النَّاس بالغِنى، وسَ عة العيش، وبالصِّ حَّة، والعافية، والقوَّة يف البدن؛ ألجل استخراج الشُّ كر هلل وحده على المسارِّ، وإظهار توحيد اهلل بحمده والثَّناء عليه يف تدبير األمور، وتفريج الهموم والغموم، واالعرتاف بنعمته ومنَّته وفضله، وأنَّه ال يستطيع أحد أن يردَّ هذا الخير إال اهلل؛ إذ ال مانع لِمَا أعطى، يقول ابن تيمية &: «فمن تمام نعمة اهلل على عباده .)355/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( المؤمنين، أن ينزل هبم الشدَّة، والضُّ رَّ ، وما يُلجئهم إلى توحيده؛ فيدعونه مخلصين له الدِّين، ويرجونه، وال يرجون أحدًا سواه، وتتعلَّق قلوهبم به، ال بغيره؛ فيحصل لهم من التوكُّل عليه، واإلنابة إليه، وحالوة اإليمان، وذوق طعمه، والرباءة من (. البالء بمقصد تحقيق العبادة لله وحده ((»الشِّ رك، ما هو أعظم نعمة عليهم من زوال المرض والخوف ِ ومن المواقف العملية المأثورة عن النَّبيِّ | لدفع البالء فيما صحَّ عن أبي أنَّه قال: جاء رجل إلى النبي | فقال: يا رسول اهلل، ما لقيت من عقرب # هريرة لدغتني البارحة. قال: «أما لو قلت، حين أمسيت: أعوذ بكلمات اهلل التَّامَّات مِن (، ويف رواية أخرى عن خَ ولة بنت حكيم السُّ لَمِيَّة، أهنا ((»شَ رِّ ما خلق، لم تضرَّ ك سمعت رسول اهلل |، يقول: «إذا نزل أحدكم منزلً ، فليقل: أعوذ بكلمات اهلل (. ورُوي عن أبان بن ((»التَّامَّات من شرِّ ما خلق، فإنَّه ال يضرُّ ه شيء حتى يرتحل منه يقول: قال رسول اهلل |: «ما من # قال: سمعت عثمان بن عفان# عثمان عبد يقول يف صباح كلِّ يوم ومساء كلَّ ليلة: بسم اهلل الذي ال يضرُّ مع اسمه شيء يف األرض وال يف السَّ ماء، وهو السَّ ميع العليم ثالث مرات، فيضرُّ ه شيء» وكان أَبَان، قد أصابه طَرَ فُ فالج، فجعل الرجل ينظر إليه، فقال له أبان: «ما تنظر؟ أما (، ومن ((»»إنَّ الحديث كما حدثتك، ولكني لم أقله يومئذ؛ ليُمضيَ اهلل علَيَّ قَدَره = .)285/5( ( الفتاوى الكربى، البن تيمية(( ( أخرجه مسلم يف صحيحه: كتاب الذكر والدعاء والتوبة واالستغفار، باب يف التعوذ من سوء القضاء(( .)2709( ودرك الشقاء وغيره، برقم ).2708( (المصدر السابق نفسه(( ،)3388( ( أخرجه الرتمذي يف سننه: أبواب الدعوات، باب ما جاء يف الدعاء إذا أصبح وإذا أمسى، برقم(( وقال الرتمذي: هذا حديث حسن صحيح غريب، وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي ). كما أخرجه ابن ماجه يف سُ ننه: كتاب الدعاء، باب ما يدعو به الرجل إذا أصبح وإذا 3388( برقم .)285/5( ( الفتاوى الكربى، البن تيمية(( ( أخرجه مسلم يف صحيحه: كتاب الذكر والدعاء والتوبة واالستغفار، باب يف التعوذ من سوء القضاء(( .)2709( ودرك الشقاء وغيره، برقم = ،)3388( ( أخرجه الرتمذي يف سننه: أبواب الدعوات، باب ما جاء يف الدعاء إذا أصبح وإذا أمسى، برقم(( وقال الرتمذي: هذا حديث حسن صحيح غريب، وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي ). البالء بمقصد تحقيق العبادة لله وحده كما أخرجه ابن ماجه يف سُ ننه: كتاب الدعاء، باب ما يدعو به الرجل إذا أصبح وإذا 3388( برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف خُ بَيْبٍ عن ل ل ل األذكار التي تقي من السُّ وء وتدفع الضَّ رر بإذن اهلل، ما رواه عبد اهلل بن خُ بَيْبٍ عن أبيه، قال: خرجنا يف ليلة مطيرة وظلمة شديدة نطلب رسول اهلل | يصلِّي لنا، قال: فأدركته، فقال: «قل»، فلم أقل شيئًا، ثم قال: «قل»، فلم أقل شيئًا، قال: «قل»، فقلت: ما أقول؟ قال: «قل: ﴿ﭑ ﭒ ﭓ ﭔ﴾، والمعوذتَيْن حين تمسي وتصبح ثالث (. ويف الصحيح عن ابن عباس ^ أن نبي اهلل | ((»مرَّ ات، تكفيك من كلِّ شيء كان يقول عند الكرب: «ال إله إال اهلل العظيم الحليم، ال إله إال اهلل رب العرش (.((»العظيم، ال إله إال اهلل رب السموات ورب األرض ورب العرش الكريم فالحاصل أنَّ األدعية، واألذكار السَّ ابقة، تحفظ المسلم من الضُّ رِّ ، واألذى، بجميع أنواعه، بإذن اهلل تعالى، ولكن ليس على وجه اللُّزوم، فمَن أصابه من البالء مع محافظته على هذه األذكار؛ فذلك بقَدَر اهلل تعالى، وله سبحانه الحِكمة البالغة يف أمره وقَدَرِه. البالء بمقصد تحقيق العبادة لله وحده = .)3828( )، وصححه األلباين يف صحيح وضعيف سنن ابن ماجه برقم3869( أمسى، برقم )، وحسَّ نه األلباين يف صحيح 3575( ( أخرجه الرتمذي يف سننه: أبواب الدعوات، لم يسمِّ بابه، برقم(( ،)، كما أخرجه عبد بن حميد يف منتخبه: عبداهلل بن خبيب3575( وضعيف سنن الرتمذي برقم ).494( برقم ( أخرجه مسلم يف صحيحه: كتاب الذِّكر والدُّ عاء والتوبة واالستغفار، باب دعاء الكرب، برقم (( .)2730( ورد لفظ «الصَّ رب» يف مائة وثالثة مواضع من آي الذِّكر الحكيم بصياغات (.((واشتقاقات مختلفة «الصَّ رب» يف اللُّغة: مصدر الفعل الثالثي: صَ بَرَ ، يصبِرُ ، صربًا، فهو صابر، والمفعول مصبور، وأصل الصَّ رب مركَّب من: «(صَ بَر) الصاد والباء والراء أصول ثالثة، األول الحبس، والثاين أعالي الشيء، والثالث جنس من الحجارة، فاألول: الصَّ رب ، وهو الحبس، يقال: صربت نفسي على ذلك األمر، أي: حبستها، والمصبورة المحبوسة على الموت، ومن الباب: الصبير، هو الكفيل، وإنما سُ مي بذلك؛ ألنه يصرب على الغُرم، يقال: صربت نفسي به أَصْ بُرُ صَ بْرً ا، إذا كفلت به، فأنا به صبير، (، وجاء يف اللِّسان: «صَ بَرَ ه عن الشيء ((»وصربت اإلنسان، إذا حلَّفته باهلل جهد القسم يَصْ بِرُ ه صربًا، حبسه؛ والصَّ رب: نقيض الجزع، وقد صرب فالن عند المصيبة يصرب صربًا، فهو صابِرٌ وصَ بَّار وصَ بِيرٌ وصَ بُور، وصربته أنا: حَ بَستُه، والتصبُّر: تكلُّف الصَّ رب؛ ]؛ معناه: وتواصوا بالصَّ رب على طاعة اهلل، 3 :وقوله تعالى: ﴿ﭟ ﭠ﴾ [العصر ]؛ 200 :والصَّ رب على الدُّخول يف معاصيه، وقوله ×: ﴿ﯭ ﯮ﴾ [آل عمران أي: اصربوا واثبتوا على دينكم، وصابروا أي: صابروا أعداءكم يف الجهاد، وقوله ]؛ 153 :×: ﴿ﯰ ﯱ ﯲ ﯳ ﯴ ﯵﯶ ﯷ ﯸ ﯹ ﯺ﴾ [البقرة أي: بالثبات على ما أنتم عليه من اإليمان، وشهر الصَّ رب: هو شهر رمضان، وأصل .401-399 ( المعجم المفهرس أللفاظ القرآن الكريم، ص(( .)329/3( ( معجم مقاييس اللغة، البن فارس(( .401-399 ( المعجم المفهرس أللفاظ القرآن الكريم، ص(( .)329/3( ( معجم مقاييس اللغة، البن فارس(( .401-399 ( المعجم المفهرس أللفاظ القرآن الكريم، ص(( .)329/3( ( معجم مقاييس اللغة، البن فارس(( م والشَّ راب ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف الصَّ رب الحبس، وسمي الصوم صربًا لِمَا فيه من حبس النَّفس عن الطَّعام والشَّ راب (، ويف أسماء اهلل تعالى الحسنى: الصَّ بور، وهو: «الذي ال يعاجل العصاة ((»والنِّكاح باالنتقام، وهو من أبنية المبالغة، ومعناه قريب من معنى الحليم، والفرق بينهما أن (، والصَّ رب ((»المذنب ال يأمن العقوبة يف صفة الصَّ بور، كما يأمنها يف صفة الحليم يف اصطالح المفسِّ رين هو: «اإلمساك يف ضيق، وحبس النَّفس على ما يقتضيه (، وعبَّر عنه آخر بأنَّه: «ثبات النَّفس، وتحمُّلها المشاقَّ واآلالم ((»العقل والشَّ رع (. البالء بمقصد تحقيق العبادة لله وحده والحاصل أنَّ الصَّ رب هو: تحمُّل المبتلَى التكاليف التشريعية الشَّ اقة ((»ونحوها من األوامر والنواهي والضِّ يق، أو الصَّ رب على الدُّنيا. البالء بمقصد تحقيق العبادة لله وحده عمَّا مَنَّ به على بني إسرائيل؛ إذ جعل منهم رؤساء يف الخير، H لقد أخرب اهلل وقدوات يُقتدى هبم؛ ألجل صربهم على فعل المأمورات؛ وترك المنهيات، وإيقاهنم بآيات اهلل، وتصديقهم هبا، فقال: ﭐ﴿ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ﮀﮁ ]؛ وقوله: ﭐ﴿ﭿ ﮀﮁ﴾ فمعناه: «صربُهم 24 :ﮂ ﮃ ﮄ﴾ [السَّ جدة (، ((»على مشاقِّ الطَّاعات، ومُقاساة الشَّ دائدِ يف نُصرةِ الدِّينِ، أو صربُهم عن الدُّنيا ويف اآلية: «تعريض بالبشارة ألصحاب رسول اهلل |؛ بأهنم يكونون أئمَّة لدين اإلسالم، وهداة للمسلمين، إذا صربوا على ما لحقهم يف ذات اهلل من أذى قومهم، (، ((»وصربوا على مشاقِّ التَّكليف، ومعاداة أهلهم، وقومهم، وظلمهم إيَّاهم .)439-438/4( ( لسان العرب، البن منظور(( .)439-438/4( ( لسان العرب، البن منظور(( .)437/4( ،( المرجع السَّ ابق(( .)474/1( ( المفردات يف غريب القرآن، للراغب(( .)299/29( ( التحرير والتنوير، البن عاشور(( .)87/7( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)237/21( ( التحرير والتنوير، البن عاشور(( ا .)437/4( ،( المرجع السَّ ابق(( .)474/1( ( المفردات يف غريب القرآن، للراغب(( .)299/29( ( التحرير والتنوير، البن عاشور(( .)87/7( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)237/21( ( التحرير والتنوير، البن عاشور(( ا .)87/7( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)237/21( ( التحرير والتنوير، البن عاشور(( ﴾وقد دعا القرآن الكريم إلى الثبات والصَّ رب لوجه اهلل تعالى فقال: ﴿ﯠ ﯡ (، واآلية: «تثبيت ((»× ] بمعنى: «اجعل صربك على أذاهم لوجه ربِّك7:[المدثر (، وقد ((»للنَّبي | على تحمُّل ما يلقاه من أذى المشركين، وعلى مشاقِّ الدَّعوة أمر اهلل تعالى عباده المؤمنين بالصَّ رب على طاعة اهلل، ورسوله، فيما أمرا به من جهاد األعداء، ثم هناهم عن التَّنازع واالختالف؛ ألنَّه يبعث على الفشل والجبن أمام األعداء فقال: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘﭙ ﭚﭛ ﭜ ]، ويف اآلية إيماء إلى: «إعانة اهلل لمن صرب؛ امتثالً 46 :ﭝ ﭞ ﭟ﴾ [األنفال (، وقد أمر اهلل تعالى بالمواظبة ((»ألمره، وهذا مُشاهَد يف تصرَّ فات الحياة كلِّها على العبادة، وشدَّة الصَّ رب عليها فقال: ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ (، وقوله: ((» ِّ]، واالصطبار هو: «شدَّة الصَّ رب على األمر الشَّ اق65 :ﭘﭙ﴾ [مريم ﴿ﭗ ﭘﭙ﴾ أي: «اثبت للعبادة، ألنَّ العبادة مراتب كثيرة، من مجاهدة النَّفس، وقد يغلب بعضها بعض النُّفوس؛ فتستطيع الصَّ رب على بعض العبادات دون (؛ لقد أقسم تعالى بأنَّه مبتلٍ عباده المسلمين يف أموالهم، وأنفسهم، وسماع ((»بعض ما يكرهون من أهل الكتاب فيقول: ﴿ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ ﯨ ﯩ ﯪﯫ ﯬ ﯭ ﯮ ﯯ ]، فحثَّهم سبحانه يف اآلية على مالزمة الصَّ رب، 186 :ﯰ ﯱ ﯲ ﯳ﴾ [آل عمران والتقوى عند مواجهة تحدِّيات البالء، وأنَّ ذلك: ﴿ﯱ ﯲ ﯳ﴾ أي: «مما أمر .)264/8( ( تفسير القرآن العظيم، البن كثير(( .)299/29( ( التحرير والتنوير، البن عاشور(( .)32/10( ( المرجع السَّ ابق(( .)142/16( ( المرجع السَّ ابق(( .)142/16( ( المرجع السَّ ابق(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،(((»[اهلل] به وبالغ فيه، والعزم يف األصل ثبات الرَّ أي على الشَّ يء نحو إمضائه واآلية داللة واضحة على أنَّ من مقاصد البالء؛ استخراج الصَّ رب، وأنه ال يمكن للعباد أن يستمرُّ وا على أداء الطَّاعات إذا لم يستعينوا بالصَّ رب؛ ألنَّ الصَّ رب حبس النَّفس عن الشَّ كوى، وثباهتا، وتحمُّلها مشاقَّ الطاعات والدَّعوة إلى اهلل والجهاد يف سبيله، كما أقسم أيضً ا بأنه سيبتلي عباده المسلمين باألمر بالجهاد، ونحوه من التَّكاليف التَّشريعية الشَّ اقَّة من األوامر والنَّواهي؛ حتى يستخرج منهم الصَّ رب، ويظهر حالهم للنَّاس؛ فيتميَّز قوي اإليمان من ضعيفه، والصَّ ادق من المنافق، والمجاهد من المتخلِّف فقال: ﭐ﴿ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ﴾ ]، وحرف الغاية: ﭐ﴿ﭡ﴾ متعلِّق بـقوله: ﭐ﴿ﭠ﴾، والمعنى: «أنَّ 31 :[محمد اهلل تعالى يبلو النَّاس؛ أي: يختربهم بالتَّكاليف، كبذل األنفس، واألموال يف الجهاد؛ (، ونظيره قوله تعالى: ﭐ﴿ﭘ ((»ليتميَّز بذلك صادقهم من كاذهبم، ومؤمنهم من كافرهم ]، 142:ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ﴾ [آل عمران وحسبك بفضيلة الصَّ رب أن اهلل جعله سببًا للنَّجاح، والظَّفر على ما يبلو اهلل به عباده من أنواع االبتالءات والمصائب، فقال: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ]، وقوله: ﭐ﴿ﭟ 3-1:ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ﴾ [العصر ﭠ﴾ فإنَّه يعني: «وتواصَ وْا بالصَّ رب عن المعاصي، وعلى الطَّاعات، وعلى ما (؛ ويستشفُّ من هذه اآليات وما جاء موضَّ حًا يف آيات أُخَ رَ ؛ أنَّ ((»يبلو اهلل به عباده الصَّ رب شرط أساسي لتحقيق النَّصر على أنواع االبتالءات والمصائب، ويؤيِّد هذا المعنى ما رواه ابن عباس ^، قال: قال لي رسول اهلل |: «... البالء بمقصد تحقيق العبادة لله وحده واعلم أنَّ النَّصر مع .)53/2( ( أنوار التنزيل وأسرار التأويل، للبيضاوي(( .)384/7( ( أضواء البيان يف إيضاح القرآن بالقرآن، للشنقيطي(( .)794/4( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( (. ويالحظ يف الحديث أنَّ النبي | قرن بين النصر والصَّ رب؛ للدِّاللة((»...الصَّ بر على أنَّه ال نصر على أنواع الباليا والمصائب إال بالصَّ رب؛ ألنه سبب يف النَّجاح واالنتصار، والحديث قاعدة ثابتة مطَّردة المعنى، ال تتغيَّر وال تتبدَّل؛ حيث يدركها (، ((»العقالء بعقولهم، والمجرِّ بون بتجارهبم. ولقد قيل: «الشَّ جاعة صرب ساعة وقال زفر بن الحارث الكالبي، يعتذر عن انتصار أعدائهم عليهم: «ســقــيــنــاهــم كــأسً ــا ســقــونــا بمثلها (((»ولكنهم كانوا على الموت أصبرا مخربًا عن طاعة أصحاب طالوت الصَّ ادقين؛ لقتال جالوت - ويقول تعالى وأصحابه الكافرين، مُعتربين أنَّ النَّصر ليس من كثرة عَدد، وال من عُدد، وإنَّما بالصَّ رب على لَ ْواء الجهاد يف سبيل اهلل، فقال: ﭐ﴿ﭾ ﭿ ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ]، وكان 249:ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌﮍ ﮎ ﮏ ﮐ﴾ [البقرة من دعائهم يف تلكم المعركة الحاسمة: ﭐ﴿ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ].250 :ﮝ ﮞ ﮟ ﮠ﴾ [البقرة وقد استفاضت السُّ نَّة النبوية باألحاديث التي تحثُّ على الصَّ رب، وتأمر به، ، قال: قال رسول اهلل |: «عجبًا ألمر المؤمن، إنَّ أمره كلَّه # فمنها ما رواه صهيب خير، وليس ذاك ألحد إلَّ للمؤمن، إنْ أصابته سرَّ اء شَ كَر، فكان خيرً ا له، وإن أصابته ، أنَّ رسول اهلل |، # (، وما رواه أنس بن مالك((»ضرَّ اء، صَ بَر، فكان خيرً ا له ،^ ( أخرجه الحاكم يف مستدركه: كتاب معرفة الصحابة ÷، ذكر عبداهلل بن عباس بن عبدالمطلب(( ،)، كما أخرجه الطرباين يف معجمه: باب العين، عبيد بن أبي مليكة، عن ابن عباس6304( برقم ). 2382( )، وقد صححه األلباين يف سلسلة األحاديث الصحيحة برقم11243( برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ا قال : أتى على امرأة تبكي على صبيٍّ لها، فقال لها: «اتقي اهلل واصربي»، فقالت: وما تُبالي بمصيبتي. فلما ذهب، قيل لها: إنَّه رسول اهلل |. فأخذها مثل الموت، فأتت بابه، فلم تجد على بابه بوَّابين، فقالت: يا رسول اهلل، لم أعرفك. البالء بمقصد تحقيق العبادة لله وحده فقال: «إنما الصَّ رب ، أنه: لَمَّا كان # (، ورَوى عبداهلل((»عند أوَّل صدمة»، أو قال: «عند أوَّل الصدمة يوم حُ نين، آثر النبي | أُناسً ا يف القسمة، فأعطى األقرع بن حابس مائة من اإلبل، وأعطى عيينة مثل ذلك، وأعطى أناسً ا من أشراف العرب، فآثرهم يومئذ يف القسمة، قال رجل: واهلل إن هذه القسمة ما عُدل فيها، وما أُريد هبا وجه اهلل. فقلت: واهلل ألُخربنَّ النبي |. فأتيته، فأخربته، فقال: «فمَن يعدل إذا لم يعدلِ اهلل ورسوله، رحم (.((»اهلل موسى، قد أُوذي بأكثر من هذا فصبر :المطلب الخامس البالء بمقصد استخراج الرِّ ضا وردت مادة «رَضِ يَ » يف ثالثة وسبعين موضعًا من آي الذِّكر الحكيم، بصياغات، (. ((واشتقاقات مختلفة و«الرِّ ضا» يف اللُّغة مصدر الفعل الثالثي معتل اآلخر: رَضيَ ، يَرْ ضَ ى، ارْضَ ، رِضً ا وإرضاء، فهو رَاضٍ، والمفعول مَرْ ضِ يٌّ ، ومادة (رضي): «الرَّ اء والضاد (؛ ويف اللِّسان: «الرِّ ضا ((»والحرف المعتلُّ أصل واحد يدلُّ على خالف السُّ خط .)926( ( أخرجه مسلم يف صحيحه: كتاب الجنائز، باب يف الصَّ رب على المصيبة عند أول الصدمة، برقم(( ( أخرجه البخاري يف صحيحه: كتاب فرض الخمس، باب ما كان النبي | يعطي المؤلفة قلوهبم(( .)3150( وغيرهم من الخمس ونحوه، برقم م م ).322-321( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)402/2( ( معجم مقاييس اللغة، البن فارس(( ]؛ تأويله أنَّ اهلل100 :ضدُّ السُّ خط، وقوله ×: ﭐ﴿ﭙ ﭚ ﭛ ﭜ ﭝ﴾ [التوبة تعالى رضي عنهم أفعالهم، ورضوا عنه ما جازاهم به، وأرضاه: أعطاه ما يرضى به، وترضَّ اه: طلب رضاه، وارتضاه: رآه له أهلً ، وترضَّ يته؛ أي: أرضيته بعد جهد، (، ويف اصطالح المفسِّ رين: ((» ٌّواسرتضيته؛ فأرضاين، ورجل رِضً ى: قُنْعانٌ مَرضي «رضا العبد عن اهلل: ألَّ يكره ما يجري به قضاؤه، ورضا اهلل عن العبد: أن يراه (. ويقول آخر: «وأصل الرِّ ضا أنَّه ضدُّ الغضب، ((»مؤتمرً ا ألمره، ومنتهيًا عن هنيه فهو المحبَّة وأثرها من اإلكرام واإلحسان، فرضا اهلل مستعمَل يف إكرامه وإحسانه ]، ورضا الخلق عن اهلل هو محبَّته وحصول 54 :مثل محبَّته يف قوله: ﴿ﮨ﴾ [المائدة (. ((»ما أملوه منه بحيث ال يبقى يف نفوسهم متطلَّع والحاصل أنَّ الرِّ ضا هو: التَّسليم الكلِّي؛ لِمَا قَسَ مه اهلل تعالى، وقَدَّره على عباده، من غير امتعاض من قسمته، وال اعرتاض على أقداره، والتَّسليم الكلِّي؛ ألحكامه الشَّ رعيَّة، من غير شكٍّ يف حِكَمها، وال منازعة يف أحكَامها، واالنقياد الكلِّي لرسوله |، من غير تقدُّم على هَدْيه، وال افتئات على سُ نَّته. البالء بمقصد تحقيق العبادة لله وحده ُأهَالقد أخرب اهلل تعالى عن عباده المؤمنين أنَّهم راضون كلَّ الرِّ ضا بما ساقت والحاصل أنَّ الرِّ ضا هو: التَّسليم الكلِّي؛ لِمَا قَسَ مه اهلل تعالى، وقَدَّره على عباده، من غير امتعاض من قسمته، وال اعرتاض على أقداره، والتَّسليم الكلِّي؛ ألحكامه الشَّ رعيَّة، من غير شكٍّ يف حِكَمها، وال منازعة يف أحكَامها، واالنقياد الكلِّي لرسوله |، من غير تقدُّم على هَدْيه، وال افتئات على سُ نَّته. َاُ لقد أخرب اهلل تعالى عن عباده المؤمنين أنَّهم راضون كلَّ الرِّ ضا بما ساقت إليهم أقداره، من همٍّ، وغمٍّ، وحَ زَ ن، وغيرها من مصائب الدُّنيا؛ ألهنم يعلمون أنَّه ال يصيبهم شيء من المصائب إلَّ وهو مقدَّر عند اهلل يف كتاب، فقال: ﴿ﮆ ﮇ ﮈ ]، واآلية 51 :ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏﮐ ﮑ ﮒ ﮓ ﮔ﴾ [التوبة تعليم للمسلمين بأن يرضَ وْا بما قَدَّر اهلل لهم وقضاه؛ ألنَّ الرِّ ضا مزيل للبالء، ومؤذن بالفرج، بينما السَّ خط مطيل للبالء، ومجلب للغُمَّة، وما تضمنته هذه اآلية الكريمة ﭡ ﭢ ﭣ ^ نابنع ا امد ي ل أوضحه اهلل تعالى يف غير هذا الموضع، كقوله تعالى: ﴿ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ]، عن ابن عباس ^ 11 :ﭤﭥ ﭦ ﭧ ﭨ ﭩ ﭪﭫ ﭬ ﭭ ﭮ ﭯ﴾ [التغابن قال: ﴿ﭦ ﭧ ﭨ ﭩ ﭪﭫ﴾ يعني: «يهد قلبه لليقين؛ فيعلم أنَّ ما أصابه لم (، وعن علقمة & قال: «هو الرَّ جل ((»يكن ليخطئه، وما أخطأه لم يكن ليصيبه (، واآليتان دلَّتا داللة ((»تصيبه المصيبة؛ فيعلم أنَّها من عند اهلل؛ فيسلم لها ويرضَ ى واضحة على أنَّ كلَّ ما أصاب النَّاس من مصائب يف األرض، كالقحط والجدب، ويف األنفس، كاألمراض واألوصاب، إنَّما هو بقضاء اهلل وقدره، وإذا أيقن المبتَلَى أنَّ البالء من عند اهلل؛ فإنَّه سيرضى حتمًا عن كلِّ شيء أصابه يف حياته، ألنَّه يعلم أنَّ الغرض من جميع البالء هو إظهار المبتَلَى تسليمه التَّامَّ، ورضاه الكامل عن كلِّ شيء أصابه يف حياته لوجه اهلل تعالى. .)421/23( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)421/23( ( المرجع السابق(( )، كما2396( ( أخرجه الرتمذي يف سُ ننه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( )، وحسَّ نه4031( أخرجه ابن ماجه يف سننه: كتاب الفتن، باب الصَّ رب على البالء، يوم النحر، برقم ).2396( األلباين يف صحيح وضعيف سنن الرتمذي، برقم البالء بمقصد تحقيق العبادة لله وحده هذا ويُستفاد من اآليتَيْن أنَّ كلَّ ما يصاب به النَّاس من المصائب يف األرض، واألنفس، واألموال، واقع ال محالة، وأهنا مقدَّرة قبل وقوعها، وأنَّ مِن بعض حِكَمها: استخراج الرِّ ضا، أو السَّ خط على المصائب، وقد روى سعد بن سنان &، ، قال: قال رسول اهلل |: «إنَّ عظم الجزاء مع عظم البالء، وإنَّ اهلل # عن أنس (، ولهذا ((»إذا أحبَّ قومًا ابتالهم، فمن رضي فله الرِّ ضا، ومن سخط فله السخط فإنَّه ينبغي على المؤمنين االستعداد ألقدار اهلل، حلوها ومرِّ ها، ومقابلتها بالرِّ ضا يف االعتقاد والقول والعمل، وإن كان خالفَ هواهم، فإهنا مثبَتة يف كتاب اهلل، ولهذا .)421/23( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)421/23( ( المرجع السابق(( )، كما2396( ( أخرجه الرتمذي يف سُ ننه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( )، وحسَّ نه4031( أخرجه ابن ماجه يف سننه: كتاب الفتن، باب الصَّ رب على البالء، يوم النحر، برقم ).2396( األلباين يف صحيح وضعيف سنن الرتمذي، برقم َقال النبي | قَدَّ َ اهلل :قال النبي |: «إن أصابك شيء فال تقل: لو أين فعلت كان كذا وكذا، ولكن قل (، وقد قال تعالى ذكره: ((»قَدَّ رَ اهلل وما شاء فعل، فإنَّ «لو» تفتح عمل الشيطان ﭐ﴿ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦﭧ ﭨ ﭩ ] وقال: ﴿ﯧ ﯨ ﯩ ﯪ ﯫ ﯬ ﯭ ﯮ 216 :ﭪ ﭫ ﭬ﴾ [البقرة ] يقول ابن عاشور &: «إنَّ حكمة التَّكليف تعتمد المصالحَ 19 :ﯯ﴾ [النساء ودرءَ المفاسد، وال تعتمد مالءمة الطَّبع ومنافرته؛ إذ يكره الطَّبع شيئًا وفيه نفعه، وقد يحبُّ شيئًا وفيه هالكه، وذلك باعتبار العواقب والغايات... وشأن جمهور النَّاس الغفلة عن العاقبة والغاية، أو جهلهما، فكانت الشَّ رائع وحملتها من العلماء (؛ ((»والحكماء تحرِّ ض النَّاس على األفعال، والتُّروك، باعتبار الغايات، والعواقب ذلك وقد بشَّ ر اهلل تعالى عباده المؤمنين بالفوز العظيم؛ إذا استسلموا لجميع أقدار اهلل، وأحكامه الشَّ رعية، من األوامر والنواهي، فقال: ﭐ﴿ﰎ ﰏ ﰐ ﰑ ﰒﰓ ﰔ ] وقوله: ﭐ﴿ﰎ ﰏ ﰐ﴾ فمعناه: «رضي اهلل عن هؤالء 119 :ﰕ ﰖ﴾ [المائدة الصَّ ادقين الذين صدقوا يف الوفاء له بما وعدوه، من العمل بطاعته، واجتناب (، وقوله: ﭐ﴿ﰑ ﰒﰓ﴾ فمعناه: «ورضوا هم عن اهلل تعالى ذكره يف ((»معاصيه (. البالء بمقصد تحقيق العبادة لله وحده ((»وفائه لهم بما وعدهم على طاعتهم إياه فيما أمرهم وهناهم، من جزيل ثوابه وقد عاب اهلل تعالى على المنافقين ضجرهم من تقسيم رسول اهلل | مصارف الزَّ كاة وتوزيعها على مستحقِّيها بالعدل، فقال: ﴿ﭻ ﭼ ﭽ ﭾ ﭿ ( أخرجه مسلم يف صحيحه: كتاب القدر، باب يف األمر بالقوة وترك العجز واالستعانة باهلل وتفويض(( .)2664( المقادير هلل، برقم ). 322-321/2( ( التحرير والتنوير، البن عاشور(( .)245-244/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه مسلم يف صحيحه: كتاب القدر، باب يف األمر بالقوة وترك العجز واالستعانة باهلل وتفويض(( .)2664( المقادير هلل، برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ] هذا وقد أرشد اهلل58 :ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ﴾ [التوبة تعالى المنافقين إلى ما كان ينبغي أن يكونوا عليه فقال: ﭐ﴿ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ] 59 :ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ﴾ [التوبة ويف اآلية: «إخبار بأنَّ الرِّ ضا بفعل اهلل؛ يوجب المزيد من الخير جزاء للرَّ اضي (، وأنَّ السَّ خط بفعل اهلل؛ يوجب المزيد من الشرور والمصائب ((»على فعله قال: قال رسول # جزاء للسَّ اخط على فعله. ويؤيِّد هذا ما ورد عن أبي هريرة (. ومن مواقف رسول اهلل ((»اهلل |: «وارْضَ بما قَسَ م اهلل لك تكن أغنى الناس ، قال: دخلنا مع رسول اهلل | على # | يف الرِّ ضا ما صح عن أنس بن مالك ، فأخذ رسول اهلل | إبراهيم، فقبَّله، + ( إلبراهيم((أبي سيف القَيْنِ، وكان ظِئْرً ا وشمَّه، ثم دخلنا عليه بعد ذلك وإبراهيم يجود بنفسه، فجعلت عينا رسول اهلل | : وأنت يا رسول اهلل؟ فقال: «يا ابن # تذرِفان، فقال له عبد الرحمن بن عوف عوف، إهنا رحمة»، ثم أتبعها بأخرى، فقال |: «إن العين تدمع، والقلب يحزن، (، ومن أعظم ((»وال نقول إال ما يَرضَ ى ربنا، وإنا بفراقك يا إبراهيم لمحزونون .)322/4( ( أحكام القرآن، للرازي(( ،)2305( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( :). كما أخرجه أحمد يف مسنده2305( وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).8096( ، برقم# مسند المكثرين من الصحابة، أبي هريرة ( أي مرضعا، وأطلق عليه ذلك ألنه كان زوج المرضعة، وأصل الظئر من ظأرت الناقة إذا عطفت (( على غير ولدها، فقيل ذلك للتي ترضع غير ولدها، وأطلق ذلك على زوجها ألنه يشاركها يف تربيته ).173 /3( غالبًا. البالء بمقصد تحقيق العبادة لله وحده فتح الباري شرح صحيح البخاري، البن حجر ( أخرجه البخاري يف صحيحه: كتاب الجنائز، باب قول النبي |: «إنا بك لمحزونون»، برقم (( .)1303( .)322/4( ( أحكام القرآن، للرازي(( ،)2305( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( :). كما أخرجه أحمد يف مسنده2305( وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).8096( ، برقم# مسند المكثرين من الصحابة، أبي هريرة ( أي مرضعا، وأطلق عليه ذلك ألنه كان زوج المرضعة، وأصل الظئر من ظأرت الناقة إذا عطفت (( على غير ولدها، فقيل ذلك للتي ترضع غير ولدها، وأطلق ذلك على زوجها ألنه يشاركها يف تربيته ).173 /3( غالبًا. فتح الباري شرح صحيح البخاري، البن حجر ،$ المواقف التي خلَّدها القرآن الكريم: حادثة اإلفك، يف شأن عائشة أم المؤمنين حين رماها أهل اإلفك والبهتان من المنافقين؛ فصربت على غمِّها؛ طلبًا لمرضاة اهلل تعالى، وكذلك صرب رسول اهلل | والمؤمنون ÷ على ما صربت عليه؛ حتى أنزل اهلل براءهتا يف عشر آيات تُتلى على مسامع الناس إلى يوم القيامة، فقال: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖﭗ ﭘ ﭙ ﭚ ﭛﭜ ﭝ ﭞ ﭟ ﭠﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨﭩ ]، وقوله تعالى: ﭐ﴿ﭘ ﭙ ﭚ ﭛﭜ ﭝ 11 :ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ﴾ [النور (، ومعنى كونه خيرً ا ((» ِّﭞ ﭟ ﭠﭡ﴾؛ أي: «لرجحان النَّفع والخير على جانب الشَّ ر لهم: «أهنم اكتسبوا فيه الثواب العظيم، ألنه كان بالء مبينًا ومحنة ظاهرة، وأنه نزلت فيه ثماين عشرة آية، كل واحدة منها مستقلة بما هو تعظيم لشأن رسول اهلل |، وتسلية له، وتنزيه ألم المؤمنين رضوان اهلل عليها، وتطهير ألهل البيت، وهتويل لمن تكلم يف ذلك أو سمع به، فلم تمجه أذناه، وعِدَّة ألطاف للسامعين والتالين إلى (، هذا وإنَّ صرب ((»يوم القيامة، وفوائد دينية، وأحكام وآداب ال تخفى على متأمليها -طلبًا لمرضاة اهلل تعالى- وثباهتا يف هذه المحنة العظيمة$ أمِّ المؤمنين عائشة لَداللة واضحة على فضلها، وقد عبَّرت بنفسها عن هذا حين قالت: «واهلل ما كنت أظنُّ أنَّ اهلل منزل يف شأين وَحيًا يُتلى، وَلَشأين يف نفسي كان أحقر من أن يتكلَّم اهلل يفَّ (. البالء بمقصد تحقيق العبادة لله وحده ((»بأمر يُتلى، ولكن كنت أرجو أن يرى رسول اهلل | يف النَّوم رؤيا يُربِّئني اهلل هبا : «وأسألك الرِّ ضا بعد # وقد كان من دعائه | كما نقل عنه سماعًا عمَّار بن ياسر .)198/12( ( الجامع ألحكام القرآن، للقرطبي(( .)217/3( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب ﴿ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ(( .101 ، ص6، ج4750 ]، برقم105 :] إلى قوله: ﴿ﭻ﴾ [النحل12 :ﭻ ﭼ ﭽ ﴾ [النور ).2770( وأخرجه مسلم يف صحيحه: كتاب التوبة، باب يف حديث اإلفك وقبول توبة القاذف، برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، وكان مِن ذكره | حين يسمع تشهد المؤذن كما يف صحيح مسلم عن((»القضاء عن رسول اهلل | أنه قال: «من قال حين يسمع المؤذن: # سعد بن أبي وقاص أشهد أن ال إله إال اهلل وحده ال شريك له، وأن محمدًا عبده ورسوله، رضيت باهلل (.((»ربًّا وبمحمد رسولً ، وباإلسالم دينًا، غُفر له ذنبه ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، وكان مِن ذكره | حين يسمع تشهد المؤذن كما يف صحيح مسلم عن((»القضاء عن رسول اهلل | أنه قال: «من قال حين يسمع المؤذن: # سعد بن أبي وقاص أشهد أن ال إله إال اهلل وحده ال شريك له، وأن محمدًا عبده ورسوله، رضيت باهلل (.((»ربًّا وبمحمد رسولً ، وباإلسالم دينًا، غُفر له ذنبه اإ :المطلب السَّ ادس البالء بمقصد استخراج الشُّ كر جاء لفظ «الشُّ كر» يف خمسة وسبعين موضعًا من آي الذِّكر الحكيم، بعدَّة (.((صيغ، واشتقاقات الشُّ كر يف اللُّغة مصدر الفعل الثالثي: شَ كَرَ ، يشكر، اشْ كُرْ ، شكرً ا، فهو شاكر، والمفعول مشكور، وأصل كلمة الشُّ كر مركَّبة من: «الشين والكاف والراء، أصول أربعة متباينة، بعيدة القياس. فاألول: الشُّ كر: الثَّناء على اإلنسان بمعروف (، ويف اللِّسان: «الشُّ كر: عرفان اإلحسان ونشره، والشُّ كر من اهلل: ((»ُيُولِيكَه المجازاة والثَّناء الجميل، وشكره لعباده: مغفرته لهم. والشَّ كور: من أبنية المبالغة. ،)1923( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( ،)1971( وقال: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه ابن حبان يف صحيحه برقم وقال شعيب األرنؤوط: إسناده قوي. ،)1923( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( ،)1971( وقال: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه ابن حبان يف صحيحه برقم وقال شعيب األرنؤوط: إسناده قوي. البالء بمقصد تحقيق العبادة لله وحده ( أخرجه مسلم يف صحيحه: كتاب الصالة، باب القول مثل قول المؤذن لمن سمعه، ثم يصلي على (( .)386( النبي | ثم يسأل له الوسيلة، برقم ).386-385( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)207/3( ( معجم مقاييس اللغة، البن فارس(( وأما الشَّ كور من عباد اهلل فهو الذي يجتهد يف شكر ربه بطاعته وأدائه ما وَظَّفَ عليه ]، 13 :من عبادته. وقال اهلل تعالى: ﭐ﴿ﯮ ﯯ ﯰ ﯱﯲ ﯳ ﯴ ﯵ ﯶ﴾ [سبأ والشُّ كر: مثل الحمد، إال أنَّ الحمد أعمُّ منه، فإنَّك تحمد اإلنسان على صفاته الجميلة وعلى معروفه، وال تشكره إال على معروفه دون صفاته. والشُّ كر: مقابلة النِّعمة بالقول والفعل والنيَّة، فيثني على المنعم بلسانه ويذيب نفسه يف طاعته ويعتقد (، إذن فالشُّ كر لغة يدور حول الثَّناء؛ لذا يقول ابن منظور: «والشُّ كر: ((»أنه مُولِيها (، ومن أسماء اهلل الحسنى الشَّ كور، ((»الثَّناء على المحسن بما أَوْالكَهُ من المعروف ومعناه: «هو الذي يُجازي بيسير الطَّاعات؛ كثير الدَّرجات، ويعطي بالعمل يف أيام (، ويف اصطالح المفسِّ رين: الشُّ كر هلل هو ((»معدودة نعيمًا يف اآلخرة غير محدود (، والشُّ كر للرَّ جل هو الثَّناء عليه ((االستخذاء هلل، واإلقرار بنعمته وهدايته وابتدائه (، ويقول آخر: «الشُّ كر تصوُّر النِّعمة وإظهارها، وهو ثالثة ((بأفعاله المحمودة أضرب: شكر القلب، وهو تصور النِّعمة، وشكر اللِّسان، وهو الثَّناء على المنعم، (، ويقول غيره: «الشُّ كر ((»وشكر سائر الجوارح، وهو مكافأة النِّعمة بقدر استحقاقه (، ويرى آخر أنَّ: «شكر العبد هلل تعالى ((»االعرتاف بحق المنعم، مع الثَّناء عليه ثناؤه عليه بذكر إحسانه إليه، وشكر الحقِّ سبحانه للعبد ثناؤه عليه بطاعته له، إلَّ .)424-423/4( ( لسان العرب، البن منظور(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، وعرَّ فه((»أنَّ شكر العبد نطق باللِّسان، وإقرار بالقلب بإنعام الربِّ ، مع الطَّاعات غيره بقوله: «شكر العبد لربِّه ينحصر معناه يف استعماله جميع نعمه فيما يرضيه (. ((»تعالى، وأما شكر الرَّ بِّ لعبده فهو أن يثيبه الثَّواب الجزيل من عمله القليل والحاصل أن الشكر يأيت بمعنيين، األوّل: شكر العبد لربه؛ باعرتافه بحق المنعم، والثناء عليه، والعمل بطاعته، واآلخر: شكر الرّ ب لعبده؛ بإثابته؛ إذا اعرتف العبد بالنعم، وأثنى على باريها، وعمل بطاعته. البالء بمقصد تحقيق العبادة لله وحده لقد أخرب تعالى ذكره أنه يف غنًى عن تعذيب عباده إنْ هم تابوا إليه وأطاعوه يف أمره وهنيه، وأنه إنما يعذهبم بذنوهبم ومخالفتهم أمره وهنيه فقال: ﴿ﯲ ﯳ ]، يقول 147:ﯴ ﯵ ﯶ ﯷ ﯸﯹ ﯺ ﯻ ﯼ ﯽ﴾ [النساء الزَّ مخشري &: «فإن قمتم بشكر نعمته وآمنتم به فقد أبعدتم عن أنفسكم استحقاق (، هذا ((»(، قال قتادة &: «إنَّ اهلل جلَّ ثناؤه ال يعذِّب شاكرً ا وال مؤمنًا((»العذاب ويف اآلية داللة واضحة على أن الشُّ كر هلل طريق إلى معرفة اهلل واإليمان به، وهو أمان من نزول الباليا والمصائب، ولهذا أخرب تعالى عن قوم لوط كيف -أي: الشُّ كر هلل- أخذهم بالعذاب الشَّ ديد؛ بسبب مخالفتهم أمر اهلل، غير أهل لوط الذين شكروا اهلل فصدَّقوا لوطًا واتبعوه على دينه، فقال: ﭐ﴿ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ ﮃ ]، وقوله: ﭐ﴿ﮊ ﮋ ﮌ 35 -34 :ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ﴾ [القمر ﮍ﴾ فمعناه: «كذلك نثيب من شكرنا على نعمتنا عليه، فأطاعنا وانتهى إلى أمرنا .)172/2( ( الجامع ألحكام القرآن، للقرطبي(( .)534/7( ( أضواء البيان يف إيضاح القرآن بالقرآن، للشنقيطي(( .)582/1( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)343/9( ( جامع البيان عن تأويل آي القرآن، للطربي(( (. البالء بمقصد تحقيق العبادة لله وحده وقد امتنَّ اهلل تعالى على بني اسرائيل بنعمة اإلنجاء من((»وهنينا من جميع خلقنا آل فرعون بعدما كانوا فيه من العذاب، وذلك ألجل استخراج شكرهم على المسارِّ فقال: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤﭥ ﭦ ﭧ ﭨ ﭩ ]، وقد بين تعالى أن الشُّ كر يُربي النعم، والكفر يزيلها، 6:ﭪ ﭫ﴾ [إبراهيم إال ما كان منها على وجه االستدراج، فقال يف شكر النعمة: ﭐ﴿ﭭ ﭮ ﭯ ﭰ ]، وضرب مثلً بأهل 7:ﭱ ﭲﭳ ﭴ ﭵ ﭶ ﭷ ﭸ﴾ [إبراهيم القرى الذين كفروا بأنعم اهلل التي أنعم هبا عليهم، فقال يف قرية مكَّة التي سكنها أهل الشِّ رك باهلل، والتي كانت آمنة: ﭐ﴿ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ]، وأخرب اهلل تعالى عن قوم سبأ الذين أعرضوا عن 112:ﭸ ﭹ﴾ [النحل شكر المنعم، فقال: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ I ]، ووجه الدِّاللة من اآليات: «النَّحل» و«سبأ»؛ أنَّ اهلل17-15:ﮂ﴾ [سبأ يبتلي عباده بالنِّعم والخيرات؛ ألجل استخراج شكرهم على المسارِّ، وأنَّهم إن لم يقابلوا بالء اهلل الحسن بالشُّ كر والطَّاعة؛ فإنَّ مآلهم مآل تلك القرى التي هانت على اهلل غاية الهوان، وحلَّ عليها سَ خَط اهلل، وغضبه، بعد جحود أهلها لكلِّ نعم اهلل وعدم شكره، وقد أمر اهلل تعالى آل داود = بعد امتنانه عليهم بأصناف من النِّعم، وألوان من المنن؛ بأن يشكروه حقَّ الشُّ كر على نِعَمه التي سخرها لهم ما لم ]، 13 :يسخر مثلها لغيرهم، فقال: ﭐ﴿ﯮ ﯯ ﯰ ﯱﯲ ﯳ ﯴ ﯵ ﯶ﴾ [سبأ )596/22(ال َّ ا ق ( ال(( .)596/22( جع السَّ ابق ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف والمعنى: «اشكروا ربكم بطاعتكم إياه يا آل داود؛ على ما أنعم عليكم من النِّعم (، واآلية داللة واضحة على أنَّ شكر النعم بالحال والمقال؛ ((»][يف الدِّين والدُّنيا مؤذن بحفظ النِّعم، ورفع النِّقم، وقد كان آل داود قائمين بشكر اهلل قولً وعملً ، ففي الصَّ حيحين أنَّ عبد اهلل بن عمرو بن العاص ^، أخربه: أنَّ رسول اهلل | قال ، وأحبُّ الصِّ يام إلى اهلل صيام داود، وكان + له: «أحبُّ الصَّ الة إلى اهلل صالة داود (.((»ينام نصف اللَّيل ويقوم ثلثه، وينام سدسه، ويصوم يومًا، ويفطر يومًا َ إلى ربِّه؛ ليوفِّقه على شكر نعمه التي أنعمها عليه وعلى + وقد ابتهل سليمان والديه؛ لِمَا يف الشُّ كر من الثواب، ومن ازدياد النعم، ومن اندثار النِّقم فقال: ﭐ﴿ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ فضل اهلل عليه + ]، كما استشعر سليمان19:ﯗ ﯘ ﯙ ﯚ﴾ [النمل بالنُّبوَّة، والملك، والعلم، وتسخير الجنِّ، واإلنس، والطَّير له، وأنَّ ذلك بالء من ربِّه عظيم؛ ليرى منه أيشكر على نعمائه، أم أيكفر، فقال: ﭐ﴿ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ]. .)385/3( ( تفسير القرآن العظيم، البن كثير(( .)448/13( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب: ﭐ﴿ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ(( .135 ، ص6، ج4837 ]، برقم2 :ﭢ ﭣ ﭤ ﭥ ﴾ [الفتح )، 1840( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( وقال: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه ابن ماجه يف سننه: كتاب األدب، باب ).3803( )، وحسنه األلباين يف صحيح وضعيف ابن ماجه برقم3803( فضل الحامدين ، برقم البالء بمقصد تحقيق العبادة لله وحده يقول النَّسفي & 40:ﮧ ﮨﮩ ﮪ ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل ﭐ﴿ﮪ ﮫ ﮬ ﮭ ﮮﮯ﴾: «فالشُّ كر قيد للنِّعمة + يف تعليقه على قول سليمان (. ويخرب تعالى ذكره بأنه اخترب عباده بأن ((»الموجودة، وصيد للنِّعمة المفقودة فاوت بينهم يف األرزاق، والقوَّة، والجاه، واألخالق، وغير ذلك؛ ليستخرج منهم الشُّ كر على المسارِّ والصَّ رب على المضارِّ، فقال: ﴿ﰍ ﰎ ﰏ ﰐ ﰑ .)368/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( )، وأخرجه1131( ( أخرجه البخاري يف صحيحه: كتاب التهجد، باب: من نام عند السحر، برقم(( مسلم يف صحيحه: كتاب الصِّ يام، باب: النهي عن صوم الدهر لمن تضرر به أو فوَّت به حقًّا أو لم ).1159( يفطر العيدَيْن والتشريق، وبيان تفضيل صوم يوم، وإفطار يوم، برقم ).607/2( ( مدارك التنزيل وحقائق التأويل، للنسفي(( َّ] وقوله: ﴿ﰒ ﰓ ﰔ ﰕﰖ﴾ أي: «ليخترب الغني165 :ﰒ ﰓ ﰔ ﰕﰖ﴾ [األنعام (، وقد اخترب ((»يف غناه، ويسأله عن شكره، والفقير يف فقره، ويسأله عن صربه اهلل عباده المؤمنين بنعمة النَّصر والغنيمة يوم بدر؛ إلظهار الشُّ كر منهم؛ فيزدادوا ] ويعني بالبالء 17 :شكرً ا فقال: ﭐ﴿ﭟ ﭠ ﭡ ﭢ ﭣ﴾ [األنفال (. ((»الحسن: «النِّعمة الحسنة الجميلة : $ ومن التطبيقات النَّبويَّة للشُّ كر على النِّعمة الحسنة الجميلة ما صح عن عائشة : لِـمَ تصنع هذا يا $ أنَّ نبي اهلل | كان يقوم من اللَّيل حتى تتفطَّر قدماه، فقالت عائشة رسول اهلل، وقد غفر اهلل لك ما تقدَّم من ذنبك وما تأخَّ ر؟ قال: «أفال أحبُّ أن أكون عبدًا (، ومن دعائه ((شكورًا»، فلما كثر لحمه صلَّى جالسً ا، فإذا أراد أن يركع قام فقرأ ثم ركع أنَّ: $ المأثور | يف التعامل مع السَّ رَّ اء تارةً، والضَّ رَّ اء تارة أخرى، ما روته أمُّنا عائشة النَّبيَّ | كان إذا أتاه األمر يسرُّ ه قال: «الحمد هلل الذي بنعمته تتم الصالحات»، وإذا أتاه (. البالء بمقصد تحقيق العبادة لله وحده ((»األمر يكرهه، قال: «الحمد هلل على كل حال .)385/3( ( تفسير القرآن العظيم، البن كثير(( .)448/13( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب: ﭐ﴿ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ(( .135 ، ص6، ج4837 ]، برقم2 :ﭢ ﭣ ﭤ ﭥ ﴾ [الفتح )، 1840( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( وقال: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه ابن ماجه يف سننه: كتاب األدب، باب ).3803( )، وحسنه األلباين يف صحيح وضعيف ابن ماجه برقم3803( فضل الحامدين ، برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف جاء لفظ «التَّوبة» يف سبعة وثمانين موضعًا من آيات الذِّكر الحكيم، بعدَّة (.((صيغ، واشتقاقات التَّوبة يف اللُّغة مصدر الفعل الثالثي: تابَ ، يتوب، تُبْ ، توبةً، فهو تائب، والمفعول مَتُوب، وأصل كلمة التَّوبة مركَّبة من: «التاء والواو والباء كلمة واحدة تدلُّ على الرُّ جوع، يقال: تاب من ذنبه؛ أي رجع عنه، يتوب إلى اهلل توبةً ومَتابًا، (، ويف اللِّسان: «أصل تاب: عاد ((»فهو تائب، والتَّوْب: التَّوبة، وهو العودة إلى اهلل إلى اهلل ورجع وأناب، وتاب اهلل عليه، أي: عاد عليه بالمغفرة، وقوله تعالى: ﭐ﴿ﯻ ]، والتَّوبة: الرُّ جوع من الذَّنب، وتاب اهلل عليه: وفَّقه لها، 31:ﯼ ﯽ ﯾ﴾ [النُّور ورجل توَّاب: تائب إلى اهلل، واهلل توَّاب: يتوب على عبده بفضله إذا تاب إليه من ذنبه، واستتبت فالنًا: عرضت عليه التَّوبة مما اقرتف؛ أي الرُّ جوع والنَّدم على ما (، ويف الحديث عن ابن مَعْقِلٍ، وأبيه، عن ((»فَرَ طَ منه، واستتابه: سأله أن يتوب (، ومن ((»عبداهلل بن عمر بن الخطاب ^ قال: قال رسول اهلل |: «النَّدم توبة .)456-455 ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي (ص(( .)357/1( ( معجم مقاييس اللغة، البن فارس(( .)233/1( ( لسان العرب، البن منظور(( )، وصححه األلباين يف صحيح4252( ( أخرجه ابن ماجه يف سننه: كتاب الزهد، باب ذكر التوبة، برقم(( ،). كما أخرجه أحمد يف مسنده: مسند المكثرين من الصحابة4252( وضعيف ابن ماجه برقم )، وقال عنه محققو المسند: 4123( :مسند عبداهلل بن مسعود رضي اهلل تعالى عنه، برقم الحديث «صحيح، وهذا إسناد حسن». ا )، وصححه األلباين يف صحيح4252( ( أخرجه ابن ماجه يف سننه: كتاب الزهد، باب ذكر التوبة، برقم(( ،). كما أخرجه أحمد يف مسنده: مسند المكثرين من الصحابة4252( وضعيف ابن ماجه برقم )، وقال عنه محققو المسند: 4123( :مسند عبداهلل بن مسعود رضي اهلل تعالى عنه، برقم الحديث «صحيح، وهذا إسناد حسن». البالء بمقصد تحقيق العبادة لله وحده أسماء اهلل الحسنى التوَّاب، ومعناه: «هو الذي يرجع إلى تيسير أسباب التوبة لعباده مرة بعد أخرى، بما يُظهر لهم من آياته، ويسوق إليهم من تنبيهاته، ويُطلعهم عليه من تخويفاته، وتحذيراته؛ حتى إذا اطَّلعوا بتعريفه على غوائل الذُّنوب، استشعروا (، بينما ((»الخوف بتخويفه؛ فرجعوا إلى التَّوبة؛ فرجع إليهم فضل اهلل تعالى بالقبول التَّوبة يف اصطالح المفسِّ رين هي: «ترك الذَّنب لقُبحه، والنَّدم على ما فرط منه، والعزيمة على ترك المعاودة، وتدارك ما أمكنه أن يتدارك من األعمال باألعمال (، ويقول آخر: هي: «أن يكون العبد نادمًا على ما مضى مجمعًا على ((»باإلعادة (، ويقول غيره: «العزم على عدم العود إلى العصيان مع النَّدم على ((»أال يعود إليه (، وقد أورد محمد بن كعب القرظي & أنَّ التوبة تنعقد ((»ما فرط منه فيما مضى بتوافر أربعة أمور، وهي: «االستغفار باللِّسان، واإلقالع باألبدان، وإضمار ترك (. والحاصل أنّ التوبة هي: الرجوع إلى ((»العَوْد بالجنان، ومهاجرة سَ يِّئِ اإلخوان ه؛ عا لً غ آ ل ا ت ك الً ل انًا طاعة اهلل ت الى قل ًا إِ طاعة اهلل تعالى قلبًا، ولسانًا، وحالً ، وترك معاصيه؛ عاجلً غير آجل. كلمات التوبة؛ فتلقَّفها بالقبول، والعمل، + لقد أخرب اهلل تعالى أنَّه علَّم آدم ]، 37:والتَّسليم، فقال: ﭐ﴿ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄﰅ ﰆ ﰇ ﰈ ﰉ﴾ [البقرة وهذه الكلمات التي تلقَّاها آدم من ربِّه × مفسَّ رة بقوله تعالى: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ]، ووجه الدِّاللة من اآلية أنَّ 23 :ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ﴾ [األعراف المقصد من ابتالء آدم وزوجه @ باألكل من الشجرة؛ هو استخراج التوبة منهما، .)139/1( ( المقصد األسنى يف شرح معاين أسماء اهلل الحسنى، للغزالي(( .)169/1( ( المفردات يف غريب القرآن، للراغب(( .)316/4( ( لباب التأويل يف معاين التنزيل، للخازن(( .)367/28( ( التحرير والتنوير، البن عاشور(( .)350/9( ( الكشف والبيان عن تفسير القرآن، للثعلبي(( .)139/1( ( المقصد األسنى يف شرح معاين أسماء اهلل الحسنى، للغزالي(( .)169/1( ( المفردات يف غريب القرآن، للراغب(( .)316/4( ( لباب التأويل يف معاين التنزيل، للخازن(( .)367/28( ( التحرير والتنوير، البن عاشور(( .)350/9( ( الكشف والبيان عن تفسير القرآن، للثعلبي(( ،+ ن آدم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،+ وبيان أنَّ عداوة إبليس للناس جميعًا ممتدة جذورها يف عمق التاريخ، من آدم وقد قام آدم وزوجه بواجب التوبة تجاه رهبما؛ فأنعم اهلل عليهما بالرَّ حمة والمغفرة، بينما أعرض إبليس عن التوبة إلى اهلل؛ فسخط اهلل عليه، ولعنه، وطرده من رحمته. .)109/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)544/14( ( المرجع السابق(( .)544/14( ( المرجع السابق(( .)579/14( ( المرجع السابق(( البالء بمقصد تحقيق العبادة لله وحده يف كتابه أنَّ من مقاصد البالء استخراج التوبة من عباده فقال: I هذا وقد بيَّن المولى ] ويعني بالحسنات: 168 :﴿ﮧ ﮨ ﮩ ﮪ ﮫ﴾ [األعراف (، ويعني ((»«الرخاء يف العيش، والخفض يف الدُّنيا والدَّعة، والسَّ عة يف الرزق (، ((»بالسيِّئات: «الشِّ دَّة يف العيش، والشَّ ظف فيه، والمصائب والرَّ زايا يف األموال وجملة قوله تعالى: ﴿ﮪ ﮫ﴾ تعليل لقوله تعالى: ﴿ﮧ ﮨ (، ((»ﮩ﴾ والمعنى: «ليرجعوا إلى طاعة رهبم وينيبوا إليه، ويتوبوا من معاصيه ]، وقوله: ﭐ﴿ﭑ 35 :ونظيره: ﴿ﯿ ﰀ ﰁ ﰂﰃ ﰄ ﰅ﴾ [األنبياء ]، عن ابن عباس ^ 21 :ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ﴾ [السجدة ﴿ﭑ ﭒ ﭓ ﭔ﴾ يقول: «مصائب الدُّنيا، وأسقامها، وبالؤها مما أن الغرض من ابتالء عباده I (، وقد بيَّن اهلل((»يبتلي اهلل هبا العباد؛ حتى يتوبوا بظهور الفساد يف برِّ األرض وبحرها؛ استخراج التوبة، كما قال تعالى: ﭐ﴿ﯾ ﯿ ]، 41 :ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ﴾ [الروم قال أبو العالية &: «من عَصى اهلل يف األرض فقد أفسد يف األرض؛ ألنَّ صالح (، ومعنى قوله تعالى: ﭐ﴿ﰋ ﰌ﴾ أي: «كي ينيبوا ((»األرض والسَّ ماء بالطَّاعة .)208/13( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)209/13( ( المرجع السَّ ابق(( .)209/13( ( المرجع السَّ ابق(( .)189/20( ( المرجع السَّ ابق(( .)320/6( ( تفسير القرآن العظيم، البن كثير(( .)208/13( ( جامع البيان عن تأويل آي القرآن، للطربي(( َ .)209/13( ( المرجع السَّ ابق(( َ .)320/6( ( تفسير القرآن العظيم، البن كثير(( (، ومن أروع النَّماذج التي((»إلى الحق، ويرجعوا إلى التوبة، ويرتكوا معاصي اهلل تَروي لنا صورًا رائعة عن التوبة بعد البالء، ما قَصَّ ه القرآن الكريم يف حقِّ ثالثة من صحابة رسول اهلل |، وهم: « كعب بن مالك، وهالل بن أمية، ومُرارة بن الربيع (، الذين تخلَّفوا عن الخروج ((»[رضوان اهلل عليهم جميعًا]، وكلُّهم من األنصار معه يف غزوة تبوك، قال اهلل تعالى: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪﭫ ﭬ ]، وقوله: ﭐ﴿ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ 118 :ﭭ ﭮ ﭯ ﭰ﴾ [التوبة ﭩ ﭪﭫ﴾ يقول ابن جرير &: «وأيقنوا بقلوهبم أنْ ال شيء لهم يلجؤون إليه مما نزل هبم من أمر اهلل من البالء؛ بتخلفهم خِ الفَ رسول اهلل |، ينجيهم من كربه، وال مما يحذرون من عذاب اهلل، إال اهلل، ثم رزقهم اإلنابة إلى طاعته، والرُّ جوع إلى (، يف ((»ما يُرضيه عنهم، لينيبوا إليه، ويرجعوا إلى طاعته واالنتهاء إلى أمره وهنيه حين ذمَّ اهلل تعالى المنافقين؛ لتخلُّفهم عن التَّوبة من المعاصي بقوله: ﭐ﴿ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ﴾ ]، وقوله: ﭐ﴿ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ﴾ فإنه يعني: «ثم هم 126 :[التوبة مع البالء الذي يحلُّ هبم من اهلل، واالختبار الذي يعرض لهم، ال ينيبون من نفاقهم، وال يتوبون من كفرهم، وال هم يتذكرون بما يرون من حجج اهلل ويعاينون من آياته؛ (، هذا، واآليتان داللة واضحة على أنَّ ((»فيتعظوا هبا، ولكنهم مصرُّ ون على نفاقهم اهلل تعالى يبتلي عباده بأنواع الباليا والمصائب؛ ألجل أن يستخرج منهم التوبة وقت .)109/20( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)544/14( ( المرجع السابق(( .)544/14( ( المرجع السابق(( .)579/14( ( المرجع السابق(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف .البالء، أو عدمها، فيميز التائب من المصرِّ ، والطيِّب من الخبيث : # ومن األدعية النَّبويَّة الجامعة لمعاين التَّوبة ما صحَّ عن شدَّاد بن أوس عن النَّبيِّ |: «سيِّد االستغفار أن تقول: اللَّهمَّ أنت ربِّي ال إله إال أنت، خلقتني وأنا عبدك، وأنا على عهدك ووعدك ما استطعت، أعوذ بك من شرِّ ما صنعت، أبوء لك بنعمتك علَيَّ ، وأبوء لك بذنبي فاغفر لي، فإنَّه ال يغفر الذُّنوب إال أنت»، قال: «ومن قالها من النهار موقنًا هبا، فمات من يومه قبل أن يمسي، فهو من أهل الجنَّة، (.((»ومن قالها من اللَّيل وهو موقن هبا، فمات قبل أن يصبح، فهو من أهل الجنَّة .البالء، أو عدمها، فيميز التائب من المصرِّ ، والطيِّب من الخبيث : # ومن األدعية النَّبويَّة الجامعة لمعاين التَّوبة ما صحَّ عن شدَّاد بن أوس عن النَّبيِّ |: «سيِّد االستغفار أن تقول: اللَّهمَّ أنت ربِّي ال إله إال أنت، خلقتني وأنا عبدك، وأنا على عهدك ووعدك ما استطعت، أعوذ بك من شرِّ ما صنعت، أبوء لك بنعمتك علَيَّ ، وأبوء لك بذنبي فاغفر لي، فإنَّه ال يغفر الذُّنوب إال أنت»، قال: «ومن قالها من النهار موقنًا هبا، فمات من يومه قبل أن يمسي، فهو من أهل الجنَّة، (.((»ومن قالها من اللَّيل وهو موقن هبا، فمات قبل أن يصبح، فهو من أهل الجنَّة :المطلب الثَّامن البالء بمقصد الرَّ حمة َ لقد وردت مادة «رحم» يف ثالثمائة وتسعة وثالثين موضعًا من آي الذِّكر (. البالء بمقصد تحقيق العبادة لله وحده ((الحكيم، بصياغات، واشتقاقات مختلفة و«الرَّ حمة» يف اللُّغة مصدر الفعل الثالثي المتعدّي: رَحِم، يرحَ م، ارْحَ مْ، رحمة، فهو رَاحِم، والمفعول مَرحُ وم، وأصل مادة (رحم) يدلُّ على: «الرِّ قَّة والعطف والرأفة، يقال من ذلك: رحمه يرحمه، إذا رقَّ له وتعطَّف عليه، وَالرُّ حْ مُ وَالْمَرْ حَ مَةُ (؛ ويف اللِّسان: «الرَّ حمة: الرِّ قَّة والتعطُّف، والمرحمة مثله، وقد ((»والرَّ حمة بمعنًى (، ((»رحمته وترحَّ مت عليه، وتراحم القوم: رحم بعضهم بعضً ا، والرَّ حمة: المغفرة .)6306( ( أخرجه البخاري يف صحيحه: كتاب الدَّعوات، باب أفضل االستغفار، برقم(( .)309-304( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)498/2( ( معجم مقاييس اللغة، البن فارس(( .)230/12( ( لسان العرب، ابن منظور(( لقد وردت مادة «رحم» يف ثالثمائة وتسعة وثالثين موضعًا من آي الذِّكر (. ((الحكيم، بصياغات، واشتقاقات مختلفة و«الرَّ حمة» يف اللُّغة مصدر الفعل الثالثي المتعدّي: رَحِم، يرحَ م، ارْحَ مْ، رحمة، فهو رَاحِم، والمفعول مَرحُ وم، وأصل مادة (رحم) يدلُّ على: «الرِّ قَّة والعطف والرأفة، يقال من ذلك: رحمه يرحمه، إذا رقَّ له وتعطَّف عليه، وَالرُّ حْ مُ وَالْمَرْ حَ مَةُ (؛ ويف اللِّسان: «الرَّ حمة: الرِّ قَّة والتعطُّف، والمرحمة مثله، وقد ((»والرَّ حمة بمعنًى (، ((»ارحمته وترحَّ مت عليه، وتراحم القوم: رحم بعضهم بعضً ا، والرَّ حمة: المغفرة َّي لقد وردت مادة «رحم» يف ثالثمائة وتسعة وثالثين موضعًا من آي الذِّكر (. البالء بمقصد تحقيق العبادة لله وحده لقد أوجب اهلل تعالى على نفسه الكريمة تفضُّ لً منه، وتكرُّ مًا؛ أن يرحم ويغفر؛ لمن تاب من عباده، وأصلح العمل، وأن يُمهل، وال يعجِّل العقوبة؛ لِمَن لم يتب من عباده، فقال: ﴿ﭾ ﭿ ﮀ ﮁﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉﮊ ﮋ ]، وقوله: ﴿ﭾ ﭿ ﮀ ﮁﮂ﴾ 12 :ﮌ ﮍ ﮎ ﮏ ﮐ﴾ [األنعام معناه: «قضى أنَّه بعباده رحيم، ال يعجِّل عليهم بالعقوبة، ويقبل منهم اإلنابة والتوبة، (، ((» استعطاف للمُعرضين عنه إلى اإلقبال إليه بالتوبة-تعالى ذِكره- وهذا من اهلل ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ونظيره قوله تعالى: ﴿ﭫ ﭬ ﭭ ﭮ ﭯ # ]، ويف الصحيح عن أبي هريرة54 :ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ﴾ [األنعام عن النبي |، قال «إنَّ اهلل تعالى كتب كتابًا فهو عنده فوق العرش، إنَّ رحمتي (، وهبذا اإلسناد عن النبي | يقول: «جعل اهلل الرَّ حمة مائة ((»سبقت غضبي جزء، فأمسك عنده تسعةً وتسعين جزءًا، وأنزل يف األرض جزءًا واحدًا، فمن ذلك (، ((»الجزءِ يرتاحمُ الخلقُ ، حتى ترفعَ الفرسُ حافِرَ ها عن ولدها، خشية أن تصيبه اواآليتان مع الحديثَيْن داللة واضحة على أنَّ رحمة اهلل تسع جميع خلقه يف عاجل ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، والحاصل((» ِّبالمرحوم، واإلحسان إليه، ودفع الضرِّ عنه، وإعانته على المشاق أنَّ الرَّ حمة المقصودة يف بحثنا تأيت بمعنيَيْن؛ األول: اإلفضال واإلمهال، وهي التي يشرتك فيها جميع الخلق يف عاجل الدُّنيا، واآلخر: التطهير والتَّوفيق، وهي التي تخصُّ المؤمنين، دون غيرهم يف عاجل الدُّنيا. البالء بمقصد تحقيق العبادة لله وحده ((الحكيم، بصياغات، واشتقاقات مختلفة و«الرَّ حمة» يف اللُّغة مصدر الفعل الثالثي المتعدّي: رَحِم، يرحَ م، ارْحَ مْ، رحمة، فهو رَاحِم، والمفعول مَرحُ وم، وأصل مادة (رحم) يدلُّ على: «الرِّ قَّة والعطف والرأفة، يقال من ذلك: رحمه يرحمه، إذا رقَّ له وتعطَّف عليه، وَالرُّ حْ مُ وَالْمَرْ حَ مَةُ (؛ ويف اللِّسان: «الرَّ حمة: الرِّ قَّة والتعطُّف، والمرحمة مثله، وقد ((»والرَّ حمة بمعنًى (، ((»رحمته وترحَّ مت عليه، وتراحم القوم: رحم بعضهم بعضً ا، والرَّ حمة: المغفرة .)6306( ( أخرجه البخاري يف صحيحه: كتاب الدَّعوات، باب أفضل االستغفار، برقم(( .)309-304( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)498/2( ( معجم مقاييس اللغة، البن فارس(( .)6306( ( أخرجه البخاري يف صحيحه: كتاب الدَّعوات، باب أفضل االستغفار، برقم(( .)309-304( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( ا .)230/12( ( لسان العرب، ابن منظور(( ومن أسماء اهلل تعالى الحسنى: الرَّ حمن، والرَّ حيم، وهما اسمان مشتقَّان من الرَّ حمة على وجه المبالغة، والرَّ حمن أشدُّ مبالغةً من الرَّ حيم؛ ألنَّ «ربَّنا جلَّ ثناؤه رحمنُ جميع خلقه يف الدُّنيا واآلخرة، ورحيمُ المؤمنين خاصَّ ةً يف الدُّنيا واآلخرة، فأمَّا الذي عمَّ جميعَهم به يف الدُّنيا من رحمته فكان رحمانًا لهم به، كما قال جلَّ ثناؤه: ] ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ ﭱﭲ﴾ 34 :ﭐ﴿ﭗ ﭘ ﭙ ﭚ ﭛ ﭜﭝ﴾ [سورة إبراهيم ]، يف البَسْ ط يف الرزق، وتسخير السَّ حاب بالغَيْثِ ، وإخراج النَّبات 18 :[سورة النحل من األرض، وصحَّة األجسام والعقول، وسائر النِّعم التي ال تُحصى، التي يشرتك فيها المؤمنون والكافرون، وأمَّا يف اآلخرة، فالذي عمَّ جميعهم به فيها من رحمته، فكان لهم رحمانًا، تسويته بين جميعهم جلَّ ذكرُ ه يف عَدله وقضائه، فال يظلم أحدًا منهم مِثْقال ذَرَّة، فذلك معنى عمومه يف اآلخرة جميعَهم برحمته، وأمَّا ما خصَّ به المؤمنين يف عاجل الدُّنيا من رحمته، الذي كان به رحيمًا لهم فيها، كما قال جلَّ ] بما لطف هبم من توفيقه إيَّاهم 43 :ذكره: ﴿ﰑ ﰒ ﰓ﴾ [سورة األحزاب لطاعته، واإليمان به وبرسله، واتِّباع أمره واجتناب معاصيه، ممَّا خُ ذِل عنه من أشرك به، وكفر وخالف ما أمره به، وركب معاصيَه؛ وكان مع ذلك قد جعل جلَّ ثناؤه، ما أعدَّ يف آجل اآلخرة يف جنَّاته من النَّعيم المقيم والفوز المبين، لِمَن آمن به، (؛ أمَّا الرَّ حمة يف ((»وصدَّق رسله، وعمل بطاعته، خالصً ا، دون من أشرك وكفر به اصطالح المفسِّ رين فهي: «رقَّة تقتضي اإلحسان إلى المرحوم، وقد تستعمل تارة يف الرِّ قَّة المجرَّ دة، وتارة يف اإلحسان المجرَّ د عن الرِّ قَّة، وعلى هذا رُوي أنَّ الرَّ حمة (، ويقول آخر: هي: «الرِّ فق ((»رمن اهلل إنعام وإفضال، ومن اآلدميِّين رقَّة وتعطَّف .)129-128/1( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)347/1( ( المفردات يف غريب القرآن، للراغب(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (، والحاصل((» ِّبالمرحوم، واإلحسان إليه، ودفع الضرِّ عنه، وإعانته على المشاق أنَّ الرَّ حمة المقصودة يف بحثنا تأيت بمعنيَيْن؛ األول: اإلفضال واإلمهال، وهي التي يشرتك فيها جميع الخلق يف عاجل الدُّنيا، واآلخر: التطهير والتَّوفيق، وهي التي تخصُّ المؤمنين، دون غيرهم يف عاجل الدُّنيا. البالء بمقصد تحقيق العبادة لله وحده يُ جل ون ير م يف ُؤ ين ص لقد أوجب اهلل تعالى على نفسه الكريمة تفضُّ لً منه، وتكرُّ مًا؛ أن يرحم ويغفر؛ لمن تاب من عباده، وأصلح العمل، وأن يُمهل، وال يعجِّل العقوبة؛ لِمَن لم يتب من عباده، فقال: ﴿ﭾ ﭿ ﮀ ﮁﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉﮊ ﮋ ]، وقوله: ﴿ﭾ ﭿ ﮀ ﮁﮂ﴾ 12 :ﮌ ﮍ ﮎ ﮏ ﮐ﴾ [األنعام معناه: «قضى أنَّه بعباده رحيم، ال يعجِّل عليهم بالعقوبة، ويقبل منهم اإلنابة والتوبة، (، ((» استعطاف للمُعرضين عنه إلى اإلقبال إليه بالتوبة-تعالى ذِكره- وهذا من اهلل ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ونظيره قوله تعالى: ﴿ﭫ ﭬ ﭭ ﭮ ﭯ # ]، ويف الصحيح عن أبي هريرة54 :ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ﴾ [األنعام عن النبي |، قال «إنَّ اهلل تعالى كتب كتابًا فهو عنده فوق العرش، إنَّ رحمتي (، وهبذا اإلسناد عن النبي | يقول: «جعل اهلل الرَّ حمة مائة ((»سبقت غضبي جزء، فأمسك عنده تسعةً وتسعين جزءًا، وأنزل يف األرض جزءًا واحدًا، فمن ذلك (، ((»الجزءِ يرتاحمُ الخلقُ ، حتى ترفعَ الفرسُ حافِرَ ها عن ولدها، خشية أن تصيبه واآليتان مع الحديثَيْن داللة واضحة على أنَّ رحمة اهلل تسع جميع خلقه يف عاجل .)169/1( ( التحرير والتنوير، البن عاشور(( .)273/11( ( جامع البيان عن تأويل آي القرآن، للطربي(( ]، ﴿ﯩ ﯪ7 :( أخرجه البخاري يف صحيحه: كتاب التوحيد، باب: ﴿ﭬ ﭭ ﭮ ﭯ﴾ [هود(( .11)7422( ]، برقم129 :ﯫ ﯬ﴾ [التوبة ).6000( ( أخرجه البخاري يف صحيحه: كتاب األدب، باب: جعل اهلل الرحمة مائة جزء، برقم(( ).6000( ( أخرجه البخاري يف صحيحه: كتاب األدب، باب: جعل اهلل الرحمة مائة جزء، برقم(( دنياهم، بطريق اإلفضال، واإلنعام عليهم بالذَّات المقدَّسة، فيرحم أهل الكفر والظُّلم والطُّغيان بإمهالهم، واستعطاف قلوهبم؛ إلى اإلقبال إليه بالتَّوبة، واإلنابة، مع إفراطهم يف الكفر والظُّلم والطُّغيان ومحاربتهم اهلل ورسوله والمؤمنين، ويرحم أهل المعصية؛ بتوفيقهم لإلنابة إليه، ومغفرة ذنوهبم، مع إفراطهم يف هتك محارم اهلل، ويرحم أهل طاعته؛ بتثبيتهم على العمل الصَّ الح، واالستقامة يف الدِّين، كما أُمروا، مع تقصيرهم يف العبادة. دليلَ رحمته بجميع خلقه، مؤمنهم وكافرهم، وهو كونه -تعالى ذكره- ثم ذكر تعالى لو يعاقب النَّاس على ما اقرتفوه من المعاصي واآلثام؛ لعجَّل لهم العذاب يف الدُّنيا، غير أنَّه سبحانه أمهلهم لوقت معلوم؛ حتى يتوبوا من سوء أعمالهم فقال: ﴿ﮫ ﮬ ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗﯘ ﯙ ﯚ ﯛ ﯜ ﯝ ﯞ ( ((»]، وقوله: ﴿ﮭ ﮮﮯ﴾ فمعناه: «يؤخِّ ر العذاب عنهم58 :ﯟ ﯠ﴾ [الكهف (. البالء بمقصد تحقيق العبادة لله وحده ((»و«يقبل توبتهم إذا تابوا لقد أوضح اهلل تعالى يف سورتَيِ األعراف، وهود، ومواضع أخرى؛ أنَّه أنجى هودًا، وصالحًا، وشعيبًا، وسائر أنبيائه =، والذين آمنوا معهم، برحمة منه، وتفضُّ لٍ، ، ومن آمن معه: ﴿ﮦ ﮧ + وتكرُّ م، من بطش الذين كفروا، فقال يف هود ]، 72 :ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯﮰ ﮱ ﯓ ﯔ﴾ [األعراف ، ومن آمن معه: ﭐ﴿ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ + وقال يف صالح ، + ]، وقال يف شعيب66 :ﮐ ﮑ ﮒ ﮓ ﮔﮕ ﮖ ﮗ ﮘ ﮙ ﮚ﴾ [هود ومن آمن معه: ﴿ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ﯘ ﯙ ﯚ ﯛ .)352/2( ( بحر العلوم، للسمرقندي(( .)189/7( ( تأويالت أهل السنة، ألبي منصور الماتريدي(( ،]، ويستفاد من آيات اإلنجاء94 :ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ﴾ [هود أنه من تمام رحمة اهلل بعباده عند اشتداد البالء، أنه ال يسلِّط أعداءه على أوليائه؛ ألنَّهم إذا ظفروا؛ طغوا يف البالد؛ فأكثروا فيها الفساد، وأهلكوا الحرث والنسل. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وهبذا اإلسناد عن النبي |، قال: «إنَّ عِظَم الجزاء مع عِظَم البالء، وإنَّ ((»ورقها (.((»اهلل إذا أحبَّ قومًا ابتالهم، فمن رضي فله الرِّ ضا، ومن سخط فله السخط تكفير السيِّئات، لقوله تعالى: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ -2 ﭙ ﭚ ﭛ ﭜ ﭝﭞ ﭟ ﭠ ﭡﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹﭺ ]، ويف الصَّ حيح عن أبي سعيد الخدري 195 :ﭻ ﭼ ﭽ ﭾ﴾ [آل عمران وأبي هريرة ^: عن النبي | قال: «ما يصيب المسلم، من نصب وال وصب، وال (.((»هم وال حزن وال أذًى وال غم، حتى الشوكة يشاكها، إال كفر اهلل بها من خطاياه إرادة الخير بالناس، لِمَا رواه محمد بن عبداهلل بن عبدالرحمن بن أبي -3 ،، أنه قال: سمعت سعيد بن يسار أبا الحباب، يقول: سمعت أبا هريرة# صعصعة (، وروى الرتمذي يف ((»يقول: قال رسول اهلل |: «من يُرِد اهلل به خيرً ا يُصِ ب منه ، قال: قال رسول اهلل |: «إذا أراد اهلل بعبده الخير عجل له العقوبة # سُ ننه عن أنس .)5661( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما يقال للمريض، وما يجيب، برقم(( ،)2396( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( :). كما أخرجه ابن ماجه يف سننه2396( :وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).4031( كتاب الفتن، باب الصَّ رب على البالء، يوم النحر، برقم ).5641( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما جاء يف كفارة المرض، برقم(( .)5645( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما جاء يف كفارة المرض، برقم(( إرادة الخير بالناس، لِمَا رواه محمد بن عبداهلل بن عبدالرحمن بن أبي -3 ،، أنه قال: سمعت سعيد بن يسار أبا الحباب، يقول: سمعت أبا هريرة# صعصعة (، وروى الرتمذي يف ((»يقول: قال رسول اهلل |: «من يُرِد اهلل به خيرً ا يُصِ ب منه ، قال: قال رسول اهلل |: «إذا أراد اهلل بعبده الخير عجل له العقوبة # سُ ننه عن أنس .)5661( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما يقال للمريض، وما يجيب، برقم(( ،)2396( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( :). وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: آِيَااَآ زيادة الثواب ومضاعفة األجر؛ لقوله تعالى: ﭐ﴿ﭮ ﭯ ﭰ ﭱ ﭲ -1 ﴾ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ ]، ووجه الدِّاللة من اآلية؛ أنَّ اهلل يبتلي عباده بصنوف المصائب، 157-156 :[البقرة واالبتالءات يف األرض، ويف أنفسهم؛ ألنَّ أعمالنا وطاعاتنا ال تؤهلنا لنيل مغفرة اهلل ورضوانه، وألجل هذا قضى اهلل علينا برحمة منه، وتفضُّ ل، وتكرُّ م، أن نمرض ونعتلَّ ، ونصاب بأنواع المصائب، والباليا؛ حتى نستكمل جانب النَّقص فينا؛ إذ لو قال: سمعت # لم نُبتَلَ ؛ لَمَا تلذَّذ مؤمن قطُّ بنعيم الجنَّة، وقد صح أن أبا هريرة رسول اهلل | يقول: «لن يُدخِ ل أحدًا عمله الجنة»، قالوا: وال أنت يا رسول اهلل؟ قال: «ال، وال أنا، إال أن يتغمدين اهلل بفضل ورحمة، فسددوا وقاربوا، وال يتمنَيَنَّ (. ((»أحدكم الموت: إما محسنًا فلعله أن يزداد خيرً ا، وإما مسيئًا فلعله أن يستعتب أهنا قالت: سمعت رسول اهلل | يقول: «ما من عبد $ وقد ورد يف عن أم سلمة تصيبه مصيبة فيقول: ﭐ﴿ﭳ ﭴ ﭵ ﭶ ﭷ﴾ اللهم اؤجُ رْ ين يف مصيبتي، وَأَخْ لِفْ لي خيرً ا منها، إال آجره اهلل من مصيبته، وأخلف له خيرً ا منها» قالت: فلما تُوُيف أبو (، ((| سلمة، قلت كما أمرين رسول اهلل |، فأخلف اهلل لي خيرً ا منه، رسول اهلل قال: دخلت على رسول اهلل | # روي يف الصَّ حيح من حديث عبد اهلل بن مسعود .)5673( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: تمني المريض الموت، برقم(( .)918( ( أخرجه مسلم يف صحيحه: كتاب الجنائز، باب ما يقال عند المصيبة، برقم(( وهو يوعك وعكًا شديدًا، فمسسته بيدي، فقلت: يا رسول اهلل، إنك لتوعك وعكًا شديدًا؟ فقال رسول اهلل |: «أجل، إين أُوعك كما يوعك رجالن منكم» فقلت: ذلك أن لك أجرَ يْن؟ فقال رسول اهلل |: «أجل»، ثم قال رسول اهلل |: «ما من مسلم يصيبه أذًى، مرض فما سواه، إال حط اهلل له سيئاته، كما تحط الشجرة (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وهبذا اإلسناد عن النبي |، قال: «إنَّ عِظَم الجزاء مع عِظَم البالء، وإنَّ ((»ورقها (.((»اهلل إذا أحبَّ قومًا ابتالهم، فمن رضي فله الرِّ ضا، ومن سخط فله السخط تكفير السيِّئات، لقوله تعالى: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ -2 ﭙ ﭚ ﭛ ﭜ ﭝﭞ ﭟ ﭠ ﭡﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹﭺ ]، ويف الصَّ حيح عن أبي سعيد الخدري 195 :ﭻ ﭼ ﭽ ﭾ﴾ [آل عمران وأبي هريرة ^: عن النبي | قال: «ما يصيب المسلم، من نصب وال وصب، وال (.((»هم وال حزن وال أذًى وال غم، حتى الشوكة يشاكها، إال كفر اهلل بها من خطاياه إرادة الخير بالناس، لِمَا رواه محمد بن عبداهلل بن عبدالرحمن بن أبي -3 ،، أنه قال: سمعت سعيد بن يسار أبا الحباب، يقول: سمعت أبا هريرة# صعصعة (، وروى الرتمذي يف ((»يقول: قال رسول اهلل |: «من يُرِد اهلل به خيرً ا يُصِ ب منه ، قال: قال رسول اهلل |: «إذا أراد اهلل بعبده الخير عجل له العقوبة # سُ ننه عن أنس وهو يوعك وعكًا شديدًا، فمسسته بيدي، فقلت: يا رسول اهلل، إنك لتوعك وعكًا شديدًا؟ فقال رسول اهلل |: «أجل، إين أُوعك كما يوعك رجالن منكم» فقلت: ذلك أن لك أجرَ يْن؟ فقال رسول اهلل |: «أجل»، ثم قال رسول اهلل |: «ما من مسلم يصيبه أذًى، مرض فما سواه، إال حط اهلل له سيئاته، كما تحط الشجرة (. وهبذا اإلسناد عن النبي |، قال: «إنَّ عِظَم الجزاء مع عِظَم البالء، وإنَّ ((»ورقها (.((»اهلل إذا أحبَّ قومًا ابتالهم، فمن رضي فله الرِّ ضا، ومن سخط فله السخط ايله ذلك أن لك أجرَ يْن؟ فقال رسول اهلل |: «أجل»، ثم قال رسول اهلل |: «ما من مسلم يصيبه أذًى، مرض فما سواه، إال حط اهلل له سيئاته، كما تحط الشجرة (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: كما أخرجه ابن ماجه يف سننه2396( :وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).4031( كتاب الفتن، باب الصَّ رب على البالء، يوم النحر، برقم ).5641( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما جاء يف كفارة المرض، برقم(( .)5645( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما جاء يف كفارة المرض، برقم(( .)5661( ( أخرجه البخاري يف صحيحه: كتاب المرضى، باب: ما يقال للمريض، وما يجيب، برقم(( ،)2396( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب من اتقى المحارم فهو أعبد الناس، برقم(( :). كما أخرجه ابن ماجه يف سننه2396( :وحسَّ نه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).4031( كتاب الفتن، باب الصَّ رب على البالء، يوم النحر، برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف .(((»يف الدنيا، وإذا أراد اهلل بعبده الشر أمسك عنه بذنبه حتى يوايف به يوم القيامة نيل أجر الشهيد لِمَن أُصيب باألوباء والطَّواعين، لِمَا رُوي يف الصحيح -4 قالت: سألت رسول اهلل | عن الطاعون، فأخربين «أنه عذاب يبعثه$ عن عائشة اهلل على من يشاء، وأن اهلل جعله رحمة للمؤمنين، ليس من أحد يقع الطاعون، فيمكث يف بلده صابرً ا محتسبًا، يعلم أنه ال يصيبه إال ما كتب اهلل له، إال كان له مثل (.((»أجر شهيد فيمكث يف بلده صابرا محتسبا، يعلم أنه ال يصيبه إال ما كتب اهلل له، إال كان له مثل (.((»أجر شهيد رفع الدَّرجات للمبتَلَى كما هو يف حق األنبياء =، وشواهد ذلك متعددة -5 ، الذي ابتاله اهلل بالمرض يف جسده+ يف القرآن الكريم، ومن ذلك نبي اهلل أيوب فصرب واحتسب؛ حتى فرَّ ج اهلل عنه، قال تعالى: ﭐ﴿ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍ ﰎ ﰏ ﰐ ﰑ ﰒ ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ﴾ ]، قال ابن كثير: «هذه تذكرة لِمَن ابتُلِي يف جسده أو ماله أو ولده، فله أُسوة 44 -41 :[ص بنبي اهلل أيوب؛ حيث ابتاله اهلل بما هو أعظم من ذلك فصرب واحتسب، حتى فَرَّ ج اهلل (، وكما هو يف حقِّ الجهاد يف سبيل اهلل، الذي فيه أصناف من األذى واالبتالء، يف ((»عنه األموال بنقصها وهالكها، ويف األنفس بالقروح واآلالم والقتل، قال تعالى: ﴿ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ ﯨ ،)2396( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب ما جاء يف الصَّ رب على البالء، برقم(( ). وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: كما أخرجه الحاكم يف2396( وقد صححه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).8799( مستدركه: كتاب العلم، برقم ).3474( ( أخرجه البخاري يف صحيحه: كتاب فضائل األنبياء، باب: حديث الغار، برقم(( .)224/1( ( تفسير القرآن العظيم، البن كثير(( رفع الدَّرجات للمبتَلَى كما هو يف حق األنبياء =، وشواهد ذلك متعددة -5 ، الذي ابتاله اهلل بالمرض يف جسده+ يف القرآن الكريم، ومن ذلك نبي اهلل أيوب فصرب واحتسب؛ حتى فرَّ ج اهلل عنه، قال تعالى: ﭐ﴿ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍ ﰎ ﰏ ﰐ ﰑ ﰒ ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ﴾ ]، قال ابن كثير: «هذه تذكرة لِمَن ابتُلِي يف جسده أو ماله أو ولده، فله أُسوة 44 -41 :[ص بنبي اهلل أيوب؛ حيث ابتاله اهلل بما هو أعظم من ذلك فصرب واحتسب، حتى فَرَّ ج اهلل (، وكما هو يف حقِّ الجهاد يف سبيل اهلل، الذي فيه أصناف من األذى واالبتالء، يف ((»عنه األموال بنقصها وهالكها، ويف األنفس بالقروح واآلالم والقتل، قال تعالى: ﴿ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ ﯨ ،)2396( ( أخرجه الرتمذي يف صحيحه: أبواب الزهد، باب ما جاء يف الصَّ رب على البالء، برقم(( ). وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ((»وأسباب هنوضهم، وال يلزم من إظهاره على األديان أن تنقرض تلك األديان ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف .(((»-أو: هذا أيسر- رسول اهلل |: «هذا أهون إظهار اإلسالم على الدِّين كلِّه، وإقامة الحُجَّة على جميع الخلق ليميِّزوا -8 بين الحقِّ والباطل، والكفر والضَّ الل، والزيغ واإليمان، يقول تعالى: ﴿ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ﴾ ]، ونظيره قوله: ﴿ﯰ ﯱ ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ 33 :[التوبة ]، يقول ابن عاشور: «وظهور اإلسالم على 28 :ﯺﯻ ﯼ ﯽ ﯾ﴾ [الفتح الدِّين كلِّه حصل يف العالم باتِّباع أهل الملل إيَّاه يف سائر األقطار، بالرَّ غم على كراهية أقوامهم وعظماء مللهم ذلك، ومقاومتهم إيَّاه بكل حيلة، ومع ذلك فقد ظهر وعال وبان فضله على األديان التي جاورها، وسالمته من الخرافات واألوهام التي تعلَّقوا هبا، وما صلحت بعض أمورهم إلَّ فيما حاكوه من أحوال المسلمين (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: كما أخرجه الحاكم يف2396( وقد صححه األلباين يف صحيح وضعيف سنن الرتمذي برقم ).8799( مستدركه: كتاب العلم، برقم م م ).3474( ( أخرجه البخاري يف صحيحه: كتاب فضائل األنبياء، باب: حديث الغار، برقم(( .)224/1( ( تفسير القرآن العظيم، البن كثير(( ]، وقوله:ﭐ﴿ﮗ186 :ﯩ ﯪﯫ ﯬ ﯭ ﯮ ﯯ ﯰ ﯱ ﯲ ﯳ﴾ [آل عمران ]، وقوله: ﭐ﴿ﭠ ﭡ ﭢ 4 :ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ﴾ [محمد ].31 :ﭣ ﭤ ﭥ ﭦ ﭧ﴾ [محمد تطهير القلوب من الكرب والخيالء، كما حدث يوم حنين، قال تعالى: ﭐ﴿ﮞ -6 ﮟ ﮠ ﮡ ﮢ ﮣﮤ ﮥ ﮦﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ].25 :ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ﴾ [التوبة تطهير القلوب من الكرب والخيالء، كما حدث يوم حنين، قال تعالى: ﭐ﴿ﮞ -6 ﮟ ﮠ ﮡ ﮢ ﮣﮤ ﮥ ﮦﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ].25 :ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ﴾ [التوبة الرَّ دع عن القبائح، واآلثام، والظُّلم، والطُّغيان، لذا أخرب اهلل تعالى بأنه -7 قادر على أن يذيق الجاحدين بألوهيته ألوان المصائب واالبتالءات، فال يدفعه عنهم أحد، فقال: ﴿ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ]، وقوله: 65 :ﯘ ﯙ ﯚ ﯛ ﯜﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ﴾ [األنعام ﴿ﯢ ﯣ﴾ قال أبو السُّ عود &: «كي يفقَهوا ويقِفوا على جلية األمر فيرجعوا (، ووجه الدِّاللة من هذه اآلية؛ أنَّ هذا ((»عمَّا هُم عليهِ من المكابرة والعِناد التهديد للمشركين، هو رحمة من رحمات اهلل تعالى عليهم؛ حتى يصرفهم عمَّا هم فيه من الشرك، وعبادة األوثان، واألهواء، إلى ما هم مكلَّفون به من أنواع العبادة، كما يُستفاد من اآلية الكريمة أنَّ اهلل تعالى رحم هذه األمة، وحفظها من اإلهالك العام، وعذاب االستئصال، كحال األمم السابقة، ودلَّ على هذا ما رواه ، قال: لما نزلت هذه اآلية: ﴿ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ﴾ # جابر ]، 65 :]، قال رسول اهلل |: «أعوذ وجهك»، قال: ﴿ﮱ ﯓ ﯔ ﯕ﴾ [األنعام65 :[األنعام ] قال 65 :قال: «أعوذ بوجهك» ﴿ﯖ ﯗ ﯘ ﯙ ﯚ ﯛ ﯜﯝ﴾ [األنعام .)146/3( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف .(((»-أو: هذا أيسر- رسول اهلل |: «هذا أهون إظهار اإلسالم على الدِّين كلِّه، وإقامة الحُجَّة على جميع الخلق ليميِّزوا -8 بين الحقِّ والباطل، والكفر والضَّ الل، والزيغ واإليمان، يقول تعالى: ﴿ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ﴾ ]، ونظيره قوله: ﴿ﯰ ﯱ ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ 33 :[التوبة ]، يقول ابن عاشور: «وظهور اإلسالم على 28 :ﯺﯻ ﯼ ﯽ ﯾ﴾ [الفتح الدِّين كلِّه حصل يف العالم باتِّباع أهل الملل إيَّاه يف سائر األقطار، بالرَّ غم على كراهية أقوامهم وعظماء مللهم ذلك، ومقاومتهم إيَّاه بكل حيلة، ومع ذلك فقد ظهر وعال وبان فضله على األديان التي جاورها، وسالمته من الخرافات واألوهام التي تعلَّقوا هبا، وما صلحت بعض أمورهم إلَّ فيما حاكوه من أحوال المسلمين (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ((»وأسباب هنوضهم، وال يلزم من إظهاره على األديان أن تنقرض تلك األديان ذلك أنَّ إقامة اهلل حُ جَّته على الكفَّار بإظهار اإلسالم على الدِّين كلِّه، وبإرسال آياته الدَّالَّة عليه، لهو من تمام رحمة اهلل تعالى المقتضية إمهال عباده، وعدم تعجيل العقوبة على كفرهم وفسقهم، وتذكيرهم بين الحين واآلخر بأحقِّيَّة ملَّة اإلسالم على الدِّين كلِّه، واستعطاف قلوهبم إلى اإلقبال إليه بالتَّوبة واإلنابة، يقول تعالى: ﭐ﴿ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬﭭ ﭮ ﭯ ﭰ ﭱﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ]، ويقول: ﴿ﭑ ﭒ ﭓ ﭔ 35 :ﭺ ﭻ ﭼ ﭽ ﭾ ﭿﮀ ﮁ ﮂ ﮃ ﮄ﴾ [يونس ﭕ ﭖ ﭗ ﭘﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ]، ويقول: 125 :ﭣ ﭤ ﭥﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ﴾ [األنعام ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب: باب قوله: ﴿ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ(( .)4628( ] اآلية، برقم65 :ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ﴾ [األنعام ).174-173/10( ( التحرير والتنوير، البن عاشور(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف أأاه ذلك أنَّ إقامة اهلل حُ جَّته على الكفَّار بإظهار اإلسالم على الدِّين كلِّه، وبإرسال آياته الدَّالَّة عليه، لهو من تمام رحمة اهلل تعالى المقتضية إمهال عباده، وعدم تعجيل العقوبة على كفرهم وفسقهم، وتذكيرهم بين الحين واآلخر بأحقِّيَّة ملَّة اإلسالم على الدِّين كلِّه، واستعطاف قلوهبم إلى اإلقبال إليه بالتَّوبة واإلنابة، يقول تعالى: ﭐ﴿ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬﭭ ﭮ ﭯ ﭰ ﭱﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ]، ويقول: ﴿ﭑ ﭒ ﭓ ﭔ 35 :ﭺ ﭻ ﭼ ﭽ ﭾ ﭿﮀ ﮁ ﮂ ﮃ ﮄ﴾ [يونس ﭕ ﭖ ﭗ ﭘﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ]، ويقول: 125 :ﭣ ﭤ ﭥﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ﴾ [األنعام ( أخرجه البخاري يف صحيحه: كتاب تفسير القرآن، باب: باب قوله: ﴿ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ(( .)4628( ] اآلية، برقم65 :ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ﴾ [األنعام ).174-173/10( ( التحرير والتنوير، البن عاشور(( .]53 :﴿ﲽ ﲾ ﲿ ﳀ ﳁ ﳂ ﳃ ﳄ ﳅ ﳆ ﳇ﴾ [فصلت إذَنْ فبناء على ما تقدَّم، يتبيَّن لنا أنَّ اإلصابة باالبتالء من تمام رحمة اهلل بعباده، وحبِّه لهم، وشفقته عليهم، حتى يوقظهم من غفلتهم، فيقيم عليهم الحُجَّة، فيظهر لهم الحقَّ من الباطل، فيوفِّقهم للتوبة، فيربِّيهم على طاعته، فيكفِّر عنهم سيِّئاهتم، فيضاعف لهم حسناهتم، فيرفع درجاهتم، فيزيدهم من فضله، فيرضى عنهم. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وقد تعلَّمنا من هَدْي األنبياء عليهم الصالة والسالم يف القرآن الكريم عامَّة، وهَدْي النبيِّ | على وجه الخصوص؛ كثرة التعوُّذ من كلِّ أنواع البالء واالبتالء، ، مع كثرة التضرُّ ع إليه يف حال اإلصابة بالبالء، والصَّ رب I واللُّجوء إلى اهلل واالحتساب على ذلك، مع اإليقان التَّامِّ أنَّه: ﭐ﴿ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ]، واتخاذ اإلصابة بالبالء، 51 :ﮎ ﮏﮐ ﮑ ﮒ ﮓ ﮔ﴾ [التوبة فرصة للتقرُّ ب إلى اهلل تعالى بفعل الخيرات، وترك المنكرات، والتكثير من أنواع الطَّاعات، والقربات، مع العناية الكاملة بغسل أدران النَّفس، والقلب، صباحً ا ومساءً؛ حتى نظفر عند اهلل بالسَّ عادة الدُّنيويَّة، واألخرويَّة. ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف :المطلب التَّاسع البالء بمقصد التَّمحيص :المطلب التَّاسع البالء بمقصد التَّمحيص و«التَّمحيص» يف اللُّغة مصدر الفعل الثالثي المضعَّف: محَّص يُمحِّص، تمحيصً ا، فهو مُمحِّص، والمفعول مُمحَّص، أصل التَّمحيص يف اللُّغة مركَّب من: «(محص) الميم والحاء والصاد أصل واحد صحيح يدلُّ على تخليص شيئًا وتنقيته. ومَحَصَ هُ مَحْصً ا: خلَّصه من كل عيب، [و] محَّص اهلل العبد من الذَّنب: طهَّره منه (، ويف اللِّسان: ((»ونقَّاه، ومحَّصه، ومحَّصت الذَّهب بالنار: خلَّصته من الشَّ وب «ومحَّص الشَّ يء يمحِّصه محصً ا، ومحَّصه: خلَّصه من كلِّ عيب، والمحص يف اللُّغة: التَّخليص والتَّنقية، وتمحيص الذُّنوب: تطهيرها، ومعنى التَّمحيص النَّقص. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: يقول ابن القيم &: «وهذا التَّمحيص يكون يف دار الدُّنيا بأربعة أشياء: بالتوبة، واالستغفار، وعمل الحسنات الماحية، والمصائب المكفرة، وإن لم تفِ هذه األربعة بتمحيصه وتخليصه، محص يف الربزخ بثالثة أشياء: بصالة أهل اإليمان الجنازة عليه، وبفتنة القرب، وبما يهدي إخوانه المسلمون إليه من هدايا األعمال، وجعل ثواب ذلك له، فإن لم تفِ هذه بالتَّمحيص، مُحِّص بين يدَيْ ربِّه يف الموقف بأربعة أشياء: أهوال القيامة، وشدَّة الموقف، وشفاعة الشُّ فعاء، وعفو اهلل ×، فإن لم تفِ هذه الثالثة بتمحيصه فال بدَّ له من دخول الكير، رحمة يف حقِّه؛ ليتخلَّص ويتمحَّص، ويتطهَّر يف النَّار، ويكون مكثه فيها على حسب كثرة الخبث وقلَّته، فإذا (.((»خرج خبثه وصار خالصً ا طيِّبًا، أُخرج من النَّار، وأُدخل الجنَّة ِ لقد أخرب اهلل تعالى يف كتابه أنَّ سُ نته جارية يف امتحان النَّاس بضروب الفتن ]، 2 :والمِحن فقال: ﴿ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ﴾ [العنكبوت فتارة يكون االمتحان بشدائد التَّكليف؛ حتى يطهِّر قلوب المؤمنين، ويخلِّصها من .)936/3( ( تفسير الراغب األصفهاين، للراغب(( .)139/4( ( التحرير والتنوير، البن عاشور(( .)91/2( ( إرشاد العقل السليم إلى مزايا الكتاب الكريم، ألبي السعود العمادي(( .)163/1( ( مدارج السالكين بين منازل ﴿ﭢ ﭣ ﭤ ﭥ﴾، البن قيم(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف العيوب، أو يكرمها بالشَّ هادة؛ لتنال الدَّرجات العُال، يقول اهلل: ﭐ﴿ﭑ ﭒ ﭓ ]، وقوله: ﭐ﴿ﭑ ﭒ ﭓ ﭔ﴾ 141 :ﭔ ﭕ ﭖ﴾ [آل عمران معناه: «يكفِّر عنهم من ذنوهبم، إن كان لهم ذنوب، وإال رفع لهم يف درجاهتم بحسب أنه قال: لَمَّا نزلت ﭐ﴿ﭰ ﭱ # (، وهبذا المعنى صحَّ عن أبي هريرة((»ما أصيبوا به ] بلغت من المسلمين مبلغًا شديدًا، فقال رسول اهلل |: 123 :ﭲ ﭳ ﭴ﴾ [النساء «قاربوا، وسدِّ دوا؛ ففي كلِّ ما يُصاب به المسلم كفَّارة، حتى النَّكبة ينكبها، أو أنَّ رسول اهلل |، # (، وفيه أيضً ا عن جابر بن عبد اهلل((»الشَّ وكة يشاكها -أو: يا أم المسيِّب- دخل على أم السَّ ائب، أو أمِّ الْمُسَ يِّبِ فقال: «ما لك يا أم السَّ ائب تزفزفين؟» قالت: الحمَّى، ال بارك اهلل فيها، فقال: «ال تسبِّي الحمَّى؛ فإهنا تُذهب (، ونظير هذا قد ذُكر يف السُّ نة يف ((»خطايا بني آدم، كما يُذهب الكير خبث الحديد غير موضع. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: يقال: محَّص اهلل عنك ذنوبك؛ أي نقصها، فسمَّى اهلل ما أصاب المسلمين من بالء (، أمَّا التمحيص ((»تمحيصً ا؛ ألنَّه ينقص به ذنوهبم، والتَّمحيص: االختبار واالبتالء (، ويقول غيره: هو: «إزالة ما قد ((»يف اصطالح المفسِّ رين فهو: «التَّطهير والتَّصفية انفصل من الخير عن الشرِّ ، وكان المقصود به ما ذكره اهلل تعالى يف قوله: ﭐ﴿ﮏ .)662( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)300/5( ( معجم مقاييس اللغة، البن فارس(( .)90/7( ( لسان العرب، البن منظور(( .)420/1( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)662( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)300/5( ( معجم مقاييس اللغة، البن فارس(( .)90/7( ( لسان العرب، البن منظور(( .)420/1( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( ا .)420/1( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( (، ويرى آخر أنَّه: «تخليص الشيء مما((»]37 :ﮐ ﮑ ﮒ ﮓ﴾ [األنفال (، وعبَّر عنه آخر بأنه: «محو لآلثار وإزالة ((»يخالطه مما فيه عيب له، فهو كالتَّزكية (، إذَنْ مما سبق من تعريفات للتَّحميص لغةً واصطالحً ا؛ يتبيَّن لنا أن ((»لألوضار التَّمحيص هو عبارة عن اختبار قلوب النَّاس بتنقيتها من المعايب والمثالب؛ حتى يتميَّز المؤمن من غيره يف الدُّنيا واآلخرة، أو يتطهَّر المؤمن من الذَّنب إن كان له ذنب، وإال فهو رفع لدرجاته. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وتارة يكون االمتحان بشدائد التَّكليف حتى يميَّز الصَّ ادق يف إيمانه من غيره، ويظهر أمره للنَّاس؛ ألجل أخذ الحذر والحيطة، ممن يدَّعي شيئًا ليس فيه، فيقول: ﭐ﴿ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞﮟ ﮠ ﮡ ﮢ ﮣ﴾ ] وقوله: ﭐ﴿ﮛ ﮜ ﮝ ﮞﮟ﴾ أي: «وليميز الخبيث من الطيِّب، 154 :[أل عمران (، وهذا تمامًا مثل ما ((»ويظهر أمر المؤمن والمنافق للنَّاس يف األقوال واألفعال حصل يوم أُحد عندما اشتدَّت الحرب بين المسلمين وكفَّار قريش، فكاد االنتصار .)127/2( ( تفسير القرآن العظيم، البن كثير(( ،( أخرجه مسلم يف صحيحه: كتاب الرب والصلة واآلداب، باب ثواب المؤمن فيما يصيبه من مرض(( .)2574( أو حزن، أو نحو ذلك، حتى الشوكة يشاكها، برقم ( أخرجه مسلم يف صحيحه: كتاب الرب والصلة واآلداب، باب ثواب المؤمن فيما يصيبه من مرض، (( .)2575( أو حزن، أو نحو ذلك حتى الشوكة يُشاكها، برقم ).146/2( ( تفسير القرآن العظيم، البن كثير(( وقتئذ يكون حليف المومنين، لوال معصية الرُّ ماة أمر رسول اهلل |، ومخالفتهم ] وقوله: 152 :طاعته، فقال: ﭐ﴿ﮛ ﮜ ﮝ ﮞ﴾ [آل عمران ﭐ﴿ﮞﮟ﴾ فمعناه: «ليختربكم، فيتميَّز المنافق منكم من المخلص الصَّ ادق (، ورُوي أنَّ رأس النِّفاق عبد اهلل بن أبيّ  بن سلول انفصل وقتئذ ((»يف إيمانه منكم بثلث الجيش، أو قريب منه، فعن مَعْمَر عن الزهري عن عروة يف قوله تعالى: ] قوله: «حتى إذا كان 152 :ﭐ﴿ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐﮑ﴾ [آل عمران بالشَّ وط من الْجَبَّانَةِ انخزل عبداهلل بن أبيٍّ ، ابن سلول بثلث الجيش، أو قريب من (، ويدخل يف معنى التمحيص تطهير قلوب المؤمنين الصَّ ادقين من ((»ثلث الجيش الكِرب والخيالء، كما حدث يوم حنين، قال تعالى: ﭐ﴿ﮞ ﮟ ﮠ ﮡ ﮢ ﮣﮤ ﮥ ﮦﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ]، ويف اآلية داللة على «أنَّ النصر بيده [أي: اهلل 25 :ﯔ ﯕ ﯖ ﯗ﴾ [التوبة (.((»تعالى] ومِن عنده، وأنه ليس بكثرة العدد وشدَّة البطش ومن خالل هذا التَّمحيص تتمايز العناصر المؤمنة الصَّ الحة من العناصر السيِّئة، فيَظهر: الخبيث من الطيب؛ لقوله تعالى: ﭐ﴿ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ -1 .(((»] وقوله: ﭐ﴿ﯓ ﯔ﴾ أي: «حتى يفرِّ ق179 :ﯓ ﯔ ﯕ ﯖ ﯗﯘ﴾ [أل عمران وقتئذ يكون حليف المومنين، لوال معصية الرُّ ماة أمر رسول اهلل |، ومخالفتهم ] وقوله: 152 :طاعته، فقال: ﭐ﴿ﮛ ﮜ ﮝ ﮞ﴾ [آل عمران ﭐ﴿ﮞﮟ﴾ فمعناه: «ليختربكم، فيتميَّز المنافق منكم من المخلص الصَّ ادق (، ورُوي أنَّ رأس النِّفاق عبد اهلل بن أبيّ  بن سلول انفصل وقتئذ ((»يف إيمانه منكم بثلث الجيش، أو قريب منه، فعن مَعْمَر عن الزهري عن عروة يف قوله تعالى: ] قوله: «حتى إذا كان 152 :ﭐ﴿ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐﮑ﴾ [آل عمران بالشَّ وط من الْجَبَّانَةِ انخزل عبداهلل بن أبيٍّ ، ابن سلول بثلث الجيش، أو قريب من (، ويدخل يف معنى التمحيص تطهير قلوب المؤمنين الصَّ ادقين من ((»ثلث الجيش الكِرب والخيالء، كما حدث يوم حنين، قال تعالى: ﭐ﴿ﮞ ﮟ ﮠ ﮡ ﮢ ﮣﮤ ﮥ ﮦﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ]، ويف اآلية داللة على «أنَّ النصر بيده [أي: اهلل 25 :ﯔ ﯕ ﯖ ﯗ﴾ [التوبة (.((»تعالى] ومِن عنده، وأنه ليس بكثرة العدد وشدَّة البطش َ ومن خالل هذا التَّمحيص تتمايز العناصر المؤمنة الصَّ الحة من العناصر السيِّئة، فيَظهر: ِ الخبيث من الطيب؛ لقوله تعالى: ﭐ﴿ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ -1 .(((»] وقوله: ﭐ﴿ﯓ ﯔ﴾ أي: «حتى يفرِّ ق179 :ﯓ ﯔ ﯕ ﯖ ﯗﯘ﴾ [أل عمران .)298/7( ( جامع البيان عن تأويل آي القرآن، للطربي(( ( أخرجه الصنعاين يف مصنفه: كتاب المغازي، باب ما جاء يف حفر زمزم، وقد دخل يف الحج أول ما(( .)371/2( )، وتفسير القرآن العظيم، البن كثير9735( ذكر من عبدالمطلب، وقعة أحد، برقم ).179/14( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)535/13( ( المرجع السَّ ابق(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف الصادق من الكاذب؛ لقوله: ﴿ﮮ ﮯ ﮰ ﮱ ﯓﯔ ﯕ ﯖ ﯗ ﯘ-2 .]3 :ﯙ ﯚ﴾ [العنكبوت ﯕ ﯖ ﯗ ﯘ ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف الشَّ اكر من الجاحد؛ لقوله: ﭐ﴿ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ -3 ﮘ ﮙ ﮚﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ].40:ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل الشَّ اكر من الجاحد؛ لقوله: ﭐ﴿ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ -3 ﮘ ﮙ ﮚﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ].40:ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل الشَّ اكر من الجاحد؛ لقوله: ﭐ﴿ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ -3 ﮘ ﮙ ﮚﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨﮩ ﮪ ﮫ ﮬ ].40:ﮭ ﮮﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ﴾ [النمل الصَّ ابر على مناجزة األعداء من الفارِّ؛ لقوله: ﴿ﯤ ﯥ ﯦ ﯧ -4 ]، وقوله: ﭐ﴿ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ140 :ﯨ ﯩ ﯪﯫ﴾ [آل عمران ].142 :ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ﴾ [آل عمران المؤمن من المنافق؛ لقوله: ﭐ﴿ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ﴾ -5 ]، وقوله: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ11 :[العنكبوت ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ ﭹ ﭺ ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ﴾ ].167-166 :[آل عمران ].167-166 :[آل عمران ].167-166 :[آل عمران الخائف من اهلل بالغيب من الجريء؛ لقوله: ﭐ﴿ﮠ ﮡ ﮢ ﮣ -6 ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ].94 :ﯗ ﯘ﴾ [المائدة الخائف من اهلل بالغيب من الجريء؛ لقوله: ﭐ﴿ﮠ ﮡ ﮢ ﮣ -6 ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ].94 :ﯗ ﯘ﴾ [المائدة النَّاصر لدين اهلل من المتقاعس؛ لقوله: ﴿ﭤ ﭥ ﭦ ﭧ ﭨ ﭩﭪ -7 .]25 :ﭫ ﭬ ﭭ ﭮ﴾ [الحديد النَّاصر لدين اهلل من المتقاعس؛ لقوله: ﴿ﭤ ﭥ ﭦ ﭧ ﭨ ﭩﭪ -7 .]25 :ﭫ ﭬ ﭭ ﭮ﴾ [الحديد الـمُحسن من الـمُسيء؛ لقوله تعالى: ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ -8 ]، وقوله: ﭐ﴿ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ7 :ﭱ ﭲ ﭳﭴ﴾ [هود الـمُحسن من الـمُسيء؛ لقوله تعالى: ﭐ﴿ﭬ ﭭ ﭮ ﭯ ﭰ -8 ]، وقوله: ﭐ﴿ﭰ ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ7 :ﭱ ﭲ ﭳﭴ﴾ [هود ]، وقوله: ﭐ﴿ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ﭢﭣ ﭤ7 :ﭹ ﭺ﴾، [الكهف ].2 :ﭥ ﭦ﴾ [الملك المفسد من المصلح؛ لقوله تعالى: ﭐ﴿ﭕ ﭖ ﭗﭘ ﭙ ﭚ ﭛ -9 ]، واآلية داللة220 :ﭜﭝ ﭞ ﭟ ﭠﭡ ﭢ ﭣ ﭤ ﭥ ﭦ﴾ [البقرة واضحة على أنَّ اهلل تعالى ابتلى األوصياء بجواز مخالطة أموالهم مع أموال اليتامى؛ ليظهر منهم المفسد من المصلح؛ لهذا رُوي عن ابن زيد يف قول اهلل تعالى ذكره: ﭐ﴿ﭢ ﭣ ﭤ ﭥ ﭦﭧ﴾ أنه قال: «اهلل يعلم حين تخلط مالك بماله: أتريد أن (.((»تصلح ماله، أو تفسده، فتأكله بغير حق إذَنْ فالمقصد من ابتالء التَّمحيص كما دلَّت اآليات؛ هو تنقية القلوب وتخليصها من العيوب، وتكفير السيِّئات؛ ألنَّ كلَّ ما يصاب به المسلم يف الدُّنيا من (، هذا من جهة، ومن جهة ((المصائب واألحزان هو كفَّارة له، كما تقدَّم يف الحديث أخرى المقصد من ابتالء التَّمحيص هو التَّفريق بين الصَّ ادق يف إيمانه والكاذب فيه، وبين الشَّ اكر ألنعُمِ اهلل والجاحد لها، وبين الصَّ ابر على أنواع الباليا، والجازع لها، وبين المخلص يف عبادته والمنافق فيها، وبين الثَّابت يف الدِّين والمضطرب فيه، وبين الناصر لدين اهلل والخاذل له، وبين الخائف من اهلل بالغيب والجريء، وبين المحسن يف عمله والمسيء فيه، وبين المصلح يف تعامله والمفسد فيه. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: يي هذا وإنَّ المؤمن الصادق إذا أصابته المحنة؛ صرب واحتسب، وأحسن الظنَّ باهلل؛ ألنه يعلم أنه ال يصيبه إال ما كُتب له، وأنَّ المِحن واإلحن تربيه، وتنقيه، وتخلِّصه، وهتذِّبه، فتزيده إيمانًا وثباتًا، أما المنافق، أو الكافر، أو الفاسق، أو الجاهل، ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،فإذا أصابه شرٌّ وبالءٌ يف جسده وضيق يف معيشته؛ فزع واضطرب، وجزع وغضب وأساء الظنَّ باهلل تعالى، يقول ابن القيم &: «إنَّ اهلل سبحانه اقتضت حكمته أنه ال بد أن يمتحن النُّفوس ويبتليها، فيظهر باالمتحان طيِّبها من خبيثها، ومن يصلح لمواالته وكراماته ومن ال يصلح، وليمحِّص النُّفوس التي تصلح له، ويخلصها بكير االمتحان، كالذَّهب الذي ال يخلص وال يصفو من غشِّ ه إلَّ باالمتحان؛ إذِ النَّفس يف األصل جاهلة ظالمة، وقد حصل لها بالجهل والظُّلم من الخبث ما يحتاج خروجه إلى السَّ بك والتَّصفية، فإن خرج يف هذه الدَّار وإلَّ ففي كير جهنَّم، فإذا هُذِّب العبد (.((»ونُقِّيَ أُذن له يف دخول الجنَّة ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،فإذا أصابه شرٌّ وبالءٌ يف جسده وضيق يف معيشته؛ فزع واضطرب، وجزع وغضب وأساء الظنَّ باهلل تعالى، يقول ابن القيم &: «إنَّ اهلل سبحانه اقتضت حكمته أنه ال بد أن يمتحن النُّفوس ويبتليها، فيظهر باالمتحان طيِّبها من خبيثها، ومن يصلح لمواالته وكراماته ومن ال يصلح، وليمحِّص النُّفوس التي تصلح له، ويخلصها بكير االمتحان، كالذَّهب الذي ال يخلص وال يصفو من غشِّ ه إلَّ باالمتحان؛ إذِ النَّفس يف األصل جاهلة ظالمة، وقد حصل لها بالجهل والظُّلم من الخبث ما يحتاج خروجه إلى السَّ بك والتَّصفية، فإن خرج يف هذه الدَّار وإلَّ ففي كير جهنَّم، فإذا هُذِّب العبد (.((»ونُقِّيَ أُذن له يف دخول الجنَّة :المطلب العاشر البالء بمقصد االستدراج (، بصيغة الفعل ((لقد وردت لفظة «استدرج» يف موضعين من القرآن الكريم المضارع المبدوء بسين االستقبال، وفاعله «نحن»؛ للتعظيم. (، بصيغة الفعل ((لقد وردت لفظة «استدرج» يف موضعين من القرآن الكريم المضارع المبدوء بسين االستقبال، وفاعله «نحن»؛ للتعظيم. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: «االستدراج» يف اللُّغة مصدر الفعل الثالثي (درج) المزيد بثالثة أحرف: استدر ج، يستدرج، استَدْرِج، استدراجً ا، فهو مُستدرِج، والمفعول مُستدرَج ، وأصل مادة (درج) يدلُّ على: «مُضيِّ الشَّ يء، والمضيِّ يف الشَّ يء، من ذلك قولهم: درج الشيء، إذا مضى لسبيله، ورجع فالن أدراجه، إذا رجع يف الطَّريق الذي جاء منه، ودرج (؛ ويف اللِّسان: «استدرجه؛ أي أدناه منه على التَّدريج، ((»الصَّ بي، إذا مشى مشيته .)17-16/3( ( زاد المعاد يف هدي خير العباد، ابن القيم(( .)255( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)78-77/4( ( معجم مقاييس اللغة، ابن فارس(( ]؛182 :فتدرَّج هو، ويف التنزيل العزيز: ﴿ﮏ ﮐ ﮑ ﮒ ﮓ﴾ [األعراف قال بعضهم: معناه سنأخذهم قليلً قليلً وال نباغتهم؛ وقيل: معناه سنأخذهم من حيث ال يحتسبون؛ وذلك أنَّ اهلل تعالى يفتح عليهم من النَّعيم ما يغتبطون به فيركنون إليه ويأنسون به، فال يذكرون الموت، فيأخذهم على غِرَّ تِهم أغفل ما كانوا، ورُوي عن أبي الهيثم: امتنع فالن من كذا وكذا حتى أتاه فالن فاستدرجه؛ أي خَ دَعَه حتى حَ مَلَه على أنْ دَرَجَ يف ذلك، أبو سعيد: استدرجه كالمي؛ أي أقلقه حتى تركه يدرج على األرض؛ قال األعشى: لَيَستدرِجَ نَّك القول حتى تَهُزَّ ه... وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وتعلم أين منكم غير (، ويف اصطالح المفسِّ رين، االستدراج: «أن تأتيه من حيث ال يعلم، ومِن ((»ِمُلْجَم (، ويقول آخر: «اغرتارُ المستدرَج بلطف من استدرجه، ((»حيث تُلَطِّف له حتى تغرتَّه (، ويرى ((»حيث يرى المستدرَج أن المستدرِج إليه محسنٌ، حتى يورِّطه مكروهًا أحدهم أنَّه عبارة عن: «اإلمداد بالنِّعم وإنساء الشُّ كر عليها، فإذا سكنوا وحجبوا عن (، ويرى آخر أنَّ االستدراج: «هو األخذ يف حال الغفلة، من حيث ((»المنعم أُخِ ذوا (، ويرى ابن عجيبة & أنَّ االستدراج ليس خاصًّ ا بالكفَّار، بل ((»أمِنَ الرَّ جل بغتة يكون يف المؤمنين خواصِّ هم وعوامِّهم، ثم نقل عن ابن عبَّاد & قوله: «الخوف من االستدراج بالنِّعم من صفة المؤمنين، وعدم الخوف منه مع الدَّوام على اإلساءة من (، وبعد الوقوف على معنى االستدراج يف اللُّغة واالصطالح، نجد ((»صفة الكافرين أنَّ االستدراج لغةً يدور حول معنى االستدناء والتقريب، وحاصل معناه يف االصطالح .)268/2( ( لسان العرب، البن منظور(( .)268/2( ( لسان العرب، البن منظور(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،هو: سوق الجاحدين، والماردين على المعاصي، شيئًا بعد شيء، ودرجة بعد درجة إلى ما يهلكهم، ويضاعف لهم العذاب، دون أن يعلموا ما يراد هبم، وذلك باإلفضال عليهم بازدياد النِّعمة، ورخاء العيش، واإلمهال لهم باإلنساء يف األجل، واإلطالة يف العمر، مع إدامة الصِّ حَّة؛ حتى يزعموا أنَّه تكريم لهم من اهلل، وإيثار لهم على سائر المخلوقين؛ فيتمادوا يف المعاصي؛ «ليبلغوا بمعصيتهم ربَّهم، المقدارَ الذي قد كتبه ( يف حال غفلة، أو فتور.((»لهم من العقاب والعذاب، ثم يقبضهم إليه لقد ورد لفظ االستدراج كما بيَّنَّا آنفًا يف موضعَيْن يف القرآن الكريم، األول يف قوله تعالى: ﭐ﴿ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ]، واآلخر يف قوله: ﭐ﴿ﭞ ﭟ ﭠ ﭡ ﭢﭣ 183-182 :ﮙ ﮚ﴾ [األعراف ]، وقوله يف 45-44 :ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ﴾ [القلم اآليتَيْن: ﭐ﴿ﱔ ﱕ ﱖ ﱗ ﱘ﴾ معناه: «سنستدنيهم قليلً قليلً إلى ما يهلكهم ويضاعف عقاهبم مِنْ حيث ال يعلمون ما يراد هبم، وذلك أن يواتر اهلل نعمه عليهم مع اهنماكهم يف الغيِّ ، فكلما جدَّد عليهم نِعمة ازدادوا بطرً ا وجدَّدوا معصية، فيتدرَّجون يف المعاصي بسبب ترادف النِّعم، ظانِّين أنَّ مواترة النِّعم أثرة من اهلل وتقريب، وإنما هي خذالن منه وتبعيد، فهو استدراج اهلل تعالى، نعوذ باهلل (، ويقول آخر: «أي: سنُمهِلهم بغرَّ هتم، ونزيِّن لهم سوء أعمالهم؛ حتى ((»منه يحسب أنه يف كفره محسن، فإذا بلغ الغاية التي كُتبت له، أُخذ بأعماله السَّ يِّئة من (، قال ابن قتيبة &: «االستدراج أن يأخذهم قليلً قليلً ، وال ((»حيث ال يعلم .)288/13( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)182/2( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( ( الهداية إلى بلوغ النهاية يف علم معاين القرآن وتفسيره، وأحكامه، وجمل من فنون علومه، ألبي(( .)2653/4( محمد مكي (، وقال((»(، وقال الضَّ حَّاك &: «كلما جدَّدوا معصية جدَّدنا لهم نعمة((»يباغتهم # (، ولهذا قال عمر((»سفيان الثوري &: «نسبغ عليهم النعمة وننسيهم الشُّ كر لَمَّا حُ مل إليه كنوز كسرى: «اللهمَّ إين أعوذ بك أن أكون مستدرجً ا؛ فإين أسمعك (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ((»]182 :تقول: ﭐ﴿ﭤ ﭥ ﭦ ﭧ ﭨ﴾ [األعراف وأمَّا قوله يف اآليتَيْن: ﭐ﴿ﭪ ﭫﭬ﴾ فمعناه: «أُمهِلهم، وأُطيل لهم مدة عمرهم؛ ليتمادوا يف المعاصي، وال أعاجلهم بالعقوبة على المعصية؛ ليقلعوا عنها بالتوبة (. وما تضمنته هاتان اآليتان الكريمتان، قد أوضحه اهلل تعالى يف أكثر ((»واإلنابة من موضع بأسماء أخرى، وقد ذكر أهل التفسير أربعة أسماء لالستدراج، وهي: (، كما ظهر لنا خمسة أخرى، وهي: اإلمهال، ((»المكر، الكيد، اإلمالء، اإلهالك الخداع، اإلمداد، الرتك، الفتح، هذا هو بياهنا: وأمَّا قوله يف اآليتَيْن: ﭐ﴿ﭪ ﭫﭬ﴾ فمعناه: «أُمهِلهم، وأُطيل لهم مدة عمرهم؛ ليتمادوا يف المعاصي، وال أعاجلهم بالعقوبة على المعصية؛ ليقلعوا عنها بالتوبة (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وما تضمنته هاتان اآليتان الكريمتان، قد أوضحه اهلل تعالى يف أكثر ((»واإلنابة من موضع بأسماء أخرى، وقد ذكر أهل التفسير أربعة أسماء لالستدراج، وهي: (، كما ظهر لنا خمسة أخرى، وهي: اإلمهال، ((»المكر، الكيد، اإلمالء، اإلهالك الخداع، اإلمداد، الرتك، الفتح، هذا هو بياهنا: المكر: كقوله: ﭐ﴿ﭸ ﭹ ﭺﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ﴾ -1 :﴾(، و ﭐ﴿ﭹ ﭺﭻ((»]، أي: «أن يستدرجهم بالنِّعم حتى يأخذهم بغتة99 :[األعراف (.((»«استعارة ألخذه العبد من حيث ال يشعر، والستدراجه هرإ المكر: كقوله: ﭐ﴿ﭸ ﭹ ﭺﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ﴾-1 :﴾(، و ﭐ﴿ﭹ ﭺﭻ((»]، أي: «أن يستدرجهم بالنِّعم حتى يأخذهم بغتة99 :[األعراف (.((»«استعارة ألخذه العبد من حيث ال يشعر، والستدراجه .)411/1( ( غريب القرآن، البن قتيبة(( 1 .)411/1( ( غريب القرآن، البن قتيبة(( .)255/2( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)255/2( ( المرجع السَّ ابق(( )، وقد أخرجه البيهقي يف سننه: كتاب أبواب تفريق ما أخذ من أربعة418/15( ( مفاتيح الغيب، للرازي(( .)13033( أخماس الفيء غير الموجف عليه، باب االختيار يف التعجيل بقسمة مال الفيء إذا اجتمع، برقم )،418/15( ( المرجع السَّ ابق(( .)438/21( ( المرجع السَّ ابق(( .)241/2( ( البحر المديد يف تفسير القرآن المجيد، البن عجيبة(( .)134/2( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)411/1( ( غريب القرآن، البن قتيبة(( .)255/2( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)255/2( ( المرجع السَّ ابق(( )، وقد أخرجه البيهقي يف سننه: كتاب أبواب تفريق ما أخذ من أربعة418/15( ( مفاتيح الغيب، للرازي(( .)13033( أخماس الفيء غير الموجف عليه، باب االختيار يف التعجيل بقسمة مال الفيء إذا اجتمع، برقم )،418/15( ( المرجع السَّ ابق(( .)438/21( ( المرجع السَّ ابق(( .)241/2( ( البحر المديد يف تفسير القرآن المجيد، البن عجيبة(( .)134/2( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)411/1( ( غريب القرآن، البن قتيبة(( .)255/2( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)255/2( ( المرجع السَّ ابق(( )، وقد أخرجه البيهقي يف سننه: كتاب أبواب تفريق ما أخذ من أربعة418/15( ( مفاتيح الغيب، للرازي(( .)13033( أخماس الفيء غير الموجف عليه، باب االختيار يف التعجيل بقسمة مال الفيء إذا اجتمع، برقم )،418/15( ( المرجع السَّ ابق(( .)438/21( ( المرجع السَّ ابق(( .)241/2( ( البحر المديد يف تفسير القرآن المجيد، البن عجيبة(( .)134/2( ( الكشاف عن حقائق التزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( َ )، وقد أخرجه البيهقي يف سننه: كتاب أبواب تفريق ما أخذ من أربعة418/15( ( مفاتيح الغيب، للرازي(( .)13033( أخماس الفيء غير الموجف عليه، باب االختيار يف التعجيل بقسمة مال الفيء إذا اجتمع، برقم )41 /1 (ال َّ ا ( ال( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ]، أي: «أمهلهم يف بطرهم45 : الكيد: كقوله: ﭐ﴿ﭪ ﭫﭬ ﭭ ﭮ ﭯ﴾ [القلم-2 .(((»وغفلتهم إلى حيث ازدادوا على نفوسهم العتوَّ والعناد الموجب لشدَّة العذاب اإلمالء: كقوله: ﭐ﴿ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝﮞ ﮟ ﮠ ﮡ -3 ]، أي: «نؤخر العذاب عنهم ليزدادوا178 :ﮢ ﮣﮤ ﮥ ﮦ ﮧ﴾ [آل عمران (، وقوله: ﴿ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ((»إثمًا؛ أي جرأة على المعاصي ].48 :ﭩ ﭪ ﭫ﴾ [الحج ]، والمعنى: 40 : اإلهالك: كقوله: ﴿ﮠ ﮡ ﮢ ﮣ ﮤﮥ﴾ [القصص-4 ،(((»«انظر بعين قلبك، وفكر بفهمك، فكذلك نفعل بمن كذبك فقتلهم اهلل بالسيف واآلية فيها استدراج بالنِّعم لمن كذب بمحمد | بأن يأخذه اهلل فجأة، كإغداقه العطاء على فرعون وشيعته ثم إهالكهم فجأة. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ((»من كل ما يختارون، وهذا استدراج منه تعالى وإمالء لهم، عياذًا باهلل من مكره هذا وما ذكرناه يف معنى البالء باالستدراج واإلمالء؛ أنَّ أهل الكفر والزَّ يغ كلما ازدادوا تماديًا يف الكفر والفسوق والعصيان، زادهم اهلل نعمة، ورغدًا يف العيش، وإدامة الصِّ حَّة؛ حتى يظنُّوا أنَّ هذا من تقريب اهلل لهم، وكرامته، وإيثاره، فيصير ذلك اإلنعام واإلمهال سببًا لتماديهم يف االنكفاء عن ذكر اهلل، واتِّباع السُّ نَّة، والبعد عن الرجوع إلى طاعة اهلل، واالئتساء بنبيِّه، وهذه الحالة نشاهدها يف كثير من الكفرة، ويف بعضٍ من فسقة المسلمين كالمبتدعة وغيرهم؛ حيث يُستدرجون يف الطَّاعات، مع ثناء النَّاس عليهم؛ حتى يحسبون أهنم على خير عظيم، وأنه من تكريم اهلل لهم، فال يزالون على هذه الحالة؛ حتى يأخذهم اهلل على غِرّ ة، أو فرتة، إلَّ من تاب منهم، وأناب إلى اهلل، وعمل صالحًا قبل األخذ، وقد كان النبيُّ | يسأل اهلل الثبات على الطَّاعة واإلعانة على شكرها والعصمة من االستدراج هبا، كما رُوي .)307/1( ( جامع البيان عن تأويل آي القرآن، للطربي(( وقوله: ﴿ﯯ﴾: «بمعنى يزيدهم، على وجه اإلمالء والرتك لهم يف عُتوِّهم (، ونظيره قوله: ﭐ﴿ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ((»وتمرُّ دهم ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍ ﰎ ﰏ ﰐ﴾ ]. وغيرها من اآليات.17 - 11 :[المدثر وقوله: ﴿ﯯ﴾: «بمعنى يزيدهم، على وجه اإلمالء والرتك لهم يف عُتوِّهم (، ونظيره قوله: ﭐ﴿ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ((»وتمرُّ دهم ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍ ﰎ ﰏ ﰐ﴾ ]. وغيرها من اآليات.17 - 11 :[المدثر ]، والمعنى: 110 : التَّرك: كقوله: ﴿ﰉ ﰊ ﰋ ﰌ﴾ [األنعام-8 .(((»«نذرُهم ونرتكهم فيه، ونملي لهم ليزدادوا إثمًا إلى إثمهم الفتح: كقوله: ﭐ﴿ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ -9 ]، أي: «فتحنا عليهم أبواب الرزق44 :ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ﴾ [األنعام (. ((»من كل ما يختارون، وهذا استدراج منه تعالى وإمالء لهم، عياذًا باهلل من مكره ]، والمعنى: 110 : التَّرك: كقوله: ﴿ﰉ ﰊ ﰋ ﰌ﴾ [األنعام-8 .(((»«نذرُهم ونرتكهم فيه، ونملي لهم ليزدادوا إثمًا إلى إثمهم الفتح: كقوله: ﭐ﴿ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ -9 ]، أي: «فتحنا عليهم أبواب الرزق44 :ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ﴾ [األنعام (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ]، أي: 17 : اإلمهال: كقوله: ﭐ﴿ﮚ ﮛ ﮜ ﮝ﴾ [الطارق-5 .(((»«أخِّ رهم، وال تسأل اهلل تعجيل إهالكهم ]، أي: 17 : اإلمهال: كقوله: ﭐ﴿ﮚ ﮛ ﮜ ﮝ﴾ [الطارق-5 .(((»«أخِّ رهم، وال تسأل اهلل تعجيل إهالكهم ]، أي: 9 : الخداع: كقوله: ﴿ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ﴾ [البقرة-6 .(((»«باالستدراج واإلِمهال الذي يزيدهم عذابًا ]، 15 : اإلمداد: كقوله تعالى: ﴿ﯬ ﯭ ﯮ ﯯ ﯰ ﯱ ﯲ﴾ [البقرة-7 .)275/1( ( الفواتح اإللهية والمفاتح الغيبية الموضحة للكلم القرآنية والحكم الفرقانية، للنخجواين(( .)267/1( ( بحر العلوم، للسمرقندي(( .)275/1( ( الفواتح اإللهية والمفاتح الغيبية الموضحة للكلم القرآنية والحكم الفرقانية، للنخجواين(( .)267/1( ( بحر العلوم، للسمرقندي(( ( الهداية إلى بلوغ النهاية يف علم معاين القرآن وتفسيره، وأحكامه، وجمل من فنون علومه، ألبي(( .)5536/8( محمد مكي )/ (لل ط ل آ أل ك ( ل( ( الهداية إلى بلوغ النهاية يف علم معاين القرآن وتفسيره، وأحكامه، وجمل من فنون علومه، ألبي(( .)5536/8( محمد مكي وقوله: ﴿ﯯ﴾: «بمعنى يزيدهم، على وجه اإلمالء والرتك لهم يف عُتوِّهم (، ونظيره قوله: ﭐ﴿ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ((»وتمرُّ دهم ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ ﰌ ﰍ ﰎ ﰏ ﰐ﴾ ]. وغيرها من اآليات.17 - 11 :[المدثر ]، والمعنى: 110 : التَّرك: كقوله: ﴿ﰉ ﰊ ﰋ ﰌ﴾ [األنعام-8 .(((»«نذرُهم ونرتكهم فيه، ونملي لهم ليزدادوا إثمًا إلى إثمهم الفتح: كقوله: ﭐ﴿ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ -9 ]، أي: «فتحنا عليهم أبواب الرزق44 :ﰅ ﰆ ﰇ ﰈ ﰉ ﰊ ﰋ﴾ [األنعام (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ((»من كل ما يختارون، وهذا استدراج منه تعالى وإمالء لهم، عياذًا باهلل من مكره هذا وما ذكرناه يف معنى البالء باالستدراج واإلمالء؛ أنَّ أهل الكفر والزَّ يغ كلما ازدادوا تماديًا يف الكفر والفسوق والعصيان، زادهم اهلل نعمة، ورغدًا يف العيش، وإدامة الصِّ حَّة؛ حتى يظنُّوا أنَّ هذا من تقريب اهلل لهم، وكرامته، وإيثاره، فيصير ذلك اإلنعام واإلمهال سببًا لتماديهم يف االنكفاء عن ذكر اهلل، واتِّباع السُّ نَّة، والبعد عن الرجوع إلى طاعة اهلل، واالئتساء بنبيِّه، وهذه الحالة نشاهدها يف كثير من الكفرة، ويف بعضٍ من فسقة المسلمين كالمبتدعة وغيرهم؛ حيث يُستدرجون يف الطَّاعات، مع ثناء النَّاس عليهم؛ حتى يحسبون أهنم على خير عظيم، وأنه من تكريم اهلل لهم، فال يزالون على هذه الحالة؛ حتى يأخذهم اهلل على غِرّ ة، أو فرتة، إلَّ من تاب منهم، وأناب إلى اهلل، وعمل صالحًا قبل األخذ، وقد كان النبيُّ | يسأل اهلل الثبات على الطَّاعة واإلعانة على شكرها والعصمة من االستدراج هبا، كما رُوي ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف عن ابن عباس ^، قال: كان النبي | يدعو: «ربِّ أعني وال تُعِن علَيَّ ، وانصرين وال تنصر علَيَّ ، وامكر لي وال تمكر علَيَّ ، واهدين ويَسِّ ر هداي إليَّ ، وانصرين على من بغى علَيَّ ، اللهم اجعلني لك شاكرً ا، لك ذاكرً ا، لك راهبًا، لك مطواعًا، إليك مخبتًا، أو منيبًا، رب تقبل توبتي، واغسل حوبتي، وأجب دعويت، وثبت حجتي، (، والشَّ اهد قوله: «وامكر لي وال ((»واهد قلبي، وسدد لساين، واسلل سخيمة قلبي تمكر علَيَّ » قال الطيبي: «المكر: الخداع، وهو من اهلل إيقاع بالئه بأعدائه من حيث (.((»ال يشعرون، وقيل: استدراج العبد بالطاعة فيتوهَّم أهنا مقبولة وهي مردودة :المطلب الحادي عشر البالء بمقصد التَّخويف وردت مادة «خوف» يف مائة وأربعة وعشرين موضعًا من آي الذِّكر الحكيم (. ((بصياغات واشتقاقات مختلفة و«التَّخويف» يف اللُّغة مصدر الفعل الثالثي المضعَّف: خوَّفَ ، يخوِّف، تخويفًا، فهو مُخوِّف، والمفعول مُخوَّف، ومادة (خوف): «الخاء والواو والفاء أصل واحد (؛ ويف اللِّسان: «الخوف: الفزع، خافه يخافه خوفًا ((»يدل على الذعر والفزع )، وصححه1510( ( أخرجه أبو داود يف سننه: أبواب تفريع أبواب الوتر، باب ما يقول الرجل إذا سلم، برقم(( ،)، كما أخرجه الرتمذي يف سننه: أبواب الدعوات1510( األلباين يف صحيح وضعيف سنن أبي داود برقم ). = .)230/12( ،( لسان العرب، البن منظور(( .)303/1( ( انظر: المفردات يف غريب القرآن، للراغب(( .)191/13( ( التحرير والتنوير، البن عاشور(( .)4409/8( ( زهرة التفاسير، ألبي زهرة(( .)478/17( ( جامع البيان عن تأويل آي القرآن، للطربي(( ،»( أخرجه البخاري يف صحيحه: أبواب الكسوف، باب قول النبي |: «يخوف اهلل عباده بالكسوف(( وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: 3551( )، وصحَّ حه األلباين يف صحيح وضعيف سنن الرتمذي برقم3551( لم يسم بابه، برقم /لآ أ )، وصححه1510( ( أخرجه أبو داود يف سننه: أبواب تفريع أبواب الوتر، باب ما يقول الرجل إذا سلم، برقم(( ،)، كما أخرجه الرتمذي يف سننه: أبواب الدعوات1510( األلباين يف صحيح وضعيف سنن أبي داود برقم ). 3551( )، وصحَّ حه األلباين يف صحيح وضعيف سنن الرتمذي برقم3551( لم يسم بابه، برقم ).263/4( ( عون المعبود شرح سنن أبي داود، لآلبادي الصديقي(( .)248-246( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)100-99/9( ( معجم مقاييس اللغة، البن فارس(( وخيفة ومخافة، وخَ وَّفَ الرجل إذا جعل فيه الخوف، وخَ وَّفْتُه إذا جعلته بحالة (، ويف اصطالح المفسِّ رين هو: «إدخال ((»يخافه الناس، واإلخافة: التخويف (، ويقول آخر: ((»الفزع يف قلب المخاطب؛ حثًّا على التَّحرُّ ز من ارتكاب محظور (، ويقول ((»«بعث النفس على تحمُّل معاكسة هواها خيفة الوقوع يف سوء العاقبة (، مما ((»غيره: «هو ما تدل عليه من الرسالة المنذرة المخوفة من عذاب اهَّلل تعالى سبق من تعريفات للتَّخويف يف اللُّغة واالصطالح يتبيَّن لنا أنه يدور حول الذُّعر والفزع، وإخافة النَّاس من الوقوع يف الشُّ رور واآلثام. إذَنْ، فالتَّخويف هو: إفزاع النَّفس بأنواع المصائب والباليا يف الحياة الدُّنيا، وبسوء العاقبة يوم القيامة، يف حال استمرارها على فعل المنهيات وترك المأمورات. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: لقد خوَّف اهلل عباده يف كتابه بإنزال اآليات عليهم ترتى، كالجوائح السَّ ماوية، وانتشار األمراض الفتَّاكة، وغير ذلك؛ ليتَّعظوا، ويعتربوا فقال: ﭐ﴿ﭣ ﭤ ﭥ ﭦ ]، قال قتادة &: «وإن اهلل يخوِّف الناس بما شاء من آية؛ لعلهم 59 :ﭧ﴾ [اإلسراء # يعتربون، أو يذكَّرون، أو يرجعون، ذُكر لنا أن الكوفة رجفت على عهد ابن مسعود (، ويف الحديث المتَّفق عليه ((»فقال: يا أيها الناس، إنَّ ربَّكم يستعتبكم فأعتبوه قال: قال رسول اهلل |: «إنَّ الشَّ مس والقمر آيتان من آيات اهلل، # عن أبي بكرة (، وعن ((»ال ينكسفان لموت أحد وال لحياته، ولكنَّ اهلل تعالى يخوِّف بها عباده = .)230/12( ،( لسان العرب، البن منظور(( .)303/1( ( انظر: المفردات يف غريب القرآن، للراغب(( .)191/13( ( التحرير والتنوير، البن عاشور(( .)4409/8( ( زهرة التفاسير، ألبي زهرة(( .)478/17( ( جامع البيان عن تأويل آي القرآن، للطربي(( ،»( أخرجه البخاري يف صحيحه: أبواب الكسوف، باب قول النبي |: «يخوف اهلل عباده بالكسوف(( = .)230/12( ،( لسان العرب، البن منظور(( .)303/1( ( انظر: المفردات يف غريب القرآن، للراغب(( .)191/13( ( التحرير والتنوير، البن عاشور(( .)4409/8( ( زهرة التفاسير، ألبي زهرة(( .)478/17( ( جامع البيان عن تأويل آي القرآن، للطربي(( ،»( أخرجه البخاري يف صحيحه: أبواب الكسوف، باب قول النبي |: «يخوف اهلل عباده بالكسوف(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف (. والغرض من هذا((»الحسن ﭐ﴿ﭣ ﭤ ﭥ ﭦ ﭧ﴾ قال: «الموت الذريع التخويف اإللهي للبشرية جميعًا؛ حتى تتَّعظ وتتذكَّر وترجع إلى بارئها، فتؤمن به إيمانًا جازمًا ال يخالطه ريب، وتؤدِّي ما هي مكلَّفة به من حقوق اهلل يف العبوديَّة، وتوحيده بالرُّ بوبية، واأللوهيَّة، واألسماء والصفات، ونفي الشريك عنه الذي هو ، إلى + أصل الدَّعوة اإلسالمية ومحور رسالة جميع أنبيائه ورسله من لدن آدم محمد |، فإنَّه تعالى يكشف الضُّ رَّ عمن تضرَّ ع إليه وتذلَّل وتمسكن، وال يُخيَّب مقصود من توكَّل عليه وأظهر فقره وعجزه بين يديه. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: سواء أكان ذلك - كما حذَّر اهلل تعالى الذين يخالفون أمره ويقعون فيما يغضبه من اإلصابة بأنواع من المصائب واالبتالءات فقال: ﴿ﮍ -باطنًا أم ظاهرً ا ]، وقوله: ﴿ﮒ 63 :ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ﴾ [النور ﮓ ﮔ﴾ يقول الشوكاين: «والفتنة هنا: غير مقيدة بنوع من أنواع الفتن، وقيل: هي القتل، وقيل: الزالزل، وقيل: تسلَّط سلطان جائر عليهم، وقيل: الطَّبع على (، وقوله: ﴿ﮕ ﮖ ﮗ ﮘ﴾ فمعناه: «أو يصيبهم يف عاجل الدُّنيا ((»قلوهبم (، وقد ((»| عذاب من اهلل موجع، على صنيعهم ذلك، وخالفهم أمر رسول اهلل يكون من هذا القبيل ظهور األمراض واألوجاع التي لم تكن يف أسالفنا، وقد عبَّر القرآن الكريم عن هذا بقوله: ﭐ﴿ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ]، 134:ﮐﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ﴾ [األعراف = )، وأخرجه مسلم يف صحيحه: كتاب الكسوف، باب ذكر النداء بصالة الكسوف1048( برقم ).911( الصالة جامعة، برقم ا ).478/17( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)68/4( ( فتح القدير، للشوكاين(( . »وقال سعيد بن جبير: «الرِجز الطَاعون وحذَّر اهلل تعالى عباده عقوبته يف حال ركوهبم ما يغضبه، فقال: ﭐ﴿ﯳ ﯴ ] والمعنى: «ويخوِّفكم اهلل من نفسه أن تَرْ كبوا معاصيه، أو توالوا 28 :ﯵﯶ﴾ [آل عمران (، ذلك وقد سجَّل القرآن الكريم أنَّ عباده الذين ال يُتوقَّع إيماهنم، ال تنفع فيهم ((»أعداءه آياته، ومخوِّفاته، وال تُجدي معهم، فقال: ﭐ﴿ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ﴾ (.((»]؛ أي: «ال تنجع فيهم اآليات، واألدلَّة، وال النُّذر والمخوِّفات101 :[يونس هذا وإنَّ الناس إذا اتَّعظوا بما خُ وِّفوا به، وحُ ذِّروا منه، وأُنذروا به، دعاهم هذا إلى النَّظر يف أحوالهم؛ حتى يتوصَّ لوا إلى التَّوحيد الخالص، واإلنابة الصَّ ادقة، ولزوم الطاعة، وترك المنكر. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وقد كان من هَدْي نبيِّنا محمد | يف التَّعامل مع المُخوِّفات اإللهيَّة ما صح زوج النبي |، أهنا قالت: كان النبي | إذا عصفت الريح قال: $ عن عائشة «اللهم إين أسألك خيرها، وخير ما فيها، وخير ما أُرسلت به، وأعوذ بك من شرها، وشر ما فيها، وشر ما أُرسلت به»، قالت: وإذا تَخَيَّلَتِ السماء، تغير لونه، وخرج ودخل، وأقبل وأدبر، فإذا مطرت، سُ رِّ يَ عنه، فعرفت ذلك يف وجهه، قالت عائشة: فسألته، فقال: «لعلَّه، يا عائشة كما قال قوم عاد: ﴿ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ (.((»]24 :ﮍ ﮎ ﮏﮐ﴾ [األحقاف وال يخفى أنَّ السُّ نَّة النَّبوية حذَّرت من االبتالءات التي قد يسلِّطها اهلل على .)2253/2( ( معالم التنزيل يف تفسير القرآن، للبغوي(( .)317/6( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)297/11( ،( التحرير والتنوير، البن عاشور(( ( أخرجه مسلم يف صحيحه: كتاب صالة االستسقاء، باب التعوذ عند رؤية الريح والغيم، والفرح(( .)899( بالمطر، برقم ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف له عباده يف حال إعراضهم عن طاعته، وركوهبم المعاصي، فقد رُوي عن عبداهلل بن عمر ^ أنه قال: أقبل علينا رسول اهلل |، فقال: «يا معشر المهاجرين، خمس إذا ابتُليتم بهن، وأعوذ باهلل أن تدركوهن: لم تظهر الفاحشة يف قوم قط، حتى يعلنوا بها، إال فشا فيهم الطاعون، واألوجاع التي لم تكن مضت يف أسالفهم الذين مضوا، ولم ينقصوا المكيال والميزان، إال أُخذوا بالسنين، وشدة المؤونة، وجور السلطان عليهم، ولم يمنعوا زكاة أموالهم، إال منعوا القطر من السماء، ولوال البهائم لم يمطروا، ولم ينقضوا عهد اهلل، وعهد رسوله، إال سلط اهلل عليهم عدوًّا من غيرهم، فأخذوا بعض ما يف أيديهم، وما لم تحكم أئمتهم بكتاب اهلل، ويتخيروا مما أنزل اهلل، إال جعل اهلل (. وقد كان من هديه | التعوُّذ من الرَّ وعات، فعن جبير بن أبي ((»بأسهم بينهم سليمان بن جبير بن مطعم، قال: سمعت ابن عمر ^ يقول: لم يكن رسول اهلل | يدع هؤالء الكلمات حين يصبح وحين يمسي: «اللَّهمَّ إنِّي أسألك العفو والعافية يف ديني ودنياي، وأهلي ومالي، اللهم استر عوراتي، وآمن روعاتي، اللَّهمَّ احفظني من بين يدَ يَّ، ومن خلفي، وعن يميني، وعن شمالي، ومِن فوقي، وأعوذ بعظمتك أن (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: والشَّ اهد قوله: «اللَّهمَّ آمن روعاتي»، قال ابن األثير يف النِّهاية: ((»أغتال من تحتي (.((»«هي جمع روعة، وهي المرَّ ة الواحدة من الرَّ وع: الفزع )، وحسَّ نه األلباين يف صحيح4019( ( أخرجه ابن ماجه يف سننه: أبواب الفتن، باب العقوبات، برقم(( ،)، كما أخرجه الحاكم يف مستدركه: كتاب الفتن والمالحم4019( وضعيف سنن أبي داود برقم ).8623( أما حديث أبي عوانة، برقم )، وحسَّ نه األلباين يف صحيح4019( ( أخرجه ابن ماجه يف سننه: أبواب الفتن، باب العقوبات، برقم(( ،)، كما أخرجه الحاكم يف مستدركه: كتاب الفتن والمالحم4019( وضعيف سنن أبي داود برقم ).8623( أما حديث أبي عوانة، برقم )، 1902( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( وقال الحاكم: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه أحمد يف مسنده: مسند )، وقال عنه محقِّقو اإلسناد: إسناده 4785( المكثرين من الصَّ حابة، عبداهلل بن عمر ^، برقم صحيح، رجاله ثقات. ).277/2( ( النهاية يف غريب الحديث واألثر، البن األثير(( )، 1902( ( أخرجه الحاكم يف مستدركه: كتاب الدعاء، والتكبير، والتهليل، والتسبيح والذكر، برقم(( وقال الحاكم: هذا حديث صحيح اإلسناد، ولم يخرجاه، كما أخرجه أحمد يف مسنده: مسند )، وقال عنه محقِّقو اإلسناد: إسناده 4785( المكثرين من الصَّ حابة، عبداهلل بن عمر ^، برقم صحيح، رجاله ثقات. )277/2(األث لا ال د ث األث ( الن ا ة يف غ(( لقد وردت مادة «عقب» يف ثمانين موضعًا من آي الذِّكر الحكيم بصياغات (. ((واشتقاقات مختلفة و«العقوبة» يف اللُّغة مصدر الفعل الرباعي المزيد بحرف: عاقبَ ، يعاقب، عِقابًا، ومُعاقبةً، وعقوبةً، فهو مُعاقِب، والمفعول مُعَاقَب، وأصل مادة (عقب) يدلُّ على: «تأخير شىءٍ وإتيانه بعد غيره، كلُّ شيء يعقب شيئًا فهو عقيبه، وإنَّما سمِّيت (؛ أي: تأتى بعد الذَّنب، ويف الفروق: ((»عقوبةً ألنَّها تكون آخرً ا وثاين الذَّنب «العقاب ينبئ عن استحقاق، وسُ مِّي بذلك ألنَّ الفاعل يستحقُّه عُقَيْبَ فعله، وأصل العقاب التِّلو، وهو تأدية األوَّل إلى الثَّاين، يقال: عقب الثاين األوَّل إذا تاله، ( ويف اللِّسان: «العقاب والمعاقبة أن ((»وعاقبت اللِّصَّ بالقطع الذي يتلو سرقته تجزي الرَّ جل بما فعل سوءًا؛ واالسم العقوبة، وعاقبه بذنبه معاقبةً وعقابًا: أخذه به، (، ويف اصطالح القرآن الكريم، العقوبة ((»وتعقَّبت الرَّ جل إذا أخذته بذنب كان منه هي: ما يلقاه اإلنسان يف الدُّنيا من األحزان، والمصائب، والعقوبات الشَّ رعية، وما يلقاه يف اآلخرة من عذاب أليم؛ جزاءً عن سوء أفعاله. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: .)486-467( ( المعجم المفهرس أللفاظ القرآن الكريم، لعبدالباقي(( .)78-77/4( ( معجم مقاييس اللغة، البن فارس(( .)240-239/1( ( الفروق اللغوية، ألبي هالل العسكري(( .)619/1( ( لسان العرب، البن منظور(( ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ا يف الدُّنيا؛ ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف يخربنا اهلل تعالى أنه يعاقب الناس بالمصائب، والشَّ دائد، والباليا يف الدُّنيا؛ ] 123 :مجازاة لهم عن سوء أعمالهم فقال: ﭐ﴿ﭰ ﭱ ﭲ ﭳ ﭴ﴾ [النساء (، ومعنى ﭐ﴿ﭳ ﭴ﴾: «ما يلقاه اإلنسان ((»ومعنى ﭐ﴿ﭲ﴾: «ما يسوء من القبائح (، ويقول أيضً ا: ﴿ﭯ ﭰ ((»يف الدنيا من األحزان والمصائب جزاءً عن سيئاته ] وقوله: ﴿ﭳ﴾ فمعناه: 59 :ﭱ ﭲ ﭳ ﭴ ﭵ ﭶ ﭷ ﭸ﴾ [البقرة «ما يعاف عنه، وكذلك الرِّ جس، والمراد به الطَّاعون، رُوي أنَّه مات يف ساعة: أنه قال: قال # (، ويؤيِّد هذا ما رواه عن أسامة بن زيد((»أربعة وعشرون ألفًا رسول اهلل |: «الطَّاعون رجز، أو عذاب أُرسل على بني إسرائيل، أو على من كان (، هذا وإنَّ اإلصابة هبذه األمراض الفتَّاكة هي نوع من أنواع العقاب الذي ((»قبلكم كان يرسله اهلل على األمم قبلنا، وإلى اآلن، وكانت سنن اهلل فيهم أن يمتِّعهم بمتاع الدُّنيا؛ حتى يظنُّوا أهنم ما متِّعوا به من خير، إلَّ لعُلوِّ منزلتهم عند اهلل؛ فيتمادوا يف طغياهنم، ثم يأخذهم اهلل فجأة بأنواع العذاب وهم ال يشعرون. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: وقد صحَّ عن أبي قال: قال رسول اهلل |: «إن اهلل × يملي للظَّالم، فإذا أخذه لم يفلته، ثم # موسى (.((»]102 :قرأ ﴿ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔﮕ ﮖ ﮗ ﮘ ﮙ﴾ [هود وقد دعا اهلل مشركي قريش إلى التَّدبُّر يف حال األمم التي أهلكها بسبب كفرها وتكذيبها رسله، وأنه قادر على إهالكهم، ثم إدخالهم نارًا خالدين فيها، إنْ هم استمرُّ وا على شركهم فقال: ﭐ﴿ﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ .)531/1( ( النكت والعيون، الماوردي(( .)531/1( ( المرجع السَّ ابق(( .)83/1( ( أنوار التنزيل وأسرار التأويل، للبيضاوي(( .)2218( ( أخرجه مسلم يف صحيحه: كتاب السالم، باب الطاعون والطيرة والكهانة ونحوها، برقم(( .)2583( ( أخرجه مسلم يف صحيحه: كتاب الرب والصلة واآلداب، باب تحريم الظلم، برقم(( .)531/1( ( النكت والعيون، الماوردي(( َ .)83/1( ( أنوار التنزيل وأسرار التأويل، للبيضاوي(( .)2218( ( أخرجه مسلم يف صحيحه: كتاب السالم، باب الطاعون والطيرة والكهانة ونحوها، برقم(( .)2583( ( أخرجه مسلم يف صحيحه: كتاب الرب والصلة واآلداب، باب تحريم الظلم، برقم(( ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ ]، ونظيره قوله 10-9 :ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ﴾ [الروم تعالى: ﴿ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ ﰉ ﰊﰋ ﰌ ]، 44 :ﰍ ﰎ ﰏ ﰐ ﰑ ﰒ ﰓ ﰔ ﰕ ﰖﰗ ﰘ ﰙ ﰚ ﰛ﴾ [فاطر ويف المفردات: «والعاقبة إطالقها يختص بالثواب، وباإلضافة قد تُستعمل يف (، وقد أوضح اهلل تعالى يف سورة الشُّ عراء، ومواضع أخرى، عاقبة األمم ((»العقوبة الخالية بسبب ظلمها، كحكايته عن إغراق فرعون وقومه، وإكباب قوم إبراهيم وأبيه يف الجحيم، وإهالك قوم نوح باإلغراق، وإهالك قوم هود، وهم قبيلة عاد، بريح صرصر، وأخذ قوم صالح وهم قبيلة ثمود بالصَّ اعقة، وإهالك قوم لوط بإقالب األرض عليهم، وإهالك قوم شعيب وهم أصحاب األيكة بالصَّ يحة، وغيرها من األمم التي انتقم اهلل منها بعذاب حسِّ يٍّ ، أو جسميٍّ ؛ بسبب ظلمها وكفرها بأنعم اهلل، وأنَّ سُ نَّته جلَّ وعزَّ ماضية يف إلحاق العقوبة بالمتمرِّ دين عن طاعته، والماردين يف معصيته، وأنَّها تجري على جميع خلقه من لدن آدم إلى قيام الساعة فقال: ﭐ﴿ﯪ ]، وقد ينتقم 43 :ﯫ ﯬ ﯭ ﯮﯯ ﯰ ﯱ ﯲ ﯳ ﯴﯵ ﯶ ﯷ ﯸ ﯹ ﯺ﴾ [فاطر اهلل تعالى من العصاة بعذاب معنويٍّ ، أو قلبيٍّ كما هو حال المنافقين، وهذا النوع من العذاب أشدُّ من سابقه، وقد كان رسول اهلل | كثير التعوُّذ منه، وأرشد أمَّته إلى ذلك، ويتمثَّل هذا النَّوع من العذاب يف الطَّبع، والختم، والوقر، والغشاوة، واألكنَّة، والطمس، المانعة من فهم ما ينفع، كما قال تعالى يف شأن المنافقين: ﭐ﴿ﮓ ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ ﮣ ﮤ ﮥ ﮦ ﮧ ﮨ ﮩ ﮪ ﮫ ﮬ ﮭ ﮮ ﮯ ﮰ ﮱ ﯓ ﯔ .)575/1( ( المفردات يف غريب القرآن، للراغب(( .)575/1( ( المفردات يف غريب القرآن، للراغب(( :ﮫ﴾؛ أي ﮫ﴾ أ ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف :]، وقوله: ﭐ﴿ﮪ ﮫ﴾؛ أي77-75 :ﯕ ﯖ ﯗ ﯘ ﯙ﴾ [التوبة (، ((»(، وهذا يستلزم أنه: «أضلهم اهلل بفعلهم((»«جعل نفاقًا عقب ذلك؛ أي إثره ويقول ابن عاشور &: «جعل فعلهم ذلك؛ سببًا يف بقاء النِّفاق يف قلوهبم إلى موهتم، (؛ ولذلك قال اهلل تعالى: ﭐ﴿ﭬ ﭭ ﭮ ((»وذلك جزاء تمرُّ دهم على النِّفاق ﭵ ﭶ ﭷ ﭸ ﭹ ﭺﭻ ﭼ ﭽﭾ ﭿ ﮀ ﭯ ﭰﭱ ﭲ ﭳ ﭴ ]، وقوله: ﭐ﴿ﭶ ﭷﭸ﴾ فمعناه: «مرَ نُوا 101 :ﮁ ﮂ ﮃ ﮄ ﮅ﴾ [التوبة (، وأحسن ما وقفت عليهم قول من قال: ((»(، و«تمهَّروا فيه((»عليه ودَرِبوا به (، ومعنى الخرِّ يج يف اللُّغة: «أدَّبه كما يُخَرِّ جُ ((»«أخرب عنهم أهنم خِ رِّ يجُونَ يف النِّفاق المعلم تلميذه، وفالن خَ رِيجُ مال وخِ رِّ يجُه، بالتشديد، وهو فِعِّيلٌ بمعنى مفعول، إذا (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: هذا وإنَّ اآلية داللة واضحة على ((»درَّبه وعلَّمه، وقد خرَّ جه يف األدب فتخرَّ ج أنَّ كلَّ من أقام على الذَّنب، واستمرَّ عليه، وتمهَّر فيه، فلم يتب منه ويستغفر، ولم صفة متأصِّ لةً متجذِّرةً فيه إلى درجة صَ يْرِه خرِّ يج ذنبه؛ -أي: الذَّنب- يقرَّ به، صار أي: متخرِّ جً ا فيه، فيُخْتَمُ له به إلى موته جزاء تمرُّ سه فيه، فيكون هبذا الفعل قد جمع العاصي المتمادي على نفسه عذابَيْن: األول يف الدُّنيا بأنواع المصائب والمحن، واآلخر يف األُخرى بعذاب أليم، عياذًا باهلل من الخذالن. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: .)273-272/10( ( التحرير والتنوير، البن عاشور(( .)462/2( ( معاين القرآن وإعرابه، للزجاج(( .)273-272 /10( ( التحرير والتنوير، البن عاشور(( .)440/14( ( جامع البيان عن تأويل آي القرآن، للطربي(( .)305/2( ( الكشاف عن حقائق التنزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)496/5( ( البحر المحيط يف التفسير، ألبي حيَّان األندلسي(( .)250/2( ،( لسان العرب، البن منظور(( .)273-272/10( ( التحرير والتنوير، البن عاشور(( ا .)462/2( ( معاين القرآن وإعرابه، للزجاج(( ي .)273-272 /10( ( التحرير والتنوير، البن عاشور(( ر .)305/2( ( الكشاف عن حقائق التنزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)496/5( ( البحر المحيط يف التفسير، ألبي حيَّان األندلسي(( ،كما قد ينتقم اهلل من الفسقة بعذاب جسديٍّ ، كما هو حال مرتكبي الجرائم والسَّ اعين يف األرض فسادًا، ويتمثَّل هذا يف العقوبات الشَّ رعيَّة من حدود وقصاص وتعازير شرعيَّة؛ ألنَّ «إقامة الحدود من المصائب التي تصيب األنفس كما يف قوله (، قال × ((»]22 :تعالى: ﭐ﴿ﮯ ﮰ ﮱ ﯓ ﯔ ﯕ ﯖ ﯗ ﯘ﴾ [الحديد عن عقوبة الحرابة: ﴿ﭻ ﭼ ﭽ ﭾ ﭿ ﮀ ﮁ ﮂ ﮃ ﮄ ﮅ ﮆ ﮇ ﮈ ﮉ ﮊ ﮋ ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒﮓ ]، وقال عن 33 :ﮔ ﮕ ﮖ ﮗ ﮘﮙ ﮚ ﮛ ﮜ ﮝ ﮞ﴾ [المائدة عقوبة السَّ رقة: ﴿ﭟ ﭠ ﭡ ﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ﭨﭩ ]، وقال عن عقوبة الصَّ يد يف حال اإلحرام، أو يف 38 :ﭪ ﭫ ﭬ﴾ [المائدة أرض الحرم: ﭐ﴿ﯚ ﯛ ﯜ ﯝ ﯞ ﯟ ﯠ ﯡﯢ ﯣ ﯤ ﯥ ﯦ ﯧ ﯨ ﯩ ﯪ ﯫ ﯬ ﯭ ﯮ ﯯ ﯰ ﯱ ﯲ ﯳ ﯴ ﯵ ﯶ ﯷ ﯸ ﯹ ﯺ ﯻ ﯼ ﯽ ﯾ ﯿﰀ ﰁ ﰂ ﰃ ﰄﰅ ﰆ ﰇ ﰈ ﰉ ﰊﰋ ﰌ ﰍ ]، وقال عن عقوبة القتل العمد: ﴿ﮓ ﮔ ﮕ ﮖ 95 :ﰎ ﰏ﴾ [المائدة ﮗ ﮘ ﮙ ﮚ ﮛ ﮜ ﮝ ﮞ ﮟ ﮠ ﮡ ﮢ﴾ ] ويُعنى بالجزاء يف اآليات: «معاملة العامل بما يعادل أعماله المجزي 93 :[النساء (، وقال عن عقوبة الزنا: ﴿ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡ ((»عليها يف الخير والشر ﭢﭣ ﭤ ﭥ ﭦ ﭧ ﭨ ﭩ ﭪ ﭫ ﭬ ﭭ ﭮ ﭯ ﭰﭱ ﭲ ﭳ ﭴ ﭵ ﭶ﴾ ]، وقال عن عقوبة القذف: ﭐ﴿ﮌ ﮍ ﮎ ﮏ ﮐ ﮑ ﮒ ﮓ 2 :[النور ]، وغير ذلك 4 :ﮔ ﮕ ﮖ ﮗ ﮘ ﮙ ﮚ ﮛﮜ ﮝ ﮞ ﮟ﴾ [النور من الجرائم االجتماعية التي رتَّب عليها الشارع عقوبات مغلَّظة. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ءالبلا دصاقم :يناثلا ثحبملا لا نآرقل ا يف ،وقد قرَّ ر اهلل تعالى أنَّ ما يصيب النَّاس من أنواع المصائب، والمحن يف أنفسهم وأهليهم، وأموالهم، والعقوبات الشَّ رعيَّة، وشيوع األمراض النَّفسية، والبدنيَّة، والعقليَّة؛ فإنَّما يصيبهم ذلك عقوبة من اهلل لهم على ما اقرتفوه من المعاصي، واآلثام، والبعد عن شرع اهلل تعالى، ومخالفتهم أمره، وارتكاهبم هنيه فقال: ﴿ﯽ ]، ونظيره قوله: 30 :ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ﴾ [الشورى ]، أي: «من بلية ومصيبة فمن عندك، 79 :ﭐ﴿ﰌ ﰍ ﰎ ﰏ ﰐ ﰑ﴾ [النساء (، وقد عاتب اهلل تعالى الصَّ حابة رضي اهلل ((»ألنَّك السَّ بب فيها بما اكتسبت يداك عنهم أجمعين على ما أصاهبم يوم أحد من هزيمة، وقتل، وجرح، وأسر، فقال: ﭐ﴿ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅﰆ ﰇ ﰈ ﰉ ﰊ ﰋﰌ ﰍ ﰎ ﰏ ]، وقوله ﭐ﴿ﰇ ﰈ ﰉ ﰊ ﰋ﴾؛ أي: «أصابكم 165 :ﰐ ﰑ ﰒ﴾ [آل عمران (.((»| َّبمعصيتكم النبي َ أنَّ كلَّ ما يرتكبه الناس من كُفر ألنعم اهلل، I هذا وقد اقتضت رحمة اهلل ومن فساد يف بَرِّ األرض وبحرها، ومن ظلم، وطغيان، وغير ذلك من الذُّنوب الفَّظيعة، التي لو عاقب اهللُ النَّاسَ عليها ما أبقى أحدًا على ظهر األرض، غير أنَّ اهلل حليم بعباده، فال يعجِّل عليهم العقوبة، وإنَّما يمهلهم؛ حتى يتوبوا، ويستدركوا يف الدُّنيا ما فرَّ طوا يف جنب اهلل، يقول تعالى ذكره: ﭐ﴿ﭑ ﭒ ﭓ ﭔ ﭕ ﭖ ﭗ ﭘ ﭙ ﭚ ﭛ ﭜ ﭝ ﭞ ﭟ ﭠ ﭡﭢ ﭣ ﭤ ﭥ ﭦ ﭧ ].45 :ﭨ ﭩ ﭪ﴾ [فاطر وقد كان من هديه | التعوُّذ باهلل من العقوبة، فعن جبير بن أبي سليمان بن جبير بن مطعم، قال: سمعت ابن عمر ^ يقول: لم يكن رسول اهلل | يدع .)538/1( ( الكشاف عن حقائق التنزيل وعيون األقاويل يف وجوه التأويل، للزمخشري(( .)488/1( ( معاين القرآن وإعرابه، للزجاج(( هؤالء الكلمات حين يصبح وحين يمسي: «اللَّهمَّ إنِّي أسألك العفو والعافية يف ديني ودنياي، وأهلي ومالي، اللهم اسرت عورايت، وآمن روعايت، اللَّهمَّ احفظني من بين يدي، ومن خلفي، وعن يميني، وعن شمالي، ومن فوقي، وأعوذ بعظمتك أن (. وسنبرز اآلن أهمَّ مقاصد االبتالء بغرض الرَّ حمة يف النِّقاط اآلتية: والشَّ اهد قوله: «وأعوذ بعظمتك أن أُغتال من تحتي»، قال ابن ((»أُغتال من تحتي (.((»األثير يف النِّهاية: «أي أُدهى من حيث ال أشعر، يريد به الخسف وكان من هديه | التعوُّذ وهو ساجد، من غضب اهلل، وسخطه، وعقوبته كما قالت: فقدت رسول اهلل | ليلة من الفراش فالتمسته فوقعت $ صحَّ عن عائشة يدي على بطن قدميه وهو يف المسجد، وهما منصوبتان وهو يقول: «اللَّهمَّ أعوذ برضاك من سخطك، وبمعافاتك من عقوبتك، وأعوذ بك منك، ال أُحصي ثناء (.((»عليك أنت كما أثنيت على نفسك هؤالء الكلمات حين يصبح وحين يمسي: «اللَّهمَّ إنِّي أسألك العفو والعافية يف ديني ودنياي، وأهلي ومالي، اللهم اسرت عورايت، وآمن روعايت، اللَّهمَّ احفظني من بين يدي، ومن خلفي، وعن يميني، وعن شمالي، ومن فوقي، وأعوذ بعظمتك أن (. والشَّ اهد قوله: «وأعوذ بعظمتك أن أُغتال من تحتي»، قال ابن ((»أُغتال من تحتي (.((»األثير يف النِّهاية: «أي أُدهى من حيث ال أشعر، يريد به الخسف ار يري ب ى ن ي ي ِه ي أير يف وكان من هديه | التعوُّذ وهو ساجد، من غضب اهلل، وسخطه، وعقوبته كما قالت: فقدت رسول اهلل | ليلة من الفراش فالتمسته فوقعت $ صحَّ عن عائشة يدي على بطن قدميه وهو يف المسجد، وهما منصوبتان وهو يقول: «اللَّهمَّ أعوذ برضاك من سخطك، وبمعافاتك من عقوبتك، وأعوذ بك منك، ال أُحصي ثناء (.((»عليك أنت كما أثنيت على نفسك 1 .)65 ، (ص3( سبق تخريجه يف مطلب االبتالء بمقصد التخويف، هامش(( .)403/3( ( النهاية يف غريب الحديث واألثر، البن األثير(( .)486( ( أخرجه مسلم يف صحيحه: كتاب الصالة، باب ما يقال يف الركوع والسجود، برقم(( 1 .)65 ، (ص3( سبق تخريجه يف مطلب االبتالء بمقصد التخويف، هامش(( .)403/3( ( النهاية يف غريب الحديث واألثر، البن األثير(( .)486( ( أخرجه مسلم يف صحيحه: كتاب الصالة، باب ما يقال يف الركوع والسجود، برقم(( الحمد هلل وحده، والصَّ الة والسَّ الم على من ال نبيَّ بعده، أمَّا بعد؛ فبعد هذه اإلشراقة على مقاصد البالء التي تمَّ إبرازها من خالل هذه الدِّراسة الموضوعيَّة آليات من الذِّكر الحكيم، نصل إلى عدَّة نتائج وتوصيات، وهذا بياهنا: �أوَّلً : �أهمُّ النتائج يُعنى بالمقاصد القرآنية: الغايات واألهداف التي أُنزل القرآن الكريم • من أجلها؛ تحقيقًا لجلب مصالح العباد يف المعاش والمعاد من جهة، وتحقيقًا لدرء مفاسد العباد يف المعاش والمعاد من جهة أخرى. يُعنى بمقاصد البالء يف القرآن الكريم: الغايات والحكم التي يدور حولها • اختبار أحوال الناس يف تلقِّي التَّكاليف، وأنواع النِّعم، والنِّقم. يستنتج أنَّ بين البالء واالبتالء عمومًا وخصوصً ا، فالبالء أعمُّ من االبتالء، • واالبتالء أخصُّ منه؛ إذ فيه زيادة مشقَّة وكلفة، وكالهما يكون يف الخير والشَّ رِّ معًا، من غير فرق بين فعليهما. ِ يستنتج أنَّ البالء يظهر حال البشر، ومدى تطبيقهم للتَّكاليف والنَّواهي، • وتتجلَّى به نيَّاهتم يف سرعة االستجابة هلل، وللرسول |، ويختلف ذلك من شخص آلخر، حسب قوة اإليمان يف القلب، وحسب إدراك المعاين والحكم للبالء يف الخير والشَّ رِّ . يستنتج أنَّ المقصد الرَّ ئيس من البالء؛ استخراج ما عند المبتَلَى من معاين • يستنتج أنَّ من مقاصد إصابة اإلنسان بالبالء؛ يكون: • بالطَّاعة قولً ، وفعلً ، واعتقادًا.H . إلفراد المبتَلَى من بيده األمر1 .. إلظهار المبتَلَى الحاجة إلى اهلل وحده لتدبير أمره2 يستنتج أنَّ من مقاصد إصابة اإلنسان بالبالء؛ يكون: • بالطَّاعة قولً ، وفعلً ، واعتقادًا.H . إلفراد المبتَلَى من بيده األمر1 اي و ب ب ب إل إ نَ ج ي بالطَّاعة قولً ، وفعلً ، واعتقادًا.H . إلفراد المبتَلَى من بيده األمر1 بالطَّاعة قولً ، وفعلً ، واعتقادًا.H . إلفراد المبتَلَى من بيده األمر1 .. إلظهار المبتَلَى الحاجة إلى اهلل وحده لتدبير أمره2 . العرتاف المبتلى بقدرة اهلل يف قضاء حوائجه وكشف كرباته؛ بحيث3 .يتوجَّ ه إليه وحده بالدُّعاء َ . لتحمُّل المبتَلَى التكاليف التشريعية الشَّ اقة من األوامر والنواهي 4 .والضِّ يق، واآلالم َ . لتحمُّل المبتَلَى التكاليف التشريعية الشَّ اقة من األوامر والنواهي 4 .والضِّ يق، واآلالم . إلظهار المبتَلَى تسليمه الكلِّي لقضاء اهلل، وأحكامه الشَّ رعيَّة من غير 5 .شكٍّ يف حِكَمها، وال منازعة يف أحكَامها . إلقرار المبتَلَى بنعمة اهلل وهدايته، واستعمال جميع نِعَمه فيما يرضيه 6 .تعالى ، واالنتهاء عن المعاصي.I . لرجوع المبتَلَى إلى طاعة اهلل7 . العرتاف المبتَلَى أنَّ ما يصيبه من المصائب هو من تمام رحمة اهلل8 .عليه؛ حتى يستيقظ من غفلته . إلقرار المبتَلَى بنعمة اهلل وهدايته، واستعمال جميع نِعَمه فيما يرضيه 6 .تعالى ، واالنتهاء عن المعاصي.I . لرجوع المبتَلَى إلى طاعة اهلل7 . العرتاف المبتَلَى أنَّ ما يصيبه من المصائب هو من تمام رحمة اهلل8 .عليه؛ حتى يستيقظ من غفلته ، واالنتهاء عن المعاصي.I . لرجوع المبتَلَى إلى طاعة اهلل7 . �أوَّلً : �أهمُّ النتائج العرتاف المبتَلَى أنَّ ما يصيبه من المصائب هو من تمام رحمة اهلل8 .عليه؛ حتى يستيقظ من غفلته . لتمحيص المبتَلَى، وبيان حدِّ المفاصلة بينه وبين أهل الكفر، إن كان 9 .من أهل اإليمان . لتمحيص المبتَلَى، وبيان حدِّ المفاصلة بينه وبين أهل الكفر، إن كان 9 .من أهل اإليمان . لتنبيه المبتَلَى أنَّ اهلل قد يمدُّ الفاسق بالنِّعم، وإنساء الشُّ كر عليها؛ 10 .ليبلغ أقصى مراتب العقوبة والعذاب . لتنبيه المبتَلَى أنَّ اهلل قد يمدُّ الفاسق بالنِّعم، وإنساء الشُّ كر عليها؛ 10 .ليبلغ أقصى مراتب العقوبة والعذاب . لتنبيه المبتَلَى أنَّ اهلل قد يمدُّ الفاسق بالنِّعم، وإنساء الشُّ كر عليها؛ 10 .ليبلغ أقصى مراتب العقوبة والعذاب ،لحياة الدُّنيا ،. لتهديد المبتَلَى بأنَّ اهلل يفزع األنفس بأنواع المصائب يف الحياة الدُّنيا11 .وبسوء العاقبة يوم القيامة يف حال إصرارها على الذُّنوب . إلنذار المبتلى أنَّ ما يلقاه اإلنسان يف الدُّنيا من األحزان، والمصائب، 12 والعقوبات الشَّ رعية، وما يلقاه يف اآلخرة من عذاب أليم؛ جزاء عن سوء أفعاله. : ثانيًا: �أهمُّ التَّو9صيات َُو ي م ي . يوصي الباحثُ بعَقْد مؤتمرات علميَّة عن مقاصد البالء يف ضوء1 .الوحيَيْن، وأثرها يف حياة الفرد والمجتمع . يوصي الباحث بإدراج موضوع مقاصد البالء ضمن مفردات أحد 2 .مقررات الثقافة اإلسالمية على سبيل المثال . يوصي الباحث المجلَّ ت العلميَّة العالميَّة المحكَّمة بإفراد عدد خاص 3 .عن مقاصد البالء يف القرآن والسُّ نَّة . يوصي الباحثُ بعَقْد مؤتمرات علميَّة عن مقاصد البالء يف ضوء1 .الوحيَيْن، وأثرها يف حياة الفرد والمجتمع . يوصي الباحث بإدراج موضوع مقاصد البالء ضمن مفردات أحد 2 .مقررات الثقافة اإلسالمية على سبيل المثال . يوصي الباحث المجلَّ ت العلميَّة العالميَّة المحكَّمة بإفراد عدد خاص 3 .عن مقاصد البالء يف القرآن والسُّ نَّة . يوصي الباحثُ بعَقْد مؤتمرات علميَّة عن مقاصد البالء يف ضوء1 .الوحيَيْن، وأثرها يف حياة الفرد والمجتمع ُ سائلين اهلل × أن يعرِّ فنا مقاصد ابتالءاتنا، وأن يعيننا على حسن التعامل معها، وأن يرفعنا هبا درجات يف دنيانا وأخرانا. تمَّت الدِّراسة وهلل الحمد والمِنَّة، اللَّهمَّ هذا الجهد، وعليك التُّكالن، وصلَّى اهلل وسلَّم على نبيِّنا محمَّد، وعلى آله وصحبه. واهلل من وراء القصد، وهو يهدي السبيل. ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ﴾ ]١٨٢ - ١٨٠ :[الصافات ُ سائلين اهلل × أن يعرِّ فنا مقاصد ابتالءاتنا، وأن يعيننا على حسن التعامل معها، وأن يرفعنا هبا درجات يف دنيانا وأخرانا. تمَّت الدِّراسة وهلل الحمد والمِنَّة، اللَّهمَّ هذا الجهد، وعليك التُّكالن، وصلَّى اهلل وسلَّم على نبيِّنا محمَّد، وعلى آله وصحبه. �أوَّلً : �أهمُّ النتائج واهلل من وراء القصد، وهو يهدي السبيل. ﴿ﯺ ﯻ ﯼ ﯽ ﯾ ﯿ ﰀ ﰁ ﰂ ﰃ ﰄ ﰅ ﰆ ﰇ ﰈ﴾ ]١٨٢ - ١٨٠ :[الصافات «أحكام القرآن». الرازي، أبو بكر، تحقيق: محمد صادق القمحاوي، (د.ط)، بيروت: دار -1 .هـ1405 ،إحياء الرتاث العربي «إرشاد العقل السليم إلى مزايا الكتاب الكريم». العمادي محمد، أبو السعود، (د.ط)، -2 .بيروت: دار إحياء الرتاث العربي، د.ت «أسباب نزول القرآن». الواحدي، أبو الحسن علي، تحقيق: عصام بن عبدالمحسن -3 .1992 ،2يأالحميدان، الدمام: دار اإلصالح، ط «أحكام القرآن». الرازي، أبو بكر، تحقيق: محمد صادق القمحاوي، (د.ط)، بيروت: دار -1 .هـ1405 ،إحياء الرتاث العربي ر «إرشاد العقل السليم إلى مزايا الكتاب الكريم». العمادي محمد، أبو السعود، (د.ط)، -2 .بيروت: دار إحياء الرتاث العربي، د.ت «أسباب نزول القرآن». الواحدي، أبو الحسن علي، تحقيق: عصام بن عبدالمحسن -3 .1992 ،2الحميدان، الدمام: دار اإلصالح، ط ر «أسباب نزول القرآن». الواحدي، أبو الحسن علي، تحقيق: عصام بن عبدالمحسن -3 .1992 ،2الحميدان، الدمام: دار اإلصالح، ط اإ «أضواء البيان يف إيضاح القرآن بالقرآن». الشنقيطي، محمد األمين. (د. ط)، بيروت: دار -4 .م1995 ،الفكر اإ «أضواء البيان يف إيضاح القرآن بالقرآن». الشنقيطي، محمد األمين. (د. ط)، بيروت: دار -4 .م1995 ،الفكر «أنوار التنزيل وأسرار التأويل». البيضاوي، ناصر الدين، تحقيق: محمد عبدالرحمن -5 .هـ1418 ،)، بيروت: دار إحياء الرتاث العربي1يأالمرعشلي، (ط «أنوار التنزيل وأسرار التأويل». البيضاوي، ناصر الدين، تحقيق: محمد عبدالرحمن -5 .هـ1418 ،)، بيروت: دار إحياء الرتاث العربي1المرعشلي، (ط ر «البحر المحيط يف التفسير». أبو حيان األندلسي، محمد بن يوسف، تحقيق: صدقي محمد -6 .هـ1420 ،جميل، (د.ط)، بيروت: دار الفكر «البحر المديد يف تفسير القرآن المجيد». ابن عجيبة، أبو العباس، تحقيق: أحمد عبداهلل -7 .هـ1429 ،القرشي، (د.ط)، د.ن )، بيروت: 1 «تأويالت أهل السُّ نة». الماتريدي، أبو منصور. تحقيق: مجدي باسلوم، (ط-8 .م2005 ،دار الكتب العلمية م.1984 ، «التحرير والتنوير». ابن عاشور، الطَّاهر. (د. ط)، تونس: الدار التونسية للنشر-9 ،)1 «تفسير التسرتي». التُسرتي، أبو محمد، تحقيق: محمد باسل عيون السود، (ط-10 .هـ1423 ،بيروت: دار الكتب العلمية «تفسير الراغب األصفهاين». الراغب األصفهانى، أبو القاسم، تحقيق: عادل بن علي -11 .م2003 ،)، الرياض: دار الوطن1الشِّ دِّي، (ط «تفسير القرآن الحكيم». رشيد رضا، محمد. (د. ط)، مصر: الهيئة المصرية العامة-12 .م1990 ،للكتاب )، لبنان: دار طيبة للنشر 2 «تفسير القرآن العظيم». ابن كثير، أبو الفداء إسماعيل. (ط-13 .م1999 ،والتوزيع )، مصر: مكتبة مصطفى البابي 1 «تفسير المراغي». المراغي، أحمد بن مصطفى، (ط-14 .م1946 ،الحلبي )، الجيزة: دار الهجر، 1 «جامع البيان عن تأويل آي القرآن». الطربي، محمد بن جرير. �أوَّلً : �أهمُّ النتائج (ط-15 2 1 «سلسلة األحاديث الصحيحة وشيء من فقهها وفوائدها». األلباين، أبو عبدالرحمن -22 .م1995 ،)، الرياض: مكتبة المعارف1محمد ناصر الدين. (ط )، 1 «سنن ابن ماجه». ابن ماجه، أبو عبداهلل، تحقيق: شعيب األرنؤوط وآخرين، (ط-23 .م2009 ،بيروت: دار الرسالة ،)، بيروت: دار الكتب العلمية1 «سنن أبي داود». أبو داود، سليمان بن األشعت. (ط-24 .م1990 ،)3 «السنن الكربى». البيهقي، أحمد بن الحسين، تحقيق: محمد عبدالقادر عطا، (ط-25 .م2003 ،بيروت: دار الكتب العلمية «الصِّ حاح تاج اللغة وصحاح العربية». الجوهري، أبو نصر إسماعيل، تحقيق: أحمد -26 .1987 ،4عبدالغفور عطار، بيروت: دار العلم للماليين، ط ا م «صحيح ابن حبان برتتيب ابن بلبان». ابن حبان، أبو حاتم، تحقيق: شعيب األرنؤوط، -27 .م1993 ،)، بيروت: مؤسسة الرسالة2(ط م.1987 ،)، بيروت: دار الكتاب العربي1 «العبودية». ابن تيمية، تقي الدين ، (ط-28 )، بيروت: دار الكتب2 «عون المعبود شرح سنن أبي داود». العظيم آبادي، الصديقي، (ط-29 .)1415 ،العلمية «غريب القرآن البن قتيبة». ابن قتيبة، أبو محمد عبداهلل، تحقيق: سعيد اللحام، (د.ط)، -30 .د.ت م.1987 ،)، بيروت: دار الكتب العلمية1 «الفتاوى الكربى». ابن تيمية، تقي الدين، (ط-31 ، «فتح الباري شرح صحيح البخاري«. العسقالين، أحمد بن علي بن حجر أبو الفضل-32 .1979 ،(د.ط)، بيروت: دار المعرفة هـ.1414 ،)، بيروت: دار الكلم الطيب1 «فتح القدير». الشوكاين، محمد بن علي، (ط-33 «الفروق اللغوية». العسكري، أبو هالل، (د.ط)، القاهرة: دار العلم والثقافة للنشر-34 .والتوزيع، د.ت «الكشاف عن حقائق التنزيل وعيون األقاويل يف وجوه التأويل». الزمخشري، محمود بن-38 .هـ1407 ،)، بيروت: دار الكتاب العربي3عمر، (ط «الكشف والبيان عن تفسير القرآن». الثعلبي، أبو إسحاق، تحقيق: محمد بن عاشور، -39 .م2002 ،)، بيروت: دار إحياء الرتاث العربي1(ط )، بيروت: دار الكتب العلمية، 1 «لباب التأويل يف معاين التنزيل». الخازن، عالء الدين، (ط-40 .هـ1415 «الكشاف عن حقائق التنزيل وعيون األقاويل يف وجوه التأويل». الزمخشري، محمود بن-38 .هـ1407 ،)، بيروت: دار الكتاب العربي3عمر، (ط «الكشف والبيان عن تفسير القرآن». الثعلبي، أبو إسحاق، تحقيق: محمد بن عاشور، -39 .م2002 ،)، بيروت: دار إحياء الرتاث العربي1(ط )، بيروت: دار الكتب العلمية، 1 «لباب التأويل يف معاين التنزيل». الخازن، عالء الدين، (ط-40 .هـ1415 «اللباب يف علوم الكتاب». النعماين، أبو حفص سراج الدين، تحقيق: عادل أحمد-41 .م1998 ،)، بيروت: دار الكتب العلمية1عبدالموجود وعلي محمد معوض، (ط هـ.1414 ،)، بيروت: دار صادر3 «لسان العرب». ابن منظور، محمد بن مكرم. (ط-42 :)، القاهرة2 «مجاز القرآن». معمر بن المثنى، أبو عبيدة. تحقيق: عبدالفتاح أبو غدة، (ط-43 .م1962 ،مكتبة الخانجي ، 1 «المحكم والمحيط األعظم». المرسي، أبو الحسن، بيروت: دار الكتب العلمية، ط-44 .2000 «مدارج السالكين بين منازل إياك نعبد وإياك نستعين». �أوَّلً : �أهمُّ النتائج ابن قيم الجوزية، محمد بن أبي-45 .م1996 ،)، بيروت: دار الكتاب العربي3ربكر، (ط «مدارج السالكين بين منازل إياك نعبد وإياك نستعين». ابن قيم الجوزية، محمد بن أبي-45 .م1996 ،)، بيروت: دار الكتاب العربي3بكر، (ط )، بيروت: دار الكلم 1 «مدارك التنزيل وحقائق التأويل». النسفي، أبو الربكات، (ط-46 .م1998 ،الطيب )، بيروت: دار الكتب العلمية، 1 «المستدرك على الصحيحين». الحاكم، أبو عبداهلل. (ط-47 .م1990لهإ «مدارج السالكين بين منازل إياك نعبد وإياك نستعين». ابن قيم الجوزية، محمد بن أبي-45 .م1996 ،)، بيروت: دار الكتاب العربي3بكر، (ط )، بيروت: دار الكلم 1 «مدارك التنزيل وحقائق التأويل». النسفي، أبو الربكات، (ط-46 .م1998 ،الطيب )، بيروت: دار الكتب العلمية، 1 «المستدرك على الصحيحين». الحاكم، أبو عبداهلل. (ط-47 .م1990لهإ : «مسند اإلمام أحمد بن حنبل». أحمد، أبو عبداهلل أحمد بن محمد بن حنبل. تحقيق-48 .م2001 ،)1شعيب األرنؤوط وعادل مرشد، وآخرين، (ط أ «المسند الصحيح المختصر بنقل العدل عن العدل إلى رسول اهلل |». مسلم، أبو -49 .الحسن. تحقيق: محمد فؤاد عبدالباقي، (د. ط)، بيروت: دار إحياء الرتاث العربي، د. ت )، 2 «المصنف». الصنعاين، أبو بكر عبدالرزاق، تحقيق: حبيب الرحمن األعظمي، (ط-50 .م1983 ،كراتشي باكستان: المجلس العلمي «معالم التنزيل يف تفسير القرآن». البغوي، أبو محمد الحسين، تحقيق: عبدالرزاق-51 .هـ1420 ،)، بيروت: دار إحياء الرتاث العربي1المهدي، (ط )، 1 «معاين القرآن وإعرابه». الزجاج، أبو إسحاق. تحقيق: عبدالجليل عبده شلبي. (ط-52 .م1988 ،بيروت: عالم الكتب «المعجم الكبير». الطرباين، سليمان بن أحمد. تحقيق: حمدي بن عبدالمجيد السلفي، -53 .م1994 ،)، الرياض: دار الصميعي2(ط م.2008 ،)، بيروت: عالم الكتب1 «معجم اللغة العربية المعاصرة». مختار، أحمد، (ط-54 «المعجم المفهرس أللفاظ القرآن الكريم». عبدالباقي، محمد فؤاد، (د.ط)، مصر: مطبعة-55 .م1945 ،دار الكتب المصرية «معجم مقاييس اللغة». ابن فارس، أبو الحسين، تحقيق: عبدالسالم محمد هارون، -56 .م1979 ،(د.ط)، بيروت: دار الفكر هـ.1420 ،)، بيروت: دار إحياء الرتاث العربي3 «مفاتيح الغيب». الرازي، أبو عبداهلل. (ط-57 ،)، بيروت: دار القلم1 «مفردات يف غريب القرآن». راغب األصفهاين، أبو القاسم. (ط-58 .م1992 «مقاصد الشريعة اإلسالمية ومكارمها». عاشور، وصفي أبو زيد، الهند: مجلة وحدة-59 .2017 األمة، العدد التاسع، ديسمرب «المقصد األسنى يف شرح معاين أسماء اهلل الحسنى». الغزالي، أبو حامد محمد بن محمد -60 .م1987 ،)، قربص: الجفان والجابي1الطوسي، تحقيق: بسام عبدالوهاب الجابي، (ط «المنتخب من مسند عبد بن حميد». عبد بن حميد، أبو محمد، تحقيق: صبحي البدري -61 .م1988 ،)، القاهرة: مكتبة السنة1السامرائي، محمود محمد خليل الصعيدي، (ط «الموطأ». مالك، أنس بن مالك، تحقيق: عبدالوهاب عبداللطيف، (د.ط)، بيروت: -62 م ب م بيرو «المعجم الكبير». الطرباين، سليمان بن أحمد. �أوَّلً : �أهمُّ النتائج تحقيق: حمدي بن عبدالمجيد السلفي، -53 .م1994 ،)، الرياض: دار الصميعي2(ط م.2008 ،)، بيروت: عالم الكتب1 «معجم اللغة العربية المعاصرة». مختار، أحمد، (ط-54 «المعجم المفهرس أللفاظ القرآن الكريم». عبدالباقي، محمد فؤاد، (د.ط)، مصر: مطبعة-55 .م1945 ،دار الكتب المصرية م «معجم مقاييس اللغة». ابن فارس، أبو الحسين، تحقيق: عبدالسالم محمد هارون، -56 .م1979 ،(د.ط)، بيروت: دار الفكر هـ.1420 ،)، بيروت: دار إحياء الرتاث العربي3 «مفاتيح الغيب». الرازي، أبو عبداهلل. (ط-57 ،)، بيروت: دار القلم1 «مفردات يف غريب القرآن». راغب األصفهاين، أبو القاسم. (ط-58 «معجم مقاييس اللغة». ابن فارس، أبو الحسين، تحقيق: عبدالسالم محمد-56 .م1979 ،(د.ط)، بيروت: دار الفكر هـ.1420 ،)، بيروت: دار إحياء الرتاث العربي3 «مفاتيح الغيب». الرازي، أبو عبداهلل. (ط-57 ،)، بيروت: دار القلم1 «مفردات يف غريب القرآن». راغب األصفهاين، أبو القاسم. (ط-58 .م1992 «مقاصد الشريعة اإلسالمية ومكارمها». عاشور، وصفي أبو زيد، الهند: مجلة وحدة-59 .2017 األمة، العدد التاسع، ديسمرب رأ «المقصد األسنى يف شرح معاين أسماء اهلل الحسنى». الغزالي، أبو حامد محمد بن محمد -60 .م1987 ،)، قربص: الجفان والجابي1الطوسي، تحقيق: بسام عبدالوهاب الجابي، (ط «المنتخب من مسند عبد بن حميد». عبد بن حميد، أبو محمد، تحقيق: صبحي البدري -61 .م1988 ،)، القاهرة: مكتبة السنة1السامرائي، محمود محمد خليل الصعيدي، (ط «الموطأ». مالك، أنس بن مالك، تحقيق: عبدالوهاب عبداللطيف، (د.ط)، بيروت: -62 .المكتبة العلمية، د.ت «نزهة األعين النواظر يف علم الوجوه والنظائر». ابن الجوزي، أبو الفرج عبدالرحمن، -63 .1984 ،1تحقيق: محمد عبدالكريم كاظم الراضي، بيروت: مؤسسة الرسالة، ط «نزهة األعين النواظر يف علم الوجوه والنظائر». ابن الجوزي، أبو الفرج عبدالرحمن، -63 .1984 ،1تحقيق: محمد عبدالكريم كاظم الراضي، بيروت: مؤسسة الرسالة، ط «النكت والعيون». الماوردي، أبو الحسن. تحقيق: السيد بن عبدالمقصود بن عبدالرحيم. -64 .(د. ط)، بيروت: دار الكتب العلمية، د. ت «النهاية يف غريب الحديث واألثر». ابن األثير، مجد الدين أبو السعادات، تحقيق: طاهر -65 .م1979 ، محمود محمد الطناحي، (د.ط)، بيروت: المكتبة العلمية- أحمد الزاوي «الهداية إلى بلوغ النهاية يف علم معاين القرآن وتفسيره، وأحكامه، وجمل من فنون -66 )، جامعة الشارقة: مجموعة بحوث الكتاب1علومه». القيرواين، أبو محمد مكي، (ط م. 2008 ،والسنة )، القاهرة: مكتبة 1 «الوجوه والنظائر». العسكري، أبو هالل، تحقيق: محمد عثمان، (ط-67 .م2007 ،الثقافة الدينية .(د. ط)، بيروت: دار الكتب العلمية، د. ت «النهاية يف غريب الحديث واألثر». ابن األثير، مجد الدين أبو السعادات، تحقيق: طاهر -65 .م1979 ، محمود محمد الطناحي، (د.ط)، بيروت: المكتبة العلمية- أحمد الزاوي «الهداية إلى بلوغ النهاية يف علم معاين القرآن وتفسيره، وأحكامه، وجمل من فنون -66 )، جامعة الشارقة: مجموعة بحوث الكتاب1علومه». القيرواين، أبو محمد مكي، (ط م. �أوَّلً : �أهمُّ النتائج 2008 ،والسنة )، القاهرة: مكتبة 1 «الوجوه والنظائر». العسكري، أبو هالل، تحقيق: محمد عثمان، (ط-67 .م2007 ،الثقافة الدينية References and Sources 1. «Ahkamu Al-Quran». 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Muammar bin Al-Muthanna, Abu Obeida. investigated by: Abdel Fattah Abu Ghadda, (2nd Edition), Cairo: Al-Khanji Library, 1962. 43. “Al-Mohkam wal Moheet al-Azam” Al-Mursi, Abu Al-Hassan, Beirut: Dar Al-Kutub Al-Ilmia, 1, 2000. 44. “Madaraj Assalikeen baina Manazil Iyyaka Nabodu wa Iyyaka Nastaeen”. Ibn Qayyim al-Jawziyya, Mohammed ibn Abi Bakr, (third edition), Beirut: Dar al-Kitab al-Arabi, 1996 AD. 45. «Madarik Al-Tanzil wa Haqaiqu Al-Taweel”.Al-Nasafi, Abu Al-Barakat, (1st ed.), Beirut: Dar Al-Kalam Al-Tayyib, 1998 AD. No edition number 46. “Al-Mostadrak al-Assahihain”. Al-Hakim, Abu Abdullah. (1st edition), Beirut: Dar al-Kutub al-Ilmiyya, 1990 AD. 47. “ Musnad al-Imam Ahmad bin Hanbal». Ahmed, Abu Abdullah Ahmed bin Mohammed bin Hanbal. investigated by: Shuaib Al-Arnaout, Adel Murshid, et al (1st edition), 2001 AD. 48. “Al-Mosnad Al-Sahihi Al-Mokhtasar Bi’Naql Al-Adl a’n Al-Adl ela Ar- rasoul (PBUH). Muslim, Abul-Hasan. investigated by: Mohammed Fouad Abdel-Baqi, (No edition number), Beirut: Dar Ihia Atturath Al-Arabi, without publishing date. 49. “Al-Mosannaf”. Al-San’ani, Abu Bakr Abdul-Razzaq, investigated by: Habib Al-Rahman Al-Azami, (2nd edition), Karachi, Pakistan: The Academic Board, 1983 AD. 50. “Maalimu Tanzil fi Tafseer al-Quran”. Al-Baghawi, Abu Mohammed Al-Hussein, investigated by: Abdul Razzaq Al-Mahdi, (1st edition), Beirut: Dar Ihia Atturath Alarabi, 1420 AH. 51. “Maani Al-Quran wa Eaboh”. Al-Zaggag, Abu Is’haq. investigated by: Ab- del-Jalil Abdo Shalaby. (1st edition), Beirut: Alam Al-Kutub, 1988 AD. 52. “Al-Mojamu Al-Kabeer”. Al-Tabarani, Suleiman bin Ahmed. investigated by: Hamdi bin Abdul Majeed Al-Salafi, (2nd Edition), Riyadh: Dar Al-Sumaei, 1994 AD. 53. “Mojam Al-Lughah al-Arabiyah Al-Moasirah”. Mokhtar, Ahmed, (1st Edi- tion), Beirut: Alam Al-Kutub, 2008. 54. “Al-Mojam Al-Mofahras Lalfaz Al-Quran Al-Kareem”. Abdel-Baqi, Mo- hammed Fouad, (No edition number), Egypt: The Egyptian House of Books Press, 1945 AD. 55. “Mujam Maqaeis Al-Lughah”. Ibn Faris, Abu Al-Hussein, investigated by: Abdel Salam Mohammed Haroun, (No edition number), Beirut: Dar Al-Fikr, 1979 AD. 56. “Mafatihu el-Ghaib”. Al-Razi, Abu Abdullah. References and Sources (3rd Edition), Beirut: Dar Ihia Atturath Al-Arabi, 1420 AH. 57. “Mofradat fi Gharibul Quran”. Ragheb Al-Asfahani, Abu Al-Qasim. (1st edi- tion.), Beirut: Dar Al-Qalam, 1992 AD. 58. “The Objectives of Islamic Sharia and its Merits.” Ashour, Wasfi Abu Zaid, India: The Nation Unity Magazine, Issue No. 9, December 2017. 59. “The Most High Purpose in Explaining the Meanings of Allah’s Most Beautiful Names”. Al-Ghazali, Abu Hamid Mohammed bin Mohammed Al-Tusi, investigated by: Bassam Abdel-Wahhab Al-Jabi, (1st Edition), Cyprus: Al-Jafan and Al-Jabi, 1987 AD. 60. “Al-Montakhab m’n Musnad Abd ibn Hamid». Abd bin Hamid, Abu Mo- hammed, investigated by: Subhi Al-Badri Al-Samarrai, Mahmoud Moham- med Khalil Al-Saidi, (1st edition), Cairo: Maktabat Al-Sunna, 1988 AD. 61. “Al-Muwatta”. Malik, Anas bin Malik, investigated by: Abdel Wahab Abdel Latif, (d.), Beirut: The Scientific Library, d.T. 62. “Nozhat Al-Oyoun Al-Nawazir fi Elm Alwojoh wan-Nawazir». Ibn al-Jaw- zi, Abu al-Faraj Abdurrahman, investigated by: Mohammed Abd al-Karim Kazem al-Radi, Beirut: Al-Resala Foundation, 1st edition, 1984. 63. “Al-Nokat wal-Oyoun”. Al-Mawardi, Abul-Hasan. investigated by: Al-Sayyid bin Abdul-Maqsoud bin Abdul-Rahim. (No edition number), Beirut: Dar Al-Kotub al-Elmiyah, 64. “The End in Strange Hadith and Impact”. Ibn al-Atheer, Majd al-Din Abu al-Saadat, investigated by: Taher Ahmad al-Zawi - Mahmoud Mohammed al-Tanahi, (No edition number), Beirut: Al-Maktabah El-Elmiyah, 1979. AD 65. “Al-Hidayah ela Bolough Al-Nihayah fi Elm Maani Al-Quran wa Taf- seerih wa Ahkamih wa Jomalon m’n Olomih”. Al-Qayrawani, Abu Mo- hammed Makki, (1st Edition), University of Sharjah: Al-Kitab and Al-Sunnah Research Group, 2008. 66. “Al-Wojoh wal Nazair”. Al-Askari, Abu Hilal, investigated by: Mohammed Othman, (1st Edition), Cairo: Religious Culture Library, 2007 AD. فهرس الموضوعات 23...................................................................الـمستخلص 27....................................................................الـمـقــدِّمــــة املبحث األوَّل: تعريف املقاصد القرآنية، وتعريف البالء ومواطن وروده يف القرآن 35........................................................................ الكريم 36..................................المطلب األول: تعريف المقاصد القرآنية 39.............................المطلب الثاين: تعريف البالء يف القرآن الكريم 40...............المطلب الثالث: مفهوم مقاصد البالء يف ضوء القرآن الكريم 41...............المطلب الرابع: األلفاظ ذات الصِّ لة بالبالء يف القرآن الكريم 41......................................................أوَّلً : البالء بالخير 43....................................................... References and Sources ِّثانيًا: البالء بالشَّ ر 47.................المطلب الخامس: الفرق بين ابتالء الرَّ حمة وابتالء العقوبة 49.......المطلب السادس: اشتقاقات مادة «بال» وتصريفاهتا يف القرآن الكريم المطلب السابع: رسومات بيانية تبيِّن الصِّ يغ التصريفية لمادة «بال» يف سور 50..............................................................القرآن الكريم 55...........................:المطلب الثامن: تحليل نتائج الرُّ سومات البيانية 63..................................لبحث الثاين:مقاصد البالء يف القرآن الكريم 65......................المطلب األوَّل: البالء بمقصد تحقيق العبادة هلل وحده 70.............................المطلب الثَّاين: البالء بمقصد استخراج التوكُّل 74............................المطلب الثَّالث: البالء بمقصد استخراج الدُّعاء 82.............................المطلب الرَّ ابع: البالء بمقصد استخراج الصَّ رب 87..........................المطلب الخامس: البالء بمقصد استخراج الرِّ ضا 93..........................المطلب السَّ ادس: البالء بمقصد استخراج الشُّ كر 99............................المطلب السَّ ابع: البالء بمقصد استخراج التَّوبة 103...................................المطلب الثَّامن: البالء بمقصد الرَّ حمة 113................................المطلب التَّاسع: البالء بمقصد التَّمحيص 119...............................المطلب العاشر: البالء بمقصد االستدراج 125..........................المطلب الحادي عشر: البالء بمقصد التَّخويف 130...............................المطلب الثاين عشر: البالء بمقصد العقوبة 137..................................................................لـخـــاتـمــــــة 140...........................................................ثبت املصادر واملراجع 146.......................................................رومنة املصادر واملراجع 152............................................................فهرس املوضوعات
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Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii
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Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii Andreas Bracher*☯, Thomas Hauser☯, Cuimin Liu¤, F. Ulrich Hartl, Manajit Hayer-Hartl* Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany Andreas Bracher*☯, Thomas Hauser☯, Cuimin Liu¤, F. Ulrich Hartl, Manajit Hayer-Hartl* Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany ☯These authors contributed equally to this work. ¤ Current address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China * bracher@biochem.mpg.de (AB); mhartl@biochem.mpg.de (MH-H) ☯These authors contributed equally to this work. ¤ Current address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China * bracher@biochem.mpg.de (AB); mhartl@biochem.mpg.de (MH-H) OPEN ACCESS Citation: Bracher A, Hauser T, Liu C, Hartl FU, Hayer-Hartl M (2015) Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii. PLoS ONE 10(8): e0135448. doi:10.1371/journal.pone.0135448 Editor: Yong-Bin Yan, Tsinghua University, CHINA Editor: Yong-Bin Yan, Tsinghua University, CHINA Received: June 3, 2015 Accepted: July 22, 2015 Published: August 25, 2015 Editor: Yong-Bin Yan, Tsinghua University, CHINA Received: June 3, 2015 Accepted: July 22, 2015 Published: August 25, 2015 Copyright: © 2015 Bracher 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. RESEARCH ARTICLE Abstract The most prevalent form of the Rubisco enzyme is a complex of eight catalytic large sub- units (RbcL) and eight regulatory small subunits (RbcS). Rubisco biogenesis depends on the assistance by specific molecular chaperones. The assembly chaperone RbcX stabilizes the RbcL subunits after folding by chaperonin and mediates their assembly to the RbcL8 core complex, from which RbcX is displaced by RbcS to form active holoenzyme. Two iso- forms of RbcX are found in eukaryotes, RbcX-I, which is more closely related to cyanobac- terial RbcX, and the more distant RbcX-II. The green algae Chlamydomonas reinhardtii contains only RbcX-II isoforms, CrRbcX-IIa and CrRbcX-IIb. Here we solved the crystal structure of CrRbcX-IIa and show that it forms an arc-shaped dimer with a central hydropho- bic cleft for binding the C-terminal sequence of RbcL. Like other RbcX proteins, CrRbcX-IIa supports the assembly of cyanobacterial Rubisco in vitro, albeit with reduced activity rela- tive to cyanobacterial RbcX-I. Structural analysis of a fusion protein of CrRbcX-IIa and the C-terminal peptide of RbcL suggests that the peptide binding mode of RbcX-II may differ from that of cyanobacterial RbcX. RbcX homologs appear to have adapted to their cognate Rubisco clients as a result of co-evolution. RbcX from Chlamydomonas reinhardtii regulatory small subunits (RbcS), capping the RbcL8 complex at both ends [1]. RbcL sequences exhibit remarkable conservation across phyla. Nevertheless, based on sequence diversity of the RbcL subunits, four subgroups of form I Rubisco, IA-ID, can be distinguished [2, 3]. The eco- nomically most important form IB is found in so-called green organisms: cyanobacteria, green algae and plants. While there is a plethora of data on Rubisco structure, function and catalysis [1, 4], the path- ways of subunit folding and oligomeric assembly are only beginning to emerge [5]. In green algae and plants, the RbcL subunits are chloroplast encoded and synthesized in the chloroplast stroma, the site of carbon fixation. In contrast, the RbcS subunits are nuclear-encoded, trans- lated in the cytosol and imported into chloroplasts [6]. Newly-synthesized RbcL subunits asso- ciate with the chloroplast chaperonin Cpn60 [7], the homolog of bacterial GroEL, initially suggesting that the chaperonin mediates Rubisco assembly [8]. Recent reconstitution of cyanobacterial form I Rubisco in vitro demonstrated that the cha- peronin mediates RbcL folding, while assembly of the RbcL8 core complex requires the addi- tional factor RbcX [9, 10]. Co-expression of RbcX was also required for the recombinant production of the Rubisco from the cyanobacterial species Synechococcus sp. PCC7002 (Syn7002) and increased the efficiency of functional expression of Synechococcus elongatus PCC6301 (Syn6301) Rubisco [11, 12]. In most cyanobacteria, the gene for RbcX is located between the rbcL and rbcS genes within a single operon [13]. Mutation or deletion of rbcX was found to reduce the level of functional Rubisco in PCC7002 and Synechococcus elongatus PCC7942 [11, 14]. RbcX is highly conserved in all prokaryotes and eukaryotes containing form 1B Rubisco [15]. Structural analysis showed that RbcX is a dimeric, α-helical protein of *15 kDa subunits [12, 16–18]. The dimer structure has a central hydrophobic cleft which serves as binding site for the C-terminal sequence motif EIKFEF(E/D) in RbcL sequences [12, 15]. The peptide binds in an extended conformation with the Phe sidechains reaching into hydrophobic pockets [10, 12]. In addition, the boomerang-shaped RbcX dimer has conserved residues at the corners that mediate interactions with the adjacent RbcL subunit [10, 12]. Thus, RbcX binding clamps the RbcL anti-parallel dimer together and facilitates the assembly of the RbcL8 core complex. The RbcL-RbcX interaction is dynamic, allowing the displacement of RbcX from RbcL8 complexes by RbcS to form the holoenzyme. RbcX therefore functions as a Rubisco assembly chaperone. Many eukaryotes have two RbcX homologs, one that closely resembles the cyanobacterial ortholog, RbcX-I, and a more distantly related homolog, RbcX-II [12]. The RbcX-I and RbcX-II from Arabidopsis thaliana have been characterized and crystallized, named AtRbcX2 and AtRbcX1, respectively, in these studies [18, 19]. The green algae Chlamydomonas reinhard- tii contains two RbcX-II sequences (CrRbcX-IIa and CrRbcX-IIb, orthologs of AtRbcX-II) and no RbcX-I ortholog. Here we biochemically and structurally characterize CrRbcX-IIa. The crystal structures of CrRbcX-IIa alone and in complex with the C-terminal peptide of RbcL show that CrRbcX-IIa shares the structural topology with cyanobacterial and plant RbcX homologs. However, the RbcL peptide bound to CrRbcX-IIa only occupies part of the central hydrophobic cleft of the RbcX dimer, in contrast to the structure of the cyanobacterial RbcX- peptide complex. Nevertheless, we find that CrRbcX-IIa supports the assembly of cyanobacter- ial Rubisco, although with reduced efficiency compared to cyanobacterial RbcX-I. Introduction Data Availability Statement: Data for this study are accessible through the RCSB Protein Data Bank at (http://www.rcsb.org/pdb/explore/explore.do? structureId=5BS1) and (http://www.rcsb.org/pdb/ explore/explore.do?structureId=5BS2). Life on earth depends on fixation of atmospheric CO2 into organic compounds by bacteria, algae and plants. The key enzyme for this process ribulose-1,5-bisphosphate carboxylase/oxy- genase (Rubisco) catalyzes the carboxylation of the five-carbon sugar ribulose-1,5-bispho- sphate (RuBP) which is converted into two molecules of 3-phosphoglycerate. The other enzymes of the Calvin–Benson–Bassham cycle subsequently use reduction equivalents and ATP produced in the light reaction of photosynthesis to regenerate RuBP and produce triose phosphate to fuel anabolic pathways. The most prevalent form of Rubisco (form I) consists of a complex of eight catalytic large subunits (RbcL), forming a D4-symmetric core, and eight Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 1 / 17 Expression and Purification of CrRbcX-IIa RbcX proteins were expressed as N-terminal His6-ubiquitin (His6-Ub) fusion proteins in E. coli BL21 (DE3) cells from pHue expression plasmids. Cells were grown to an OD600 of 0.5 at 37°C in LB medium followed by induction for 16 h with 0.5 mM isopropyl-D-thiogalactoside (IPTG) at 23°C. Cells were lysed in 50 mM Tris-HCl pH 8.0, 20 mM NaCl, 1 mM EDTA, 0.5 mg/ml lysozyme and 5 mM phenylmethylsulfonyl fluoride (PMSF) for 30 min on ice, followed by ultrasonication (Misonix Sonicator 3000). The supernatant obtained after high-speed cen- trifugation (48 000 x g, 40 min, 4°C) was applied to a Ni-IMAC column (GE Biotech) to cap- ture the His6-Ub protein, followed by overnight cleavage of the His6-Ub moiety at 23°C using the deubiquitinating enzyme Usp2 [21]. All subsequent steps were performed at 4°C. The supernatant was dialyzed against buffer A (20 mM Tris-HCl pH 8.0, 50 mM NaCl) and applied to a pre-equilibrated MonoQ column (GE Biotech). Proteins were eluted with a linear salt gra- dient from 50 mM to 1 M NaCl. Fractions containing RbcX were combined and concentrated, 5% glycerol was added, followed by flash-freezing in liquid nitrogen and storage at –80°C. RbcX for crystallographic studies was purified further by Superdex200 (GE Biotech) size exclusion chromatography in buffer A. Protein concentration was determined spectrophoto- metrically at 280 nm using calculated extinction coefficients. y g For selenomethionine (SeMet) labeling by the catabolite repression method [23], the bacte- ria were grown to mid-log phase at 37°C in M9 medium containing 100 mg L-1 ampicillin. Methionine biosynthesis repression was induced by addition of amino acids as follows: 125 mg L-1 L-Lys, 100 mg L-1 L-Phe, 100 mg L-1 L-Tyr, 50 mg L-1 L-Ile, 50 mg L-1 L-Leu, 50 mg L-1 L- Val and 60 mg L-1 L-Se-Met. 15 min later the temperature was reduced to 23°C and protein synthesis was induced with 0.5 mM IPTG for 20 h. Cells were harvested and re-suspended in lysis buffer (50 mM Na-phosphate pH 9.0, 300 mM NaCl, 10 mM imidazole and 1 mM β-mer- captoethanol) containing Complete protease (Roche Biotech) inhibitor cocktail. The cells were disrupted by ultrasonication and SeMet-labeled His6-Ub RbcX was purified essentially as described above. The protein solution was dialyzed against buffer A containing 1 mM β-mer- captoethanol (β-ME) and applied to a pre-equilibrated MonoQ column. Proteins were eluted with a linear salt gradient from 50 to 400 mM NaCl. Plasmids and Proteins Open reading frames for CrRbcX-IIa were amplified by PCR from Chlamydomonas reinhardtii cDNA [20], and cloned between the SacII and SacI restriction sites of the pHue plasmid [21], 2 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 RbcX from Chlamydomonas reinhardtii resulting in the following constructs: pHueCrRbcX-IIa(33–189); pHueCrRbcX-IIa(34–156); pHueCrRbcX-IIa(34–189); pHueCrRbcL(462–474)-RbcX-IIa(37–156). The cleavage site for the chloroplast transit peptide of CrRbcX-IIa was predicted based on homology with AtRbcX-II (see Fig 1). The Quik-Change protocol (Stratagene) was used to produce the mutant pHueCrRbcX-IIa(33–189)(R118A). All plasmid inserts were verified by DNA sequencing. S. elongatus PCC6301 RbcL8S8, RbcL8, RbcS, RbcL, GroEL and GroES were purified as pre- viously described [9, 12, 22]. Rabbit antibody against S. elongatus PCC6301 RbcL was produced using standard procedures. S. elongatus PCC6301 RbcL8S8, RbcL8, RbcS, RbcL, GroEL and GroES were purified as pre- viously described [9, 12, 22]. Rabbit antibody against S. elongatus PCC6301 RbcL was produced using standard procedures. Expression and Purification of CrRbcX-IIa Fractions containing SeMet-labeled CrRbcX-IIa(34–156) were subsequently dialyzed against buffer A/β-ME and concentrated. After flash-freezing in liquid N2, the protein was stored at -80°C. Native Mass Spectrometry (Native-MS) Purified CrRbcX-IIa(33–189); CrRbcX-IIa(34–156) and CrRbcX-IIa(34–189) (15 μM mono- mer each) were buffer-exchanged into 100 mM ammonium acetate pH 8.5 (Fluka, Sigma), using Micro Bio-Spin 6 chromatography columns (BioRad). Native-MS analyses were per- formed in positive ion mode on an electrospray ionization quadrupole time-of-flight (ESI-- TOF) hybrid mass spectrometer (Synapt G2-Si, Waters Corp., Manchester, UK) equipped with a Z-spray nano-ESI source. The instrument was mass calibrated using a solution of 30 mg ml-1 3 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Crystallization Crystals of CrRbcX-IIa(34–156) were grown using the hanging drop vapor diffusion method at 20°C by mixing 1 μl protein sample at 6 g L-1 and 1 μl reservoir solution. Crystals of SeMet- labeled CrRbcX-IIa(34–156) resembling shields were obtained with a reservoir solution con- taining 5% PEG-3350/0.2 M MgCl2/50 mM Tris-HCl pH 8.0. For cryo-protection, the crystals were transferred into mother liquor containing 15% PEG-3350/0.2 M MgCl2/50 mM Tris-HCl pH 8.0, followed by stepwise increase to 20% glycerol content and flash-freezing in liquid nitrogen. Crystals of the CrRbcL(462–473)-RbcX-IIa(37–156) fusion protein were grown by the hanging drop vapor diffusion method at 20°C using 0.1M Tris-HCl pH 8.5, 25% PEG2000 monomethyl ether as precipitant. RbcX from Chlamydomonas reinhardtii residues are shown in red and identical residues in white using bold lettering on red background. Blue frames indicate homologous regions. The consensus sequence is shown at the bottom. The forward arrow designates the beginning of the mature RbcX-II proteins. The diamond symbol at the end of the CrRbcX-IIb sequence indicates that the sequence continues with 130 amino acids not displayed. Asterisks denote residues known to be essential for RbcX function. doi:10.1371/journal.pone.0135448.g001 cesium iodide dissolved in 1:1 acetonitrile:water. Gold-plated 10 μm nano-ESI pipettes (Mas- com, Bremen) were used as capillaries. Optimized capillary and sample cone voltages were 1–1.3 kV and 100–150 V, respectively. cesium iodide dissolved in 1:1 acetonitrile:water. Gold-plated 10 μm nano-ESI pipettes (Mas- com, Bremen) were used as capillaries. Optimized capillary and sample cone voltages were 1–1.3 kV and 100–150 V, respectively. Rubisco Reconstitution GroEL/ES-mediated RbcL folding was performed as in Liu et al. (2010) with modifications. Denatured S. elongatus PCC6301 RbcL was diluted 200-fold from 6 M GuHCl (final RbcL con- centration 0.5 μM) into ice-cold buffer B (20 mM MOPS-KOH pH 7.5, 100 mM KCl, 5 mM MgOAc2) containing GroEL (1 μM oligomer), 1 mg/ml BSA and 5 mM DTT. The reaction was incubated on ice for 60 min, followed by centrifugation to remove any aggregated RbcL. GroES (2 μM oligomer), RbcX (2 μM AnaCa-RbcX or 30 μM CrRbcX dimer) and S. elongatus PCC6301 RbcS (5 μM) were added to the supernatant containing GroEL bound Syn6301-RbcL as indicated in Figure legend. Reconstitution was initiated by addition of 4 mM ATP at 25°C. Reactions were stopped by addition of apyrase (Sigma) to a final concentration of 0.25 U/μl to inhibit GroEL/ES activity. For measurement of Rubisco enzymatic activity at 25°C, the reaction was supplemented with Syn6301-RbcS (5 μM) and C-terminal RbcL peptide (KEIKFEFETMD) of S. elongatus PCC6301 (200 μM) when indicated, and assembly of RbcL8S8 allowed to proceed for 15 min before enzymatic assay. Rubisco carboxylation activity was determined after incubation for 10 min in 50 mM Tris-HCl pH 8.0, 10 mM MgCl2, 30 mM NaH14CO3 (25 Bq/nmol) and the amount of carbon fixed was quantified [24]. Activities are expressed as percent of purified Syn6301-RbcL8 (~0.06 μM oligomer) standard supplemented with RbcS (5 μM). RbcX from Chlamydomonas reinhardtii Fig 1. Sequence alignment of RbcX-II from green algae. Amino acid sequences of selected RbcX-II homologs from green algae, mosses aligned using Clustal-Ω. Note that for the green algae Coccomyxa subellipsoidea, Chlorella variabilis, Volvox carteri, Ostreococcus tauri and pusilla only one RbcX-II sequence is shown. For comparison, RbcX-I from A. thaliana, Synechococcus sp. PCC7002 and Anabaena sp. CA All sequence numbering is based on the open reading frames. Secondary structure elements are indicated above the sequences. In the alig Fig 1. Sequence alignment of RbcX-II from green algae. Amino acid sequences of selected RbcX-II homologs from green algae, mosses a aligned using Clustal-Ω. Note that for the green algae Coccomyxa subellipsoidea, Chlorella variabilis, Volvox carteri, Ostreococcus tauri and M pusilla only one RbcX-II sequence is shown. For comparison, RbcX-I from A. thaliana, Synechococcus sp. PCC7002 and Anabaena sp. CA ar All sequence numbering is based on the open reading frames. Secondary structure elements are indicated above the sequences. In the alignm Fig 1. Sequence alignment of RbcX-II from green algae. Amino acid sequences of selected RbcX-II homologs from green algae, mosses and plants were aligned using Clustal-Ω. Note that for the green algae Coccomyxa subellipsoidea, Chlorella variabilis, Volvox carteri, Ostreococcus tauri and Micromonas pusilla only one RbcX-II sequence is shown. For comparison, RbcX-I from A. thaliana, Synechococcus sp. PCC7002 and Anabaena sp. CA are also aligned. All sequence numbering is based on the open reading frames. Secondary structure elements are indicated above the sequences. In the alignment, similar Fig 1. Sequence alignment of RbcX-II from green algae. Amino acid sequences of selected RbcX-II homologs from green algae, mosses and plants were aligned using Clustal-Ω. Note that for the green algae Coccomyxa subellipsoidea, Chlorella variabilis, Volvox carteri, Ostreococcus tauri and Micromonas pusilla only one RbcX-II sequence is shown. For comparison, RbcX-I from A. thaliana, Synechococcus sp. PCC7002 and Anabaena sp. CA are also aligned. All sequence numbering is based on the open reading frames. Secondary structure elements are indicated above the sequences. In the alignment, similar PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 4 / 17 NE | DOI:10.1371/journal.pone.0135448 August 25, 201 Structural Analysis of Chlamydononas reinhardtii RbcX The genome of C. reinhardtii contains no RbcX-I, but instead has two RbcX-II genes, g688.t1 (locus Cre01.g030350) and g7885.t1 (locus Cre07.g339000). We refer to the gene products as CrRbcX-IIa and CrRbcX-IIb, respectively. Note that in the most recent genome annotation CrRbcX-IIa would start at amino-acid residue 34 and lacks the sequence encoding the transit peptide. CrRbcX-IIb, on the other hand, has a putative transit peptide but the annotated gene codes for a protein twice the length of other RbcX homologs (~290 residues) with only the first ~160 amino acids displaying homology to RbcX proteins (Fig 1). The additional sequence in CrRbcX-IIb probably represents an intron, and thus the sequence for CrRbcX-IIb is apparently incorrectly annotated. We focused our analysis on CrRbcX-IIa, which was previously anno- tated with a putative transit peptide. Based on sequence alignment with the mature form of A. thaliana RbcX-II (also known as AtRbcX1), which begins with Lys46 [19], we cloned CrRbcX-IIa starting at Arg33 (Fig 1), generating a protein of ~17 kDa. CrRbcX-IIa(33–189) was recombinantly expressed and purified from the soluble fraction. Analysis by native-MS showed that CrRbcX-IIa is a dimer in solution, as expected (Fig 2A). Full-length CrRbcX-IIa failed to crystallize. A stable fragment comprising residues 34–156 lacking the flexible C-terminal 33 residues was produced by subtilisin treatment, as determined by mass spectrometry (MS). An unstructured C-terminus was also found to be present in the cyanobacterial Syn7002-RbcX and was not required for function in Rubisco assembly [12]. We recombinantly expressed and purified the truncated CrRbcX-IIa(34–156) protein for further structural analysis. The structure of the selenomethionine (SeMet)-labeled CrRbcX-IIa(34– 156) protein was solved by selenium-single-wavelength anomalous dispersion (Se-SAD) at 2.0 Å resolution. The experimental electron density was readily interpretable (Fig 3A). The structural model was built against data to 1.6 Å resolution and refined to final R and Rfree val- ues of 0.177 and 0.206, respectively (see Table 1 for data collection and refinement statistics). The asymmetric unit of the monoclinic unit cell contains four copies of CrRbcX-IIa(34–156) in a two-fold symmetric topology (Fig 3B). Each chain consists of a succession of five α-helices. In three of the subunits the insertion after helix α1, residues 73–77, is disordered. This inser- tion is typical for RbcX-II sequences from green algae (Fig 1). Apart from the N-terminal 10 residues (see below), the backbones of the CrRbcX-IIa(34–156) subunits are closely similar (r. m.s.d. Structure Solution and Refinement The diffraction data were collected at beamline X10SA of the Swiss Light Source (SLS) in Villi- gen, Switzerland. Diffraction data were integrated and scaled with XDS [25]. Pointless [26], Scala [27] and Truncate [28] were used to convert the data to CCP4 format, as implemented in the CCP4i interface [29]. The structure of CrRbcX-IIa(34–156) was solved by Se-SAD using crystals from SeMet- labeled protein at 2.0 Å resolution. 36 selenium sites were found by direct methods using 5 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 RbcX from Chlamydomonas reinhardtii SHELXD as implemented in HKL2MAP [30, 31]. SHELXE was used for density modification and auto-building of a poly-alanine model. The resulting map was readily interpretable and the sequence was docked using Coot [32]. The final model was created by iterative Coot model building and Refmac5 refinement cycles [33]. The structure of the fusion protein CrRbcL(462– 474)-RbcX-IIa(37–156) was solved by molecular replacement using Molrep [34], and the mod- els modified and refined as above. Residues facing solvent channels with disordered side chains were modeled as alanines. Coordinates were aligned with Lsqkab and Lsqman [35]. Figures were generated with the program PyMOL [36] and ESPript [37]. Coordinates and structure factor amplitudes were deposited to Protein Data Bank under accession codes 5BS1 and 5BS2. PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Structural Analysis of Chlamydononas reinhardtii RbcX of Cα positions of 0.267 to 0.577 Å). The subunits form arch-shaped, two-fold symmet- ric dimers with a hydrophobic cleft in the center (Fig 4A), similar to other known RbcX struc- tures [12, 17, 18]. In each subunit helices α1-α4 form a four-helix bundle, which associates with helix α5 of the opposing subunit in the dimer (Fig 4A). The N-terminal sequence of one subunit binds into the central cleft, with residues Met34 and Ile36 reaching into hydrophobic pockets located between the anti-parallel helices α1 and α1’ at the bottom of the cleft (Fig 4B). The N-terminal ammonium group of Met34 engages in a tight salt bridge (lengths 2.53 and PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 6 / 17 RbcX from Chlamydomonas reinhardtii Fig 2. Oligomeric state of CrRbcX-IIa analyzed by native-MS. Nano-ESI native-MS spectra of CrRbcX-IIa (33–189) (A) and CrRbcX-IIa(34–156) (B). Symbols indicate the charge state distributions with the charge states shown for some peaks; the calculated mass around the m/z values of the respective protein complexes is reported. The accuracy of mass values calculated from the different m/z peaks is indicated. doi:10.1371/journal.pone.0135448.g002 Fig 2. Oligomeric state of CrRbcX-IIa analyzed by native-MS. Nano-ESI native-MS spectra of CrRbcX-IIa (33–189) (A) and CrRbcX-IIa(34–156) (B). Symbols indicate the charge state distributions with the charge states shown for some peaks; the calculated mass around the m/z values of the respective protein complexes is reported. The accuracy of mass values calculated from the different m/z peaks is indicated. doi:10.1371/journal.pone.0135448.g002 doi:10.1371/journal.pone.0135448.g002 2.58 Å) with Asp90 from the opposing dimer, which presumably stabilizes the tetramer arrangement. The other N-terminal peptide inserts into a cleft between neighboring tetramers in the crystal lattice. The dimers in the asymmetric unit interact substantially (1370 Å2 accessi- ble surface area buried on each dimer). Indeed, CrRbcX-IIa(34–156) formed mainly tetramers in solution as detected by native-MS (Fig 2B). However, this interaction is unlikely to be func- tionally relevant since full-length CrRbcX-IIa behaved as a dimer in solution (Fig 2A). PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Comparison with Other RbcX Structures On the left, a view along the two-fold molecular axis is shown. CrRbcX-IIa(34–156) is shown in ribbon representation. In each dimer, one of the chains is colored blue and the other gold or silver, respectively. Chain termini and secondary structure elements are indicated. The N- termini of the golden/silver subunits reach into the clefts (roughly horizontal); the N-termini of the blue subunits towards crystallographic symmetry mates. doi:10.1371/journal.pone.0135448.g003 which form the “walls” of the hydrophobic cleft, are rotated outwards in comparison to cyano- bacterial RbcX (Fig 5C), widening the cleft. Comparison with Other RbcX Structures The crystal structure of the dimer of CrRbcX-IIa(34–156) is closely similar to that of the plant ortholog AtRbcX-II (AtRbcX1) [18] (Fig 5A). 175 Cα positions could be superposed with a r. m.s.d. of 1.239 Å. In contrast, the structure of CrRbcX-IIa(34–156) differs more substantially from the structures of cyanobacterial RbcX and AtRbcX-I. For example, while one four-helix bundle and the associated C-terminal helix from the other subunit of the dimer of AtRbcX-I are reasonably well superimposable with CrRbcX-IIa(34–156) (r.m.s.d. 1.414 Å for 120 match- ing Cα atom positions), the other helical bundle is markedly shifted (Fig 5B). The situation is closely similar when comparing with the cyanobacterial Anabaena sp. CA RbcX (Ana- CA-RbcX) with an r.m.s.d. 1.453 Å for 134 matching Cα atom positions (Fig 5C). The rear- rangement displaces helices α1 and α1’ in the protomers longitudinally, which moves the symmetry-related pairs of hydrophobic pockets apart by ~5 Å. This becomes apparent from comparing the positions of residues Leu57 and Phe62, which line the hydrophobic pockets (spheres in Fig 5). Consequently, a pseudo-symmetrical binding of the FEF motif in the RbcL C-terminal peptide across the dyad axis is not possible in CrRbcX, in contrast to the binding mode of the FEF motif to cyanobacterial RbcX [10, 12]. The helices α2 of CrRbcX-IIa(34–156), PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 7 / 17 RbcX from Chlamydomonas reinhardtii Fig 3. Asymmetric unit of the CrRbcX-IIa(34–156) crystal. (A) Stereoview of a representative portion of the experimental density map at 1.0 σ. The final model is superposed in stick representation. (B) Tetrameric complex of the SeMet-labeled oligomer in the asymmetric unit of the crystal lattice. Two perpendicular views are shown. On the left, a view along the two-fold molecular axis is shown. CrRbcX-IIa(34–156) is shown in ribbon representation. In each dimer, one of the chains is colored blue and the other gold or silver, respectively. Chain termini and secondary structure elements are indicated. The N- termini of the golden/silver subunits reach into the clefts (roughly horizontal); the N-termini of the blue subunits towards crystallographic symmetry mates. Fig 3. Asymmetric unit of the CrRbcX-IIa(34–156) crystal. (A) Stereoview of a representative portion of the experimental density map at 1.0 σ. The final model is superposed in stick representation. (B) Tetrameric complex of the SeMet-labeled oligomer in the asymmetric unit of the crystal lattice. Two perpendicular views are shown. RbcX from Chlamydomonas reinhardtii Table 1. Crystallographic data collection and model refinement statistics. Dataset CrRbcX-IIa(34–156) (SeMet) CrRbcL(462–474)-CrRbcX-IIa(37–156) Data collection Wavelength (Å) 0.9790 0.9999 Space group P1 P1 Cell dimensions a, b, c (Å); 36.13, 52.99, 61.56; 34.22, 38.53, 50.36; α, β, γ (°) 76.49, 81.10, 70.10 88.47, 81.53, 67.92 Resolution limits (Å)* 59.66–1.6 (1.69–1.6) 35.68–1.97 (2.07–1.97) Rmerge * 0.059 (0.332) 0.081 (0.494) I/sigma * 18.3 (4.6) 10.4 (2.0) Multiplicity * 7.1 (6.7) 2.4 (2.2) Completeness (%) * 94.1 (77.2) 94.2 (87.9) Wilson B-factor (Å2) 15.3 22.8 Refinement Resolution range 30–1.6 30–1.97 Reflections ** 49112 (2585) 15009 (1887) Rwork / Rfree 0.177 / 0.206 0.200 / 0.222 Number of atoms 4185 1887 Average B-factor (Å2) 19.0 31.0 r.m.s. deviations Bond length (Å) 0.011 0.013 Bond angle (°) 1.509 1.423 Ramachandran plot *** Favoured (%) 97.7 97.3 Allowed (%) 2.1 2.2 Outliers (%) 0.2 0.4 * Values in parenthesis for outer shell. ** Values in parenthesis for test set. *** Values from Molprobity 4.02. doi:10 1371/journal pone 0135448 t001 Table 1. Crystallographic data collection and model refinement statistics. doi:10.1371/journal.pone.0135448.t001 was solved at 1.97 Å resolution (Table 1). The structural core of CrRbcX-IIa(37–156) in the fusion protein is virtually identical to that obtained for CrRbcX-IIa(34–156) (r.m.s.d. 0.425 Å for 211 matching Cα positions). Thus it is unlikely that the contact area with the RbcL peptide is distorted by crystal packing. Difference electron density along the hydrophobic cleft could be assigned to the RbcL residues 462–467 (WKEIKF). Residues 468–473 (EFDTID) of RbcL as well as residues 37–43 of CrRbcX-IIa were disordered (Fig 6A). Notably, Phe469 was among the disordered residues, consistent with the finding that the corresponding Phe464 in Syn7002-RbcL is functionally less important for RbcX binding than Phe462 (Phe467 in CrRbcL) [12]. The sidechains of Ile465 and Phe467 point into hydrophobic pockets sur- rounded by Phe60/Arg64/Leu67/Leu92 and Leu57/Phe60/Met96, respectively (Fig 6B). The sidechain of Lys463 points towards the C-terminal end of helix α2 and Asp90. The indole moi- ety of Trp462 interacts with Tyr85 and Met89, but also with a neighboring CrRbcX-IIa mole- cule (not shown), and thus these interactions seem to be influenced by crystal packing. was solved at 1.97 Å resolution (Table 1). The structural core of CrRbcX-IIa(37–156) in the fusion protein is virtually identical to that obtained for CrRbcX-IIa(34–156) (r.m.s.d. 0.425 Å for 211 matching Cα positions). Structural Basis of RbcL Peptide Recognition Attempts to obtain a co-crystal between CrRbcXIIa(34–159) and the C-terminal RbcL peptide failed, presumably due to low peptide binding affinity. Taking advantage of the finding that the N-terminus of RbcX binds into the central cleft (Fig 4), we therefore generated a fusion con- struct between CrRbcX-IIa and the C-terminal recognition motif in CrRbcL. In this construct, residues 462–473 of CrRbcL (sequence WKEIKFEFDTID) are directly linked to residue Pro37 at the N-terminus of CrRbcX-IIa(37–156), with the new N-terminus of the fusion protein start- ing with Trp462 of the RbcL sequence. This fusion protein readily crystallized and the structure PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 8 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Thus it is unlikely that the contact area with the RbcL peptide is distorted by crystal packing. Difference electron density along the hydrophobic cleft could be assigned to the RbcL residues 462–467 (WKEIKF). Residues 468–473 (EFDTID) of RbcL as well as residues 37–43 of CrRbcX-IIa were disordered (Fig 6A). Notably, Phe469 was among the disordered residues, consistent with the finding that the corresponding Phe464 in Syn7002-RbcL is functionally less important for RbcX binding than Phe462 (Phe467 in CrRbcL) [12]. The sidechains of Ile465 and Phe467 point into hydrophobic pockets sur- rounded by Phe60/Arg64/Leu67/Leu92 and Leu57/Phe60/Met96, respectively (Fig 6B). The sidechain of Lys463 points towards the C-terminal end of helix α2 and Asp90. The indole moi- ety of Trp462 interacts with Tyr85 and Met89, but also with a neighboring CrRbcX-IIa mole- cule (not shown), and thus these interactions seem to be influenced by crystal packing. Superposition with the structure of the heterologous cyanobacterial Syn6301-RbcL8/Ana- CA-RbcX8 assembly intermediate [10] shows that Ile465 and Phe467 of CrRbcL are recognized by similar sites on CrRbcX-IIa (Fig 6C). The peptide is oriented more towards helix α2 in the cyanobacterial structure, whereas it assumes a deeper and more central position in the PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 9 / 17 hydrophobic cleft of CrRbcX IIa (Fig 6C) The indole ring of Trp462 is at roughly the same Fig 4. Crystal structure of the CrRbcX-IIa(34–156) dimer. (A) Ribbon representation of the CrRbcX-IIa(34–156) dimer. Two perpendicular views are shown, the first along the molecular two-fold axis. (B) Interactions of the N-terminal tail with the hydrophobic cleft in CrRbcX-IIa(34–156). A zoom-in on the boxed area in panel (A) is shown. The N-terminal tail is shown as a coil with prominent sidechains in stick representation. The bulk of the CrRbcX-IIa(34–156) is represented as a molecular surface. doi:10.1371/journal.pone.0135448.g004 RbcX from Chlamydomonas reinhardtii RbcX from Chlamydomonas reinhardtii Fig 4. Crystal structure of the CrRbcX-IIa(34–156) dimer. (A) Ribbon representation of the CrRbcX-IIa(34–156) dimer. Two perp shown, the first along the molecular two-fold axis. (B) Interactions of the N-terminal tail with the hydrophobic cleft in CrRbcX-IIa(34– boxed area in panel (A) is shown. The N-terminal tail is shown as a coil with prominent sidechains in stick representation. The bulk Fig 4. Crystal structure of the CrRbcX-IIa(34–156) dimer. (A) Ribbon representation of the CrRbcX-IIa(34–156) dimer. Two perpendicular views are shown, the first along the molecular two-fold axis. PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 (B) Interactions of the N-terminal tail with the hydrophobic cleft in CrRbcX-IIa(34–156). A zoom-in on the boxed area in panel (A) is shown. The N-terminal tail is shown as a coil with prominent sidechains in stick representation. The bulk of the CrRbcX-IIa(34–156) is represented as a molecular surface. doi:10.1371/journal.pone.0135448.g004 hydrophobic cleft of CrRbcX-IIa (Fig 6C). The indole ring of Trp462 is at roughly the same place in the superposition, but the backbone conformations differ strongly at this segment. We note that in the context of the RbcL subunit this residue would be connected, whereas it forms the N-terminal residue in the fusion construct. This difference in sequence topology may influ- ence the binding mode. The superposed CrRbcX-IIa is compatible with the surface of the RbcL anti-parallel dimer in the context of the RbcL8 core complex (Fig 6D), in a topology similar to that observed for the cyanobacterial RbcX [10]. The C-terminal sequence of one RbcL subunit reaches into the central cleft of CrRbcX-IIa and the functionally critical, conserved residues Gln69 and Arg118 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 10 / 17 RbcX from Chlamydomonas reinhardtii Fig 5. Comparison of the CrRbcX-IIa(34–156) structure with RbcX-II and RbcX-I homologs. (A) Comparison with the A. thaliana homolog AtRbcX-II. The backbones of the subunits of CrRbcX-IIa(34–156) are represented as a Cα trace in the same views as in Fig 4A. Spheres designate the Cα atoms of Leu57 and Phe60 in CrRbcX-IIa, or the respective sequence positions in the homologous proteins. CrRbcX-IIa and Fi 5 C i f th C Rb X II (34 156) t t ith Rb X II d Rb X I h l (A) Fig 5. Comparison of the CrRbcX-IIa(34–156) structure with RbcX-II and RbcX-I homologs. (A) Comparison with the A. thaliana homolog AtRbcX-II. The backbones of the subunits of CrRbcX-IIa(34–156) are represented as a Cα trace in the same views as in Fig 4A. Spheres designate the Cα atoms of Leu57 and Phe60 in CrRbcX-IIa, or the respective sequence positions in the homologous proteins. CrRbcX-IIa and 11 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 RbcX from Chlamydomonas reinhardtii AtRbcX-II are shown in blue and dark grey, respectively. (B) Comparison with the A. thaliana homolog AtRbcX-I, which is shown in light grey. (C) Comparison with cyanobacterial AnaCA-RbcX which is shown in red. Arrows indicate the direction of displacement of the second 4-helix bundle of CrRbcX-IIa(34–156). doi:10.1371/journal.pone.0135448.g005 Fig 6. doi:10.1371/journal.pone.0135448.g006 RbcX from Chlamydomonas reinhardtii (Fig 1) are positioned correctly for interaction with the second RbcL subunit (Fig 6D). The loop insertion between helices α1 and α2 of CrRbcX-IIa, which is ordered in the structure of the CrRbcL(462–474)-RbcX-IIa(37–156) fusion protein, would extend into a shallow groove of the RbcL dimer surface (Fig 6D). We speculate that this loop insertion found in RbcX sequences of green algae might modulate the interaction with RbcL. Functional Characterization of CrRbcX We used the previously reconstituted Rubisco from S. elongatus PCC6301 [9] and the bacterial chaperonin system GroEL/ES to assess the functionality of CrRbcX-IIa in Rubisco assembly. Unfolded RbcL was bound to GroEL upon dilution from denaturant. Assembly was initiated by adding GroES, ATP and RbcX for 60 min at 25°C, followed by addition of RbcS for Rubisco activity assay. The formation of holoenzyme was dependent on RbcX as shown previously [9], reaching a yield of ~20% with AnaCA-RbcX (Fig 7A). Addition of the C-terminal RbcL peptide prior to RbcS doubled the yield to ~40% by facilitating the displacement of RbcX from the RbcL8RbcX8 assembly intermediate by RbcS [9, 10]. A lower yield of enzyme activity of ~7% was obtained with full-length CrRbcX-IIa(33–189) protein, but only when present at a high molar excess (30 μM dimer) over RbcL. Again the activity doubled in the presence of the C-ter- minal RbcL peptide (Fig 7A). The mutant CrRbcX-IIa(R118A) did not support assembly, con- sistent with this conserved residue being involved in the stabilization of the RbcL dimer [9, 10, 12]. Notably, CrRbcX-IIa(34–189), lacking the N-terminal residue Arg33 of the full-length protein was inactive (Fig 7A). Arg or Lys is conserved at this position among most RbcX-II homologs (Fig 1). Arg33 is also missing in the C-terminally truncated, crystallized CrRbcX-IIa (34–156) protein. In the crystal structure, the amino group of the N-terminal Met34 forms a short salt bridge (2.53–2.58 Å) with Asp90 from the other RbcX dimer, which appears to stabi- lize the tetramer. In addition, Arg33 would clash with the other dimer, consistent with the MS data showing that deletion of Arg33 favors tetramer formation in solution (Fig 2). We suggest that in the absence of Arg33, the N-terminus of RbcX may bind into the central cleft, rendering the protein non-functional in Rubisco assembly (Fig 7A), consistent with the formation of non-functional tetramers (Fig 7B). PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Crystal structure of a fusion protein revealing the interactions between CrRbcX-IIa and the C-terminal tail of CrRbcL. (A) Unbiased omit difference electron density for the RbcL tail residues of the CrRbcL(462–474)-RbcX-IIa(37–156) fusion protein. The C-terminal sequence of CrRbcL is sho as a coil and the sidechains in stick representation. The difference electron density at 1.5 σ level is shown as orange meshwork. CrRbcX-IIa(37–156) is represented as a molecular surface. (B) Detailed view of the RbcL-RbcX interactions. The area boxed in panel (A) is shown. (C) Superposition of the CrRbcX-IIa(37–156) onto the Syn6301-RbcL8/AnaCA-RbcX8 crystal structure [10]. The structures are shown in ribbon representation. The RbcL subunits are shown in brown and siena; the AnaCA-RbcX dimer in red; CrRbcX-IIa dimer in blue. (D) Putative contacts of CrRbcX-IIa(37–156) with the surface of th Syn6301-RbcL8 complex. The same view as in panel (C) is shown. d i 10 1371/j l 0135448 006 Fig 6. Crystal structure of a fusion protein revealing the interactions between CrRbcX-IIa and the C-terminal tail of CrRbcL. (A) Unbiased omit difference electron density for the RbcL tail residues of the CrRbcL(462–474)-RbcX-IIa(37–156) fusion protein. The C-terminal sequence of CrRbcL is shown as a coil and the sidechains in stick representation. The difference electron density at 1.5 σ level is shown as orange meshwork. CrRbcX-IIa(37–156) is represented as a molecular surface. (B) Detailed view of the RbcL-RbcX interactions. The area boxed in panel (A) is shown. (C) Superposition of the CrRbcX-IIa(37–156) onto the Syn6301-RbcL8/AnaCA-RbcX8 crystal structure [10]. The structures are shown in ribbon representation. The RbcL subunits are shown in brown and siena; the AnaCA-RbcX dimer in red; CrRbcX-IIa dimer in blue. (D) Putative contacts of CrRbcX-IIa(37–156) with the surface of the Syn6301-RbcL8 complex. The same view as in panel (C) is shown. doi:10.1371/journal.pone.0135448.g006 12 / 17 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 Discussion Our data demonstrate that RbcX-II from the green algae C. reinhardtii functions as a bona fide Rubisco assembly chaperone, despite its considerable evolutionary distance from cyanobacter- ial and eukaryotic RbcX-I proteins. Like all other known RbcX proteins, CrRbcX-IIa is an arc- shaped dimer with a central hydrophobic cleft that binds the C-terminal sequence of the RbcL subunit. Conserved polar residues at the corners of RbcX make critical contacts to the N- domain of an adjacent RbcL, thereby stabilizing the RbcL anti-parallel dimer in a state compe- tent for assembly to the RbcL8 core complex of Rubisco. The crystal structure of CrRbcX-IIa differs from the structures of cyanobacterial RbcX homologs in several aspects. The adjacent helices α1, which form the floor of the hydrophobic cleft, are shifted with respect to each other, moving the binding pockets for the two Phe side- chains in the C-terminal RbcL binding motif apart. Consistently, density for the bound peptide sequence is only discernible until the first Phe residue (Phe467) in the complex structure. There are additional hydrophobic cavities between the helices close to the symmetry axis, resulting from the conserved substitution of Thr10 in cyanobacterial RbcX by Ala in RbcX-II (residue 50 in CrRbcX-IIa sequence numbering), but these volumes are not occupied in the complex with peptide. In the apo-structure, the sidechains of the conserved residues Met34 and Ile36 point into these pockets, but the functional significance of this interaction, if any, is PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 13 / 17 Fig 7. Rubisco reconstitution of CrRbcX-IIa and oligomeric state of CrRbcX-IIa(34–189) analyzed by native-MS. (A) Rubisco reconstitution. Chemically denatured RbcL from S. elongatus PCC6301 (at 100 μM) was diluted 200-fold into ice-cold buffer containing GroEL (1.0 μM). The components (2 μM GroES oligomer; 2 μM AnaCa-RbcX or 30 μM CrRbcX dimer) were added as indicated and refolding/assembly initiated by addition of 4 mM ATP at 25°C (see Materials and Methods). After incubation for 60 min, RbcS (5 μM) was added with or without C-terminal RbcL peptide (200 μM) for 15 min, followed by Rubisco enzyme assay. The activity of RbcL8 core complex (~0.06 μM oligomer) incubated with RbcS (5 μM) was set to 100%. Error bars s.d. (n = 3 independent experiments). (B) Nano-ESI native-MS spectra of CrRbcX-IIa(34–189). Discussion Symbols indicate the charge state distributions with the charge states shown for some peaks; the calculated mass around the m/z values of the respective protein complexes is reported. The accuracy of mass values calculated from the different m/z peaks is indicated. doi:10.1371/journal.pone.0135448.g007 RbcX from Chlamydomonas reinhardtii RbcX from Chlamydomonas reinhardtii Fig 7. Rubisco reconstitution of CrRbcX-IIa and oligomeric state of CrRbcX-IIa(34–189) analyzed by native-MS. (A) Rubisco reconstitution. Chemically denatured RbcL from S. elongatus PCC6301 (at 100 μM) was diluted 200-fold into ice-cold buffer containing GroEL (1.0 μM). The components (2 μM GroES oligomer; 2 μM AnaCa-RbcX or 30 μM CrRbcX dimer) were added as indicated and refolding/assembly initiated by addition of 4 mM ATP at 25°C (see Materials and Methods). After incubation for 60 min, RbcS (5 μM) was added with or without C-terminal RbcL peptide (200 μM) for 15 min, followed by Rubisco enzyme assay. The activity of RbcL8 core complex (~0.06 μM oligomer) incubated with RbcS (5 μM) was set to 100%. Error bars s.d. (n = 3 independent experiments). (B) Nano-ESI native-MS spectra of CrRbcX-IIa(34–189). Symbols indicate the charge state distributions with the charge states shown for some peaks; the calculated mass around the m/z values of the respective protein complexes is reported. The accuracy of mass values calculated from the different m/z peaks is indicated. doi:10.1371/journal.pone.0135448.g007 PLOS ONE | DOI:10.1371/journal.pone.0135448 August 25, 2015 14 / 17 14 / 17 RbcX from Chlamydomonas reinhardtii unclear. Interestingly, in the structure of the A. thaliana ortholog, which has essentially the same backbone conformation, the pockets are smaller and intra-molecular binding of the N- terminus into the central cleft is not observed. Besides the RbcX homologs, a recent screen of a Maize mutant library identified several additional Rubisco accumulation factors, including Bsd2, Raf1 and Raf2 [38–42]. RbcX and Raf1 are generally conserved in photosynthetic organisms containing form IB Rubisco [2, 3], but mediate assembly by different mechanisms [43]. Whether RbcX and Raf1 cooperate in a coherent assembly pathway or act in parallel pathways is still unknown. Acknowledgments C. reinhardtii cDNA was obtained from the Kazusa Institute and from E. Lorentzen. We thank R. Körner for performing the mass spectroscopy analysis of the protease-treated CrRbcX-IIa, J. Y. Bhat and D. Balchin for the native-MS analysis. We also thank the staff at the Core and Crystallization Facilities at the MPI of Biochemistry for their services and acknowledge support by the staff at beamline X10SA of the Swiss Light Source (SLS) in Villigen, Switzerland. Author Contributions Conceived and designed the experiments: AB MH-H. Performed the experiments: AB TH CL. Analyzed the data: AB TH CL FUH MH-H. Contributed reagents/materials/analysis tools: AB TH CL. Wrote the paper: AB FUH MH-H. 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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
Briefings in bioinformatics
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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications mtchouk, Edmund Weitz, Peter D. Karp and Claes Wahlestedt Bohdan B. Khomtchouk, Edmund Weitz, Peter D. Karp and Clae Bohdan B. Khomtchouk, Edmund Weitz, Peter D. Karp and Claes Wahlestedt Corresponding author: Bohdan Khomtchouk, Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St, Miami, FL 33136, USA. Tel.: +1 786-501-9121; E-mail: b.khomtchouk@med.miami.edu Corresponding author: Bohdan Khomtchouk, Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St, Miami, FL 33136, USA. Tel.: +1 786-501-9121; E-mail: b.khomtchouk@med.miami.edu Abstract We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and com- putational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSLs): languages that are specialized to a particular area, and thus not only facili- tate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the ‘programmable programming language’. We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and artificial intelligence research in bioinformatics and computational biology. Key words: lisp; software engineering; bioinformatics; computational biology; programming languages Briefings in Bioinformatics, 19(3), 2018, 537–543 Briefings in Bioinformatics, 19(3), 2018, 537–543 doi: 10.1093/bib/bbw130 Advance Access Publication Date: 31 December 2016 Opinion Note Bohdan B. Khomtchouk is an NDSEG Fellow and PhD candidate in the Human Genetics and Genomics Graduate Program at the University of Miami Miller School of Medicine. His research interests include bioinformatics and computational biology applications in HPC, integrative multi-omics, artificial intelli- gence, machine learning, mathematical genetics, biostatistics, epigenetics, visualization, search engines and databases. Edmund Weitz is full professor at the University of Applied Sciences in Hamburg, Germany. He is a mathematician and his research interests include set theory, logic and combinatorics. Rewards and challenges In general, early adopters of a language framework are better poised to reap the scientific benefits, as they are the first to set out building the critical libraries, ultimately attracting and re- taining a growing share of the research and developer commu- nity. As library support for bioinformatics tasks in the Lisp family of programming languages (Clojure, Common Lisp and Scheme) is yet in its early stages and on the rise, and there is (as of yet) no officially established bioinformatics Lisp community, there is plenty of opportunity for high-impact work in this direction. It is well known that the best language to choose from should be the one that is most well suited to the job at hand. Yet, in practice, few programmers may consider a nonmain- stream programming language for a project, unless it offers strong, community-tested benefits over its popular contenders for the specific task under study. Often times, the choice comes down to library support: does language X already offer well- written, optimized code to help solve my research problem, as opposed to language Y (or perhaps language Z)? In general, new language adoption boils down to a chicken-and-egg problem: without a large user base, it is difficult to create and maintain large-scale, reproducible tools and libraries. But without these tools and libraries, there can never be a large user base. Hence, a new language must have a big advantage over the existing ones and/or a powerful corporate sponsorship behind it to com- pete [42]. Most often, a positive feedback loop is generated by repositories of useful libraries attracting users, who, in turn, add more functional libraries, thereby raising a programming language’s popularity, rather than reflecting its theoretical potential. Programmers often test a language’s mettle by how success- fully it has fared in commercial settings, where big money is often on the line. To this end, Lisp has been successfully adopted by commercial vendors such as the Roomba vacuum- ing robot [24, 25], Viaweb (acquired by Yahoo! Store) [26], ITA Software (acquired by Google Inc. and in use at Orbitz, Bing Travel, United Airlines, US Airways, etc.) [27], Mirai (used to model the Gollum character for the Lord of the Rings movies) [28], Boeing [29], AutoCAD [30], among others. Introduction and background As a programming language, Lisp supports many different programming paradigms, each of which can be used exclusively or intermixed with others; this includes functional and procedural programming, object orien- tation, meta programming and reflection. Lisp’s dominance over mainstream programming languages like R and Python, we refer the reader to Sections 4 and 5 of Ross Ihaka’s (creator of the R programming language) seminal paper [34]. Scheme [35] is an elegant and compact version of Common Lisp that supports a minimalistic core language and an excel- lent suite of language extension tools. However, Scheme has traditionally mainly been used in teaching and computer sci- ence research and its implementors have thus prioritized small size, the functional programming paradigm and a certain kind of ‘cleanliness’ over more pragmatic features. As such, Scheme is considered far less popular than Common Lisp for building large-scale applications [24]. But more to the point, we have empirical evidence that Lisp is a more productive general-purpose programming language than the other usual suspects, and that most Lisp programs run faster than their counterparts in other languages. Gat [3] com- pared the run times, development times and memory usage of 16 programs written by 14 programmers in Lisp, C/C þþ and Java. Development times for the Lisp programs ranged from 2 to 8.5 h, compared with 2 to 25 h for C/C þþ and 4 to 63 h for Java (programmer experience alone does not account for the differ- ences). The Lisp programs were also significantly shorter than the other programs. The third most common LFL, Clojure [36, 37], is a rising star language in the modern software development community. Clojure specializes in the parallel processing of big data through the Java Virtual Machine (JVM), recently making its debut in bio- informatics and computational biology research [38, 39, 40]. Most recently, Clojure was used to parallelize the processing and analysis of SAM/BAM files [39]. Furthermore, the BioClojure project provides seeds for the bioinformatics community that can be used as building blocks for writing LFL applications. As of now, BioClojure consists of parsers for various kinds of file for- mats (UniProtXML, Genbank XML, FASTA and FASTQ), as well as wrappers of select data analysis programs (BLAST, SignalP, TMHMM and InterProScan) [39]. Introduction and background date. Concepts such as tree data structures, automatic storage management, dynamic typing, conditionals, exception han- dling, higher-order functions, recursion and more have all shaped the foundations of today’s software engineering date. Concepts such as tree data structures, automatic storage management, dynamic typing, conditionals, exception han- dling, higher-order functions, recursion and more have all shaped the foundations of today’s software engineering The programming language Lisp is credited for pioneering fun- damental computer science concepts that have influenced the development of nearly every modern programming language to Bohdan B. Khomtchouk is an NDSEG Fellow and PhD candidate in the Human Genetics and Genomics Graduate Program at the University of Miami Miller School of Medicine. His research interests include bioinformatics and computational biology applications in HPC, integrative multi-omics, artificial intelli- gence, machine learning, mathematical genetics, biostatistics, epigenetics, visualization, search engines and databases. Edmund Weitz is full professor at the University of Applied Sciences in Hamburg, Germany. He is a mathematician and his research interests include set theory, logic and combinatorics. Claes Wahlestedt is Leonard M. Miller Professor at the University of Miami Miller School of Medicine and is working on a range of basic science and trans- lational efforts in his roles as Associate Dean and Center Director for Therapeutic Innovation. The author of some 250 peer-reviewed scientific publica- tions, his ongoing research projects concern bioinformatics, epigenetics, genomics and drug/biomarker discovery across several therapeutic areas. He has experience not only from academia but also from leadership positions in the pharmaceutical and biotechnology industry. S b itt d 18 A t 2016 R i d (i i d f ) 16 N b 2016 y y 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 537 538 | Khomtchouk et al. 538 community. The name Lisp derives from ‘List processor’ [1], as linked lists are one of Lisp’s major data structures, and Lisp source code is composed of lists. Lists, which are a generaliza- tion of graphs, are extraordinarily well supported by Lisp. As such, programs that analyze sequence data (such as genomics), graph knowledge (such as pathways) and tabular data (such as that handled by R [2]) can be written easily, and can be made to work together naturally in Lisp. Lisp applications and dialects In bioinformatics and computational biology, Lisp has success- fully been applied to research in systems biology [4, 5], high-per- formance computing (HPC) [6], database curation [7, 8], drug discovery [9], computational chemistry and nanotechnology [10, 11], network and pathway -omics analysis [12, 13, 14, 15, 16], single-nucleotide polymorphism analysis [17, 18, 19] and RNA structure prediction [20, 21, 22]. In general, the Lisp family of programming languages, which includes Common Lisp, Scheme and Clojure, has powered multiple applications across fields as diverse as [23]: animation and graphics, artificial intel- ligence (AI), bioinformatics, B2B and e-commerce, data mining, electronic design automation/semiconductor applications, embedded systems, expert systems, finance, intelligent agents, knowledge management, mechanical computer-aided design (CAD), modeling and simulation, natural language, optimiza- tion, risk analysis, scheduling, telecommunications and Web authoring. Introduction and background And although the execution times of the fastest C/C þþ pro- grams were faster than the fastest Lisp programs, on average, the Lisp programs ran significantly faster than the C/C þþ pro- grams and much faster than the Java programs (mean runtimes were 41 s for Lisp versus 165 s for C/C þþ). As a whole, Lisp continues to develop new offshoots. A rela- tively recent addition to the family is Julia [41]. Although it is sometimes touted ‘C for scientists’ and caters to a different community because of its syntactical proximity to Python, it is a Lisp at heart and certainly worth watching. Rewards and challenges Lisp has also been the driving force behind open source applications like Emacs [31] and Maxima [32], which both have existed for decades and continue to be used worldwide. Among the Lisp-family languages (LFLs), Common Lisp has been described as the most powerful and accessible modern language for advanced biomedical concept representation and manipulation [33]. For concrete code examples of Common Strengths of Lisp-family languages 539 With mainstream languages like R [2] and Python [43] domi- nating the bioinformatics and computational biology scene for years, large-scale software development and community sup- port for other less popular language frameworks have waned to relative obscurity. Consequently, languages winning over in- creasingly growing proportions of a steadily expanding user base have the effect of shaping research paradigms and influ- encing modern research trends. For example, R programming generally promotes research that frequently leads to the de- ployment of R packages to Bioconductor [44], which has steadily grown into the largest bioinformatics package ecosystem in the world, whose package count is considerably ahead of BioPython [45], BioClojure [38], BioPerl [46], BioJava [47], BioRuby [48], BioJulia [49] or SCABIO [50]. Given the choice, R programmers interested in deploying large-scale applications are more likely to branch out to releasing Web applications (e.g. Shiny [51]) than to graphical user interface (GUI) binary executables, which are generally more popular with lower-level languages like C/ C þþ [52]. As such, language often dictates research direction, output and funding. Questions like ‘who will be able to read my code?’, ‘is it portable?’, ‘does it already have a library for that?’ or ‘can I hire someone?’ are pressing questions, often inexorably shaping the course and productivity of a project. However, des- pite its popularity, R has been severely criticized for its many shortcomings by its own creator, Ross Ihaka, who has openly proposed to scrap the language altogether and start afresh by using a Lisp-based engine as the foundation for a statistical computing system [34, 53]. matching like ML or Haskell out of the box, it is easy to add [56]) or the integration of code with markup languages (if you want you can, e.g., write code that mimics the structure of an HTML document it is supposed to emit [57, 58]). In addition to that, Common Lisp even offers access to its ‘reader’, which means that code can be manipulated (in Lisp) before it is parsed [59]. Macros and domain-specific languages Lisp is a so-called homoiconic language, which means that Lisp code is represented as a data structure of the language itself in such a way that its syntactical structure is preserved. In more technical terms, while the Lisp compiler has to parse the textual representation of the program (the ‘source code’) into a so- called abstract syntax tree (like any other compiler of any pro- gramming language has to), a Lisp program has direct access to (and can modify) this abstract syntax tree, which is presented to the program in a convenient, structured way. p g y This property enables Lisp to have a macro system that re- mains undisputed in the programming language world [55]. Although ‘macros’ in languages like C have the same name, they are essentially just text substitutions performed on the source code before it is compiled and they cannot always reli- ably preserve the lexical structure of the code. Lisp macros, on the other hand, operate at the syntactic level. They transform the program structure itself and, as opposed to C macros, are written in the same language they work on and have the full language available all the time. Lisp macros are thus not only used for moderately simple ‘find and replace’ chores but can apply extensive structural changes to a program. This includes tasks that are impossible in other languages. Examples would be the introduction of new control structures (while Python users had to wait for the language designers to introduce the ‘with’ statement in version 2.5, Lisp programmers could always add something like that to the language themselves), pattern matching capabilities (while Lisp does not have pattern • Common Lisp was designed from the ground up to create large, complex and long-running applications and thus supports soft- ware ‘hot swapping’: the code of a running program can be changed without the need to interrupt it. This includes features like the ability of the Common Lisp object system (CLOS) to change the classes of existing objects. Although Erlang and Smalltalk also support hot swapping, no mainstream compiled language does this to our knowledge. Hot swapping can be performed in Java to a certain extent, but only with the help of third-party frameworks, as it is not an intrinsic feature of the language itself. Other unique strengths In addition to homoiconicity, Lisp has several other features that set it apart from mainstream languages: • In Lisp, programmers usually work in a special incremental interactive programming environment called the read-eval-print loop (REPL) [65, 66]. This means that the Lisp system continu- ously reads expressions typed by the user, evaluates them and prints the results. The REPL enables a paradigm that allows the programmer to continually interact with their program as it is developed. This is similar to the way Smalltalk ‘images’ evolve [59] and different from the usual edit-compile-link-execute cycle of C-like languages. This approach lends itself well to explorative programming and rapid prototyping. As such, the REPL enables the programmer to write a function, test it, change it, try a differ- ent approach, etc., while never having to stop for any lengthy compilation cycles [24]. Rewards and challenges This enables Lisp programs to com- pletely change their surface syntax if necessary. Examples would be code that adds Perl-like interpolation capabilities to Lisp strings [60] or a library [61] that enables Lisp to read arith- metic in ‘infix’ notation, i.e. to understand ‘20 þ 2 * 21’ in add- ition to the usual ‘(þ 20 (* 2 21))’. These features make Lisp an ideal tool for the creation of domain-specific languages: languages that are custom-tailored to a specific problem domain but can still have access to all of Lisp. A striking example is Common Prolog [62], a professional Prolog system implemented and embedded in Common Lisp. In bioinformatics, the Biolingua [5] project (now called BioBike) built a cloud-based general symbolic biocomputing domain- specific language (DSL) entirely in Common Lisp. The system, which could be programmed entirely through the browser, was its own complete biocomputing language, which included a built-in deductive reasoner, called BioDeducta [54]. Biolingua programs, guided by the reasoner, would invisibly call tools such as BLAST [63] and Bioconductor [44] on the server-side, as needed. Symbolic biocomputing has also previously been used to create user-friendly visual tools for interactive data analysis and exploration [64]. As a community repository of bioinformatics packages, BioLisp does not yet exist as such (albeit its name currently de- notes the native language of BioBike [4, 54], a large-scale bio- informatics Lisp application), which means that there is certainly wide scope and potential for its rise and development in the bioinformatics community. Speed considerations The interactivity and flexibility of Lisp languages are something that can usually only be found (if at all) in interpreted lan- guages. This might be the origin of the old myth that Lisp is in- terpreted and must thus be slow—however, this is not true. Compilers for Lisp have existed since 1959, and all major Common Lisp implementations nowadays can compile directly to machine code, which is often on par with C code [70,71,72] or only slightly slower. Some also offer an interpreter in addition to the compiler, but examples like Clozure Common Lisp dem- onstrate that a programmer can have a compiler-only Common Lisp. For example, CL-PPCRE, a regular expression library writ- ten in Common Lisp, runs faster than Perl’s regular expression engine on some benchmarks, even though Perl’s engine is writ- ten in highly tuned C [24]. Pathway Tools consists of 680 000 lines of Common Lisp code (roughly the equivalent of 1 400 000 lines of C or Java code), organized into 20 subsystems. In addition, 30 000 lines of JavaScript code are present within the Pathway Tools Web interface. We chose Common Lisp for development of Pathway Tools because of its excellent properties as a high-level, highly productive, easy-to-debug programming language; we strongly believe that the choice of Common Lisp has been a key factor behind our ability to develop and maintain this large and com- plex software system. Although programmers who use interpreted languages like Python or Perl for their convenience and flexibility will have to re- sort to writing in C/C þþ for time-critical portions of their code, Lisp programmers can usually have their cake and eat it too. This was perhaps best shown with direct benchmarking by the creator of the R programming language, Ross Ihaka, who provided benchmarks demonstrating that Lisp’s optional type declaration and machine-code compiler allow for code that is 380 times faster than R and 150 times faster than Python [34]. And not only will the code created by Lisp compilers be efficient by default, Common Lisp, in particular, offers unique features to optimize those parts of the code (usually only a tiny fraction) that really need to be as fast as possible [59]. Macros and domain-specific languages • Common Lisp was designed from the ground up to create large, complex and long-running applications and thus supports soft- ware ‘hot swapping’: the code of a running program can be changed without the need to interrupt it. This includes features like the ability of the Common Lisp object system (CLOS) to change the classes of existing objects. Although Erlang and Smalltalk also support hot swapping, no mainstream compiled language does this to our knowledge. Hot swapping can be performed in Java to a certain extent, but only with the help of third-party frameworks, as it is not an intrinsic feature of the language itself. • Lisp invented exception handling, and Common Lisp, in particu- lar, has an error-handling facility (the ‘condition system’ [24]) that goes far beyond most other languages: it does not necessar- ily unwind the stack if an exception occurs and instead offers so- called restarts to programmatically continue ‘where the error happened’. This system makes it easy to write robust software, which is an essential ingredient to building industry-strength • Lisp invented exception handling, and Common Lisp, in particu- lar, has an error-handling facility (the ‘condition system’ [24]) that goes far beyond most other languages: it does not necessar- ily unwind the stack if an exception occurs and instead offers so- called restarts to programmatically continue ‘where the error happened’. This system makes it easy to write robust software, which is an essential ingredient to building industry-strength Khomtchouk et al. 540 fault-tolerant systems capable of handling a variety of condi- tions, a trait especially useful for artificial intelligence and ma- chine learning applications. In the Bioconductor community, error-handling facilities are ubiquitously present in practically all R/Bioconductor packages via tryCatch(), a base R function whose roots originate directly from Lisp’s condition system. fault-tolerant systems capable of handling a variety of condi- tions, a trait especially useful for artificial intelligence and ma- chine learning applications. In the Bioconductor community, error-handling facilities are ubiquitously present in practically all R/Bioconductor packages via tryCatch(), a base R function whose roots originate directly from Lisp’s condition system. analyze SAM/BAM files [39] with significantly less lines of code and almost identical speeds as SAMTools [73], which is written in the C programming language. In addition, Common Lisp was recently used to build a high-performance tool for preparing se- quence alignment/map files for variant calling in sequencing pipelines [6]. A case study: Pathway Tools Pathway Tools [74, 75] is an example of a large bioinformatics software system written in Common Lisp (Allegro Common Lisp from Franz Inc.). Pathway Tools has among the largest function- ality of any bioinformatics software system, including genome informatics, regulatory network informatics, metabolic pathway informatics and omics data analysis. For example, the software includes a genome browser that zooms from the nucleotide level to the chromosome level; it infers metabolic reconstructions from annotated genomes; it computes organism-specific layouts of metabolic map diagrams; it computes optimal routes within metabolic networks; and it can execute quantitative metabolic flux models. It has been shown that these features, together with other amenities like powerful debugging tools that Lisp programmers take for granted, offer a significant productivity boost to pro- grammers [3]. Lisp also gives programmers the ability to imple- ment complex data operations and mathematical constructs in an expressive and natural idiom [69]. The same Pathway Tools binary executable can execute as both a desktop window application and as a Web server. In Web server mode, Pathway Tools powers the BioCyc.org Web site, which contains 7600 organism-specific Pathway/Genome Databases, and services 500 000 unique visitors per year and up to 100 000 page views per day. Pathway Tools uses the ‘hot- swapping’ capabilities of Common Lisp to download and install software patches at user sites and within the running BioCyc Web server. Pathway Tools has been licensed by 7200 groups, and was found to have the best performance and documentation among multiple genome database warehousing systems [76]. Speed considerations This includes so-called com- piler macros, which can transform function calls into more effi- cient code at runtime, and a mandatory disassembler, which enables programmers to fine-tune time-critical functions until the compiled code matches their expectations. It should also be emphasized that while the C or Java compiler is ‘history’ once the compiled program is started, the Lisp compiler is always present and can thus generate new, fast code while the program is al- ready running. This is rarely used in finished applications (except for some areas of AI), but it is an important feature during devel- opment and helpful for explorative programming. Macros and domain-specific languages This HPC tool was shown to significantly outper- form SAMTools and Picard on a variety of benchmarks [6]. • Common Lisp implementations usually come with a sophisti- cated ‘foreign function interface’ (FFI) [24], which allows direct access from Lisp to code written in C or C þþ and sometimes also to Java code. This enables Lisp programmers to make use of libraries written in other languages, making those libraries a dir- ect strength of Lisp. For instance, it is simple to call Bioconductor from Lisp, just as Python and other programming languages can [67, 68]. Likewise, Clojure runs on the JVM and, thus, has immedi- ate access to all of Java’s libraries. A case study: BioBike BioBike provides an example of a large-scale application of the power of homoiconicity. In personal communication, the in- ventor of BioBike, Jeff Shrager, explained why Lisp (in this case, Common Lisp) was chosen as the implementation language, an unusual choice even for the early 2000’s. According to Shrager, Lisp-style DSL creation is uniquely suited to ‘living’ domains, such as biology, where new concepts are being introduced on an ongoing basis (as opposed to, for example, electronics, where the domain is better understood, and so the conceptual space is more at rest). Shrager pointed out that as Lisp-based DSLs are usually implemented through macros, this provides the unique capability of creating new language constructs that are embedded in the home programming language (here, in Lisp). This is a critical distinction: in most programming languages, DSLs are whole new programming languages built on top of the base language, whereas in Lisp, DSLs are built directly into the language. To further debunk the popular misconception that Lisp lan- guages are slow, Clojure was recently used to process and Strengths of Lisp-family languages 541 Lisp-based DSLs commonly show up in two sorts of domain- specific control structures: WITH-... clauses and MAP-... clauses. By virtue of Lisp’s homoiconicity, such constructs can take code as arguments, and can thereby create code-local bindings, and do various specialized manipulation directly on the code itself, in ac- cord with the semantics of the new construct. In non-homoiconic languages, users must do this either by creating new classes/ob- jects, or through function calls or via an ugly hack commonly referred to as ‘Greenspun’s 10th rule’ [77], wherein users must first implement a quasi-LFL on top of the base language, and then im- plement the DSL in that quasi-LFL. Both the object-creation and function-call means of creating new constructs lead to encapsula- tion problems, often requiring ugly manipulations such as repre- senting code as strings, passing code-conditionalizing arguments, and then having to either globalize them, or re-pass them through- out a large part of the codebase. Perspectives and outlook Historically speaking, Lisp is the second oldest (second only to Fortran) programming language still in use and has influenced nearly every major programming language to date with its con- structs [78]. For example, it may be surprising to learn that R is written atop of Scheme [79]. In fact, R borrows directly from its Lisp roots for creating embedded domain-specific languages within R’s core language set [80]. For instance, ggplot2 [81], dplyr [82] and plyr [83] are all examples of DSLs in R. This highlights the importance and relevance of Lisp as a programmable pro- gramming language, namely the ability to be user-extensible beyond the core language set. Given the wide spectrum of do- mains and subdomains in bioinformatics and computational biology research, it follows that similar applications tailored to genomics, proteomics, metabolomics or other research fields may also be developed as extensible macros in Common Lisp. By way of analogy, perhaps a genomics equivalent of ggplot2 or dplyr is in store in the not-so-distant future. Advice for when such pursuits are useful is readily available [84]. Perhaps even more importantly, it is imperative to take into the consideration the future of statistical computing [34], which will form the big data backbone of artificial intelligence and machine learning applications in bioinformatics. Key Points • Lisp empowers programmers to write faster programs faster. An empirical study shows that when program- mers tackle the same problems in Lisp, C/Cþþ and Java, that the Lisp programs are smaller (and therefore easier to maintain), take less time to develop and run faster. • Lisp empowers programmers to write faster programs faster. An empirical study shows that when program- mers tackle the same problems in Lisp, C/Cþþ and Java, that the Lisp programs are smaller (and therefore easier to maintain), take less time to develop and run faster. • Lisp empowers programmers to write faster programs faster. An empirical study shows that when program- mers tackle the same problems in Lisp, C/Cþþ and Java, that the Lisp programs are smaller (and therefore easier to maintain), take less time to develop and run faster. • Lisp empowers programmers to write faster programs faster. An empirical study shows that when program- mers tackle the same problems in Lisp, C/Cþþ and Java, that the Lisp programs are smaller (and therefore easier to maintain), take less time to develop and run faster. • The Lisp family of programming languages (Common Lisp, Scheme and Clojure) makes it easy to create extensible macros, which facilitate the creation of modularized extensions to help bioinformaticians easily create plug-ins for their software. This, in turn, paves the way for creating enterprise-level, fault-toler- ant domain-specific languages in any research area or specialization. BioBike was created by a team led by Jeff Shrager and JP Massar, and later Jeff Elhai. Its core Web listener is almost 15 000 lines of Common Lisp code in 25 modules, and the entire BioBike system is nearly 400 000 lines of code in about 850 modules, including the Web listener, many specialized bioinformatics modules, a scratch-like visual programming language (built using a specialized LFL that compiles to JavaScript, because of Peter Siebel), a specialized bioinformatics-oriented frame system (because of Mike Travers) and many other smaller modules. • The current state of Lisp research in bioinformatics and computational biology is at a point where an offi- cial BioLisp community is likely to be established soon, especially considering the documented short- comings of mainstream programming languages like R and Python when compared side by side with identical implementations in Lisp. A case study: BioBike The Lisp-like methods of embed- ding DSLs into the base language via macros, one can simply use, for example, a WITH-GENES or a MAP-GENES macro wrapper, and within these, all one need do is to write normal everyday Lisp code, and the wrapper, because it has access to and can modify the code that gets run, has no such firewalls, enabling a much more power- ful sort of computation. This greatly simplifies the incremental cre- ation and maintenance of the DSL, and it is for this reason, argues Shrager, that Lisp (and LFLs more generally) is well suited to biol- ogy. Being a science that is creating new concepts constantly, it is especially important to be able to flexibly add concepts to the DSL. Acknowledgements B.B.K. dedicates this work to the memory of his uncle, Taras Khomchuk. B.B.K. wishes to acknowledge the financial sup- port of the United States Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) Program: this research was conducted with Government support under and awarded by DoD, Army Research Office (ARO), National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a. C.W. thanks Jeff Shrager for critical review and helpful com- ments on the manuscript. Conclusions New programming language adoption in a scientific community is both a challenging and rewarding process. Here, we advocate for and propose a greater inclusion of the LFLs into large-scale bioinformatics research, outlining the benefits and opportunities of the adoption process. 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New Bounds of Ostrowski–Gruss Type Inequality for (k + 1) Points on Time Scales
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International Journal of Analysis and Applications ISSN 2291-8639 Volume 15, Number 2 (2017), 211-221 DOI: 10.28924/2291-8639-15-2017-211 International Journal of Analysis and Applications ISSN 2291-8639 Volume 15, Number 2 (2017), 211-221 DOI: 10.28924/2291-8639-15-2017-211 NEW BOUNDS OF OSTROWSKI–GR ¨USS TYPE INEQUALITY FOR (k + 1) POINTS ON TIME SCALES EZE R. NWAEZE1∗, SETH KERMAUSUOR2 Abstract. The aim of this paper is to present three new bounds of the Ostrowski–Gr¨uss type inequality for points x0, x1, x2, · · · , xk on time scales. Our results generalize result of Ngˆo and Liu, and extend results of Ujevi´c to time scales with (k + 1) points. We apply our results to the continuous, discrete, and quantum calculus to obtain many new interesting inequalities. An example is also considered. The estimates obtained in this paper will be very useful in numerical integration especially for the continuous case. 1. Introduction Received 18th August, 2017; accepted 20th October, 2017; published 1st November, 2017. 2010 Mathematics Subject Classification. 35A23, 26E70, 34N05. Key words and phrases. Montgomery identity; Ostrowski-Gr¨uss inequality; parameter; time scales. 1. Introduction In 1997, Dragomir and Wang [6] proved that if f : [a, b] →R is a differentiable function such that there exist constants γ, Γ ∈R with γ ≤f ′(x) ≤Γ for all x ∈[a, b], then we have f(x) − 1 b −a Z b a f(s)ds −f(b) −f(a) b −a  x −a + b 2  ≤1 4(b −a)(Γ −γ) (1.1) (1.1) for all x ∈[a, b]. The above inequality is known in the literature as the Ostrowski–Gr¨uss type inequality. Under the same assumption, Cheng [5] obtained the following sharp version of (1.1). for all x ∈[a, b]. The above inequality is known in the literature as the Ostrowski–Gr¨uss type inequality. Under the same assumption, Cheng [5] obtained the following sharp version of (1.1). f(x) − 1 b −a Z b a f(s)ds −f(b) −f(a) b −a  x −a + b 2  ≤1 8(b −a)(Γ −γ) (1.2) (1.2) for all x ∈[a, b]. In 2003, Ujevi´c [20] obtained another estimate of the left part of (1.2) as follows: In 2003, Ujevi´c [20] obtained another estimate of the left part of (1.2) as follows: Theorem 1.1. Let f : I →R, where I ⊂R is an interval, be a mapping differentiable in the interior IntI of I, and let a, b ∈IntI, a < b. If there exist constants γ, Γ ∈R such that γ ≤f ′(t) ≤Γ for all t ∈[a, b] and f ′ ∈L1(a, b), then, for all x ∈[a, b], we have f(x) −  x −a + b 2 f(b) −f(a) b −a − 1 b −a Z b a f(t) dt ≤b −a 2 (S −γ) f(x) −  x −a + b 2 f(b) −f(a) b −a − 1 b −a Z b a f(t) dt ≤b −a 2 (S −γ) f(x) −  x −a + b 2 f(b) −f(a) b −a − 1 b −a Z b a f(t) dt ≤b −a 2 (Γ −S), and and f(x) −  x −a + b 2 f(b) −f(a) b −a − 1 b −a Z b a f(t) dt ≤b −a 2 (Γ −S), where S = f(b)−f(a) b−a . where S = f(b)−f(a) b−a . In 2012, Feng and Meng [7] generalized Inequality (1.1) to the case involving (k + 1) points x0, x1, · · · , xk. Their result is contained in the following theorem. j fi , , Key words and phrases. Montgomery identity; Ostrowski-Gr¨uss inequality; parameter; time scales. c ⃝2017 Authors retain the copyrights o their papers, and all open access articles are distributed under the terms of the Creative Commons Attribution License Received 18th August, 2017; accepted 20th October, 2017; published 1st November, 2017. 2010 Mathematics Subject Classification 35A23 26E70 34N05 c ⃝2017 Authors retain the copyrights of their papers, and all open access articles are distributed under the terms of the Creative Commons Attribution License. c ⃝2017 Authors retain their papers, and all open access articles are distributed under the terms of the Creative Commons Att c ⃝2017 Authors retain the copyrights of their papers, and all open access articles are distributed under the terms of the Creative Commons Attribution License. 211 ds and phrases. Montgomery identity; Ostrowski-Gr¨uss inequality; parameter; time scales. ⃝ A h 1. Introduction If f ∆is rd-continuous and γ ≤f ∆(t) ≤Γ for all t ∈[a, b], then we have f(t) − 1 b −a Z b a f σ(s)∆s −f(b) −f(a) (b −a)2 " h2 (t, a) −h2 (t, b) # ≤ Γ −γ 2(b −a) Z b a p(t, x) −h2(t, a) −h2(t, b) b −a ∆x, (1.3) f(t) − 1 b −a Z b a f σ(s)∆s −f(b) −f(a) (b −a)2 " h2 (t, a) −h2 (t, b) # ≤ Γ −γ 2(b −a) Z b a p(t, x) −h2(t, a) −h2(t, b) b −a ∆x, (1.3 (1.3) where h2(t, s) is given in Definition 2.8 and p(t, x) = ( x −a, x ∈[a, t), x −b, x ∈[t, b]. (1.4) (1.4) his paper, we introduce a parameter λ ∈[0, 1] and then achieve the following goals, viz., paper, we introduce a parameter λ ∈[0, 1] and then achieve the following goals, viz., (1) firstly, we extend Theorem 1.3 to (k + 1) points. Our first result provides another estimate for the left hand side of the inequality in Theorem 1.2 for the case when λ = 0 and the time scale is the set of real numbers (see Remark 4.1). (1) firstly, we extend Theorem 1.3 to (k + 1) points. Our first result provides another estimate for the left hand side of the inequality in Theorem 1.2 for the case when λ = 0 and the time scale is the set of real numbers (see Remark 4.1). (2) Next, we generalize and extend Theorem 1.1 to time scales (see Remark 3.2). This paper is made up of five sections. In Section 2, we lay a quick foundation of the theory of time scales. Our main results (Theorems 3.1 and 3.2) are then formulated and proved in Section 3. Thereafter, we then give some applications of our results in Section 4 to obtain many new inequalities. Finally, a brief conclusion follows in Section 5. 1. Introduction 211 212 NWAEZE AND KERMAUSUOR Theorem 1.2. Let I ⊂R be an open interval, a, b ∈I, a < b, f : I →R a differentiable function such that there exist constants γ, Γ ∈R with γ ≤f ′(x) ≤Γ for all x ∈[a, b]. Furthermore, suppose that xi ∈[a, b], i = 0, 1, 2, · · · , k, Ik : a = x0 < x1 < · · · < xk = b is a division of the interval [a, b] and mi ∈[xi−1, xi], i = 1, 2, · · · , k, m0 = a, mk+1 = b. Then we have the following inequality Theorem 1.2. Let I ⊂R be an open interval, a, b ∈I, a < b, f : I →R a differentiable function such that there exist constants γ, Γ ∈R with γ ≤f ′(x) ≤Γ for all x ∈[a, b]. Furthermore, suppose that xi ∈[a, b], i = 0, 1, 2, · · · , k, Ik : a = x0 < x1 < · · · < xk = b is a division of the interval [a, b] and mi ∈[xi−1, xi], i = 1, 2, · · · , k, m0 = a, mk+1 = b. Then we have the following inequality 1 b −a k X i=0 (mi+1 −mi)f(xi) − 1 b −a Z b a f(t)dt −f(b) −f(a) (b −a)2 b2 −a2 2 − k−1 X i=0 mi+1(xi+1 −xi)  ≤1 4(b −a)(Γ −γ). To unify the theory of continuous, discrete and quantum calculus, Stefan Hilger [8] in 1988 came up with the theory of time scales (see Section 2 for a brief introduction). Ever since, many classical integral inequalities have been extended to time scales; see, for example, the references [4, 9–12, 15–17, 19]. In [13], Liu and Ngˆo extended (1.1) to time scales. Following thereafter, the same authors in [14] obtained the following theorem which sharpens their earlier result. Theorem 1.3. Let a, b, s, t ∈T with a < b and f : [a, b] →R be differentiable. 2. Time scale essentials In this section, we collect basic time scale concepts that will aid in better understanding of this work. For more on this subject, we refer the interested reader to Hilger’s Ph.D. thesis [8], the books [2, 3], and the survey [1]. finition 2.1. A time scale T is an arbitrary nonempty closed subset of the real numbers. We assume throughout that T has the topology that is inherited from the standard topology on R. It is also assumed throughout that in T the interval [a, b] means the set {t ∈T: a ≤t ≤b} for the points a < b in T. Since a time scale may not be connected, we need the following concept of jump operators. Definition 2.2. For each t ∈T, the forward jump operator σ : T →T is definied by σ(t) = inf {s ∈T: s > and the backward jump operator ρ : T →T is defined by ρ(t) = sup {s ∈T : s < t}. Definition 2.2. For each t ∈T, the forward jump operator σ : T →T is definied by σ(t) = inf and the backward jump operator ρ : T →T is defined by ρ(t) = sup {s ∈T : s < t}. Definition 2.3. If σ(t) > t, then we say that t is right-scattered, while if ρ(t) < t then we say that t is left-scattered. Points that are right-scattered and left-scattered at the same time are called isolated. If σ(t) = t, then t is called right-dense, and if ρ(t) = t then t is called left-dense. Points that are both right-dense and left-dense are called dense. NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY 213 Definition 2.4. The mapping µ : T →[0, ∞) defined by µ(t) = σ(t)−t is called the graininess function. The set Tk is defined as follows: if T has a left-scattered maximum m, then Tk = T −{m} ; otherwise, Tk = T. If T = R, then µ(t) = 0, and when T = Z, we have µ(t) = 1. Definition 2.5. Let f : T →R and t ∈Tk. Then we define f ∆(t) to be the number (provided it exists) with the property that for any given ϵ > 0 there exists a neighborhood U of t such that Definition 2.5. Let f : T →R and t ∈Tk. Then we define f ∆(t) to be the number (provided it exists) with the property that for any given ϵ > 0 there exists a neighborhood U of t such that f(σ(t)) −f(s) −f ∆(t) [σ(t) −s] ≤ϵ |σ(t) −s| , ∀s ∈U. f(σ(t)) −f(s) −f ∆(t) [σ(t) −s] ≤ϵ |σ(t) −s| , ∀s ∈U. We call f ∆(t) the delta derivative of f at t. finition 2.1. A time scale T is an arbitrary nonempty closed subset of the real numbers. Moreover, we say that f is delta differentiable (or in short: differentiable) on Tk provided f ∆(t) exists for all t ∈Tk. The function f ∆: Tk →R is then called the delta derivative of f on Tk. In the case T = R, f ∆(t) = df(t) dt . In the case T = Z, f ∆(t) = ∆f(t) = f(t + 1) −f(t), which is the usual forward difference operator. Theorem 2.1. If f, g : T →R are differentiable at t ∈Tk, then the product fg : T →R is differentiable at t and ∆ ∆ ∆ (fg)∆(t) = f ∆(t)g(t) + f(σ(t))g∆(t). Definition 2.6. The function f : T →R is said to be rd-continuous on T provided it is continuous at all right-dense points t ∈T and its left-sided limits exist at all left-dense points t ∈T. The set of all rd-continuous function f : T →R is denoted by Crd(T,R). Also, the set of functions f : T →R that are differentiable and whose derivative is rd-continuous is denoted by C1 rd(T,R). It follows from [2, Theorem 1.74] that every rd-continuous function has an anti-derivative. Definition 2.7. Let F : T →R be a function. Then F : T →R is called the anti-derivative of f on T if it satisfies F ∆(t) = f(t) for any t ∈Tk. In this case, the Cauchy integral ollows from [2, Theorem 1.74] that every rd-continuous function has an anti-derivative. Definition 2.7. Let F : T →R be a function. Then F : T →R is called the anti-derivative of f on T if it satisfies F ∆(t) = f(t) for any t ∈Tk. In this case, the Cauchy integral b Z a f(t)∆t = F(b) −F(a), a, b ∈T. Theorem 2.2. Let f, g ∈Crd(T,R), a, b, c ∈T and α, β ∈R. Then f, g rd( , ), , , , β (1) bR a [αf(t) + βg(t)] ∆t = α bR a f(t)∆t + β bR a g(t)∆t. (2) bR a f(t)∆t = − aR b f(t)∆t. (3) bR a f(t)∆t = cR a f(t)∆t + bR c f(t)∆t. (4) bR a f(t)g∆(t)∆t = (fg) (b) −(fg) (a) − bR a f ∆(t)g(σ(t))∆t. (5) If |f(t)| ≤g(t) on [a, b], then b Z a f(t)∆t ≤ b Z a g(t)∆t. Definition 2.8. finition 2.1. A time scale T is an arbitrary nonempty closed subset of the real numbers. Let hk, gk : T2 →R , k ∈N0 be defined by h0(t, s) := g0(t, s) := 1, for all s, t ∈T and then recursively by gk+1 (t, s) = tR s gk (σ (τ) , s) ∆τ, hk+1 (t, s) = tR s hk (τ, s) ∆τ, for all s, t ∈T. Definition 2.8. Let hk, gk : T2 →R , k ∈N0 be defined by h0(t, s) := g0(t, s) := 1, for all s, t ∈T and then recursively by gk+1 (t, s) = tR s gk (σ (τ) , s) ∆τ, hk+1 (t, s) = tR s hk (τ, s) ∆τ, for all s, t ∈T. In view of the above definition, we make the following remarks that will come handy in the sequel. – For T = R, h2(t, s) = (t−s)2 2 . – For T = Z, h2(t, s) = (t−s)(t−s−1) 2 . 214 NWAEZE AND KERMAUSUOR 3. Main results In order to prove our results, we will need the following lemmas. The first lemma is given in [18,21] but with some typos. We present here the correct version. Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that (1) a, b ∈T, λ ∈[0, 1], Ik : a = x0 < x1 < · · · < xk−1 < xk = b is a partition of the interval [a, b] for x0, x1, · · · , xk ∈T, (2) αi ∈T (i = 0, 1, · · · , k + 1) is k + 2 points so that α0 = a, αi ∈[xi−1, xi] (i = 1, · · · , k) and αk+1 = b, (3) f : [a, b] →R is a differentiable function. (1) a, b ∈T, λ ∈[0, 1], Ik : a = x0 < x1 < · · · < xk−1 < xk = b is a partition of the interval [a, b] for x0, x1, · · · , xk ∈T, (2) αi ∈T (i = 0, 1, · · · , k + 1) is k + 2 points so that α0 = a, αi ∈[xi−1, xi] (i = 1, · · · , k) and αk+1 = b, (3) f : [a, b] →R is a differentiable function. Then we have the following equation Then we have the following equation Then we have the following equation Z b a K(t, Ik)f ∆(t)∆t + Z b a f σ(t)∆t = (1 −λ) k X i=0  αi+1 −αi  f(xi) + λ k X i=0  αi+1 −αi f(αi) + f(αi+1) 2 , (3.1) (3.1) where K(t, Ik) =                                  t −  α1 −λ α1−a 2  , t ∈[a, α1), t −  α1 + λ α2−α1 2  , t ∈[α1, x1), t −  α2 −λ α2−α1 2  , t ∈[x1, α2), ... Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that t −  αk−1 + λ αk−αk−1 2  , t ∈[αk−1, xk−1), t −  αk −λ αk−αk−1 2  , t ∈[xk−1, αk), t −  αk + λ αk+1−αk 2  , t ∈[αk, b], (3.2)                  t −  α1 −λ α1−a 2  , t ∈[a, α1), t −  α1 + λ α2−α1 2  , t ∈[α1, x1), t −  α2 −λ α2−α1 2  , t ∈[x1, α2), (3.2)                  . t −  αk−1 + λ αk−αk−1 2  , t ∈[αk−1, xk−1), t −  αk −λ αk−αk−1 2  , t ∈[xk−1, αk), t −  αk + λ αk+1−αk 2  , t ∈[αk, b], provided for each i ∈{0, 1, 2, . . . , k −1}, αi+1 −λ αi+1−αi 2 and αi+1 + λ αi+2−αi+1 2 belong to T provided for each i ∈{0, 1, 2, . . . , k −1}, αi+1 −λ αi+1−αi 2 and αi+1 + λ αi+2−αi+1 2 belong to T. Lemma 3.2 ( [14]). Let a, b, x ∈T, f, g ∈Crd and f, g : [a, b] →R with γ ≤g(x) ≤Γ for all x ∈[a, b] and for some γ, Γ ∈R. Then we have Lemma 3.2 ( [14]). Let a, b, x ∈T, f, g ∈Crd and f, g : [a, b] →R with γ ≤g(x) ≤Γ for all x ∈[a, b] and for some γ, Γ ∈R. Then we have Z b a f(t)g(t)∆t − 1 b −a Z b a f(t)∆t Z b a g(t)∆t ≤Γ −γ 2 Z b a f(t) − 1 b −a Z b a f(s)∆s ∆t. (3.3) (3.3) Moreover, the inequality in (3.3) is sharp. Moreover, the inequality in (3.3) is sharp. We now state and justify our first result. NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY 215 Theorem 3.1. Suppose f satisfies the conditions of Lemma 3.1. Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that If, in addition, f ∆∈Crd with γ ≤f ∆(t) ≤Γ for all t ∈[a, b] and some γ, Γ ∈R, then we have the inequality (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f σ(t)∆t −f(b) −f(a) b −a k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ≤Γ −γ 2 Z b a K(t, Ik) − 1 b −a k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ∆t, (3.4) (3.4) provided for each i ∈{0, 1, 2, . . . , k −1}, αi+1 −λ αi+1−αi 2 and αi+1 + λ αi+2−αi+1 2 belong to T. The inequality in (3.4) is sharp in the sense that the constant 1/2 cannot be replaced by a smaller one. Proof By applying Lemma 3 2 to the functions f(t) := K(t Ik) and g(t) = f ∆(t) we have provided for each i ∈{0, 1, 2, . . . , k −1}, αi+1 −λ αi+1−αi 2 and αi+1 + λ αi+2−αi+1 2 belong to T. The inequality in (3.4) is sharp in the sense that the constant 1/2 cannot be replaced by a smaller one. Proof. By applying Lemma 3.2 to the functions f(t) := K(t, Ik) and g(t) = f ∆(t), we have of. By applying Lemma 3.2 to the functions f(t) := K(t, Ik) and g(t) = f ∆(t), we have Z b a K(t, Ik)f ∆(t)∆t − 1 b −a Z b a K(t, Ik)∆t Z b a f ∆(t)∆t ≤Γ −γ 2 Z b a K(t, Ik) − 1 b −a Z b a K(s, Ik)∆s ∆t. Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that (3.5) (3.5) Now, we observe that Now, we observe that Z b a f ∆(t)∆t = f(b) −f(a), (3.6) (3.6) and (by applying the items of Theorem 2.2 and Definition 2.8) and (by applying the items of Theorem 2.2 and Definition 2.8) and (by applying the items of Theorem 2.2 and Definition 2.8) Z b a K(t, Ik)∆t = k−1 X i=0 Z xi+1 xi K(t, Ik)∆t = k−1 X i=0  Z αi+1 xi  t −  αi+1 −λαi+1 −αi 2  ∆t + Z xi+1 αi+1  t −  αi+1 + λαi+2 −αi+1 2  ∆t  = k−1 X i=0  Z αi+1−λ αi+1−αi 2 xi  t −  αi+1 −λαi+1 −αi 2  ∆t + Z αi+1 αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t + Z αi+1+λ αi+2−αi+1 2 αi+1  t −  αi+1 + λαi+2 −αi+1 2  ∆t + Z xi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t  Z b a K(t, Ik)∆t = k−1 X i=0 Z xi+1 xi K(t, Ik)∆t = k−1 X i=0  Z αi+1 xi  t −  αi+1 −λαi+1 −αi 2  ∆t + Z xi+1 αi+1  t −  αi+1 + λαi+2 −αi+1 2  ∆t  = k−1 X i=0  Z αi+1−λ αi+1−αi 2 xi  t −  αi+1 −λαi+1 −αi 2  ∆t + Z αi+1 αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t + Z αi+1+λ αi+2−αi+1 2 αi+1  t −  αi+1 + λαi+2 −αi+1 2  ∆t + Z xi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t  NWAEZE AND KERMAUSUOR 216 = k−1 X i=0  − Z xi αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t (3.7) + Z αi+1 αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t − Z αi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t + Z xi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t  = k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  . Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that (3.8) = k−1 X i=0  − Z xi αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t (3.7) + Z αi+1 αi+1−λ αi+1−αi 2  t −  αi+1 −λαi+1 −αi 2  ∆t − Z αi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t + Z xi+1 αi+1+λ αi+2−αi+1 2  t −  αi+1 + λαi+2 −αi+1 2  ∆t  (3.7) = k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  . (3.8) + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  . (3.8) (3.8) Now using Lemma 3.1, we get Now using Lemma 3.1, we get Z b a K(t, Ik)f ∆(t)∆t = (1 −λ) k X i 0 (αi+1 −α Z b a K(t, Ik)f ∆(t)∆t a = (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f σ(t)∆t. ( (3.9) (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f σ(t)∆t −f(b) −f(a) b −a k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ≤Γ −γ 2 Z b a K(t, Ik) − 1 b −a k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ∆t. (3.10 (3.10) Hence, the proof is complete. Remark 3.1. If we take λ = 0, k = 2, and x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in Theorem 3.1, then we recapture Theorem 1.3. Remark 3.1. If we take λ = 0, k = 2, and x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in Theorem 3.1, then we recapture Theorem 1.3. Remark 3.1. Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that (3.12) For C = γ, and taking absolute values of both sides of (3.12), we have by using (3.6) Z b a K(t, Ik)f ∆(t)∆t − 1 b −a Z b a K(t, Ik)∆t Z b a f ∆(t)∆t ≤ Z b a f ∆(t) −γ K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s ∆t ≤max t∈[a,b] K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s Z b a f ∆(t) −γ ∆t b Z b a K(t, Ik)f ∆(t)∆t − 1 b −a Z b a K(t, Ik)∆t Z b a f ∆(t)∆t ≤ Z b a f ∆(t) −γ K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s ∆t ≤max t∈[a,b] K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s Z b a f ∆(t) −γ ∆t = Mk Z b a f ∆(t) −γ  ∆t = Mk hf(b) −f(a) b −a −γ i (b −a). = Mk hf(b) −f(a) b −a −γ i (b −a). (3.13) (3.13) Similarly, for C = Γ, we get Similarly, for C = Γ, we get , g Z b a K(t, Ik)f ∆(t)∆t − 1 b −a Z b a K(t, Ik)∆t Z b a f ∆(t)∆t ≤Mk h Γ −f(b) −f(a) b −a i (b −a). (3.14) (3.14) The intended inequalities follow from Lemma 3.1 and Relations (3.13) and (3.14). □ Remark 3.2. If we take T = R, λ = 0, k = 2, and x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in Theorem 3.2, then we get Theorem 1.1. The intended inequalities follow from Lemma 3.1 and Relations (3.13) and (3.14). □ Remark 3.2. If we take T = R, λ = 0, k = 2, and x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in Theorem 3.2, then we get Theorem 1.1. □ Lemma 3.1 (Generalized Montgomery identity with a parameter). Suppose that If we take λ = 0, k = 2, and x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in Theorem 3.1, then we recapture Theorem 1.3. Next, we provide another bound for (3.4). Theorem 3 2 Under the conditions of Theorem 3 1 we obtain the following inequalities Next, we provide another bound for (3.4). Next, we provide another bound for (3.4). Theorem 3.2. Under the conditions of Theor Theorem 3.2. Under the conditions of Theorem 3.1, we obtain the following i em 3.2. Under the conditions of Theorem 3.1, we obtain the following inequalities (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f σ(t)∆t −f(b) −f(a) b −a k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  xi, αi+1 −λαi+1 −αi 2  + h2  xi+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ≤ ( Mk(b −a)(S −γ) Mk(b −a)(Γ −S), NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY 217 NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY 217 where S = f(b)−f(a) b−a , and Mk = max t∈[a,b] K(t, Ik) − 1 b−a R b a k(s, Ik)∆s . Proof. We start by observing that where S = f(b)−f(a) b−a , and Mk = max t∈[a,b] K(t, Ik) − 1 b−a R b a k(s, Ik)∆s . Proof. We start by observing that Proof. We start by observing that Z b a  K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s  ∆t = 0. (3.11) (3.11) Using (3.11), we get that for any C ∈R, Using (3.11), we get that for any C ∈R, Z b a K(t, Ik)f ∆(t)∆t − 1 b −a Z b a K(t, Ik)∆t Z b a f ∆(t)∆t = Z b a f ∆(t) −C  K(t, Ik) − 1 b −a Z b a k(s, Ik)∆s  ∆t. 4. Applications In this section, we apply our theorems to the continuous, discrete, and quantum calculus to obtain the following results. In this section, we apply our theorems to the continuous, discrete, and quantum calculus to obtain the following results. Corollary 4.1 (Continuous case). Let T = R in Theorem 3.1. Then we have the inequality (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f(t)dt −f(b) −f(a) 8(b −a) k−1 X i=0  λ2 αi+1 −αi 2 −  2xi −λαi + (λ −2)αi+1 2 +  2xi+1 −λαi+2 + (λ −2)αi+1 2 −λ2 αi+2 −αi+1 2 ≤Γ −γ 2 Z b a K(t, Ik) − 1 8(b −a) k−1 X i=0  λ2 αi+1 −αi 2 −  2xi −λαi + (λ −2)αi+1 2 +  2xi+1 −λαi+2 + (λ −2)αi+1 2 −λ2 αi+2 −αi+1 2 dt. (4.1) NWAEZE AND KERMAUSUOR 218 Applying Corollary 4.1 to different values of λ and k, we obtain some novel inequalities. We present here some of these new results. Applying Corollary 4.1 to different values of λ and k, we obtain some novel inequalities. We present here some of these new results. Remark 4.1. If we take λ = 0 in Corollary 4.1, we get mark 4.1. If we take λ = 0 in Corollary 4.1, we get k X i=0 (αi+1 −αi)f(xi) − Z b a f(t)dt −f(b) −f(a) b −a b2 −a2 2 − k−1 X i=0 αi+1(xi+1 −xi)  ≤Γ −γ 2 Z b a K(t, Ik) − 1 b −a b2 −a2 2 − k−1 X i=0 αi+1(xi+1 −xi)  dt, (4.2 (4.2) where K(t, Ik) =                t −α1, t ∈[a, x1), t −α2, t ∈[x1, x2), ... t −αk−1, t ∈[xk−2, xk−1), t −αk, t ∈[xk−1, b]. (4.3) where K(t, Ik) =                t −α1, t ∈[a, x1), t −α2, t ∈[x1, x2), ... t −αk−1, t ∈[xk−2, xk−1), t −αk, t ∈[xk−1, b]. (4.3) (4.3) The above inequality is new and sharp. This gives a new estimate for the left hand side of the inequality in Theorem 1.2. The above inequality is new and sharp. Applying the above inequality to the following example. 4. Applications This gives a new estimate for the left hand side of the inequality in Theorem 1.2. Furthermore, let k = 2 in Corollary 4.1. If in addition, one then sets x1 = x, α0 = α1 = a, α2 = α3 = x2 = b in the resulting inequality, then one gets that for all x ∈[a, b] the following inequality holds: (1 −λ)(b −a)f(x) + λ(b −a)f(a) + f(b) 2 − Z b a f(t)dt −f(b) −f(a) 8(b −a)  2x −λb + (λ −2)a 2 −  2x −λa + (λ −2)b 2 ≤Γ −γ 2 Z b a K(t, x) − 1 8(b −a)  2x −λb + (λ −2)a 2 −  2x −λa + (λ −2)b 2 dt. (4.4) (4.4) Remark 4.2. For λ = 0 in Inequality (4.4), we have the inequality Remark 4.2. For λ = 0 in Inequality (4.4), we have the inequality (b −a)f(x) −  f(b) −f(a)  x −a + b 2  − Z b a f(t)dt ≤Γ −γ 2 Z b a K(t, x) −  x −a + b 2  dt, (4.5) ( )f( )  f( ) f( )  2  Z a f( ) ≤Γ −γ 2 Z b a K(t, x) −  x −a + b 2  dt, (4.5) ≤Γ −γ 2 Z b a K(t, x) −  x −a + b 2  dt, (4.5) (4.5) where K(t, x) = ( t −a, t ∈[a, x) t −b, t ∈[x, b]. K(t, x) = ( t −a, t ∈[a, x) t −b, t ∈[x, b]. It is important to note here that Inequality (4.5) is sharper than (1.1) since max t∈[a,b] K(t, x) −  x −a + b 2  = b −a 2 . Remark 4.3. Next, we consider the case when λ = 1 in Inequality (4.4). For this, we obtain Remark 4.3. Next, we consider the case when λ = 1 in Inequality (4.4). For this, we obtain f(a) + f(b) 2 − 1 b −a Z b a f(t) dt ≤ Γ −γ 8(b −a) h (b −a)2 + (2x −a −b)2i (4.6) (4.6) for all x ∈[a, b]. Applying the above inequality to the following example. Applying the above inequality to the following example. Applying the above inequality to the following example. 219 NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY Example 4.1. 4. Applications (1) Ik := {j0, j1, · · · , jk} ⊂Z, where a = j0 < j1 < · · · < jk = b, is a partition of the set [0, n] ∩Z (2) {α0, α1, · · · , αk+1} ⊂Z is a set of k+2 points such that α0 = 0, αi ∈[ji−1, ji] for i = 1, 2, · · · , k and αk+1 = n; We have the inequality, We have the inequality, (1 −λ) k X i=0 (αi+1 −αi)xji + λ k X i=0 (αi+1 −αi)xαi + xαi+1 2 − n X j=1 xj −xn −x0 n k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  ji, αi+1 −λαi+1 −αi 2  + h2  ji+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  ≤Γ −γ 2 n−1 X j=0 K(j, Ik) −1 n k−1 X i=0  h2  αi+1, αi+1 −λαi+1 −αi 2  −h2  ji, αi+1 −λαi+1 −αi 2  + h2  ji+1, αi+1 + λαi+2 −αi+1 2  −h2  αi+1, αi+1 + λαi+2 −αi+1 2  , (4.7) (4.7) where h2(t, s) = t−s 2  = (t−s)(t−s−1) 2 for all t, s ∈Z. Corollary 4.3 (Quantum case). Let T = qN0, q > 1, a = qm, b = qn with m, n ∈N and m < n. Suppose that Corollary 4.3 (Quantum case). Let T = qN0, q > 1, a = qm, b = qn with m, n ∈N and m < n. 4. Applications Consider the function f : [0, 1] →R+ defined by f(x) = ex2. We know that the integral of f cannot be achieved via an analytic method; but we can approximate it using numerical methods. For this function, we observe that 0 ≤f ′(x) ≤6 for all x ∈[0, 1]. Choose γ = 0 and Γ = 6. Now, using (4.6), on gets Example 4.1. Consider the function f : [0, 1] →R+ defined by f(x) = ex2. We know that the integral of f cannot be achieved via an analytic method; but we can approximate it using numerical methods. For this function, we observe that 0 ≤f ′(x) ≤6 for all x ∈[0, 1]. Choose γ = 0 and Γ = 6. Now, using (4.6), on gets Z 1 0 et2 dt −e + 1 2 ≤3 2(2x2 −2x + 1) for all x ∈[0, 1]. In particular, for x = 0 or 1, we have e 2 −1 ≤ Z 1 0 et2 dt ≤e 2 + 2. Using MATLAB, one can verify that R 1 0 et2 dt ≈1.46265. This shows that the range given above is correct! Corollary 4.2 (Discrete case). Let T = Z in Theorem 3.1. Suppose a = 0, b = n and Corollary 4.2 (Discrete case). Let T = Z in Theorem 3.1. Suppose a = 0, b = n and (1) Ik := {j0, j1, · · · , jk} ⊂Z, where a = j0 < j1 < · · · < jk = b, is a partition of the set [0, n] ∩Z (2) {α0, α1, · · · , αk+1} ⊂Z is a set of k+2 points such that α0 = 0, αi ∈[ji−1, ji] for i = 1, 2, · · · , k and αk+1 = n; (3) f(k) = xk. (1) Ik := {j0, j1, · · · , jk} ⊂Z, where a = j0 < j1 < · · · < jk = b, is a partition of the set [0, n] ∩Z (2) {α0, α1, · · · , αk+1} ⊂Z is a set of k+2 points such that α0 = 0, αi ∈[ji−1, ji] for i = 1, 2, · · · , k and αk+1 = n; (3) f(k) = xk. 4. Applications Corollary 4.4 (Continuous case). Let T = R. Then we have the inequalities We close this section by applying Theorem 3.2 to the continuous calculus. Corollary 4.4 (Continuous case). Let T = R. Then we have the inequalities (1 −λ) k X i=0 (αi+1 −αi)f(xi) + λ k X i=0 (αi+1 −αi)f(αi) + f(αi+1) 2 − Z b a f(t)dt −f(b) −f(a) 8(b −a) k−1 X i=0  λ2 αi+1 −αi 2 −  2xi −λαi + (λ −2)αi+1 2 +  2xi+1 −λαi+2 + (λ −2)αi+1 2 −λ2 αi+2 −αi+1 2 ≤ ( Mk(b −a)(S −γ) Mk(b −a)(Γ −S), ≤ ( Mk(b −a)(S −γ) Mk(b −a)(Γ −S), where S = f(b)−f(a) b−a , and Mk = max t∈[a,b] K(t, Ik) − 1 b−a R b a k(s, Ik)ds . Remark 4.4. By setting λ = 0 in Corollary 4.4, we get a direct generalization of Theorem 1.1 to (k + 1) points x0, x1, · · · , xk. In fact, we obtain Remark 4.4. By setting λ = 0 in Corollary 4.4, we get a direct generalization of Theorem 1.1 to (k + 1) points x0, x1, · · · , xk. In fact, we obtain k X i=0 (αi+1 −αi)f(xi) − Z b a f(t)dt −f(b) −f(a) b −a b2 −a2 2 − k−1 X i=0 αi+1(xi+1 −xi)  ≤ ( Mk(b −a)(S −γ) Mk(b −a)(Γ −S), (4.8) ≤ ( Mk(b −a)(S −γ) (4.8) where K(t, Ik) is given by (4.3). where K(t, Ik) is given by (4.3). 5. Conclusion We have established three new Ostrowski–Gr¨uss type inequality with a parameter λ ∈[0, 1]. Loads of interesting results can be derived by choosing different values of k ∈N, and λ’s. As an application, we considered the continuous, discrete, and quantum calculus from which many novel inequalities are obtained. 4. Applications Suppose that (1) Ik : qm = qj0 < qj1 < · · · < qjk = qn, is a partition of the set [qm, qn]∩qN0 for j0, j1, · · · , jk ∈N; (2) qαi ∈qN0(i = 0, 1, · · · , k+1) is a set of k+2 points such that qα0 = qm, qαi ∈[qji−1, qji]∩qN0(i = 1, 2, · · · , k) and qαk+1 = qn; (1) Ik : qm = qj0 < qj1 < · · · < qjk = qn, is a partition of the set [qm, qn]∩qN0 for j0, j1, · · · , jk ∈N; (2) qαi ∈qN0(i = 0, 1, · · · , k+1) is a set of k+2 points such that qα0 = qm, qαi ∈[qji−1, qji]∩qN0(i = 1, 2, · · · , k) and qαk+1 = qn; (3) f [ m n] R d ff bl (1) Ik : qm = qj0 < qj1 < · · · < qjk = qn, is a partition of the set [qm, qn]∩qN0 for j0, j1, · · · , jk ∈N; (2) qαi ∈qN0(i = 0, 1, · · · , k+1) is a set of k+2 points such that qα0 = qm, qαi ∈[qji−1, qji]∩qN0(i = 1, 2, · · · , k) and qαk+1 = qn; , , ) q q ; : [qm, qn] →R is differentiable. ) (3) f : [qm, qn] →R is differentiable. NWAEZE AND KERMAUSUOR 220 (1 −λ) k X i=0 (qαi+1 −qαi)f(qji) + λ k X i=0 (qαi+1 −qαi)f(qαi) + f(qαi+1) 2 − Z qn qm f(qt)dqt −f(qn) −f(qm) qn −qm k−1 X i=0  h2  qαi+1, qαi+1 −λqαi+1 −qαi 2  −h2  qji, qαi+1 −λqαi+1 −qαi 2  + h2  qji+1, qαi+1 + λqαi+2 −qαi+1 2  −h2  qαi+1, qαi+1 + λqαi+2 −qαi+1 2  ≤Γ −γ 2 Z b a K(t, Ik) − 1 qn −qm k−1 X i=0  h2  qαi+1, qαi+1 −λqαi+1 −qαi 2  −h2  qji, qαi+1 −λqαi+1 −qαi 2  + h2  qji+1, qαi+1 + λqαi+2 −qαi+1 2  −h2  qαi+1, qαi+1 + λqαi+2 −qαi+1 2  dqt, where h2(t, s) = (t−s)(t−qs) q+1 for all t, s ∈qN0. We close this section by applying Theorem 3.2 to the continuous calculus. We close this section by applying Theorem 3.2 to the continuous calculus. [2] M. Bohner and A. Peterson, Dynamic equations on time scales, Boston (MA): Birkh¨auser Boston, 2001. References [1] R. Agarwal, M. Bohner and A. Peterson, Inequalities on time scales: a survey, Math. Inequal. Appl. 4 (2001), 535–557. M. Bohner and A. Peterson, Dynamic equations on time scales, Boston (MA): Birkh¨auser Boston, 2001. r and A. Peterson, Advances in Dynamic Equations on Time Series, Boston (MA): Birkh¨auser Boston, [3] M. Bohner and A. Peterson, Advances in Dynamic Equations on Time Series, Boston (MA): Birkh¨au 2003. NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY 221 [4] M. Bohner and T. Matthews, Ostrowski inequalities on time scales, J. Inequal. Pure Appl. Math. 9 (2008), Art. 6. [5] X. L. Cheng, Improvement of some Ostrowski-Griiss type inequalities, Compu. Math. Appli. 42 (2001), 109–114. Bohner and T. Matthews, Ostrowski inequalities on time scales, J. Inequal. Pure Appl. Math. 9 (2008), Ar L. Cheng, Improvement of some Ostrowski-Griiss type inequalities, Compu. Math. Appli. 42 (2001), 109–11 [ ] , q , q pp ( ), [5] X. L. Cheng, Improvement of some Ostrowski-Griiss type inequalities, Compu. Math. Appli. 42 (2001), 109–114. [6] S. S. Dragomir and S. Wang, An inequality of Ostrowski-Gr¨uss type and its applications to the estimation of error bounds for some special means and for some numerical quadrature rules, Compu. Math. Appli. 33(11) (1997), 15–20. [7] Q. Feng and F. Meng, Some generalized Ostrowski–Gr¨uss type integral inequalities, Compu. Math. Appli. 63 (2012), 652–659. [6] S. S. Dragomir and S. Wang, An inequality of Ostrowski-Gr¨uss type and its applications to the estimat bounds for some special means and for some numerical quadrature rules, Compu. Math. Appli. 33(11) (1997), 15–20. [7] Q. Feng and F. Meng, Some generalized Ostrowski–Gr¨uss type integral inequalities, Compu. Math. Appli. 63 (2012), 652–659. [7] Q. Feng and F. Meng, Some generalized Ostrowski–Gr¨uss type integral inequalities, Compu. Math. A 652–659. [8] S. Hilger, Ein Maβkettenkalk¨ul mit Anwendung auf Zentrumsmannigfaltigkeiten (Ph.D. thesis). W¨urzburg (Ger- many): Universit¨at W¨urzburg, 1988. [9] B. Karpuz and U. M. ¨Ozkan, Ostrowski Inequality on time scales, J. Inequal. Pure and Appl. Math. 9(4) (2008), Art. 112. 10] S. Kermausuor, E. R. Nwaeze and D. F. M. Torres, Generalized weighted Ostrowski and Ostrowski– inequalities on time scale via a parameter function, J. Math. Inequal. 11 (4) (2017), 1185–1199. [11] W. J. Liu and Q. A. Ngˆo, A generalization of Ostrowski inequality on time scales for k points, Appl. Math. Comput. 203(2) (2008), 754–760. Liu and Q. A. Ngˆo, Chen WB. A perturbed Ostrowski-type inequality on time scales for k points for function second derivatives are bounded J Inequal Appl (2008) Art ID 597241 [12] W. J. Liu and Q. A. Ngˆo, Chen WB. A perturbed Ostrowski-type inequality on time scales for k points for functions whose second derivatives are bounded, J. Inequal. Appl. (2008) Art. ID 597241. W. J. Liu and Q. A. Ngo, Chen WB. NEW BOUNDS OF OSTROWSKI–GR¨USS TYPE INEQUALITY A perturbed Ostrowski-type inequality on time scales for k points fo whose second derivatives are bounded, J. Inequal. Appl. (2008) Art. ID 597241. 13] W. J. Liu and Q. A. Ngˆo, An Ostrowski–Gr¨uss type inequality on time scales, arXiv:0804.3231. 14] Q A N ˆ d W J Li A h G ¨ i li i l d li i h h [14] Q. A. Ngˆo and W. J. Liu, A sharp Gr¨uss type inequality on time scales and application to the sharp Ostrowski-Gr¨uss inequality, Commun. Math. Anal. 6(2) (2009), 33–41. [15] E. R. Nwaeze, A new weighted Ostrowski type inequality on arbitrary time scale, J. King Saud Uni. Sci. 29(2) (2017), 230–234. Nwaeze, Generalized weighted trapezoid and Gr¨uss type inequalities on time scales, Aust. J. Math. Anal 11(1) 2017, Art. 4. ( ) [17] E. R. Nwaeze and A. M. Tameru, On weighted Montgomery identity for k points and its associates on time scales, Abstr. App. Anal. (2017), Art. ID 5234181. ( ) [18] E. R. Nwaeze, S. Kermausuor and A. M. Tameru, New time scale generalizations of the Ostrowski–Gr¨uss type inequality for k points, J. Inequal. Appl. 2017 (2017), Art. ID 245. ( ) [19] A. Tuna and D. Daghan, Generalization of Ostrowski and Ostrowski–Gr¨uss type inequalities on time scales, Comput. Math. Appl. 60 (2010), 803–811. ( ) vi´c, New bounds for the first inequality of Ostrowski–Gr¨uss type and applications, Compu. Math. Appl. 46 421–427. (2003), 421–427. [21] G. Xu and Z. B. Fang, A Generalization of Ostrowski type inequality on time scales with k points, J. Math. Inequal. 11(1) (2017), 41–48. ( ) [21] G. Xu and Z. B. Fang, A Generalization of Ostrowski type inequality on time scales with k points, J. Math. Inequal. 11(1) (2017), 41–48. 1Department of Mathematics, Tuskegee University,, Tuskegee, AL 36088, USA 1Department of Mathematics, Tuskegee University,, Tuskegee, AL 36088, USA 2Department of Mathematics and Computer Science, Alabama State University, Montgomery, AL 36104, USA ∗Corresponding author: enwaeze@tuskegee.edu ∗Corresponding author: enwaeze@tuskegee.edu
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Determination and ranking of target areas in catchments for the implementation of nitrogen reduction measures
Advances in geosciences
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Determination and ranking of target areas in catchments for the implementation of nitrogen reduction measures B. Tetzlaff1, R. Kunkel2, W. Sch¨afer2, and F. Wendland1 1Research Centre J¨ulich, Institute of Chemistry and Dynamics of the Geosphere (ICG), Institute IV: Agrosphere, 52425 J¨ulich, Germany 2State Authority for Mining, Energy and Geology, Lower Saxony, 30655 Hannover, Germany Received: 11 January 2007 – Revised: 5 April 2007 – Accepted: 22 May 2007 – Published: 13 June 2007 measures to reduce diffuse pollution from agriculture and to promote sustainable water resources management. On the basis of a pollution risk assessment, the environmental ob- jectives will be specified and measures for endangered water bodies will be specified, discussed with the local stakehold- ers and implemented at farm level. The results achieved in the pilot areas and the socio-political, financial, geograph- ical and hydrological factors influencing the impact of the measures are evaluated. On the basis of an extrapolation to Federal State level, the administrative requirements for state- wide implementation are specified and evaluated. In this pa- per we will focus on the assessment of the pollution risk and the geographical prioritization for measures in catchment ar- eas. Abstract. The implementation of the EU Water Framework Directive (EU-WFD) forms the background of the WAgriCo- project (Water Resources Management in Cooperation with Agriculture). WagriCo concentrates on the development of nitrogen management options adapted to hydrological and agro-economic site conditions and at demonstrating new par- ticipation approaches and technologies suitable for setting- up programmes of measures. The article outlines the con- ceptual model approach and its application in the pilot region “Große Aue” (Northern Germany). Furthermore the process of delineating priority areas is described, which act as spatial targets for the adaptation of regionally differentiated nutrient reduction measures. 2 Investigated area The implementation of the the EU Water Framework Di- rective (EU-WFD) forms the background of the WAgriCo- project (Water Resources Management in Cooperation with Agriculture). The implementation schedule for the EU wa- ter framework directive requires the creation of monitor- ing programmes for water bodies according to the inten- sity of the pollution risk by the end of 2006. Until 2009 river basin district management programmes have to be es- tablished followed by the implementation of measures from the management plans (until 2012). WagriCo is a collabora- tive project funded by the European Commission Life Fund 2005–2008, involving six British and four German institu- tions. The project aims are to aid the implementation of the Water Framework Directive, to develop nitrogen man- agement options adapted to hydrological and agro-economic site properties and to demonstrate the use of new participa- tion approaches and technologies suitable for programmes of Within the WAgriCo project, six pilot study areas have been selected in the UK and in Germany. One of the selected case study areas is located in the river basin Große Aue, a tribu- tary to the river Weser basin and geographically situated in the Federal State of Lower Saxony, Germany (see Fig. 1). The Große Aue pilot area is a groundwater body with a size of about 1000 km2. About 55% of the lands surface of this groundwater body is used agriculturally, in about 20% of the area peaty soils under peat cutting can be found. Therefore, the natural conditions in groundwater and surface waters are expected to be significantly influenced by anthropogenic in- terferences into N- and water balance and runoff regimes. Advances in Geosciences Advances in Geosciences Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/ © Author(s) 2007. This work is licensed under a Creative Commons License. Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/ © Author(s) 2007. This work is licensed under a Creative Commons License. Advances in Geosciences 3 Conceptual model The WAgriCo project is based around the catchment man- agement process. For basic understanding of interactions be- tween the issues mentioned in chapter 1 a conceptual inte- grated hydrological/hydrogeological model (see Fig. 2) has Correspondence to: B. Tetzlaff (b.tetzlaff@fz-juelich.de) Correspondence to: B. Tetzlaff (b.tetzlaff@fz-juelich.de) Published by Copernicus Publications on behalf of the European Geosciences Union. Published by Copernicus Publications on behalf of the European Geosciences Union. B. Tetzlaff et al.: Determination and ranking of target areas in catchments B. Tetzlaff et al.: Determination and ranking of target areas in catchments 70 tools, e.g. for water balance or reactive subsurface nutrient transport modelling. Fig. 1. German pilot study areas in the WAgriCo project. As an example for the assessment of natural characteris- tics, Fig. 3 shows the denitrification conditions in the soils for the Große Aue pilot area. This parameter has been de- rived from the soil map 1:50 000 of Lower Saxony on the ba- sis of soil type and groundwater influence information. Ap- parently, the denitrification conditions vary from very bad to very good within the pilot area. Good to very good denitrifi- cation conditions occur in peatlands of the central part and in groundwater influenced floodplains. In contrast, the north- ern Geest part of the pilot area, dominated by sandy soils, bad to very bad denitrification conditions are to be found. In those regions, nitrate inputs may reach the groundwater after a relative short period of time without any significant denitri- fication. 3.2 Monitoring data Fig. 1. German pilot study areas in the WAgriCo project. Because of anthropogenic influences the status of ground- water and surface waters is different compared to the natural characteristics. In particular, in the status review of German’s groundwater bodies according to the EU-WFD the Große Aue groundwater body has been classified as at risk because of a potential failure of good status, primarily due to high nitrate concentrations. Monitoring programs have been initi- ated to quantify the amount of anthropogenic intakes e.g. of nutrients into the soil, groundwater and surface waters. Data from different monitoring programs are available, indicating the concentrations of various substances (e.g. nutrients) in groundwater and surface waters. been set up. The model consists of three main features: nat- ural characteristic assessment, anthropogenic impact assess- ment using monitoring data and model tools providing a link- age between the first two parts. Based on the conceptual model the interactions between agricultural practice, nitrogen surpluses, nitrogen concentra- tion in both leachate and groundwater are analyzed. In the same way modelling nitrogen inputs into surface waters and, finally, the characterization of the groundwater status are car- ried out. In the following sections selected natural character- istics, monitoring data and model tool application results are presented for the Große Aue case study area. As all of the applied model tools have been already described in detail in the literature (e.g. Kunkel and Wendland, 1997, 2002, 2006) this paper will concentrate on a brief description. Figure 4 shows measured nitrate concentrations in the groundwater using data from monitoring wells. It can be seen clearly that the nitrate concentrations are typically very low. In areas covered by clay layers, concentrations are less than 2 mg NO3/l in most cases, indicating a possible denitrifica- tion due to reduced aquifer conditions. This is confirmed by an analysis of the Fe2+ and O2-concentrations in those ar- eas (Kunkel et al., 2004). In contrast uncovered surface-near stations and, in particular, withdrawal wells from water sup- pliers show much higher nitrate concentrations in groundwa- ter because of either oxidized conditions near groundwater surface or the modified flow regime due to groundwater ab- straction. 3.1 Natural characteristics The natural site conditions represent an important basis for the understanding of groundwater status. In a first step, a hy- drogeological characterization has been done using a num- ber of different data sets available on a Federal State level, e.g. from geological maps, geological/hydrogeological pro- files and the distribution of clay covers above the aquifers. A hydrochemical/hydrodynamic characterization of ground- water has been performed using data on the hydraulic con- ductivities and the groundwater pressure heads of the upper aquifers, as well as groundwater quality data related to the re- dox and salinization state of the aquifers. From all data avail- able for the Federal State of Lower Saxony a number of data sets have been selected, which are of particular importance for the assessment of natural characteristics. These data, listed in Table 1, are often not only used for natural char- acteristics assessment but also input parameters for model The monitoring in the case study area Große Aue also comprises the intakes of nutrients into the soil, biannual mea- surements of the Nmin-contents in the soil as well as mea- surements of the nitrate concentration in the leachate. Al- though these kinds of data are available only for selected sites, they allow the assessment of impacts from anthro- pogenic inputs originating from diffuse or point sources. www.adv-geosci.net/11/69/2007/ Adv. Geosci., 11, 69–75, 2007 B. Tetzlaff et al.: Determination and ranking of target areas in catchments 71 Fig. 2. The hydrological-hydrogeological conceptual model. Table 1. Used data sets for target area assessment. Data set Scale Land cover Landcover categories 1:25 000 Agricultural production Animals Cultivation Harvest Mineral fertilizer Agrarian statistical data Climate Summer precipitation levels Winter precipitation levels Potential Evaporation Interpolated point data Topography Slope Exposition 50×50 m2 raster Soil parameters Plant-available water Denitrification capacity of soils Groundwater influence 1:50 000 Hydrogeology Hydrogeological units Geological profiles Hydraulic conductivity 1:200 000 Hydrodynamics Depth to groundwater Runoff in rivers River network, drainage systems 1:200 000 or point data Hydrochemistry Groundwater monitoring data Point data 3.3 Model tools ponents were quantified area-differentiated considering cli- mate, soil, geology, topography and land use conditions us- ing the GROWA model (Kunkel and Wendland, 2002). The groundwater recharge level is an important model based pa- rameter for the assessment of natural characteristics. Addi- tionally, the ratio between groundwater recharge and total runoff levels was taken as a measure for the extent diffuse nitrogen surpluses, which are displaced from soil to ground- water (Kunkel et al., 2004; Wendland et al., 2002). For the northern and the southern parts of the pilot area, the ground- water recharge amounts to 80% or more of total runoff. In those areas, the nitrate leached out of the soil will reach the groundwater area almost complete. In the floodplains along the rivers and in the central part of the pilot area, the ground- water recharge is reduced to the advantage of direct runoff due to groundwater influence of the soils and the existence of artificial drainage systems. A significant part of the ni- trate washed out of the soils will reach the surface waters via direct or drainage runoff without leaching into groundwater. Within the conceptual model the linkage between natural characteristics, land use and status of groundwater and sur- face waters is provided by model tools. At present, three different tools are included in the model, considering N- balancing, water balance and reactive N-transport through the soil and groundwater into the surface waters (Fig. 2). Coupling between agricultural practice and N-surpluses in the soil is done by the agricultural sector model RAUMIS (Henrichsmeyer, 1996). Agricultural statistics, e.g. on crop yields, livestock farming and land use were taken to balance the nitrogen supplies and extractions for the agricultural area. The long-term nitrogen balance averaged over several vege- tation periods is calculated considering the organic nitrogen fertilization, the mineral nitrogen fertilization, the symbiotic N-fixation, the atmospheric N-inputs and the N-extractions with the crop substance. As a rule, the difference between nitrogen supplies, primarily by mineral fertilizers and farm manure, and nitrogen extractions, primarily by field crops, leads to a positive N-balance (G¨omann et al., 2004). During transport through soil and groundwater nitrogen surpluses may be denitrified to molecular nitrogen. Deni- trification losses in the soil occur mainly in the root zone in case of low oxygen and high water contents as well as high contents of organic substances. B. Tetzlaff et al.: Determination and ranking of target areas in catchments 71 Fig. 2. The hydrological-hydrogeological conceptual model. Fig. 2. The hydrological-hydrogeological conceptual model. Table 1. Used data sets for target area assessment. Data set Scale Land cover Landcover categories 1:25 000 Agricultural production Animals Cultivation Harvest Mineral fertilizer Agrarian statistical data Climate Summer precipitation levels Winter precipitation levels Potential Evaporation Interpolated point data Topography Slope Exposition 50×50 m2 raster Soil parameters Plant-available water Denitrification capacity of soils Groundwater influence 1:50 000 Hydrogeology Hydrogeological units Geological profiles Hydraulic conductivity 1:200 000 Hydrodynamics Depth to groundwater Runoff in rivers River network, drainage systems 1:200 000 or point data Hydrochemistry Groundwater monitoring data Point data Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/ B. Tetzlaff et al.: Determination and ranking of target areas in catchments B. Tetzlaff et al.: Determination and ranking of target areas in catchments B. Tetzlaff et al.: Determination and ranking of target areas in catchments 72 Fig. 3. Denitrification conditions in the soil. Fig. 4. Measured nitrate concentration in the groundwater. Fig. 3. Denitrification conditions in the soil. Fig. 4. Measured nitrate concentration in the groundwater. Fig. 3. Denitrification conditions in the soil. 3.3 Model tools In a Michaelis-Menten ki- netics approach these denitrification conditions were com- bined with the calculated nitrogen surpluses and the resi- dence times of the percolation water in the root zone cal- culated as a function of average field capacity and the perco- lation runoff level (Kunkel and Wendland, 1997). The displacement of N-surpluses from soil to groundwater and surface waters is coupled to runoff components. Against the background of a long-term treatment, runoff was distin- guished into the relevant runoff components for nitrate emis- sions to surface runoff: surface runoff, direct runoff, drainage runoff and groundwater runoff. Whereas direct and drainage runoff reaches the surface waters within short time periods (within about a week), groundwater run-off needs much more time (years) to percolate into surface waters. The runoff com- www.adv-geosci.net/11/69/2007/ www.adv-geosci.net/11/69/2007/ Adv. Geosci., 11, 69–75, 2007 B. Tetzlaff et al.: Determination and ranking of target areas in catchments B. Tetzlaff et al.: Determination and ranking of target areas in catchments 73 Fig. 5. Calculated nitrate concentration in the leachate. Fig. 6. Delineated target areas for groundwater protection mea- sures. Fig. 5. Calculated nitrate concentration in the leachate. Fig. 6. Delineated target areas for groundwater protection mea- sures. The potential nitrate concentration in recharged ground- water is a modelled parameter, which combines Nitrogen surpluses from agriculture, water balance and denitrifica- tion in the soil. It is calculated using the GROWA-WEKU- RAUMIS model tools and displayed area-differentiated in Fig. 5. As to be seen from the map, nitrate concentrations above 100 mg NO3/l are calculated for the major part of the pilot area. Only for the peaty areas and the floodplains with high denitrification potentials in the soil lower nitrate con- centrations have been calculated. This is in line with the ob- served situation in the upper part of the aquifers. implementation of certain mitigation measures and its effect on the groundwater or surface water quality. 4 Delineation of target areas For the delineation of environmental target areas for nitro- gen reduction measures it has to be distinguished whether the main focus should be on groundwater protection or surface water protection. Only under consideration of the receptors of the nitrate inputs, target areas can be defined. In the fol- lowing sections the consequences of this are demonstrated for both, surface waters and groundwater as receptor. A comparison between Figs. 4 and 5 shows, that the ob- served nitrate concentration in groundwater is much smaller than nitrate concentration in the leachate. This is due to den- itrification processes in the aquifer, which are well known for larger parts of the North-German Lowlands where the Große Aue is located (B¨ottcher et al. (1989) and Walter et al. (2004)). However, although denitrification in ground- water is relative effective – extensive field studies indicate a halving of nitrate load in groundwater after a residence time between 1.2 and 4 years – the process irreversibly con- sumes pyrite and/or organic carbon reservoirs in the aquifer. In contrast to nitrate degradation in the soil denitrification in groundwater cannot be regarded as being inexhaustible. www.adv-geosci.net/11/69/2007/ 5 Conclusions and outlook The previous sections have shown, that for the delineation of environmental target areas for nitrogen reduction measures it has to be distinguished whether groundwater protection or surface water protection is the main focus. Only under con- sideration of the receptors of the nitrate inputs targets areas can be defined. Therefore, the next steps in the WAgriCo – project are straightforward. First, it is necessary to achieve an agreement on the environmental targets in the participa- tion process between the stakeholders. Measures, which are effective for surface and/or groundwater with respect to cost and impact need to be selected and implemented in the pi- lot areas. The consequences for the farmers concerning land management and income losses need to be evaluated and pro- grammes for an effective distribution of available funding of measurements at farm level need to be compiled and imple- mented. Groundwater protection is an important part of surface wa- ter protection but, furthermore, focuses directly on issues concerning public water supply. It is an ongoing discussion between the EU-member states, whether the groundwater “as itself” needs to be protected or if the “usability” of ground- water for human demand is the main focus. This has direct implications on the environmental targets, which have to be defined prior to the delineation of target areas or the evalu- ation of protection measures. If, for example, the “usabil- ity” of groundwater is protected, the drinking water limit of 50 mg NO3/l in groundwater needs to be ensured at least for drinking water extraction areas. Because of possible nitrate degradation in the aquifers of the Große Aue, 50 mg NO3/l can be reached in most parts of the aquifer even in case of much larger nitrate concen- trations in the leachate. Only in the vicinity of withdrawal wells, higher nitrate concentrations are observed because of the modified flow regime. Hence, reduction measures to reach the environmental target of 50 mg/l would only have to be implemented in areas used for groundwater extraction. Edited by: K.-E. Lindenschmidt Reviewed by: H. Nacken and G. Petersen Edited by: K.-E. Lindenschmidt Reviewed by: H. Nacken and G. Petersen Edited by: K.-E. Lindenschmidt Reviewed by: H. Nacken and G. Petersen 4.1 Target areas for surface water protection In the case of surface water protection nitrate inputs from all runoff components – direct runoff, drainage runoff and groundwater runoff – need to be considered. Hence, tar- get areas should be delineated from those areas, which con- tribute most to nitrate intakes into the river systems. Due to denitrification processes in the aquifers of the Große Aue, groundwater-borne nitrate intakes into the surface waters play a minor role compared to intakes from direct runoff, mainly by artificial drainage systems. Thus, possible miti- gation measures for surface water protection imply either N- surplus reduction or blocking of artificial drainage systems. Reactive nitrate transport in groundwater was modelled using the stochastical WEKU model (Kunkel and Wendland, 1997) on the basis of a first order reaction depending on the nitrogen inputs into the aquifer, denitrification conditions in groundwater and groundwater residence times. These pa- rameters allow an assessment of the time-lags between the Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/ B. Tetzlaff et al.: Determination and ranking of target areas in catchments 74 B. Tetzlaff et al.: Determination and ranking of target areas in catchments 4.2 Delineation of target areas for groundwater protection 4.2 Delineation of target areas for groundwater protection than 25 kg N/(ha a) is necessary. Compared to the actual N- surpluses the required reduction would be larger than 40% in most areas. It becomes evident that this reduction could only be achieved by massive changes in agricultural produc- tion, which would lead to significant consequences for the affected farmers. In contrast possible mitigation measures to reduce nitrate concentrations in groundwater imply only the reduction of N- inputs to groundwater. Target areas for groundwater protec- tion are delineated from those areas, which contribute most to nitrate intakes into groundwater. Therefore, agricultural areas on soils with bad or very bad denitrification capacity and high portion of groundwater recharge are considered as target areas. The delineated target areas for the Große Aue pilot area are shown in Fig. 6. A large part of the arable land in the groundwater recharge areas north and south of the floodplains are selected as target areas for groundwater protection. In all of these target areas, the calculated nitrate concentration in the leachate is above 100 mg NO3/l. www.adv-geosci.net/11/69/2007/ Wendland, F., Bach, M., Behrendt, H., and Kunkel R.: Integrated modelling of groundwater-borne nitrate intakes into the river Elbe basin (German part), Proceedings of the 9th International Specialized Conference on River Basin Management, Edinburgh, Scotland, 2002. References B¨ottcher, J., Strebel, O., and Duynisveld, W. H. M.: Kinetik und Modellierung gekoppelter Stoffumsetzungen im Grundwasser eines Lockergesteinsaquifers, Geologisches Jahrbuch C, 51, 3– 40, 1989. Another aspect has to be taken into account when environ- mental targets for groundwater protection are defined. Den- itrification in groundwater is associated with the irreversible consumption of substances in the groundwater, such as pyrite and organic carbon. Once these substances are exhausted ni- trate can not be denitrified in groundwater any more. As a consequence, nitrate concentrations would start to rise, like it has been described for many sites already. Consequently, the denitrification buffer of groundwater systems has to be pre- vented from damage, which implies a reduction of N-intakes into groundwater. A capable environmental target may be the nitrate concentration in the leachate. A limit of 50 mg NO3/l would ensure a “good groundwater quality status” with re- spect to general quality standards even in the case of missing or exhausted nitrate degradation capacities in the aquifer. G¨omann, H., Kreins, P., Kunkel, R., and Wendland, F.: Model based impact analysis of policy options aiming at reducing diffuse pol- lution by agriculture: a case study for the river Ems and a sub- catchment of the Rhine, Environ. Modell. Softw., 20(2), 261– 271, 2004. Henrichsmeyer, W., Cypris, Ch., L¨ohe, W., Meudt, M., Sander, R., and v. Sothen, F.: Entwicklung eines gesamtdeutschen Agrarsek- tormodells RAUMIS 96, Endbericht zum Kooperationsprojekt, Institut f¨ur Agrarpolitik, Marktforschung und Wirtschaftssozi- ologie der Universit¨at Bonn, Institute f¨ur Betriebswirtschaft, Strukturforschung und Landwirtschaftliche Marktforschung der Bundesforschungseinrichtung f¨ur Landwirtschaft (FAL), Bonn, Braunschweig, Germany, 1996. Kunkel, R. and Wendland, F.: WEKU; a GIS-supported stochastic model of groundwater residence times in upper aquifers for the supraregional groundwater management, Environ. Geol., 30(1– 2), 1–9, 1997. Scenario analyses were conducted in order to derive the amount of N-surpluses, which has to be reduced, when a con- centration of 50 mg NO3/l in the leachate should be achieved for all individual sites. For most regions, especially in the northern part of the pilot area, a N-surplus reduction of more Kunkel, R. and Wendland, F.: The GROWA98 model for water bal- ance analysis in large river basins; the River Elbe case study, J. Hydrol., 259(1–4), 152–162, 2002. Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/ 75 B. References Tetzlaff et al.: Determination and ranking of target areas in catchments Wendland, F., Bach, M., Behrendt, H., and Kunkel R.: Integrated modelling of groundwater-borne nitrate intakes into the river Elbe basin (German part), Proceedings of the 9th International Specialized Conference on River Basin Management, Edinburgh, Scotland, 2002. Kunkel, R., Bach, M., Behrendt, H., and Wendland, F.: Groundwater-borne nitrate intakes into surface waters in Ger- many, Water Sci. Technol., 49(3), 11–19, 2004. Kunkel, R. and Wendland, F.: Diffuse Nitrateintr¨age in die Grund- und Oberfl¨achengew¨asser von Rhein und Ems, Schriften des Forschungszentrums J¨ulich, Reihe Umwelt/Environment, Band 62, Forschungszentrum J¨ulich GmbH, J¨ulich, Germany, 2006. Walther, W., Reinstorf, F., P¨atsch, F., and Weller, D.: Management tools to minimize nitrogen emissions into groundwater in agri- cultural used catchment areas, northern low plain of Germany, Proceedings of “XXX IAHR Congress: Water engineering and research in a learning society”, 24–29 August 2003, Thessa- loniki, Greece, Vol. B, 747–754, 2003. Adv. Geosci., 11, 69–75, 2007 www.adv-geosci.net/11/69/2007/
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Genomic Characterization of an Emerging Enterobacteriaceae Species: the First Case of Co-infection With a Typical Pathogen in a Human Patient
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Genomic Characterization of an Emerging Enterobacteriaceae Species: the First Case of Co- infection With a Typical Pathogen in a Human Patient Zhao Zhang  The First Affiliated Hospital of Zhengzhou University Daixi Li  Peking University People's Hospital Xing Shi  Peking University People's Hospital https://orcid.org/0000-0003-2778-5373 Yao Zhai  University of Technology Sydney Yatao Guo  The First Affiliated Hospital of Zhengzhou University Yali Zheng  Xiamen University Xiang'an Hosital Lili Zhao  Peking University People's Hospital Yukun He  Peking University People's Hospital Yusheng Chen  Fujian Provincial Hospital Zhanwei Wang  Peking University People's Hospital Jianrong Su  Beijing Friendship Hospital Yu Kang  (  kangy@big.ac.cn ) Beijing Institute of Genomics, Chinese Academy of Sciences Zhancheng Gao  Peking University People's Hospital Research article Research article Page 1/25 Keywords: Enterobacteriaceae, pathogen, whole-genome sequencing, RNA-Seq, phylogenetic Posted Date: April 1st, 2020 DOI: https://doi.org/10.21203/rs.2.22057/v4 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License DOI: https://doi.org/10.21203/rs.2.22057/v4 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 on April 15th, 2020. See the published version at https://doi.org/10.1186/s12864-020-6720-z. Page 2/25 Abstract Background Opportunistic pathogens are important for clinical practice as they often cause antibiotic- resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species strain of extended-spectrum β-lactamase- producing Enterobacteriaceae from a patient of with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause. Results The isolate grows grew very slowly but confers conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia pneumoniae . As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis , and anti- infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural wild environment and animal host, tens of over 30 mobile genetic mobile elements, and a plasmid bearing bla CTX-M-3 gene, indicating its ability to disseminate antimicrobial - resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 , which could serve as targets for novel antimicrobial strategies. Conclusions Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes i n transferring antibiotic determinants , which highlights the need for continuous monitoring for this novel species and efforts to develop controlling treatment strategies. Background Antimicrobial resistance (AMR) is an increasingly global health threat that contributes to 700,000 deaths per year [1]. Increased and often unrestricted antibiotic use in the clinical and farming settings is to blame for this issue. Growing surveillances based on genomic sequencing of microbes from the natural environment, human settlements, and clinical settings have been conducted worldwide to investigate the evolution and transfer of antibiotic resistance genes (ARGs) [2-4]. In recent years, the eco-evolutionary feedback loops between ecological and evolutionary dynamics have been increasingly recognized, where spillover of antibiotic use to natural and semi-natural environments may have profound implications on the distribution of ARGs in natural bacterial populations which serve as environmental reservoirs of resistance determinants [5, 6]. However, how resistance evolves, and how ARGs are maintained and dispersed back to clinical settings is poorly understood. Understanding the dynamics of the continuous Page 3/25 Page 3/25 feedback loops from clinical to nature and back may prove critical for preventing and controlling the problem of antibiotic resistance. The rapidly developing sequencing technology increasingly enables the identification of emerging opportunistic pathogens and taxonomical classification based on their genomic information [7-9]. Naturally, opportunistic pathogens inhabit in the natural environment and are occasionally resistant to common antibiotics. Among these previously unknown pathogens, many are belong to species of the Enterobacteriaceae family [10, 11]. Meanwhile, many Enterobacteriaceae species are commensal microbiota of human and animal guts, but under certain conditions, can be opportunistic pathogens that cause infections [12]. These species often have other animal hosts, or they can be found in more diverse environments, such as soil and sewage [13]. Enterobacteriaceae species (including E. coli, Klebsiella, and Enterobacter) are also famous for their antibiotic resistance and regarded as some of the most dangerous pathogens since they can efficiently acquire various ARGs through efficient plasmid transmission [14]. The ability of these species to disseminate between habitats and transferring ARGs highlights their importance as mediators in the eco-evolutionary feedback loops that disperse ARGs from natural environments back to clinical settings. The taxonomy of Enterobacteriaceae is complex, containing 28 genera and over 75 species [15], while novel species are continuously discovered. Recognizing and characterizing Enterobacteriaceae species, especially those of emerging opportunistic pathogens, is critical for understanding the dynamics of the evolution of AMR. Background Here, we isolated from a patient with a biliary infection a novel strain of unknown taxonomy accompanying an infectious Klebsiella pneumoniae strain, which we designated as AF18. AF18 grew slowly but provided drug-resistance to its companion by carrying a blaCTX-M-3 resistant gene. The co- infection brought perplexity in both diagnosis and treatment of the patients. In order to provide new evidence and detailed information for opportunistic pathogens about the complex issues that they may cause in clinical infections, we conducted a study with the three following objectives: (1) Clarifying the taxonomy of AF18 using whole-genome phylogenetic analysis; (2) Testing the ability of AF18 to protect K. pneumoniae from antibiotics in co-culture experiments; and (3) Analyzing the adaptation mechanisms of AF18 base on transcriptome sequencing. Finally, we find that AF18 is a strain of an undefined novel species in the family Enterobacteriaceae, and that sensitive K. pneumoniae can survive when co-cultured with AF18 in Luria-Bertani broth containing 8 μg/mL ceftriaxone. Furthermore, genomic and transcriptomic analyses reveal the genomic characteristics of this rare pathogen and the regulation mechanisms of how it adapts to multiple habitats and its association with ARGs transfer. Results Biological Identification of the Strain AF18 Biological Identification of the Strain AF18 From the bile sample of the patient, two types of colonies were isolated after serial dilutions and isolations on MacConkey agar plates. One type was mucous, entirely pink, and of 4-5mm in diameter, which was finally identified as a K. pneumoniae clone sensitive to common antibiotics (Table 1); the other Page 4/25 Page 4/25 type was composed by small (2-3mm in diameter) red-centered colonies with clear and transparent edges (Fig. 1A). The bacteria of the small colonies seemed prone to adhere to the cells of K. pneumoniae and were not able to be isolated until extensive dilutions. The taxonomy of the small colonies was not immediately identified by the microbiological laboratory in the hospital, and we designated it as strain AF18. AF18 exhibited resistance to most β-lactam antibiotics in antimicrobial susceptibility testing (Table 1). As the infection was rather intractable and finally cured by intravenous amikacin, the final diagnosis for the patient was a co-infection caused by a sensitive K. pneumoniae strain and a multidrug-resistant strain of unknown species. Microscope observation showed that AF18 was a Gram-negative bacillus (Fig. 1B), and its cells were surrounded by flagella under a transmission electron microscope (Fig. 1C). The scanning electron microscope confirmed the tubular shape of AF18 and a smooth surface with no polysaccharide particles (Fig. 1D), in line with the mucus-free characteristics of its colonies. VITEK-II in the hospital laboratory did not identify any bacterial species with identical biochemical properties to AF18 (Table S1), whereas the API20E biochemical identification system suggested AF18 as Pantoea sp. but with low reliability. The mass spectrometry which scans the protein profile of samples did not identify the species of AF18 either. Complete Genome of Enterobacteriaceae bacterium AF18 To determine the taxonomy and genetic features of AF18, we performed whole-genome sequencing using two platforms, Illumina Hiseq (generates short-reads) and PacBio sequencer (generates long-reads), obtaining a high-quality completed genome sequence. AF18 possessed a circulated chromosome and two plasmids (Table 2). By using Mash [16] to search the publicly available bacterial genomes and drafts with a cutoff of mutation distance < 0.25, we identified 33 non-redundant close relatives of AF18, all of which were in the Enterobacteriaceae family. The average nucleotide identity (ANI) matrix of the 34 strains (Fig. 2A) shows that the closest five with identity > 98.5% ( > 95% regarded as strains of the same species [17]) are nominated as [Kluyvera] intestini (GCA_001856865.3), Metakosakonia sp.(GCA_003925915.1), By using Mash [16] to search the publicly available bacterial genomes and drafts with a cutoff of mutation distance < 0.25, we identified 33 non-redundant close relatives of AF18, all of which were in the Enterobacteriaceae family. The average nucleotide identity (ANI) matrix of the 34 strains (Fig. 2A) shows that the closest five with identity > 98.5% ( > 95% regarded as strains of the same species [17]) are nominated as [Kluyvera] intestini (GCA_001856865.3), Metakosakonia sp.(GCA_003925915.1), Enterobacter sp. (GCA_000814915.1, GCA_900168315.1 ), and just Enterobacteriaceae bacterium (GCA_002903045.1). The phylogenetic relationship of these relatives was further inferred with core genome SNPs (Fig. 2B), which confirmed the relationships inferred from the ANI matrix and indicated the novel species, including AF18, possibly represents another genus than Kluyvera. Herein, we temporarily nominated our stain as Enterobacteriaceae bacterium AF18 as the nomenclature of its genus and species is still undefined. We predicted seven copies of 16S rDNA sequences in AF18. We aligned them to the 33 genomes we picked using BLASTN and calculated the average identity. We removed the genomes which do not contain high quality 16S rDNA sequence. The result shows a good congruence of 16S rDNA and whole- genome comparisons (Table S4). However, considering cutoffs commonly used for intra-species Page 5/25 Page 5/25 classification by whole-genome ANI > 95% [17] and 16S rDNA identity > 99% [18], 16S rDNA classification found two more strains of the species, namely Enterobacteriaceae bacterium ENNIH1, and Phytobacter ursingii strain CAV1151 (Table S4). Thus, we think that 16S rDNA can also be used as a marker gene to clarify the taxonomy of isolated strains, but we need to examine the identity cutoff we used carefully. Complete Genome of Enterobacteriaceae bacterium AF18 Unfortunately, due to constraints related to the outbreak of the 2019 novel coronavirus, we were unable to perform conjugation experiments. Complete Genome of Enterobacteriaceae bacterium AF18 The chromosome of AF18 possesses 5651 protein-coding genes whose functions facilitate the survival and adaptation of AF18 in various habits (Table S2, Table S3). For example, motility-related genes, including a complete flagellar gene cluster that encodes all components of flagellar, csg gene cluster that encodes curli assembly proteins to mediate adhesion, and other genes of ompA, pilRT, ibeB, icaA, htpB and fimB, together confer the ability of adhesion, invasion, chemotaxis, and escape to the host strain. Efflux pump genes which confer resistance to macrolides, quinolones and aminoglycosides were also identified. Meanwhile, the AF18 genome possesses 20 genomic islands, 11 prophages, and five CRISPR sequences (Table S3), suggesting the active transfer of stress-adaptive genes by these mobile genetic elements in this species. More importantly, markers of soil-inhabiting bacteria, including a complete nitrogen fixation gene cluster and ksgA—— a pesticide-resistant gene, were found in AF18 genome, which suggests that AF18 is able to colonize natural environments. The mobility of this strain may potentiate its dissemination to various habits. Analysis of conserved genes in plasmids shows that most of the antibiotic-resistant genes of AF18, including qnrS, dfrA, and blaCTX-M-3, are carried by the smaller plasmid pAF18_2 (Fig. 3, Table S2) which is, in major part, responsible for the antibiotic resistance profile of AF18 (Table 1). Sequence alignment shows that pAF18_2 is similar to many plasmids from other Enterobacteriaceae species, such as E. coli (KF914891.1, KC788405.1, CP028486.1), K. pneumoniae (KX928750.1, CP026179.1), and C. freundii (KT989599.1), and they contain identical replication origins, replication and transcription systems, plasmid partition systems, and a partial gene cluster responsible for plasmid conjugation, which indicates that the plasmid might be compatible with all these Enterobacteriaceae host species. Besides, these plasmids share a common anti-restriction system that ensures they would not be destroyed by the restriction-modified system in other host strains. Specifically, the pAF18_2 contains an active transposase system with complete IS elements which had acquired the blaCTX-M-3 gene and an arsenical resistant system. Many other DNA manipulating enzymes, such as integrase and DNA invertase, were also identified in the plasmid, all of which could facilitate the plasmid in efficiently acquiring and transferring antibiotic-resistance genes and other stress-adaptive genes among Enterobacteriaceae strains. Unfortunately, due to constraints related to the outbreak of the 2019 novel coronavirus, we were unable to perform conjugation experiments. Growth of AF18 in Co-cultures and Its Transcriptional Regulation To disentangle the respective contribution of AF18 and the sensitive K. pneumoniae in the co-infection, we co-cultivated the two strain in various concentration of ceftriaxone, and found that addition of 1% of Page 6/25 Page 6/25 AF18 was able to elevate the MIC from 0.125 µg/ml of pure K. pneumoniae culture to 64 µg/ml. Furthermore, when spreading the co-culture onto the MacConkey agar containing ceftriaxone, the sensitive K. pneumoniae colonies were able to withstand 8 µg/ml ceftriaxone (Fig. 4A), indicating a strong protective effect of AF18 to the co-infected K. pneumoniae. AF18 was able to elevate the MIC from 0.125 µg/ml of pure K. pneumoniae culture to 64 µg/ml. Furthermore, when spreading the co-culture onto the MacConkey agar containing ceftriaxone, the sensitive K. pneumoniae colonies were able to withstand 8 µg/ml ceftriaxone (Fig. 4A), indicating a strong protective effect of AF18 to the co-infected K. pneumoniae. Although necessary in the co-infection for antibiotic-resistance, AF18 only took less than 1% in the initial sample. Even when equally input, the proportion of AF18 decreased to 1% of the co-culture if without antibiotic pressure (Fig. 4B). It seems that AF18 may be less aggressive, and its growth rate is much slower than the co-inhabited K. pneumoniae. It has been reported that plasmid carriage may slow down growth rate due to the cellular cost imposed [19], and thus we generate a new strain—AF18-NC by deleting the resistant plasmid of AF18. Then we measured the independent growth curve of the three strains— K. pneumoniae, AF18, and AF18-NC, respectively (Fig. 4C). As expected, AF18-NC did grow faster than its mother strain AF18 since it was relieved from the plasmid-caused cellular cost. However, the growth rate of AF18-NC was still much slower than that of K. pneumoniae, suggesting that slow growth is an inherent property of the novel species. Next, we analyzed the genes involved in the regulation of the growth rate by a comparison between the transcriptomes of AF18 and AF18-NC. A total of 3,309 genes of chromosomal coding genes were significantly differentially expressed, with 1675 upregulated and 1634 downregulated in AF18 (Fig. 4D). Functional cluster analysis with GO database showed that most of the differentially expressed genes were in the categories of transcriptional regulation, biosynthesis regulation, metabolic process regulation, signal transduction, and flagellar motility (Fig. S1). Analysis of the non-coding sRNA expression profile identified a total of 15 sRNAs differentially expressed between AF18 and AF18-NC. Growth of AF18 in Co-cultures and Its Transcriptional Regulation Interestingly, two of the down-regulated sRNAs in AF18, namely sRNA00063 and sRNA00291 (Fig. S2), shared 98% of their predicted target genes which constitute up to 56% of those differentially expressed genes as mentioned above, suggesting that these two sRNAs have a key role in promoting growth. This result indicated the importance of the two sRNAs in global regulation of growth rate, and consequently, the contribution of the host AF18 in co-infections. Discussion In this study, we reported a case of co-infection caused by a typical pathogen and a rare opportunistic pathogen with taxonomical nomenclature undefined. K. pneumoniae is a common pathogen that can cause various aggressive infections [20], while the AF18 strain and its relatives have not been reported to cause infection in humans. In the pathogenic consortium of the co-infection in our study, although taking a very small proportion, AF18 provides strong protection for the entire pathogenic consortium against antibiotic damage. The cooperation between the K. pneumoniae and AF18 makes the infectious situation more complicated and difficult in terms of therapies than infections caused by either of them. Meanwhile, as the strain AF18 only took a minor proportion and closely adhered to co-infected K. pneumoniae, it was prone to be concealed by the dominant K. pneumoniae and hard to be detected and isolated, which led to inaccurate etiological diagnosis and improper anti-infective treatment at first admission. As AF18 and Page 7/25 Page 7/25 other strains of the same species are rare opportunistic pathogen with little documentation, and conventional testings for bacterial identification are not always correct for such novel species, as shown in this study, WGS comprised a straightforward approach for accurate taxonomy identification. Sequencing strategy combining both long- and short-read platforms makes it easy to obtain high-quality complete genome and plasmids, which will be helpful for the overall characterization of novel species and deep insight into the functions of the genes they harbor. Phylogenetic analysis with the whole genome of AF18 assigned it to the Enterobacteriaceae family. However, the nomenclature of this novel species is still under discussion due to very limited documentation [21]. The first report of the novel species was in 2016 when [Kluyvera] intestini str. GT-16 was isolated from the stomach of a patient with gastric cancer [22], and in the following years, strains of this species were emergingly discovered [23, 24]. Of note, AF18 is the first clear report of human infection of this novel species, as [Kluyvera] intestine GT- 16 and Matakosakonia sp. MRY16_398 were more likely a common resident in the gastrointestinal tract or a by-stander of the diverticulitis. Although the first strain of [Kluyvera] intestini str. GT-16 had been assigned to the genus Kluyvera, the ANI of strains in this novel species to typical Kluyvera spp. Discussion AF18 carries genes of the hcp-clp and mprAB system which are powerful in implementing persistence status and endows resistance to many environmental stresses including all kinds of antibiotics [29, 30]. These species can acquire various ARGs from their Enterobacteriaceae relatives in natural environments and host gut. For example, E. coli and K. pneumoniae can share these ARGs through various genetic mobile elements or even in a more efficient manner of conjugating resistant plasmids [31]. Thus, the species of AF18 may prove important in spreading ARGs and function as a mediator in the eco-evolutionary feedback loops of AMR. In this regard, the novel species and many other emerging opportunistic pathogens of Enterobacteriaceae family, such as Kluyvera spp. and Enterobacter spp., deserve more attention in clinical practice and in the field of antibiotic resistance control. In our study, the resistant AF18 does not have to transfer its resistance gene to the co-infected sensitive K. pneumoniae to confer protection. Being antibiotic-resistant by itself, we speculate that AF18 just upregulated the production of antibiotic-hydrolase to generate a niche of low antibiotic concentration for the sensitive K. pneumoniae to hide. Such co-operation between different bacteria has been deeply investigated in experiments, and relevant theories or mathematic models have been fully developed which illustrated the important role of growth regulation in maximizing the benefit and population of the entire consortium [32-34]. Our study provides empirical evidence for these hypotheses and highlights the importance of mutualistic relationships between microbes in a co-infection scenario in clinical settings. Transcriptome analysis further identified genes involved in growth regulation and pointed to two novel sRNAs that might be the key regulators of the process. As antibiotics are not always successful, especially in treating opportunistic pathogens, the sRNAs that promote the growth of host strains as we had identified may serve as targets of bacteriostatic agents and deserve further investigations. Conclusion Opportunistic pathogenic strain Enterobacteriaceae bacterium AF18 is in a novel species with little documentation. In-depth genomic analysis suggests the ability of this species to transfer between the natural environment and host habitats and in disseminating antibiotic-resistant genes, which potentiates it to be an important disseminator of antibiotic resistance to clinical pathogens. When co-infected with typical pathogens, the resistant opportunistic strain can provide temporary protection for the whole consortium and cause confusions in the etiological diagnosis and antibiotic treatment, although the strain by itself is possibly not a pernicious pathogen for immunocompetent patients. Taken together, Enterobacteriaceae bacterium AF18 and other newly emerging opportunistic pathogens complicate the situation of antibiotic resistance control in clinical practice and deserve in-depth investigation including methods for surveillance and control. Discussion are less than 80.8%, even farther than the distance to other genera, such as Kasokonia (ANI, 82.3%), and typical Enterobacter spp. (ANI, 81%), suggesting that AF18 and its species is not a typical Kluyvera species or should not be included in this genus. Except AF18 which cause a co-infection with a typical pathogen, two of the other strains of this species ( [Kluyvera] intestini str. GT-16 [25], and Matakosakonia sp.MRY16_398 [23]) were both isolated from patients in Japan, while the other three strains (Enterobacter sp.NFR05, Enterobacter sp.Bisph2, and Enterobacteriaceae bacterium ENNIH2) were isolated from rhizoplane (China), sandy soil (Algeria) [26], and hospital sewage (USA) [24], respectively, indicating a wide range of environments that this species can inhabit. 16S rDNA sequencing is also a commonly used method for species identification; however, there are some matters to consider when using 16S rDNA to determine the taxonomy of a new bacteria. Briefly speaking, we need to obtain the entire 16S rDNA gene (preferably all copies of the strain) and an up-to- date database to ensure accurate identification [18]. Another issue that requires attention is that we indeed need some online websites and databases to help us identify bacterial taxonomy and obtain genomic characteristics of pathogens quickly and accurately. An easy-to-use and convenient web service platform, such as BacWGSTdb (http://bacdb.org/BacWGSTdb) [27], can provide uniform classification criteria to help us identify the taxonomy of species, ARGs, and virulence genes. Moreover, worldwide species information can be integrated into the platform, helping us to evaluate the tracking and evolution of pathogens. Annotation of genes in the genome supports that AF18 possesses many common features to the Enterobacteriaceae family, such as the flagella that confer mobility to the bacterium, many genetic mobile elements that facilitate the transfer of stress-adaptive genes, especially ARGs. In fact, strains of this species have been identified as an important source of extended-spectrum β-lactamase-encoding genes and even carbapenem-resistant genes. For example, Enterobacteriaceae bacterium ENNIH2 is KPC-2 positive [24], Metakosakonia sp. MRY16-398 carries blaIMP-6 , blaCTX-M-2 , and aadA2 gene [23], and the Page 8/25 Page 8/25 [Kluyvera] intestini str. GT-16 contains many ARGs that even confer resistance to polymyxin [25]. A more distant relative of AF18—Pytobacter ursingii (previously named Kluyvera intermedia) was found to be KPC positive and carbapenem-resistant [28]. Bacterial isolation The bile sample was collected from a patient with obstructive jaundice who suffered an infection two days after the percutaneous transhepatic cholangial drainage (PTCD) surgery admitted to Fujian Province Hospital (N26.08, E119.30) in 2014. The original colonies isolated from the bile sample on a blood agar plate were further incubated in Luria-Bertani (LB) broth overnight. The culture was diluted 106- fold with LB broth and spread onto MacConkey agar and incubated at 37°C for 24 h. Then, the morphology of the isolated colonies were observed. The K. pneumoniae colonies were inoculated into LB broth and incubated overnight. The bacterial cultures were supplemented with glycerol before freezing and stored in a -80°C freezer. AF18 was selected by culturing overnight in LB broth containing 50 µg/ml ceftriaxone: the aforementioned method was used to pick 10 drug-resistant clones from the MacConkey agar medium; then, the clones were re-inoculated in LB broth containing 50 µg/ml ceftriaxone and cultured overnight. The selection was repeated 5 times, and each culture was supplemented with glycerol before freezing and stored in a -80°C freezer. Methods Page 9/25 Genome Sequencing AF18 cells were harvest by centrifugation from an overnight culture, and DNA was extracted with QIAamp DNA Mini Kit (Qiagen, Cat No: 51304) following manufacturer’s instruction. The extracted DNA sample was assayed with a NanoDrop spectrophotometer for quantification and then sent to Beijing Novogene Bioinformatics Technology Co., LTD for whole-genome sequencing. The genome of AF18 was both sequenced with the single-molecule real-time sequencing (SMRT) technology from Pacbio using a PacBio RSII sequencer (insert size was approximately 10 kb) for one cell, and sequenced with the short-reads Hiseq 2000 platform from Illumina (100bp pair-end reads) for 3G raw reads. The obtained raw SMRT reads were analyzed and de novo assembled using SMRT Analysis 2.3.0 software. Then, we performed the error correction of tentative complete circular sequences using Pilon (v1.18) with Illumina short reads. Genome Annotation GeneMarks (version 4.17) [35] was used to predict protein-coding genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), NCBI-NR and Gene Ontology (GO) databases were used to annotate the function of predicted genes [36-38]. Virulent genes were reliably identified by BLAST in the Virulence Factors Database (http://www.mgc.ac.cn/VFs/) with identity > 80% and E-value < 10e-50, and antibiotic-resistant genes were identified using RGI from the Comprehensive Antibiotic Resistance Database (https://card.mcmaster.ca/) with “perfect and strict hits” and “identity > 90%” [39, 40]. Circos software (Version 0.64) was used to plot a circular map of the genome [41]. Plasmid replicon typing was performed using the curated PlasmidFinder database at the CGE website (https://cge.cbs.dtu.dk/services/PlasmidFinder/) [42]. Biological Characterization of Strain AF18 net and allowed to rest for 5 min so that the bacteria could adhere to the copper net; then, the excess water was removed. The specimen was stained with 1% uranyl acetate for approximately 10 min. After the specimen dried, the flagella were observed with a JEM-1230 transmission electron microscope. Biological Characterization of Strain AF18 Gram staining: (1) A total of 10 µl of a bacterial culture that was cultured for 4 h in LB broth without antibiotics was dropped onto a sterile slide. (2) The bacteria were stained for 1 min with ammonium oxalate crystal violet and the dye was washed off with water. (3) A potassium iodide solution was dropped onto the bacteria and allowed to stain for 1 min and the excess dye was gently rinsed off with water. (4) Next, 95% ethanol was dropped onto the slide to destain for 30 s. (5) Safranin solution was dropped onto the slide to counterstain for 30 s, and the dye solution was rinsed off with water. When the slide was dry, the bacteria were observed under a microscope with an oil objective lens. Biochemical identification: The biochemical identification of AF18 was performed with the VITEK-II automated bacterial identification system and the API20E Enterobacter biochemical identification system (Biomerieux, France). The obtained biochemical properties were compared with the biochemical properties of known species. The VITEK-MS mass spectrometer and the time-of-flight detection method were used to obtain the mass spectrum of AF18, which was compared with the mass spectra of known species. Antimicrobial susceptibility of strain AF18 and K. pneumonia was investigated by broth microdilution using the E-test (Biomerieux, France) according to manufacturers’ instructions, and a total of 21 antibiotics were tested as listed in Table 1. Electron microscopy: An inoculation loop was used to scrape a bacterial colony from a blood agar plate. The colony was fixed with 2.5% glutaraldehyde, followed by 1% osmium acid, for 2 h each. After gradient dehydration with 30%, 50%, 70%, 80%, 90%, and 100% ethanol, the bacteria were dried in a desiccator. After the specimen was coated with gold, the morphology of the bacteria was observed under a Hitachi S- 3400N scanning electron microscope. Bacteria grown on a blood agar plate for approximately 6 h were scraped with an inoculation loop. A bacterial suspension prepared in saline was dropped onto a copper Page 10/25 Page 10/25 Page 10/25 net and allowed to rest for 5 min so that the bacteria could adhere to the copper net; then, the excess water was removed. The specimen was stained with 1% uranyl acetate for approximately 10 min. After the specimen dried, the flagella were observed with a JEM-1230 transmission electron microscope. Phylogenetic Analysis We used Mash [16] to compare the AF18 genome sequence to the NCBI genome assembly database, and picked 33 genomes from the non-redundant species with identity scores > 75%. Then, we used kSNP3 to identify core genome SNPs (single nucleotide polymorphisms) of each pair of the 34 genome sequences with an optimal k-mer size of 21 (determined by Kchooser) [43]. These core SNPs were used to build a maximum likelihood tree by FastTreeML [44], and iTOL was used to exhibit the phylogenetic tree (https://itol.embl.de/) [45]. We used fastANI to calculated the pairwise ANI of the 34 genome sequences Page 11/25 Page 11/25 [17]. We used RNAmmer to predict the rRNA sequences [46], and then used BLASTN to align the 16S rRNA sequences to the genomes we picked. Comparative Analysis of pAF18_2 We used BLASTN to compare pAF18_2 sequence against the NR/NT database and picked 10 non- redundant plasmids according to the query coverage (>60%) and percent identity (>99.7%) [47]. We then performed BLASTN for pAF18_2 against the above selected 10 plasmids to find out the alignment fragments with E-value < e-50 [48], and generated the comparative map using CGView (http://wishart.biology.ualberta.ca/cgview/) [49]. Drug-resistant Plasmid Elimination Test A single colony of AF18 was inoculated into LB broth medium without antibiotics and cultured for 24 hours at 37°C. Then the culture was 1:1000 diluted and re-inoculated in LB broth medium for another 24 hours. The procedure was repeated while an aliquot was collected and spread on LB agar medium for each round of re-inoculation. Colonies grown on the LB agar medium were randomly selected and tested for the presence of blaCTX-M-3 gene by PCR. DNA was extracted with QIAamp DNA Mini Kit, and PCR was performed under cycling conditions: 95℃ for 5 min, followed by 32 cycles of 95℃ for 1 min, 55℃ for 1 min, 72℃ for 1 min, followed by a single step of 72℃ for 5 min. The pair of Primers were: F 5'- CAGAATAAGGAATCCCATG-3', and R 5'-CGTCTAAGGCGATAAACA-3'. The PCR negative colonies, which might have lost their resistant plasmid pAF18-2, were functionally confirmed by inoculation in LB broth medium both with and without ceftriaxone (20 μg/ml). The strains that didn’t survive in the ceftriaxone- containing medium were believed to have lost the resistant plasmid, and one of them was preserved and named AF18-NC. A single colony of AF18 was inoculated into LB broth medium without antibiotics and cultured for 24 hours at 37°C. Then the culture was 1:1000 diluted and re-inoculated in LB broth medium for another 24 hours. The procedure was repeated while an aliquot was collected and spread on LB agar medium for each round of re-inoculation. Colonies grown on the LB agar medium were randomly selected and tested for the presence of blaCTX-M-3 gene by PCR. DNA was extracted with QIAamp DNA Mini Kit, and PCR was performed under cycling conditions: 95℃ for 5 min, followed by 32 cycles of 95℃ for 1 min, 55℃ for 1 min, 72℃ for 1 min, followed by a single step of 72℃ for 5 min. The pair of Primers were: F 5'- CAGAATAAGGAATCCCATG-3', and R 5'-CGTCTAAGGCGATAAACA-3'. The PCR negative colonies, which might have lost their resistant plasmid pAF18-2, were functionally confirmed by inoculation in LB broth medium both with and without ceftriaxone (20 μg/ml). The strains that didn’t survive in the ceftriaxone- containing medium were believed to have lost the resistant plasmid, and one of them was preserved and named AF18-NC. Transcriptome Sequencing AF18 and AF18-NC cells were harvested from its overnight LB broth medium culture by centrifugation, and total RNA of both strains were extracted with QIAGEN RNeasy Plus Mini Kit (Qiagen, Cat No.74134) following manufacturer’s instruction. The extracted RNA samples were assayed with NanoDrop spectrophotometer for quantification and then sent to Beijing Novogene Co., LTD for transcriptome sequencing. rRNA was removed using the Ribo-Zero rRNA Removal Kit (Epicentre Biotechnologies), then the transcriptome was sequenced on Hiseq 2000 platform with 1G raw reads (paired-end, 2×100bp). Low- quality reads and adaptor sequences were then removed. Using the whole genome of AF18 as the reference genome, the gene expression level for each transcript was estimated by calculating the FPKM (Fragments Per Kilobase per Million mapped fragments) value of each transcript. Functions of Differentially Expressed Genes Functions of the differentially expressed genes between AF18 and AF18-NC were annotated with GO database [36], and the probability of enrichment for each cluster was calculated by using the weight algorithm and Fisher’s exact test implemented in topGO package [51]. Clusters with a corrected p value < 0.05 were regarded as significantly enriched. Differential Gene Expression Analysis The read count data of each transcript was first normalized using DEseq [50]. According to the binomial distribution model, hypothesis testing was performed on each transcript between the AF18 strain and the AF18-NC strain, and confirmed by multiple hypothesis tests. Co-culture of AF18 and K. pneumoniae AF18 and K. pneumoniae were first co-cultured in LB broth mediums containing different concentrations of ceftriaxone (0.125-16 μg/mL) overnight, and then the bacterial solution in the tube was diluted and spread on MacConkey agar medium. We picked out the colonies of K. pneumoniae from the plates and incubated them in LB broth medium containing ceftriaxone at the same concentration overnight, and then diluted the bacterial culture with LB broth and spread onto MacConkey agar medium. Growth Rate Measurement Page 12/25 Page 12/25 Overnight cultures of the K. pneumonia strain, AF18, and AF18-NC were sampled and diluted to O.D.=0.10, and were then cultured at 37°C for 24 h in LB broth medium. The turbidity (O.D. value) of the cultures was measured by using a bacterial turbidimeter at 1 h intervals for 24 h, and the 3 bacterial growth curves were drawn based on the O.D. values. The proportion of AF18 and the K. pneumoniae strain in co-cultured samples was determined by colony counting on plates of MacConkey agar. Consent for publication Not applicable sRNA Analysis Rockhopper software was used to search new intergenic transcripts [52, 53], and those transcripts that had no hits in the NCBI-NR protein database by BLASTx were considered as candidates for non-coding sRNA. The sRNAs with two-fold increased/decreased FPKM value were regarded as up-/down-regulated. Page 13/25 Page 13/25 Secondary structures of candidate sRNAs were predicted using RNAfold software and their target genes were predicted by using IntaRNA [54, 55]. y p g g g were predicted by using IntaRNA [54, 55]. Abbreviations AMR:           Antimicrobial resistance ARGs: Antibiotic resistance genes ANI:    Average nucleotide identity COG:  Clusters of Orthologous Groups FPKM:            Fragments Per Kilobase per Million mapped fragments GO:         Gene Ontology KEGG:            Kyoto Encyclopedia of Genes and Genomes LB:          Luria-Bertani PTCD: Percutaneous transhepatic cholangial drainage SMRT:            Single-molecule real-time sequencing SNPs:  Single nucleotide polymorphisms Declaration Ethics approval and consent to participate The study protocol was approved by the ethics committee of Peking university people’s hospital (Approval No. 2015PHB037-01, 17/01/2015). Written consent was acquired from the patient. Consent for publication Not applicable   Availability of data and materials The complete, annotated genomic sequence of AF18 was deposited in a public database GenBank [5 (accession numbers: chromosome, CP025982; pAF18_1, CP025983; pAF18_2, CP025984). The clean Ethics approval and consent to participate The study protocol was approved by the ethics committee of Peking university people’s hospital (Approval No. 2015PHB037-01, 17/01/2015). Written consent was acquired from the patient. Abbreviations Abbreviations AMR:           Antimicrobial resistance ARGs: Antibiotic resistance genes ANI:    Average nucleotide identity COG:  Clusters of Orthologous Groups FPKM:            Fragments Per Kilobase per Million mapped fragments GO:         Gene Ontology KEGG:            Kyoto Encyclopedia of Genes and Genomes LB:          Luria-Bertani PTCD: Percutaneous transhepatic cholangial drainage SMRT:            Single-molecule real-time sequencing SNPs:  Single nucleotide polymorphisms D l i AMR:           Antimicrobial resistance ARGs: Antibiotic resistance genes ANI:    Average nucleotide identity COG:  Clusters of Orthologous Groups FPKM:            Fragments Per Kilobase per Million mapped fragments GO:         Gene Ontology KEGG:            Kyoto Encyclopedia of Genes and Genomes LB:          Luria-Bertani PTCD: Percutaneous transhepatic cholangial drainage SMRT:            Single-molecule real-time sequencing SNPs:  Single nucleotide polymorphisms Availability of data and materials The complete, annotated genomic sequence of AF18 was deposited in a public database GenBank [56] (accession numbers: chromosome, CP025982; pAF18_1, CP025983; pAF18_2, CP025984). The clean Acknowledgements We are thankful to Donghui Yan and Wei Sun from Department of Clinical Laboratory Center, Beijing Friendship Hospital, for their help on the biological characterization. We are also thankful to the staff of Electron Microscope Laboratory of China Agricultural University, for their help on morphological characterization. Author’s contributions ZG and YK designed and conducted the study. YC isolated the strains and organized the clinical information. ZZ, DL, YZ, YG, LZ, and YL Z performed the experiments. ZW and JS identified the isolate. ZZ, XS, and YH performed the bioinformatics analyses. ZZ, YK and XS prepared the manuscript. ZG revised the manuscript, and all authors read the manuscript and approved the submission. Funding The study was funded by National Science and Technology Major Project (2017ZX10103004-006, 2018ZX10712001-018-002), National Natural Science Foundation of China (81870010, 31970568, 31671350). Programs of the Chinese Academy of Sciences (Y8YZ02E001, QYZDY-SSW-SMC017) The funding sources had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication. The complete, annotated genomic sequence of AF18 was deposited in a public database GenBank [56] (accession numbers: chromosome, CP025982; pAF18_1, CP025983; pAF18_2, CP025984). The clean Page 14/25 Page 14/25 Page 14/25 sequence data for RNA-Seq have been deposited in the Genome Sequence Archive [57] in BIG Data Center [58], Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA002037 that are publicly accessible at https://bigd.big.ac.cn/gsa. Accession numbers of genomes and plasmids used for comparative analyses are listed in Table S5. Competing Interests All authors declare that they have no conflicts of interest. 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Heidelberg, Germany: European Molecular Biology Laboratory (EMBL) 2012. 51. Alexa A, Rahnenfuhrer J: Gene set enrichment analysis with topGO. Bioconductor Improv, 27. In.; 2019. 52. McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B: Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 2013, 41(14):e140. 53. Tjaden B: De novo assembly of bacterial transcriptomes from RNA-seq data. Genome Biol 2015, 16:1. 54. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P: Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly 1994, 125(2):167-188. Supplement Material Figure S1 The bar plot of enriched GOs in AF18 and AF18-NC Figure S1 The bar plot of enriched GOs in AF18 and AF18-NC Figure S2  The sequences and the secondary structures of sRNAs Table S1  The results of biochemical testing of AF18 isolate by VITEK II2 Table S2  The ARGs and virulence genes annotation results of AF18 Table S3  The summary statistics of genomic features of AF18 Table S4  Comparison of whole-genome ANI and 16S rDNA BLASTN results Table S5  Accession numbers of genomes and plasmids used for comparative analyses Tables Table 1. The antibiotic resistance profile of AF18 and K. pneumoniae isolate. Drug Antibiotic susceptibility AF18 K. pneumoniae strain MIC (μg/ml) Phenotype MIC (μg/ml) Phenotype Ampicillin ≥32 R 16 I Ampicillin/sulbactam ≥32 R 4 S Piperacillin ≥128 R ≤4 S Piperacillin/tazobactam ≥128 R ≤4 S Cefazolin ≥64 R ≤4 S Cefuroxime ≥64 R ≤1 S Cefuroxime axetil ≥64 R ≤1 S Cefotetan ≤4 S ≤4 S Ceftazidime 16 R ≤1 S Ceftriaxone ≥64 R ≤1 S Cefepime ≥64 R ≤1 S Aztreonam ≥64 R ≤1 S Imipenem ≤1 S ≤1 S Meropenem ≤0.25 S ≤0.25 S Amikacin ≤2 S ≤2 S Gentamicin ≤1 S ≤1 S Tobramycin 2 S ≤1 S Ciprofloxacin 2 I ≤0.25 S Levofloxacin 1 S ≤0.25 S Nitrofurantoin 256 R ≤16 S Trimethoprim/sulfamt ≤20 S ≤20 S Tables Table 2. Overview of genome information for AF18 Replicon Nucleotide length (bp) Coding Genes GC% Inc type GenBank ID Chromosome 5,676,372 5651 53.06 NA CP025982 pAF18_1 140,420 181 51.14 IncFII CP025983 pAF18_2 42,923 53 51.28 IncN CP025984 Figures Figures gure 1 he morphological characters of AF18 (A)The morphology of AF18 colonies on MacConkey agar plate. B) Gram staining of AF18 cells. (C) Flagella of AF18 photographed by transmission electron microscop D) Cells of AF18 under scanning electron microscopy. Figure 1 The morphological characters of AF18 (A)The morphology of AF18 colonies on MacConkey agar plate. (B) Gram staining of AF18 cells. (C) Flagella of AF18 photographed by transmission electron microscopy. (D) Cells of AF18 under scanning electron microscopy. The morphological characters of AF18 (A)The morphology of AF18 colonies on MacConkey agar plate. (B) Gram staining of AF18 cells. (C) Flagella of AF18 photographed by transmission electron microscopy. (D) Cells of AF18 under scanning electron microscopy. (D) Cells of AF18 under scanning electron microscopy. Page 21/25 Figure 2 Figure 2 Phylogenetic relationship of 34 strains related to AF18 A. The heatmap of ANI matrix. The color bar represents the value of ANI. The top five species (not including AF18) are the closest relatives of AF18 with ANI>98.5%. B. The maximum likelihood phylogenetic tree constructed based on the core genome SNPs. The species in the blue box are the closest relatives of AF18 in the phylogenetic tree which are the same as the top five species of ANI heatmap. ANI, average nucleotide identity. Phylogenetic relationship of 34 strains related to AF18 A. The heatmap of ANI matrix. The color bar represents the value of ANI. The top five species (not including AF18) are the closest relatives of AF18 with ANI>98.5%. B. The maximum likelihood phylogenetic tree constructed based on the core genome SNPs. The species in the blue box are the closest relatives of AF18 in the phylogenetic tree which are the same as the top five species of ANI heatmap. ANI, average nucleotide identity. Page 22/25 Page 22/25 Figure 3 The circular map of pAF18_2 and comparison to similar plasmids The outmost slot represents the predicted genes of pAF18_2, whose functions are shown in different color arrows. From outward, slot 2- 11 indicate aligned fragments from similar plasmids of IncN. Slot 12, GC content; slot 13, GC skew. Accession numbers of plasmids from outer to inner were: AP018758.1, KF914891.1, KC788405.1, KX928750.1, CP028486.1, CP026277.1, KM660724.1, CP026179.1, CP026198.1, KT989599.1. Figure 3 Figure 4 The properties and regulation of the growth rate of AF18 (A) Over-night co-culture of AF18 and the co- infected K. pneumoniae strain in LB medium was spread on MacConkey agar plates supplemented with ceftriaxone at a concentration of 2-16 μg/mL. (▲) stands for K. pneumoniae colonies. (B)Proportion of AF18 in the co-culture with the co-infected K. pneumoniae strain in LB medium without antibiotic pressure. (C) The growth curves of AF18, AF18-NC and the K. pneumoniae strain. (D) Up- and down- regulated genes in AF18 when compared to the transcriptome of AF18-NC. Figure 3 The circular map of pAF18_2 and comparison to similar plasmids The outmost slot represents the predicted genes of pAF18_2, whose functions are shown in different color arrows. From outward, slot 2- 11 indicate aligned fragments from similar plasmids of IncN. Slot 12, GC content; slot 13, GC skew. Accession numbers of plasmids from outer to inner were: AP018758.1, KF914891.1, KC788405.1, KX928750.1, CP028486.1, CP026277.1, KM660724.1, CP026179.1, CP026198.1, KT989599.1. The circular map of pAF18_2 and comparison to similar plasmids The outmost slot represents the predicted genes of pAF18_2, whose functions are shown in different color arrows. From outward, slot 2- 11 indicate aligned fragments from similar plasmids of IncN. Slot 12, GC content; slot 13, GC skew. Accession numbers of plasmids from outer to inner were: AP018758.1, KF914891.1, KC788405.1, KX928750.1, CP028486.1, CP026277.1, KM660724.1, CP026179.1, CP026198.1, KT989599.1. Page 23/25 Fi 4 TableS3.docx Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. TableS3.docx Page 24/25 FigureS2.jpg TableS2e.xlsx FigureS1.tif FigureS3.tif TableS5.docx TableS1.docx TableS4.docx Page 24/25 Page 24/25 FigureS2.jpg TableS2e.xlsx FigureS1.tif FigureS3.tif TableS5.docx TableS1.docx TableS4.docx Page 25/25
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https://cyberleninka.ru/article/n/the-concept-of-the-frontier-its-linguistic-and-cultural-significance-in-american-english/pdf
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THE CONCEPT OF THE FRONTIER: ITS LINGUISTIC AND CULTURAL SIGNIFICANCE IN AMERICAN ENGLISH
Vestnik Moskovskogo gosudarstvennogo oblastnogo universiteta. Seriâ Lingvistika/Vestnik Moskovskogo gosudarstvennogo oblastnogo universiteta. Seriâ: Lingvistika
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ÐÀÇÄÅË I. ÒÅÎÐÈß ßÇÛÊÀ УДК 811.111(73) DOI: 10.18384/2310-712X-2019-4-7-12 THE CONCEPT OF THE FRONTIER: ITS LINGUISTIC AND CULTURAL SIGNIFICANCE IN AMERICAN ENGLISH L. Baranova Lomonosov Moscow State University 1 Leninskie gory, Moscow 119991, Russian Federation Abstract. The article deals with the linguistic and cultural aspects of the concept in question. Special emphasis is made on the importance of diachronic and synchronic approach to the issue under consideration. Otherwise stated, the article is concerned with some features of the formation and evolution of the concept of the Frontier in American English, the modern state of affairs in so far as the Frontier is concerned, as well as the significance of its awareness in understanding the conceptual and linguistic worldview of the Americans. Turning to authoritative dictionaries and reference books, the author gives a concrete definition of the word “Frontier” in American English, as well as the interpretation of the term “concept” used in the article. Numerous examples illustrate the influence of the above-mentioned concept on the vocabulary of the American variant of English. Several lexical strata which have appeared as a result of the westward movement of the settlers are adduced, namely: words denoting various representatives of flora and fauna; borrowings from American Indian languages; words and word-combinations which have become phraseological units, but which had a concrete material meaning in the 19th century. Besides, a new comprehension of the analyzed concept in the second half of the 20th – the beginning of the 21st century is given. Keywords: concept, Frontier, American studies, worldview, American character. ßÇÛÊÎÂÎÅ È ÊÓËÜÒÓÐÍÎÅ ÇÍÀ×ÅÍÈÅ ÊÎÍÖÅÏÒÀ «ÔÐÎÍÒÈл  ÀÌÅÐÈÊÀÍÑÊÎÌ ÂÀÐÈÀÍÒÅ ÀÍÃËÈÉÑÊÎÃÎ ßÇÛÊÀ Баранова Л. Л. Московский государственный университет имени М. В. Ломоносова 119991, г. Москва, Ленинские горы, д. 1, Российская Федерация1 Аннотация. Статья посвящена языковым и культурным аспектам концепта «Фронтир». Особое внимание уделено важности диахронического и синхронического подходов к изучению данного вопроса: в статье освещаются некоторые черты формирования и эволю© CC BY Баранова Л. Л., 2019. 7 ISSN 2072-8379 Вестник Московского государственного областного университета. Серия: Лингвистика 2019 / № 4 ции рассматриваемого концепта в американском варианте английского языка, а также его значимость при изучении понятийной и языковой картины мира американцев. Обращаясь к авторитетным словарям и справочным изданиям, автор определяет точное значение слова “frontier” в американском английском, а также то понимание термина «концепт», которое используется в статье. Приводятся многочисленные примеры влияния концепта «Фронтир» на словарный состав американского варианта английского языка. Выделяется несколько пластов лексики, появившихся в результате освоения Дикого Запада, а именно: названия из мира флоры и фауны; слова, пришедшие из языков американских индейцев; слова и словосочетания, ставшие фразеологизмами, но имевшие конкретновещественное значение в XIX в., во время передвижения переселенцев на запад. Кроме того, в статье приводится информация о новом осмыслении данного концепта во второй половине XX – начале XXI вв. Ключевые слова: концепт, Фронтир, страноведение США, картина мира, американский характер First and foremost, it is essential to clarify what is meant by the term “concept” in the present paper. Following the definition of the term in The Concise Dictionary of Cognitive Terms, we believe that it is a mental unit of our mind and of the informational structure, reflecting the knowledge and experience of a person. Thus, concepts are directly connected with thinking processes and with our perception of the world, or worldview1. Next, it is necessary to understand the meaning of the word “frontier”. For example, in Collins COBUILD Dictionary it is defined as follows2: 1. The border between two countries. 2. When you are talking about the western part of America before the twentieth century, you use frontier to refer to the area beyond the part settled by Europeans. 3. The frontiers of something, especially knowledge, are the limits to which it extends. …pushing back the frontiers of science. …the frontiers of medicine Interestingly, the word “frontier” is one of the 10000 most commonly used words in the dictionary in question. However, it is the second meaning of the word that is relevant for the present paper. Turning to The Longman Dictionary of English Language and Culture, we can find a related definition of the word3: Frontier – the area where people have never lived before, that not much is known about, especially in the western US before the 20th century. It follows from the definitions adduced above that the concept of the Frontier is inextricably linked with the early history of the USA. When the country was first settled by Puritans, people lived mainly on the Atlantic coast of North America. But they wanted more space and tried to cross the limits of settled territories and go west. However, there were a number of barriers on their way, both geographical and political. Basically, what these people found when they went west was wilder- 1 Концепт // Краткий словарь когнитивных терминов / Е. С. Кубрякова, В. З. Демьянков, Ю. Г. Панкрац, Л. Г. Лузина. М.: МГУ им. М. В. Ломоносова, 1996. С. 90. 2 Frontier // Collins COBUILD Dictionary. London: Harper Collins Publishers, 2006. P. 585. 3 Frontier // The Longman Dictionary of English Language and Culture. Pearson Education Limited, 2005. P. 556. 8 ISSN 2072-8379 Вестник Московского государственного областного университета. Серия: Лингвистика ness, so they had to clear their own land, and build their own homes, and hunt or grow their own food. A family of settlers might be a day’s journey from another family. This pattern created frontier communities that had to rely completely on their own resources. Besides making everything they used themselves, they also developed their own music, folklore, and forms of religious worship. Such a way of life fostered independent philosophy: “I’ll do things for myself ”, “I don’t want anyone dictating what I can do”. In this setting the so-called “frontier spirit” developed. It was marked by toughness, independence, and self-reliance. It is worth mentioning that the frontier spirit has always had an enormous influence on the entire nation. It goes without saying that Frontier is a concept reflecting the national identity of American people, as it has been stated in the works by Professor T. A. Komova and her disciples [1; 3]. One of the outstanding American historians of the late 19th century, F. J. Turner, claimed that the frontier experience had shaped the American character for all time. In his opinion, the geography and environment of America – particularly the westward expansion and the availability of free land – formed American attitudes and institutions. These peculiarities of the American character are as follows: 1. A spirit of adventurous enterprise: a willingness to go through any hardship or danger to accomplish an object. 2. Independence of thought and action. 3. An apparent roughness, which some would consider to be rudeness of manners. 2019 / № 4 4. An American is always whispering to himself: “I ought to do better” [5]. It should be added that many values and attitudes – good or bad – of presentday America can be traced back to the frontier experience. The frontier stressed values of ruggedness, resourcefulness, and self-reliance. Thus, the frontier spirit is also closely connected with the concept of individualism, one of the underlying concepts of the American worldview. It is what Ralph Waldo Emerson, the leader of American Transcendentalists, referred to as “rugged individualism” [4, p. 60]. Developing this idea, the authors of the book “Impressions. America Through Academic Readings” state that the Americans are individualistic by nature, and this trait is traced back to the frontier experience [2, p. 13]: “Americans almost always express a strong preference for individual rather than group values… The emphasis on individualism means that Americans do not like to depend on others. They prefer to solve problems or make decisions themselves. Another trait of American individualism is distrust of the government. Some political observers believe this distrust came from the frontier experience. The Americans who moved west to the wild frontier were cut off from the political system. Organized government was far away. As a result, people had to survive on their own. In such an environment, self-reliance and individualism became important”. Besides, the linguistic significance of the westward movement cannot be overestimated. For example, the famous American explorers, Meriwether Lewis and William Clark, introduced over 2000 9 ISSN 2072-8379 Вестник Московского государственного областного университета. Серия: Лингвистика words in American English while travelling through the Wild West. Among these words one can mention “buffalo” (the word was known in England, but used in a different meaning – “буйвол”), “rattle-snake” (named so because of the sound it produced with the end of its tail), “rapids” (used as a noun “пороги реки, участки реки с быстрым течением”, formerly used as an adjective), “elk” (which in England meant “лось”, but in America was used to refer to a different animal – “олень вапити”), “mocking-bird” (this name was derived from the bird’s habit to imitate other birds’ songs). Quite a number of words were borrowed from American Indian languages: “moccasin”, “maize”, “opossum”, “toboggan”, “pemmican” (a mixture of meat, fat and berries). But this was just the beginning. The country was on the move and on the make. As gambling was one of the favourite pastimes of frontiersmen, a few typically American idioms sprang from this activity: “to pass the buck” (from a buckhorn knife, showing who was dealing the cards), “deal” (square deal. fair deal, New Deal, no big deal), “to have an ace up your sleeve”, “to keep a poker face”, “to scoop the jackpot”. Gambling and drinking spread across the West, together with the new words: “saloon”, “bartender”, “bootlegging” (comes from a habit of hiding a flat bottle of whiskey in a leg of a boot to be sold illegally to the natives). Certainly, frontiersmen encountered American Indians on their way west, and tensions between the two grew, adding a number of words and expressions to American English: “sculp” (a well-known English noun became a rather frightening American English verb), “tomahawk”, “war dance”, “war path”. “long knives” (a name for white men), “fire water” (a name 2019 / № 4 for alcohol). Some colloquial expressions in American English are, in fact, literal translations from American Indian languages, for example, “no can do”, “long time no see”. It is interesting to mention that a slang word for dollar “buck” is derived from buckskin – a standard unit of trade between American Indians and Europeans. One more aspect of the concept of Frontier is connected with the fact that the westward expansion was an epic journey full of hardships imposed by the distance and the weather. Frontiersmen distilled their experience through their stories, often mixing fact and fiction. This is manifested in such idioms as “tall talk” (хвастовство, бахвальство, небылицы), “to kick the bucket”, “to face the music”, “to bark up the wrong tree”, “to be in cahoots with someone”, “to stake one’s claim”, “to strike it lucky/rich”. Even in the 20th and 21st centuries Frontier continues to play an important role in the USA. Politicians have praised the frontier life. Songs and stories have described it in glowing terms. Frontier heroes, such as Daniel Boone, Meriwether Lewis and William Clark, David Crockett, have been admired by generations of the Americans. The Frontier has been described as “wild”, “final”, “new”. For example, the term “New Frontier” was used by John F. Kennedy in his acceptance speech in 1960. It was the time when the Americans were somewhat piqued by the fact that the Soviet Union outdid them in its space exploration programme. The future president of the USA promised his citizens to catch up with America’s rival: “We stand today on the edge of a New Frontier – the frontier of the 1960s, the frontier of unknown opportunities and perils, the frontier of unfilled hopes and 10 ISSN 2072-8379 Вестник Московского государственного областного университета. Серия: Лингвистика 2019 / № 4 sent it can refer not only to the westward movement of the settlers, but also to quite a few other notions, as well as artifacts – knives, guns, airlines, cars, articles of clothing, TV series. Thus, on the one hand it seems that the grand conquest of the West deteriorated into being exploited by popular culture. However, looking at it from a different perspective, it may be said that it has left an indelible mark on the American character, having shaped it for all time. unfilled threats… Beyond that frontier are uncharted areas of science and space, unsolved problems of peace and war, unconquered problems of ignorance and prejudice, unanswered questions of poverty and surplus”1. Later the term “New Frontier” developed further to refer to the Kennedy administration’s domestic and foreign programmes. To conclude: The Frontier is one of the underlying concepts of the American conceptual and linguistic worldview. At pre- Статья поступила в редакцию 11.06.2019 ЛИТЕРАТУРА 1. Ма Т. Ю. Национальное самосознание в контексте языка и культуры (на материале американского варианта английского языка): дис. … канд. филол. наук. М., 2001. 186 с. 2. Benz C., Benz S. Impressions. America Through Academic Readings. Boston, MA: Thomson Heinle, 2008. 157 p. 3. Komova T. A. On British/American Cultural Studies. Moscow: Moscow University Press, 2000. 167 p. 4. Mitchell C. E. Individualism and Its Discontents. Appropriation of Emerson. 1880–1950. Amherst: University of Massachusetts Press, 1997. 219 p. 5. Turner F. J. The Frontier in American History. New York: Dover Publications: Mineola, 2010. 174 p. REFERENCES 1. Ma T. Yu. Natsional'noe samosoznanie v kontekste yazyka i kul'tury (na materiale amerikanskogo varianta angliiskogo yazyka): dis. … kand. filol. nauk [National identity in the context of language and culture (study of American English): PhD thesis in Philological Sciences]. Moscow, 2001. 186 p. 2. Benz C., Benz S. Impressions. America Through Academic Readings. Boston, MA, Thomson Heinle, 2008. 157 p. 3. Komova T. A. On British/American Cultural Studies. Moscow, Moscow University Press, 2000. 167 p. 4. Mitchell C. E. Individualism and Its Discontents. Appropriation of Emerson. 1880–1950. Amherst, University of Massachusetts Press, 1997. 219 p. 5. Turner F. J. The Frontier in American History. New York, Dover Publications, Mineola, 2010. 174 p. 1 1 Kennedy J. F. Excerpt, 1960 Democratic National Convention, 15 July 1960. Los Angeles [Электронный ресурс]. URL: https://www.jfklibrary.org/learn/about-jfk/historic-speeches/acceptance-of-democratic-nomination-for-president (дата обращения: 10.01.2019). 11 ISSN 2072-8379 Вестник Московского государственного областного университета. Серия: Лингвистика 2019 / № 4 ИНФОРМАЦИЯ ОБ АВТОРЕ Баранова Людмила Львовна – доктор филологических наук, профессор кафедры английского языкознания филологического факультета Московского государственного университета имени М. В. Ломоносова; e-mail: ludbar2000@gmail.com INFORMATION ABOUT THE AUTHOR Ludmila L. Baranova – Doctor in Philological Sciences, Professor at the Department of English Linguistics, Faculty of Philology, Lomonosov Moscow State University; e-mail: ludbar2000@gmail.com ПРАВИЛЬНАЯ ССЫЛКА НА СТАТЬЮ Баранова Л. Л. Языковое и культурное значение концепта «фронтир» в американском варианте английского языка // Вестник Московского государственного областного университета. Серия: Лингвистика. 2019. № 4. С. 7–12. DOI: 10.18384/2310-712X-2019-4-7-12 FOR CITATION Baranova L. L. The concept of the frontier: its linguistic and cultural significance in American English. In: Bulletin of Moscow Region State University. Series: Linguistics, 2019, no. 4, рр. 7–12. DOI: 10.18384/2310-712X-2019-4-7-12 12
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https://journals.library.brocku.ca/index.php/voixplurielles/article/download/1564/1429
fr
L’heureux, Lisa. Pour l’hiver
Voix plurielles
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Voix plurielles 14.1 (2017) 158 L’heureux, Lisa. Pour l’hiver. Sudbury : Prise de parole, 2016. 106 p. Trois personnages, de trois époques différentes, se rencontrent sur scènes, amalgament leurs histoires et superposent leurs discours. Bernard a quinze ans ; il est seul, en retenue dans la bibliothèque de son école ; on est en 1955. En 1982, Valérie, âgée de seize ans, est au poste de police pour un interrogatoire. Arthur, lui, vit « aujourd’hui » ; il a trente ans et sa mère vient de mourir. Les personnages se croisent, s’affrontent et s’ignorent dans les vingt-trois scènes qui composent cette nouvelle pièce de théâtre de Lisa L’Heureux. Toutefois, ils demeurent cloisonnés dans leurs questions et leurs pensées. La solitude de Bernard est celle de l’exclu : « Quelle honte / Quelle humiliation / Comme si ce n’était pas déjà assez d’être enfermé ici entre ces quatre murs / Comme un ours en cage / Alors que vous êtes tous là / De l’autre côté du mur / A rire de moi / A me pointer du doigt en me traitant de tous les noms possibles ». L’isolement de Valérie est d’ordre social : « On souffre en banlieue / Avec nos sourires plaqués en pleine face pis nos maisons toutes pareilles [,,,] / La guerre est interne la violence est secrète / C’est pas nos voisins qui nous entendent hurler / Cracher notre désespoir contre les murs de carton / De nos osties de maisons semi-détachées / Qui vont essayer de nous aider ». Arthur est en pleine crise amoureuse : « J’ai plus de blonde qui m’attend dans mon appartement au centre-ville / Parce qu’elle m’a laissé / Comme ça l’autre jour / Pas sans raison mais c’était quand même un choc ». Les trois esseulés s’accordent, par-delà les générations, à définir ce qui est, pour eux « l’enfer » et celui-ci, comme on le sait, est logé chez autrui… ou en son absence. L’isolement de chacun est ainsi leur point commun. Que différentes générations se côtoient dans une fiction qui relève de la fantaisie, et non du possible, renforce en même temps l’impression d’extrême enfermement et celle d’une universalité de sentiments et de situations. Livrés à eux-mêmes, les personnages sont néanmoins propulsés dans des partages qui les désarment en sautant d’une époque à l’autre. Pour l’hiver est l’exploration de conflits qui naissent de ce paradoxe. Gabrielle Bonifaci
https://openalex.org/W4366314494
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The effect of seafood oil omega-3 supplementation on ulcerative colitis remission: A systematic review
Journal of Shahrekord University of Medical Sciences
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Journal of Shahrekord University of Medical Sciences 2023;25(2):104-110 http://j.sku 4172/jsums.2023.761 http://j.skums.ac.ir http://j.skums.ac.ir doi: 10.34172/jsums.2023.761 © 2023 The Author(s); Published by Shahrekord University of Medical Sciences. 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. Abstract In addition, supplementation with this oil could decrease free radicals at the cellular level and subsequently increase antioxidant activity, which also mediates the inflammatory process itself. y p Keywords: Omega-3, Fish oil, Ulcerative colitis, Inflammatory bowel disease Received: July 31, 2022, Accepted: August 13, 2022, ePublished: February 19, 2023 Received: July 31, 2022, Accepted: August 13, 2022, ePublished: February 19, 2023 Hossein Mardani-Nafchi1 ID , Atieh Mohammadi-Nafchi2* ID Hossein Mardani-Nafchi1 ID , Atieh Mohammadi-Nafchi2* ID 1Deputy of Food and Drug, Shahrekord University of Medical Sciences, Shahrekord, Iran 2MSc of Mathematical Statistics, Shahid Beheshti University of Medical Sciences, Shahid Beheshti, Iran *Corresponding Author: Atieh Mohammadi-Nafchi, Email: atiyehmoh77@gmail.com Introduction UC treatment challenges (10). Given that food enters the digestive system, it can be mentioned that diet can affect exacerbate or reduce the symptoms of UC, one of the most important of which is seafood (2). Studies show that seafood omega-3, which consists of eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) are inversely associated with UC symptoms (11-13). Nonetheless, given insufficient data and controversial results to recommend the use of omega-3 fatty acids for the remission of UC reported in a previous systematic review and a meta- analysis (14,15), this meta-analysis aimed to investigate the effect of seafood oil omega-3 supplementation on UC remission. Ulcerative colitis (UC) is a recurrent, idiopathic, and chronic disease that is considered a subtype of inflammatory bowel disease (IBD). UC is characterized by the inflammation of the gastrointestinal tract, commonly the innermost part of the colon (1), and leads to abdominal pain, bloating, diarrhea and rectal bleeding, digestive disorders, weight loss, and ultimately an impaired health- related quality of life at younger ages (2,3). Thus, it can disrupt the daily activities of affected people, including their work, school, social relationships, and daily life (4,5). Mild to moderate symptoms are most frequently reported, but in some cases, they can cause severe cases that require immediate medical attention and hospitalization (6,7). Despite significant advances in UC treatment, some patients are resistant to common treatments (8). On the other hand, these treatments are expensive and sometimes cause severe side effects. For example, corticosteroids are the most common drugs prescribed for the treatment of the disease and are associated with acne, moon face, oedema, glucose intolerance, sleep and mood disturbance, dyspepsia, posterior subcapsular cataracts, osteoporosis, myopathy, and susceptibility to infection (9). Therefore, the use of newer drugs and the study of alternative and natural therapies will be necessary for overcoming the Abstract Abstract Background and aims: Ulcerative colitis (UC) is a prevalent and long-term condition that causes inflammation, irritation, and ulcers in the colon. This systematic review aimed to evaluate the effect of seafood oil omega-3 supplementation on UC remission. Background and aims: Ulcerative colitis (UC) is a prevalent and long-term condition that causes inflammation, irritation, and ulcers in the colon. This systematic review aimed to evaluate the effect of seafood oil omega-3 supplementation on UC remission. Methods: PubMed, EMBASE, Web of Science, and Scopus databases were extensively searched on 25.5.2022 according to the PRISMA checklist The studies were imported into EndNote X9 Data were extracted in Excel form including the first author’s name study setting Background and aims: Ulcerative colitis (UC) is a prevalent and long-term condition that causes inflammation, irritation, and ulcers in the colon. This systematic review aimed to evaluate the effect of seafood oil omega-3 supplementation on UC remission. Methods: PubMed, EMBASE, Web of Science, and Scopus databases were extensively searched on 25.5.2022 according to the PRISMA checklist. The studies were imported into EndNote X9. Data were extracted in Excel form, including the first author’s name, study setting, year of publication, sample size, sea oil type, intervention, and outcomes. Methods: PubMed, EMBASE, Web of Science, and Scopus databases were extensively searched on 25.5.2022 according to the PRISMA checklist. The studies were imported into EndNote X9. Data were extracted in Excel form, including the first author’s name, study setting, year of publication, sample size, sea oil type, intervention, and outcomes. y p p yp Results: Seafood oil omega-3 supplementation reduced the levels of leukotriene B4, interleukin (IL)-2, IL-8, IL-1β, thromboxane A2, prostaglandin E2, scavenges-free radicals, and tumor necrosis factor-α (TNF-α). In addition, supplementation with this oil could decrease free radicals at the cellular level and subsequently increase antioxidant activity, which also mediates the inflammatory process itself. Conclusion: Most studies showed that omega-3 extracted from seafood can reduce inflammation and oxidative stress (OS) in intestinal cells. It also could improve clinical symptoms and scores of histological, sigmoidoscopic, and simple clinical colitis activity index (SCCAI). However, some studies reported no positive effects in this regard and confirmed that these compounds have no effect on improving UC symptoms. y p p yp Results: Seafood oil omega-3 supplementation reduced the levels of leukotriene B4, interleukin (IL)-2, IL-8, IL-1β, thromboxane A2, prostaglandin E2, scavenges-free radicals, and tumor necrosis factor-α (TNF-α). Results Marine oil omega-3 induces various mechanisms to suppress the OS onset and consequently reduce the severity of the inflammatory response. They could have favorable effects by scavenging free radicals, reducing prooxidative enzymes and cytokines, and increasing the antioxidative capabilities of cells (52). Marine oil omega-3 antioxidant activity is related to the level of intracellular antioxidants such as vitamins D and E, mucosal immune response, and genetic susceptibility (52). Search results, study characteristics of selected studies Search results, study characteristics of selected studies The PRISMA flow diagram including database searches is illustrated in Figure 1. The initial electronic search in the mentioned databases retrieved 3314 titles/abstracts. From all retrieved publications, 1854 records were deleted due to duplicate titles. Some other titles/abstracts were excluded (n = 8) as well; two manuscripts were out of the aim of the study (16,17), one IBD study was generally reviewed (18), three records did not have the desired methodology (19-21) and the full text of 2 others could not be retrieved (22,23), and finally, 25 articles were selected for the assessment. OS in UC patients occurred due to the high concentration of reactive oxygen species (ROS) produced in different mechanisms. Increasing OS can harm the oxidation in intestinal cells via a chain reaction that causes the breakage of macromolecules such as proteins, nucleic acid, and lipid structure, as well as lipid peroxidation which can cause the loss of polyunsaturated fatty acids (PUFAs) and the loss of enzymatic activity and receptors in the intestinal membrane, leading to the infraction of membrane integrity and finally disrupting the action of epithelial cells (15,36). The infiltration of the mucosal tissue with activated phagocytic immune cells causing the production of ROS and nitrogen species leads to a shift toward prooxidants. It disrupts cellular homeostasis by distracting key macromolecules and attributing to cell injury and elevated permeability of the mucosal barrier, thus precipitating and maintaining ongoing inflammation (53). Thus, antioxidants such as marine oil omega-3 can downregulate the inducible isoforms of nitric oxide, myeloperoxidase, lipoxygenases, cyclooxygenase, and nicotinamide adenine dinucleotide phosphate oxidase. Although there are various drugs such as immunosuppressive agents, 5-ASA agents, and steroids to cure UC, each of them has its own side effects. The results of the study demonstrated that the beneficial effects of omega-3 unsaturated fatty acids (EPA and DHA) are related to the anti-inflammatory effects of these compounds. Data sources and search strategy Data sources and search strategy gy This systematic review method followed PRISMA 2020 statement (http://prisma-statement.org/prismastatement/ Checklist.aspx) so that according to the instructions, an extensive search was undertaken on 25.5.2022 in PubMed, EMBASE, Web of Science, and Scopus databases. In this study, the following keywords were used for searching: ((“ulcerative colitis” OR “colitis gravis” OR “idiopathic proctocolitis” OR “inflammatory bowel disease”) AND (“fish oil” OR “seal oil” OR “marine oil” OR “omega-3” OR © 2023 The Author(s); Published by Shahrekord University of Medical Sciences. 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. Seafood oil omega-3 supplementation on ulcerative colitis “n-3 fatty acid” OR “ω-3 fatty acid” OR “docosahexaenoic acid” OR “docosahexaenoic” OR “eicosapentaenoic” OR “icosapentaenoic acid” OR “eicosapentaenoic acid”)). “n-3 fatty acid” OR “ω-3 fatty acid” OR “docosahexaenoic acid” OR “docosahexaenoic” OR “eicosapentaenoic” OR “icosapentaenoic acid” OR “eicosapentaenoic acid”)). Several mechanisms are associated with the favorable effects of seafood omega-3 on UC. The main mechanisms are as follows: Study selection y The records were imported into EndNote X9 (July 31, 2018, Thomson Reuters) to manage references and remove duplicate publications. Two researchers independently screened the records in terms of titles and abstracts according to the study inclusion and exclusion criteria. The clinical trial studies that addressed the effects of marine oil omega-3 supplementation on UC remission were included in the systematic review. Not retrieving the full text of the articles and being published in non-English languages were considered the exclusion criteria. The full texts of all screened publications were independently evaluated, and any disagreement between the authors was resolved by discussion. A PRISMA flow diagram of the search strategy was used as well. Several pathways are engaged in the inflammation and pathogenicity of UC, including increased interferon-γ, tumor necrosis factor-α (TNF-α), interleukins (ILs) (IL- 4, IL-5, IL-9, IL-17, and IL-22), and reduced levels of IL-10 and transforming growing factor-β (32,49). The main favorable effects of omega-3 as supplementation on UC are related to anti-inflammatory effects. They can induce a change in the synthesis cycle of fatty acids in the cell membrane and reduce arachidonic acid that synthesizes pro-inflammatory cytokines in 5-lipoxygenase and cyclooxygenase pathways (15). The syntheses of leukotriene B4 (LTB4), IL 8, and IL1B, as well as thromboxane A2, prostaglandin E2, scavenges free radicals, and TNF are all decreased in these pathways (15,38,50). Moreover, they can decrease the chemotaxis of T-cell and leukocyte reactivity and the activation of NF-κB (50,51). In this study, seafood omega-3 suppressed the synthesis of leukotriene B4, which is an important mediator of inflammation and a stimulus for neutrophil chemotaxis in IBD (26,27). Data extraction and quality assessment Studies were independently extracted and selected by two researchers. The data were extracted from the articles and recorded in Excel form, including the first author’s name, study setting, year of publication, sample size, sea oil type, intervention, and outcomes. Results These effects are induced by making changes in the synthesis of fatty acids in the intestinal cells. In addition to reducing pro-inflammatory factors, omega-3 can be effective in improving UC symptoms by reducing the level of free radicals and antioxidant activities. Based on data in Table 1, the results of the reviewed studies mainly emphasized that omega-3 sea oils remission effects on UC are associated with the reduction of clinical symptoms, disease-related complications, and the reduction of inflammatory cytokines and oxidative stress (OS). Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 10 105 Mardani-Nafchi and Mohammadi-Nafchi Figure 1. Flow diagram for including studies in the systematic review Records identified from databases (n = 3314) PubMed: 331 EMBASE: 1308 Web of Science: 657 Scopus: 1018 Records removed before screening: Duplicate records removed (n = 1854) Records marked as ineligible by automation tools (n = 0) Records removed for other reasons (n = 941) Records screened (n = 519) Records excluded (n = 487) Reports sought for retrieval (n = 32) Reports not retrieved (n = 2) Reports assessed for eligibility (n = 30) Reports excluded: 5 Irrelevant aim of the study (n = 3) Not having the desired methodology (n = 2) Studies included in the review (n = 25) Identification of Studies via Databases and Registers Identification Screening Included Identification of Studies via Databases and Registers Reports assessed for eligibility (n = 30) Studies included in the review (n = 25) Figure 1. Flow diagram for including studies in the systematic review Figure 1. Flow diagram for including studies in the systematic review Table 1. Characteristics of clinical trials included in this systematic review First Author Year Country Sample Size Marine omega-3 Intervention Outcome Lorenz (24) 1989 Germany 39 Fish oil 3 of the 1.2 mL fish oil capsules for 3 months. After 4 weeks, they received capsules for 7 months Clinical disease activity did not change statistically. Results A moderate fall in inflammatory lipid mediators by dietary n-3 fatty acids and a little morphological improvement in chronic IBD were observed Salomon (25) 1990 USA 10 Fish oil 15 capsules of EPA (containing 2.7 g) daily in three divided doses for 8 weeks Although some patients had an improvement in their symptoms, there was no change in some patients, and at least their condition did not worsen Hawthorne (26) 1992 UK 87 Fish oil Fish oil, 10 mL twice daily for a year Fish oil supplementation in UC patients works somewhat like corticosteroids but does not affect maintenance therapy. In addition, it synthesized detectable amounts of leukotriene B5 and suppressed leukotriene B4 Stenson (27) 1992 USA 18 Fish oil Fish oil containing 18 Max-EPA (EPA 3.24) capsules daily and DHA, 2.16 g) for 4 months Supplementation decreased rectal dialysate levels of leukotriene B4 and produced a modest corticosteroid- sparing effect on UC patients, but there was no benefit in maintenance therapy Greenfield (28) 1993 UK 43 Fish oil Max-EPA at 3 months by 3-fold and 6 months by 4 folds Improvements were observed in the acute histology index and total histology Loeschke (29) 1996 Germany 64 Fish oil 2 capsules contained fish oil (5.1 g/d n-3 fatty acids) for 3 months Actuarial relapse-free survival was ameliorated only during months 2 and 3 Campbell (30) 1997 USA 24 Fish oil The formula includes supplemental oligosaccharides fish oil, and gum arabic for 7 days EPA and DHA were increased in plasma phospholipids and the red blood cells Almallah (31) 1998 UK 18 Fish oil Patients received either fish oil extract (DHA, 2.4 g and EPA, 3.2 g) daily for 6 months Reduced the histological scores and sigmoidoscopic scores and finally improved disease activity Almallah (32) 2000 UK 18 Fish oil 15 mL of fish oil extract (5 mL 3 times a day) for 6 months Reduced NK cell cytotoxic activity, IL-2, and sIL2R Almallah (33) 2000 UK 18 Fish oil Fifteen mL of the fish oil extract (5 mL 3 times a day). This provided a total of 3·2 g of EPA and 2.4 g of DHA for 6 months Reduced the number of cells expressing HLA and CD3 and the percentage of cells containing IgM and improved the histological score Table 1. Characteristics of clinical trials included in this systematic review Clinical disease activity did not change statistically. Decrease fecal levels of calprotectin Decrease fecal levels of calprotectin Decreased necrotizing enterocolitis, the number of patients who needed treatment, and the level of treatment failure Decreased the levels of oxidative and inflammatory markers while increasing antioxidant markers in the serum No change was found in intestinal permeability, calprotectin concentration in gut lavage fluid, and lipid peroxidation. Reduced IBD-associated joint pain Decreased the duration of morning stiffness, intensity of pain, number of tender joints, and the doctor’s scoring of rheumatic disease activity Note. LTB4: Leukotriene B4; IgM: Immunoglobulin M; IBD: Irritable bowel disease; UC: Ulcerative colitis; DHA: Docosahexaenoic acid; EPA: Eicosapentaenoic acid; HLA: Human leukocyte antigens; CD3: Cluster of differentiation 3; ESR: Erythrocyte sedimentation rate; CRP: C-reactive protein; PGE2: Prostaglandin E2; SCCAI: Simple clinical colitis activity index; PUFAs: Polyunsaturated fatty acids; AIFAI: Anti-inflammatory fatty acid index; RBC: Red blood cells. Note. LTB4: Leukotriene B4; IgM: Immunoglobulin M; IBD: Irritable bowel disease; UC: Ulcerative colitis; DHA: Docosahexaenoic acid; EPA: Eicosapentaenoic acid; HLA: Human leukocyte antigens; CD3: Cluster of differentiation 3; ESR: Erythrocyte sedimentation rate; CRP: C-reactive protein; PGE2: Prostaglandin E2; SCCAI: Simple clinical colitis activity index; PUFAs: Polyunsaturated fatty acids; AIFAI: Anti-inflammatory fatty acid index; RBC: Red blood cells. They can also prevent the formation of free radicals by enhancing glutathione peroxidase, catalase, superoxide dismutase, paraoxonase, and peroxiredoxins (46,47,53). They can also prevent the formation of free radicals by enhancing glutathione peroxidase, catalase, superoxide dismutase, paraoxonase, and peroxiredoxins (46,47,53). supplements with fish oil play a role in improving IBD disease outcomes (12). The overall effects of omega-3 seafood are illustrated in Figure 2. Results A moderate fall in inflammatory lipid mediators by dietary n-3 fatty acids and a little morphological improvement in chronic IBD were observed Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 Seafood oil omega-3 supplementation on ulcerative colitis Table 1. Continued. Table 1. Continued. First Author Year Country Sample Size Marine omega-3 Intervention Outcome Dichi (34) 2000 Brazil 10 Fish oil 5.4 g/d of fish oil omega-3 fatty acids (18 capsules) for 2 months, and then 2 g/d of sulfasalazine for 2 months CRP, ESR, and platelet count increased. Moreover, an increase in fecal nitrogen and a reduction in a sigmoidoscopy score were observed Middleton (35) 2002 UK 58 Fish oil Patients received either DHA, 45 mg, per day, 500 mg/d) and trial medication (gamma-linolenic acid (1.6 g, EPA, 270 mg) for 12 months No statistical differences were in the relapse rate and the intake of dietary constituents or adverse events between the groups Barbosa (36) 2003 Brazil 18 Fish oil 4.5 g/d (30 capsules) of fish oil omega-3 fatty acids (omega-3) for 2 months No significant changes were found in any laboratory indicator or the histology scores and sigmoidoscopy. The ESR and oxidative stress represented a decrease Seidner (37) 2005 USA 121 Fish oil 18 oz of formula for 6 months A reduction in the dose of prednisone was required to control clinical symptoms for 6 months Brunborg (38) 2008 Norway 38 Fish oil + seal oil 10 mL of the seal oil (n = 18) or cod liver oil (n = 20) was given orally 3 times/day for 14 days. No significant changes were observed; but, in both groups, the changes in the plasma level of leukotriene B4, joint pain parameters, and serum fatty acid profile were favorable and reduced LTB4 plasma levels Bjørkkjaer (39) 2009 Norway 18 Fish oil + seal oil Seal and whale oils were prescribed 10 mL × 3 daily through a nasoduodenal feeding tube for 10 days in IBD patients Decreased IBD-related joint pain and disease activity. The seal oil reduced the PGE2 level in the plasma Grimstad (40) 2011 Norway 12 Fish oil 200 gr of Atlantic salmon fillet 3 times/ week for 8 weeks The anti-inflammatory fatty acid index was significantly elevated in biopsies and plasma. Based on AIFAI and SCCAI results and a tendency of reduced levels of CRP and homocysteine, UC symptoms improved. Results Scaioli (41) 2015 Italy 35 Fish oil All patients took 2 g EPA-FFA daily as 2 capsules (500 mg PUFAs) 2 times/day with food for 8 weeks The plasma n-3 PUFA levels in IBD patients were significantly increased, and the RBC n-6 PUFA content in IBD patients represented a decrease Prossomariti (42) 2017 Italy 19 Fish oil 2 g/day (90 days supplementation with two 500 mg capsules twice a day) of EPA-FFA Reduced promoted goblet cell differentiation, modulated intestinal microbiota composition, and mucosal inflammation in UC patients Scaioli (43) 2017 Italy 60 Fish oil EPA-FFA (500 mg, 2 bid) for 6 months Fecal calprotectin levels significantly decreased and ameliorated the symptom of the disease Scaioli (44) 2018 Italy 60 Fish oil Patients were administered either 2 g daily of EPA-FFA (2 x 500 mg gastro- resistant sustained-release capsules, twice daily) for 6 months Decrease fecal levels of calprotectin Bernabe-García (45) 2020 Mexico 214 Fish oil 75 mg of DHA/kg body weight for 14 days Decreased necrotizing enterocolitis, the number of patients who needed treatment, and the level of treatment failure Abhari (46) 2020 Iran 70 Algal oil 4.3 g (4800 mg) of omega-3 (4 capsules of 1200 mg)/day for 2 months Decreased the levels of oxidative and inflammatory markers while increasing antioxidant markers in the serum Arslan (47) 2002 Norway 10 Seal oil Seal oil (10 mL) was given 3 times/day No change was found in intestinal permeability, calprotectin concentration in gut lavage fluid, and lipid peroxidation. Reduced IBD-associated joint pain Bjørkkjaer (48) 2004 Norway 19 Seal oil Ten mL of seal oil 3 times daily for 10 days Decreased the duration of morning stiffness, intensity of pain, number of tender joints, and the doctor’s scoring of rheumatic disease activity Note. LTB4: Leukotriene B4; IgM: Immunoglobulin M; IBD: Irritable bowel disease; UC: Ulcerative colitis; DHA: Docosahexaenoic acid; EPA: Eicosapentaenoi acid; HLA: Human leukocyte antigens; CD3: Cluster of differentiation 3; ESR: Erythrocyte sedimentation rate; CRP: C-reactive protein; PGE2: Prostaglandin E2 SCCAI: Simple clinical colitis activity index; PUFAs: Polyunsaturated fatty acids; AIFAI: Anti-inflammatory fatty acid index; RBC: Red blood cells. Outcome CRP, ESR, and platelet count increased. Moreover, an increase in fecal nitrogen and a reduction in a sigmoidoscopy score were observed CRP, ESR, and platelet count increased. Results Moreover, an increase in fecal nitrogen and a reduction in a sigmoidoscopy score were observed No statistical differences were in the relapse rate and the intake of dietary constituents or adverse events between the groups No significant changes were found in any laboratory indicator or the histology scores and sigmoidoscopy. The ESR and oxidative stress represented a decrease A reduction in the dose of prednisone was required to control clinical symptoms for 6 months Decreased IBD-related joint pain and disease activity. The seal oil reduced the PGE2 level in the plasma The anti-inflammatory fatty acid index was significantly elevated in biopsies and plasma. Based on AIFAI and SCCAI results and a tendency of reduced levels of CRP and homocysteine, UC symptoms improved. The anti-inflammatory fatty acid index was significantly elevated in biopsies and plasma. Based on AIFAI and SCCAI results and a tendency of reduced levels of CRP and homocysteine, UC symptoms improved. The plasma n-3 PUFA levels in IBD patients were significantly increased, and the RBC n-6 PUFA content in IBD patients represented a decrease Reduced promoted goblet cell differentiation, modulated intestinal microbiota composition, and mucosal inflammation in UC patients Fecal calprotectin levels significantly decreased and ameliorated the symptom of the disease Discussion This systematic review aimed to investigate the effect of omega-3 marine oil on UC remission. Most studies showed that omega-3 extracted from seafood can reduce inflammation and OS in intestinal cells. It also improves the clinical symptoms and scores of histological, sigmoidoscopic, and SCCAI. However, some studies did not report such positive effects; they demonstrated that these compounds have no effect on improving UC symptoms. Turner et al revealed that there was no difference in the relapse rate between the fish oil omega-3 Some studies indicated that seafood omega-3 reduces the histological score, simple clinical colitis activity index (SCCAI), and sigmoidoscopic scores, and finally improves patients’ situation (31,33,34,36). Other studies reported that corticosteroid doses during treatment with the fish oil were decreased as well (37,40). In summary, seafood-derived omega-3 PUFAs can improve the clinical and laboratory findings of the disease and interact with the gut microbiota to promote the homeostasis of the gut immune system. Therefore, in general, dietary Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 107 107 Mardani-Nafchi and Mohammadi-Nafchi Figure 2. Effects and Mechanisms of Seafood Omega-3 Supplementation on the UC. Note. UC: Ulcerative colitis; LB4: Leukotriene B4; IL2: Interleukin 2; PE2: Prostaglandin E2 Sea foods Omega3 A reduce in clinical symptoms A reduce in inflammation and remission ulcerative colitis symptoms A reduce in inflammatory cytokines by reducing LTB4, IL2, IL 8 and IL1B, thromboxane A2, and E2 (PE2) A reduce in oxidative stress by reducing cellular ROS and suppressing lipid peroxidation Sea foods Omega3 A reduce in inflammatory cytokines by reducing LTB4, IL2, IL 8 and IL1B, thromboxane A2, and E2 (PE2) A reduce in clinical symptoms A reduce in oxidative stress by reducing cellular ROS and suppressing lipid peroxidation A reduce in inflammation and remission ulcerative colitis symptoms Figure 2. Effects and Mechanisms of Seafood Omega-3 Supplementation on the UC. Note. UC: Ulcerative colitis; LB4: Leukotriene B4; IL2: Interleukin 2; PE2 Prostaglandin E2 Author Contributions C li i H Author Contributions Conceptualization: Hossein Mardani-Nafchi. Data curation: Atieh Mohammadi-Nafchi. Investigation: Hossein Mardani-Nafchi. Methodology: Hossein Mardani-Nafchi. Project administration: Hossein Mardani-Nafchi. Resources: Atieh Mohammadi-Nafchi. Supervision: Atieh Mohammadi-Nafchi. Writing – original draft: Hossein Mardani-Nafchi, Atieh Mohammadi-Nafchi. Writing – review & editing: Hossein Mardani-Nafchi, Atieh Mohammadi-Nafchi. Conceptualization: Hossein Mardani-Nafchi. Data curation: Atieh Mohammadi-Nafchi. Project administration: Hossein Mardani-Nafchi. Resources: Atieh Mohammadi-Nafchi. Writing – original draft: Hossein Mardani-Nafchi, Atieh Mohammadi-Nafchi. Writing – review & editing: Hossein Mardani-Nafchi, Atieh Mohammadi-Nafchi. Writing – review & editing: Hossein Mardani-Nafchi, Atieh Mohammadi-Nafchi. Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 108 Conclusion supplementation group and control groups. They further indicated that higher rates of symptoms of the upper gastrointestinal tract and diarrhea were observed in the intervention group. Therefore, insufficient data were obtained to recommend the use of omega-3 fatty acids for remission symptoms in UC patients (14). Another review represented that diet and nutritional supplements that contribute to the development of an optimal gut microbial community hold promising effects on reducing intestinal inflammation associated with IBD. More studies are probably needed to determine the mechanisms of these nutritional supplements, including fish oil (12). One study evaluated the effects of omega-3 fatty acids on UC and reported controversial results in this regard while not conclusively stating that taking omega-3 PUFA supplementation is beneficial in the treatment of UC. This study highlighted the need for further studies in this area (15). The reasons for the difference in the results of the studies and some existing discrepancies can be due to different dosages of supplementation, different methodologies of the studies, poor absorption of sea omega-3, different chemical formulations, and poor patient adherence to the treatment (54). Overall, it was found that omega-3 extracted from seafood can reduce inflammation and OS in intestinal cells. It could also improve the clinical symptoms and scores of histological, sigmoidoscopic, and SCCAI. However, some studies reported no positive effects but indicated that these compounds have no effect on improving UC symptoms. More studies are needed to obtain clearer and more accurate results on the effects of omega-3 extracted from seafood on UC. gasn.2016.14.8.39. gasn.2016.14.8.39. gasn.2016.14.8.39. Ann Gastroenterol. 2020;33(2):125-33. doi: 10.20524/ aog.2020.0457. Ann Gastroenterol. 2020;33(2):125-33. doi: 10.20524/ aog.2020.0457. 18. 18. Bjørkkjaer T, Brun JG, Valen M, Arslan G, Lind R, Brunborg LA, et al. Short-term duodenal seal oil administration normalised n-6 to n-3 fatty acid ratio in rectal mucosa and ameliorated bodily pain in patients with inflammatory bowel disease. Lipids Health Dis. 2006;5:6. doi: 10.1186/1476-511x-5-6. 2. Seyedian SS, Nokhostin F, Malamir MD. A review of the diagnosis, prevention, and treatment methods of inflammatory bowel disease. J Med Life. 2019;12(2):113-22. doi: 10.25122/ jml-2018-0075. 19. Meister D, Ghosh S. Effect of fish oil enriched enteral diet on inflammatory bowel disease tissues in organ culture: differential effects on ulcerative colitis and Crohn’s disease. World J Gastroenterol. 2005;11(47):7466-72. doi: 10.3748/ wjg.v11.i47.7466. 3. Habibi F, Habibi ME, Gharavinia A, Baradaran Mahdavi S, Akbarpour MJ, Baghaei A, et al. Quality of life in inflammatory bowel disease patients: a cross-sectional study. J Res Med Sci. 2017;22:104. doi: 10.4103/jrms.JRMS_975_16. 4. Chaudhry NA, Pham A, Flint A, Molina I, Zaidi Z, Zimmermann EM, et al. College students with inflammatory bowel disease: a qualitative study of challenges associated with college transition and self-care. Health Equity. 2020;4(1):190-7. doi: 10.1089/heq.2019.0053. 20. Chiu CY, Gomolka B, Dierkes C, Huang NR, Schroeder M, Purschke M, et al. Omega-6 docosapentaenoic acid-derived resolvins and 17-hydroxydocosahexaenoic acid modulate macrophage function and alleviate experimental colitis. Inflamm Res. 2012;61(9):967-76. doi: 10.1007/s00011-012- 0489-8. 5. Kim YS, Jung SA, Lee KM, Park SJ, Kim TO, Choi CH, et al. Impact of inflammatory bowel disease on daily life: an online survey by the Korean Association for the Study of Intestinal Diseases. Intest Res. 2017;15(3):338-44. doi: 10.5217/ ir.2017.15.3.338. 21. Klek S, Mankowska-Wierzbicka D, Scislo L, Walewska E, Pietka M, Szczepanek K. High dose intravenous fish oil reduces inflammation-a retrospective tale from two centers. Nutrients. 2020;12(9):2865. doi: 10.3390/nu12092865. 6. Rubin DT, Traboulsi C, Rai V. A practical clinical approach to the management of high-risk ulcerative colitis. Gastroenterol Hepatol (N Y). 2021;17(2):59-66. 22. Aslan A, Triadafilopoulos G. Fish oil fatty acid supplementation in active ulcerative colitis: a double-blind, placebo-controlled, crossover study. Am J Gastroenterol. 1992;87(4):432-7. 7. Kayal M, Shah S. Ulcerative colitis: current and emerging treatment strategies. J Clin Med. 2019;9(1):94. doi: 10.3390/ jcm9010094. 23. Mantzaris GJ, Archavlis E, Zografos C, Petraki K, Spiliades C, Triantafyllou G. A prospective, randomized, placebo- controlled study of fish oil in ulcerative colitis. Hellenic J Gastroenterol. 1996;9(2):138-41. 8. gasn.2016.14.8.39. Porter RJ, Kalla R, Ho GT. Ulcerative colitis: recent advances in the understanding of disease pathogenesis. F1000Res. 2020;9:F1000 Faculty Rev-294. doi: 10.12688/ f1000research.20805.1. 24. Lorenz R, Weber PC, Szimnau P, Heldwein W, Strasser T, Loeschke K. Supplementation with n-3 fatty acids from fish oil in chronic inflammatory bowel disease--a randomized, placebo-controlled, double-blind cross-over trial. J Intern Med Suppl. 1989;731:225-32. doi: 10.1111/j.1365-2796.1989. tb01461.x. 9. Probert C. Steroids and 5-aminosalicylic acids in moderate ulcerative colitis: addressing the dilemma. Therap Adv Gastroenterol. 2013;6(1):33-8. doi: 10.1177/1756283x12461395. 25. Salomon P, Kornbluth AA, Janowitz HD. Treatment of ulcerative colitis with fish oil n--3-omega-fatty acid: an open trial. J Clin Gastroenterol. 1990;12(2):157-61. doi: 10.1097/00004836-199004000-00009. 10. Fukuda T, Naganuma M, Kanai T. Current new challenges in the management of ulcerative colitis. Intest Res. 2019;17(1):36- 44. doi: 10.5217/ir.2018.00126. 11. Carreras-Torres R, Ibáñez-Sanz G, Obón-Santacana M, Duell EJ, Moreno V. Identifying environmental risk factors for inflammatory bowel diseases: a Mendelian randomization study. Sci Rep. 2020;10(1):19273. doi: 10.1038/s41598-020- 76361-2. 26. Hawthorne AB, Daneshmend TK, Hawkey CJ, Belluzzi A, Everitt SJ, Holmes GK, et al. Treatment of ulcerative colitis with fish oil supplementation: a prospective 12 month randomised controlled trial. Gut. 1992;33(7):922-8. doi: 10.1136/gut.33.7.922. 12. Wellington VNA, Sundaram VL, Singh S, Sundaram U. Dietary supplementation with vitamin D, fish oil or resveratrol modulates the gut microbiome in inflammatory bowel disease. Int J Mol Sci. 2021;23(1):206. doi: 10.3390/ijms23010206. 27. Stenson WF, Cort D, Rodgers J, Burakoff R, DeSchryver- Kecskemeti K, Gramlich TL, et al. Dietary supplementation with fish oil in ulcerative colitis. Ann Intern Med. 1992;116(8):609- 14. doi: 10.7326/0003-4819-116-8-609. 13. Chan SS, Luben R, Olsen A, et al. Association between high dietary intake of the n-3 polyunsaturated fatty acid docosahexaenoic acid and reduced risk of Crohn’s disease. Aliment Pharmacol Ther. 2014;39(8):834-842. doi:10.1111/ apt.12670. 28. Greenfield SM, Green AT, Teare JP, Jenkins AP, Punchard NA, Ainley CC, et al. A randomized controlled study of evening primrose oil and fish oil in ulcerative colitis. Aliment Pharmacol Ther. 1993;7(2):159-66. doi: 10.1111/j.1365- 2036.1993.tb00085.x. 14. Turner D, Shah PS, Steinhart AH, Zlotkin S, Griffiths AM. Maintenance of remission in inflammatory bowel disease using omega-3 fatty acids (fish oil): a systematic review and meta-analyses. Inflamm Bowel Dis. 2011;17(1):336-45. doi: 10.1002/ibd.21374. 29. Loeschke K, Ueberschaer B, Pietsch A, Gruber E, Ewe K, Wiebecke B, et al. n-3 fatty acids only delay early relapse of ulcerative colitis in remission. Dig Dis Sci. 1996;41(10):2087- 94. doi: 10.1007/bf02093614. 15. Hassanshahi N, Masoumi SJ. Seafood oil omega-3 supplementation on ulcerative colitis Seafood oil omega-3 supplementation on ulcerative colitis Conflict of Interests We declare that we have no conflict of interests. Omega-3 and its relevant PUFAs are generally safe with benign side effects, including dyspepsia, diarrhea, nausea, eructation, gas, arthralgia, and fishy taste (55). Ethical Approval Not applicable. Funding/Support Nil. References 1. Andreou NP, Legaki E, Gazouli M. Inflammatory bowel disease pathobiology: the role of the interferon signature. One of the limitations of the present study was the investigation of omega-3 from seafood, which may have different doses of omega-3 or different bioavailability rates based on the type of fish or seafood. On the other hand, a comprehensive and detailed review of the studies conducted according to the purpose of the study was one of the strengths of this study. Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 108 108 gasn.2016.14.8.39. The effect of omega-3 fatty acids in ulcerative colitis: a systematic review. Int J Nutr Sci. 2018;3(2):58-64. 30. Campbell JM, Fahey GC Jr, Demichele SJ, Garleb KA. Metabolic characteristics of healthy adult males as affected by ingestion of a liquid nutritional formula containing fish oil, oligosaccharides, gum Arabic and antioxidant vitamins. Food Chem Toxicol. 1997;35(12):1165-76. doi: 10.1016/s0278- 6915(97)00104-x. 16. Zhang T, Li G, Duan M, Lv T, Feng D, Lu N, et al. Perioperative parenteral fish oil supplementation improves postoperative coagulation function and outcomes in patients undergoing colectomy for ulcerative colitis. JPEN J Parenter Enteral Nutr. 2022;46(4):878-86. doi: 10.1002/jpen.2269. 31. Almallah YZ, Richardson S, O’Hanrahan T, Mowat NA, Brunt PW, Sinclair TS, et al. Distal procto-colitis, natural cytotoxicity, and essential fatty acids. Am J Gastroenterol. 1998;93(5):804- 9. doi: 10.1111/j.1572-0241.1998.229_a.x. 17. McNelly AS, Nathan I, Monti M, Grimble GK, Norton C, Bredin F, et al. The effect of increasing physical activity and/or omega-3 supplementation on fatigue in inflammatory bowel disease. Gastrointest Nurs. 2016;14(8):39-50. doi: 10.12968/ 32. Almallah YZ, El-Tahir A, Heys SD, Richardson S, Eremin O. Distal procto-colitis and n-3 polyunsaturated fatty Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 10 109 Mardani-Nafchi and Mohammadi-Nafchi acids: the mechanism(s) of natural cytotoxicity inhibition. Eur J Clin Invest. 2000;30(1):58-65. doi: 10.1046/j.1365- 2362.2000.00581.x. 43. Scaioli E, Sartini A, Bellanova M, Campieri M, Festi D, Bazzoli F, et al. Highly purified eicosapentaenoic acid, as free fatty acid, reduces fecal calprotectin levels and prevents clinical relapse in ulcerative colitis patients: a double-blind, randomized, placebo controlled trial. J Crohns Colitis. 2017;11(Suppl 1):S376. doi: 10.1093/ecco-jcc/jjx002.705. 33. Almallah YZ, Ewen SW, El-Tahir A, Mowat NA, Brunt PW, Sinclair TS, et al. Distal proctocolitis and n-3 polyunsaturated fatty acids (n-3 PUFAs): the mucosal effect in situ. J Clin Immunol. 2000;20(1):68-76. doi: 10.1023/a:1006698728816. 44. Scaioli E, Sartini A, Bellanova M, Campieri M, Festi D, Bazzoli F, et al. Eicosapentaenoic acid reduces fecal levels of calprotectin and prevents relapse in patients with ulcerative colitis. Clin Gastroenterol Hepatol. 2018;16(8):1268-75.e2. doi: 10.1016/j.cgh.2018.01.036. 34. Dichi I, Frenhane P, Dichi JB, Correa CR, Angeleli AY, Bicudo MH, et al. Comparison of omega-3 fatty acids and sulfasalazine in ulcerative colitis. Nutrition. 2000;16(2):87- 90. doi: 10.1016/s0899-9007(99)00231-2. 35. Middleton SJ, Naylor S, Woolner J, Hunter JO. A double- blind, randomized, placebo-controlled trial of essential fatty acid supplementation in the maintenance of remission of ulcerative colitis. Aliment Pharmacol Ther. 2002;16(6):1131- 5. doi: 10.1046/j.1365-2036.2002.01286.x. 45. gasn.2016.14.8.39. Bernabe-García M, Calder PC, Villegas-Silva R, Rodríguez- Cruz M, Chávez-Sánchez L, Cruz-Reynoso L, et al. Efficacy of docosahexaenoic acid for the prevention of necrotizing enterocolitis in preterm infants: a randomized clinical trial. Nutrients. 2021;13(2):648. doi: 10.3390/nu13020648. 46. Biglari Abhari M, Farokhnezhad Afshar P, Alimoradzadeh R, Mirmiranpour H. Comparing the effect of including omega-3 to treatment regimen in elderly patients with ulcerative colitis with placebo: a randomized clinical tria. Immunopathol Persa. 2020;6(1):e10. doi: 10.15171/ipp.2020.10. 36. Barbosa DS, Cecchini R, El Kadri MZ, Rodríguez MA, Burini RC, Dichi I. Decreased oxidative stress in patients with ulcerative colitis supplemented with fish oil omega-3 fatty acids. Nutrition. 2003;19(10):837-42. doi: 10.1016/s0899- 9007(03)00162-x. 37. Seidner DL, Lashner BA, Brzezinski A, Banks PL, Goldblum J, Fiocchi C, et al. An oral supplement enriched with fish oil, soluble fiber, and antioxidants for corticosteroid sparing in ulcerative colitis: a randomized, controlled trial. Clin Gastroenterol Hepatol. 2005;3(4):358-69. doi: 10.1016/ s1542-3565(04)00672-x. 47. Arslan G, Brunborg LA, Frøyland L, Brun JG, Valen M, Berstad A. Effects of duodenal seal oil administration in patients with inflammatory bowel disease. Lipids. 2002;37(10):935-40. doi: 10.1007/s11745-006-0983-2. 48. Bjørkkjaer T, Brunborg LA, Arslan G, Lind RA, Brun JG, Valen M, et al. Reduced joint pain after short-term duodenal administration of seal oil in patients with inflammatory bowel disease: comparison with soy oil. Scand J Gastroenterol. 2004;39(11):1088-94. doi: 10.1080/00365520410009429. 38. Brunborg LA, Madland TM, Lind RA, Arslan G, Berstad A, Frøyland L. Effects of short-term oral administration of dietary marine oils in patients with inflammatory bowel disease and joint pain: a pilot study comparing seal oil and cod liver oil. Clin Nutr. 2008;27(4):614-22. doi: 10.1016/j. clnu.2008.01.017. 49. Marton LT, Goulart RA, Carvalho ACA, Barbalho SM. Omega fatty acids and inflammatory bowel diseases: an overview. Int J Mol Sci. 2019;20(19):4851. doi: 10.3390/ijms20194851. 39. Bjørkkjaer T, Araujo P, Madland TM, Berstad A, Frøyland L. A randomized double blind comparison of short-term duodenally administrated whale and seal blubber oils in patients with inflammatory bowel disease and joint pain. Prostaglandins Leukot Essent Fatty Acids. 2009;81(5-6):425- 32. doi: 10.1016/j.plefa.2009.07.005. 50. Tatiya-Aphiradee N, Chatuphonprasert W, Jarukamjorn K. Immune response and inflammatory pathway of ulcerative colitis. J Basic Clin Physiol Pharmacol. 2018;30(1):1-10. doi: 10.1515/jbcpp-2018-0036. 51. Luo C, Zhang H. The role of proinflammatory pathways in the pathogenesis of colitis-associated colorectal cancer. Mediators Inflamm. 2017;2017:5126048. doi: 10.1155/2017/5126048. 40. Grimstad T, Berge RK, Bohov P, Skorve J, Gøransson L, Omdal R, et al. Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 110 gasn.2016.14.8.39. Salmon diet in patients with active ulcerative colitis reduced the simple clinical colitis activity index and increased the anti-inflammatory fatty acid index--a pilot study. Scand J Clin Lab Invest. 2011;71(1):68-73. doi: 10.3109/00365513.2010.542484. 52. Guan G, Lan S. Implications of antioxidant systems in inflammatory bowel disease. Biomed Res Int. 2018;2018:1290179. doi: 10.1155/2018/1290179. 53. Krzystek-Korpacka M, Kempiński R, Bromke MA, Neubauer K. Oxidative stress markers in inflammatory bowel diseases: systematic review. Diagnostics (Basel). 2020;10(8):601. doi: 10.3390/diagnostics10080601. 41. Scaioli E, Cardamone C, Liverani E, Munarini A, Hull MA, Belluzzi A. The pharmacokinetic profile of a new gastroresistant capsule preparation of eicosapentaenoic acid as the free fatty acid. Biomed Res Int. 2015;2015:360825. doi: 10.1155/2015/360825. 54. Scaioli E, Salice M, Belluzzi A. Omega-3 as a part of the dietary guidance for patients with ulcerative colitis: beyond the natural sources. Clin Gastroenterol Hepatol. 2021;19(6):1296-7. doi: 10.1016/j.cgh.2020.05.053. 42. Prossomariti A, Scaioli E, Piazzi G, Fazio C, Bellanova M, Biagi E, et al. Short-term treatment with eicosapentaenoic acid improves inflammation and affects colonic differentiation markers and microbiota in patients with ulcerative colitis. Sci Rep. 2017;7(1):7458. doi: 10.1038/s41598-017-07992-1. 55. Krupa K, Fritz K, Parmar M. Omega-3 fatty acids. In: StatPearls. Treasure Island, FL: StatPearls Publishing; 2022. Available from: https://www.ncbi.nlm.nih.gov/books/NBK564314/. Updated July 12, 2022. Journal of Shahrekord University of Medical Sciences, Volume 25, Issue 2, 2023 110
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https://openresearch-repository.anu.edu.au/bitstream/1885/46877/5/szalayslides.pdf
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Science in an exponential world
Nature
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Australiasia eResearch Conference, Brisbane, 2007 Science in an Exponential World Alex Szalay The Johns Hopkins University Evolving Science • Thousand years ago: science was empirical describing natural phenomena • Last few hundred years: theoretical branch using models, generalizations • Last few decades: a computational branch 2 ⎛ .⎞ 4πGρ c2 ⎜a⎟ = −Κ 2 3 a ⎜⎜ a ⎟⎟ ⎝ ⎠ simulating complex phenomena • Today: data exploration (eScience) synthesizing theory, experiment and computation with advanced data management and statistics Æ new algorithms! 1 Living in an Exponential World • Astronomers have a few hundred TB now – 1 pixel (byte) / sq arc second ~ 4TB – Multi-spectral, temporal, … → 1PB • They mine it looking for 1000 new (kinds of) objects or more of interesting ones (quasars), density variations in 400-D space correlations in 400-D space 100 10 1 • Data doubles every year • Caused by the emergence of generations of inexpensive sensors + computing 0.1 1970 1975 1980 1985 1990 1995 2000 CCDs Glass The Challenges Exponential data growth: Distributed collections Soon Petabytes Data Collection Discovery and Analysis New analysis paradigm: Data federations, Move analysis to data Publishing New publishing paradigm: Scientists are publishers and Curators 2 Collecting Data • Very extended distribution of data sets: data on all scales! • Most datasets are small, and manually maintained (Excel spreadsheets) • Total amount of data dominated by the other end (large multi- TB archive facilities) • Most bytes today are collected via electronic sensors Making Discoveries • Where are discoveries made? – At the edges and boundaries – Going deeper, collecting more data, using more colors…. • Metcalfe’s law – Utility of computer networks grows as the number of possible connections: O(N2) • Federating data (the connections!!) – Federation of N archives has utility O(N2) – Possibilities for new discoveries grow as O(N2) • Current sky surveys have proven this – Very early discoveries from SDSS, 2MASS, DPOSS – Genomics+proteomics 3 Publishing Data Roles Authors Publishers Curators Consumers • Exponential growth: Traditional Scientists Journals Libraries Scientists Emerging Collaborations Project www site Bigger Archives Scientists Linear Exponential – Projects last at least 3-5 years – Data sent upwards only at the end of the project – Data will never be centralized • More responsibility on projects – Becoming Publishers and Curators (session on Data Publishing) • Data will reside with projects – Analyses must be close to the data Data Delivery: Hitting a Wall FTP and GREP are not adequate • • • • You can GREP 1 MB in a second You can GREP 1 GB in a minute You can GREP 1 TB in 2 days You can GREP 1 PB in 3 years • Oh!, and 1PB ~4,000 disks • • • • You can FTP 1 MB in 1 sec You can FTP 1 GB / min (~1 $/GB) … 2 days and 1K$ … 3 years and 1M$ • At some point you need indices to limit search parallel data search and analysis • This is where databases can help • Bring the analysis to the data!! 4 Next-Generation Data Analysis • Looking for – Needles in haystacks – the Higgs particle – Haystacks: Dark matter, Dark energy • Needles are easier than haystacks • ‘Optimal’ statistics have poor scaling – Correlation functions are N2, likelihood techniques N3 – For large data sets main errors are not statistical • As data and computers grow with Moore’s Law, we can only keep up with N logN • A way out? – Discard notion of optimal (data is fuzzy, answers are approximate) – Don’t assume infinite computational resources or memory • Requires combination of statistics & computer science The Virtual Observatory • Premise: most data is (or could be online) • The Internet is the world’s best telescope: – It has data on every part of the sky – In every measured spectral band: optical, x-ray, radio.. – As deep as the best instruments (2 years ago). – It is up when you are up – The “seeing” is always great – It’s a smart telescope: links objects and data to literature on them • Software became the capital expense – Share, standardize, reuse.. 5 National Virtual Observatory • NSF ITR project, “Building the Framework for the National Virtual Observatory” is a collaboration of 17 funded and 3 unfunded organizations – – – – – Astronomy data centers National observatories Supercomputer centers University departments Computer science/information technology specialists • Similar projects now in 15 countries world => International Virtual Observatory Alliance wd ie Sloan Digital Sky Survey Goal Create the most detailed map of the Northern sky “The Cosmic Genome Project” Two surveys in one Photometric survey in 5 bands Spectroscopic redshift survey The TheUniversity UniversityofofChicago Chicago Princeton PrincetonUniversity University The Johns The JohnsHopkins HopkinsUniversity University The TheUniversity UniversityofofWashington Washington New Mexico State University New Mexico State University Fermi FermiNational NationalAccelerator AcceleratorLaboratory Laboratory US USNaval NavalObservatory Observatory The Japanese Participation The Japanese ParticipationGroup Group The TheInstitute Institutefor forAdvanced AdvancedStudy Study Max Planck Inst, Heidelberg Max Planck Inst, Heidelberg Sloan SloanFoundation, Foundation,NSF, NSF,DOE, DOE,NASA NASA Automated data reduction 150 man-years of development High data volume 40 TB of raw data 5 TB processed catalogs Data is public 2.5 Terapixels of images 6 The SkyServer Portal • • • • Sloan Digital Sky Survey: Pixels + Objects About 500 attributes per “object”, 400M objects Currently 2.4TB fully public, June 29-> 3TB Prototype eScience lab (800 users) – Moving analysis to the data – Fast searches: color, spatial • Visual tools – Join pixels with objects • Tutorials and projects Prototype in data publishing – – – – http://skyserver.sdss.org/ Data Versions • June 2001: EDR • Now at DR5, with 2.4TB • 3 versions of the data – Target, Best, Runs – Total catalog volume 5TB • Data publishing: once published, must stay • SDSS: DR1 is still used EDR Human page view s 5.E+05 5.E+05 4.E+05 4.E+05 EDR 3.E+05 DR1 DR3 2.E+05 DR4 2.E+05 DR5 1.E+05 DR2 DR2 DR2 astro 5.E+04 2005/11 2006/03 2005/03 2005/07 2004/07 weblog 2004/11 2003/11 2004/03 2003/03 vo 2003/07 2002/07 2002/11 collab 2001/07 0.E+00 DR1 DR1 DR2 3.E+05 2001/11 • 50B rows of data delivered 250 million web hits in 5 years 930,000 distinct users 50K hours of classroom lessons 2002/03 • EDR admin DR3 DR3 DR3 DR3 weblog 7 Skyserver Sessions Vic Singh (Stanford/ MSR) Trends CMB Surveys (pixels) • 1990 COBE • 2000 Boomerang • 2002 CBI • 2003 WMAP • 2008 Planck 1000 10,000 50,000 1 Million 10 Million Time Domain • QUEST • SDSS Extension survey • Dark Energy Camera • PanStarrs • SNAP… • LSST… Angular Galaxy Surveys (obj) • 1970 Lick 1M • 1990 APM 2M • 2005 SDSS 200M • 2008 VISTA 1000M • 2012 LSST 3000M Galaxy Redshift Surveys (obj) • 1986 CfA 3500 • 1996 LCRS 23000 • 2003 2dF 250000 • 2005 SDSS 750000 Petabytes/year by the end of the decade… 8 Simulations Cosmological simulations have 109 particles and produce over 30TB of data (Millennium) • Build up dark matter halos • Track merging history of halos • Use it to assign star formation history • Combination with spectral synthesis • Realistic distribution of galaxy types • Hard to analyze the data afterwards- >need DB • What is the best way to compare to real data? Exploration of Turbulence We can finally “put it all together” • • • Large scale range, scale-ratio O(1,000) Three-dimensional in space Time-evolution and Lagrangian approach (follow the flow) Unique turbulence database • We are creating a database of O(2,000) consecutive snapshots of a 1,0243 simulation of turbulence: close to 100 Terabytes • Treat it as an experiment 9 Wireless Sensor Networks • Will use 200 wireless (Intel) computers, with 10 sensors each, monitoring • Air temperature, moisture • Soil temperature, moisture, at least in two depths (5cm, 20 cm) • Light (intensity, composition) • Gases (O2, CO2, CH4, …) • • • • • • Long-term continuous data Small (hidden) and affordable (many) Less disturbance >200 million measurements/year Collaboration with Microsoft Complex database of sensor data and samples With K.Szlavecz and A. Terzis http://lifeunderyourfeet.org Data Sharing/Publishing in the VO • What is the business model (reward/career benefit)? • Three tiers (power law!!!) (a) big projects (b) value added, refereed products (c) ad-hoc data, on-line sensors, images, outreach info • • • • • We have largely done (a), mandated Need “Journal for Data” to solve (b) Need “VO - Flickr” (a simple interface) for (c) Mashups are emerging (GalaxyZoo) Need an integrated environment for ‘virtual excursions’ for education (C. Wong) 10 ‘Journal for Data’ Experiment S. Choudhury, T. deLauro, R. Hanisch, E. Vishniac, A. Szalay, M. Kurtz, C. Lagoze Team up with the main existing journals in US astronomy and create an on-line supplement for the data related to journal articles • Easy submission process for authors • Properly linked to the journals, mostly in electronic version • Data geoplexed among university libraries, with automated replication • Data guaranteed to exist for 20 years • Curation, curation, curation!!! (P. Buenemann) Continuing Growth How long does the data growth continue? • High end always linear • Exponential comes from technology + economics, rapidly changing generations! – like CCD’s replacing plates… gene-chips • How many new generations of instruments do we have left? • Are there new growth areas emerging? • Software (collaboration) is becoming an instrument – hierarchical data replication – Value added data/ mashups – data cloning 11 Collaborative Trends • Science is aggregating into ever larger projects • VO is inevitable, a new way of doing science • Present on every physical scale today, not just astronomy (Earth/Oceans, Biology, MS, HEP) • But: there is a natural size for close collaborations • May be the only way to do 'small science' in 2020 Scholarly Communications • No ‘Einstein letters’ today… very little paper trail • Proposals and papers archived • Most large projects communicate through email exploders and phonecons • Often reaching back to the Internet Archive • Some technical info on WIKI pages • Science oriented blogs are appearing • Collaborative workbenches emerging • More instant messaging, especially next generation • What can we and what should we capture? • What will science historians do in 50 years? 12 Technology+Sociology+Economics • Technology is changing very rapidly – Sensors, Moore's Law – Trend driven by changing generations of technologies – There may not be time for a top-down design • Sociology is changing in unpredictable ways – YouTube… vs Google and Yahoo – In general, people will use a new technology if it is • Offers something entirely new • Or substantially cheaper • Or substantially simpler – Build it and they (may) come… • Funding is essentially level The Future of the VO • Technology driving Sociology (limited by Economics) • We need to keep running forward just to keep up • We must take risks – We will not get it always right – If we are right all the time, we are not taking enough risks • Surprisingly significant public involvement! • Everything is a power law! 13 Summary • Data growing exponentially, Petabytes/year by 2010 • Explosion is coming from inexpensive sensors and value added data products • Requires a new model for science – Having more data makes it harder to extract knowledge • Same thing happening in all sciences – High energy physics, genomics, cancer research, medical imaging, oceanography, remote sensing, … • Science with so much data requires a new paradigm – Computational methods, algorithmic thinking will come just as naturally as mathematics today • eScience: an emerging new branch of science 14
https://openalex.org/W2170488763
https://europepmc.org/articles/pmc4308849?pdf=render
English
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The impact of a standardized incident reporting system in the perioperative setting: a single center experience on 2,563 ‘near-misses’ and adverse events
Patient safety in surgery
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RESEARCH Open Access Open Access Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 DOI 10.1186/s13037-014-0046-1 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 DOI 10.1186/s13037-014-0046-1 * Correspondence: Anita.Heideveld-Chevalking@radboudumc.nl 1Department of Operating Theatres, Radboud University Medical Center, Geert Grooteplein-Zuid 10, Internal postal code 738, 6525, GA, Nijmegen, The Netherlands Full list of author information is available at the end of the article The impact of a standardized incident reporting system in the perioperative setting: a single center experience on 2,563 ‘near-misses’ and adverse events The impact of a standardized incident reporting system in the perioperative setting: a single center experience on 2,563 ‘near-misses’ and adverse events J Heideveld-Chevalking1*, Hiske Calsbeek2, Johan Damen3, Hein Gooszen1 and André P Wolff1,3 © 2014 Heideveld-Chevalking et al.; licensee BioMed Central. 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. 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. Methods h This retrospective study is performed in the Radboud university medical center, which has 953 beds and 25 operating rooms (ORs). All data were obtained from HIMS, a database that is developed by the Patient Safety Company (http://www.patientsafety.com), licensed to the Radboud university medical center and used by the operating department since July 2009. The study period lasted from the 1st of July 2009 to the 1st of July 2012. Incidents in HIMS are reported as a) ‘adverse events’, i.e. any unintended or unexpected event which could have led or did lead to harm of one or more patients receiving hospital care and b) ‘near-miss events’, i.e. events or cir- cumstances that nearly occurred but were prevented (through luck or intervention) and did not lead to patient harm. [1] Harm is defined as any injury to the patient which leads to an extension or increase in the treatment, to temporary or permanent physical, psychological and/or social functional loss, or to death [5]. The worsening of a patient’s condition as a result of the natural progression of an disease is not considered ‘harm’ [5]. To improve patient safety and reduce adverse events, a national safety management system has been implemen- ted in Dutch hospitals (‘Veiligheidsmanagementsysteem = VMS’) between 2008–2012. VMS focuses on the manage- ment of risks (the prevention of patient harm and its pos- sible consequences) and is described in the ‘Netherlands Technical Agreement’ (NTA) [5]. The starting point for this NTA was the report “Here you’ll work safely, or you won’t work here” [6]. VMS consists of systems for risk identification, risk analysis, risk evaluation, incident re- porting, incident analysis, and managing recommenda- tions and improvement measures. The operating department (including the clinical oper- ating and recovery rooms) of the Radboud university medical center introduced the Hospital Incident Man- agement System (HIMS) in July 2009. HIMS aimed at facilitating the voluntarily and confidentially reporting of perioperative incidents. After using HIMS for three years, we set out to analyze whether there are specific types or patterns of the reported information and to detect the areas where further efforts are required to improve perioperative patient safety. Specifically, we wished to investigate the number and characteristics of the voluntarily reported perioperative incidents. From the start of recording we noticed that Standard Operating Procedure (SOP) non-compliance was a prominent repor- ted cause of incidents. Abstract Background: The reduction of perioperative harm is a major priority of in-hospital health care and the reporting of incidents and their causes is an important source of information to improve perioperative patient safety. We explored the number, nature and causes of voluntarily reported perioperative incidents in order to highlight the areas where further efforts are required to improve patient safety. Methods: Data from the Hospital Incident Management System (HIMS), entered in the period from July 2009 to July 2012, were analyzed in a Dutch university hospital. Employees in the perioperatve field filled out a semi-structured digital form of the reporting system. The risk classification of the reported adverse events and ‘near misses’ was based on the estimated patient consequences and the risk of recurrence, according to national guidelines. Predefined reported incident causes were categorized as human, organizational, technical and patient related. Results: In total, 2,563 incidents (1,300 adverse events and 1,263 ‘near-miss’ events) were reported during 67,360 operations. Reporters were anesthesia, operating room and recovery nurses (37%), ward nurses (31%), physicians (17%), administrative personnel (5%), others (6%) and unmentioned (3%). A total of 414 (16%) adverse events had patient consequences (which affected 0,6% of all surgery patients), estimated as catastrophic in 2, very serious in 34, serious in 105, and marginally serious in 273 cases. Shortcomings in communication was the most frequent reported type of incidents. Non-compliance with Standard Operating Procedures (SOPs: instructions, regulations, protocols and guidelines) was reported with 877 (34%) of incident reports. In total, 1,194 (27%) voluntarily reported causes were SOP-related, mainly human-based (79%) and partially organization-based (21%). SOP-related incidents were not associated with more patient consequences than other voluntarily reported incidents. Furthermore ‘mistake or forgotten’ (15%) and ‘communication problems’ (11%) were frequently reported causes of incidents. Conclusions: The analysis of voluntarily reported perioperative incidents identified an association between perioperative patient safety problems and human failure, such as SOP non-compliance, mistakes, forgetting, and shortcomings in communication. The data suggest that professionals themselves indicate that SOP compliance in combination with other human failures provide room for improvement. Keywords: Hospital incident reporting, Guideline adherence, Patient safety, Perioperative care, Quality Full list of author information is available at the end of the article Page 2 of 10 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Background perioperative care. Dutch hospital record review studies suggest that at least 10-15% of AEs are directly or indir- ectly related to procedure non-compliance [9,10]. The compliance rate of the use of surgical safety checklists ranges from 12% to 100% (mean 75%) [11]. French re- search revealed that alarms are frequently ignored by the operating theatre staff [12]. English anesthesiologists wit- nessed that 22% of incidents during anaesthesia are related to protocol violations [13]. Patient safety is a global public health issue receiving rapidly increasing attention. Patient safety is the (near) absence of (the chance of) avoidable harm inflicted on the patient through the actions and/or negligence of employees or through flaws in the healthcare system [1]. Numerous medical record studies have shown that un- safe care may result in adverse events (AEs) leading to harm in 3-17% of hospital patients [2]. An AE is “an un- intended injury or complication resulting in prolonged length of hospital stay, disability at the time of discharge or death caused by health care management and not by the patients’ underlying disease” [3]. A total of 51-77% of AEs in hospitals are related to perioperative care [2]. A systematic review reveals that 14% of perioperative patients experience some form of AEs, that 38% of these AEs are preventable and that 4% of patients experiencing AEs have fatal outcomes [4]. Preventable AEs are the result of care that falls below current professional stan- dards and the expected performance of practitioners or care systems [1,2]. There is an association between undesirable periopera- tive events and subsequent critical perioperative outcomes [14]. Recent studies reveal also that better guideline com- pliance is associated with better perioperative outcomes [15,16]. Therefore, adherence to guidelines is an important target for safety improvement programs. This study was designed to provide data on the number, nature and causes of voluntarily reported perioperative incidents. Methods h At the introduction of HIMS, hospital wide appoint- ments were made for reporting of incidents, based on the national agreements [5]. All employees, including professionals working in the perioperative process were encouraged to report incidents in order to prevent them from happening again. They were requested to fill out a semi-structured digital form of the reporting system. At least the following had to be reported: date, time and location of the incident, a brief description of the event and the circumstances, the type of incident and possible causes, the potential patient impact and the estimated risk of recurrence of that incident, and the measures that may prevent the incident from repeating. The predefined categorization of incident types is illustrated in Figure 1. In Tables 1 and 2 an explanation of the used terms is Since humans are fallible, systems must be designed to prevent humans from making errors [7,8]. Standardisation, the use of guidelines and protocols, is generally considered to improve perioperative safety. Preventable patient harm may be the result of guideline non-compliance but unfor- tunately there is hardly any literature about this problem in Page 3 of 10 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 698 585 460 346 282 192 Communication Equipment Treatment Other Medication & blood products Diagnostics Type of Incidents (n=2,563) Figure 1 Predefined types of voluntarily reported perioperative incidents. Type of Incidents (n=2,563) Figure 1 Predefined types of voluntarily reported perioperative incidents. contributing factors through informal discussions with care providers, managers, and/or other expert(s), asking ‘why’ and ‘what’ influenced the occurrence of this (near)incident. Besides these analyzing actions, other activities of ORIRC are trend watching, advising to adjust products and proce- dures, providing feedback and spreading newsletters and safety alerts to all involved in perioperative care. After clos- ing a report, all information is automatically anonymized. The information in HIMS is not used for blaming, shaming or (legal) actions against the reporting professional, but for improving the quality of patient care. given, in particular of the concepts estimated risk of recurrence (Table 1) and estimated consequences for the patient (Table 2). This categorization of patient conse- quences is based on national guidelines as described in the NTA [5]. Based on the estimated patient consequen- ces and risk of recurrence, the incident is automatically classified into four risk categories (Table 3). The estimated potential patient consequences of the reported incidents. Methods h This risk classification is the basis for actions to be taken by the Operating Room Incident Reporting Committee (ORIRC) as described in Table 4. According to the Dutch con- sensus classification reported incident causes were classi- fied as human, organizational, technical, patient related and other [1,2]. Descriptive statistics were used to describe the number, nature and causes of incidents. Chi-square tests with Yates’ correction and odds ratios (ORs) with 95% confi- dence limits (CL) were applied to test differences between physicians and non-physicians and between perioperative and hospital wide reporting behaviour. A p-value < 0.05 is considered to show statistical significance. The ORIRC consists of a surgeon, two anesthesiologists, a patient safety coordinator, a recovery room nurse, two operating room nurses, an anesthesia nurse, a logistic man- ager, a logistic employee, and a technician. The ORIRC reviews and discusses incidents weekly with priority to high risk events. Estimating the risk of recurrence and potential consequences for the patient at the time of reporting and before analysis of the incident may be diffi- cult. Therefore, the ORIRC may adapt the risk score after analysis of the incident. Subsequently, the ORIRC under- takes actions, such as gathering additional information, cross-checking with the medical charts, and exploring key Table 2 Explanation of patient consequences Classification of patient consequences: Catastrophe (Expected) death or (expected) severe permanent harm Very serious (Expected) permanent harm/major intervention like (re) operation and/or (expected) extended hospitalization or treatment > 7 days/delay of treatment causing severe risk of harm Serious (Expected) temporary harm and/or severe pain, for which medical treatment is needed and/or (expected) extended hospitalization or treatment > 3 days/delay of treatment causing risk of harm Marginally serious (Expected) minimal harm and/or pain, requiring minor treatment and/or (expected) extended hospitalization or treatment < 3 days/delay of treatment causing minimal risk of harm None No harm and no delay, or (expected) delay of treatment causing no harm The estimated potential patient consequences of the reported incidents. Methods h Table 2 Explanation of patient consequences Classification of patient consequences: Catastrophe (Expected) death or (expected) severe permanent harm Very serious (Expected) permanent harm/major intervention like (re) operation and/or (expected) extended hospitalization or treatment > 7 days/delay of treatment causing severe risk of harm Serious (Expected) temporary harm and/or severe pain, for which medical treatment is needed and/or (expected) extended hospitalization or treatment > 3 days/delay of treatment causing risk of harm Marginally serious (Expected) minimal harm and/or pain, requiring minor treatment and/or (expected) extended hospitalization or treatment < 3 days/delay of treatment causing minimal risk of harm None No harm and no delay, or (expected) delay of treatment causing no harm The estimated potential patient consequences of the reported incidents. Table 2 Explanation of patient consequences Classification of patient consequences: (Expected) permanent harm/major intervention like (re) operation and/or (expected) extended hospitalization or treatment > 7 days/delay of treatment causing severe risk of harm (Expected) permanent harm/major intervention like (re) operation and/or (expected) extended hospitalization or treatment > 7 days/delay of treatment causing severe risk of harm Table 1 Explanation of risk of recurrence Classification of the estimated risk of recurrence: Almost inevitable It will probably happen again within a few hours or days Probable It will probably happen again within a week Possible It will probably happen again within a few weeks Small It will probably happen again within a few month Very small It will not happen more than once a year The estimated risk of recurrence of the reported incidents. Table 1 Explanation of risk of recurrence Classification of the estimated risk of recurrence: Almost inevitable It will probably happen again within a few hours or days Probable It will probably happen again within a week Possible It will probably happen again within a few weeks Small It will probably happen again within a few month Very small It will not happen more than once a year The estimated risk of recurrence of the reported incidents. (Expected) temporary harm and/or severe pain, for which medical treatment is needed and/or (expected) extended hospitalization or treatment > 3 days/delay of treatment causing risk of harm Classification of the estimated risk of recurrence: (Expected) minimal harm and/or pain, requiring minor treatment and/or (expected) extended hospitalization or treatment < 3 days/delay of treatment causing minimal risk of harm No harm and no delay, or (expected) delay of treatment causing no harm No harm and no delay, or (expected) delay of treatment causing no harm Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Page 4 of 10 Table 3 Explanation of risk matrix Patient consequences Catastrophe Extreme Extreme Extreme Extreme Extreme Very serious High High High High High Serious High High High Medium Medium Marginally serious High High Medium Medium Low None Medium Medium Medium Low Low Risk of recurrence Almost Inevitable Probable Possible Small Very small Risk matrix based on the estimated patient consequences and the estimated risk of recurrence of the incident. Hospital-wide voluntarily reported incidents Hospital-wide voluntarily reported incidents Hospital-wide key figures over the period July 2009-July 2012 are presented in Table 5. The occurrence of volun- tarily reported incidents associated with procedure non- compliance within the operating department was not significantly different from hospital wide reporting of non-compliance with SOPs (34% and 32,5% respectively (OR 1.087; 95% CL 0.998-1.184, p = 0.084)). Table 2 Explanation of patient consequences Classification of patient consequences: Table 3 Explanation of risk matrix Table 5 Hospital-wide key figures, July 2009-July 2012 Total number of admissions 210,507 Total number of clinical operations 67,360 Total number of voluntarily reported incidents: 27,008 by physicians 2,937 by non-physicians 23,154 by reporters that did not mention their position 917 Number of voluntarily reported incidents per type: medication & blood-related 6,932 communication-related 6,053 diagnostics-related 4,183 treatment-related 3,751 equipment-related 2,421 other type-related 3,668 Total number of voluntarily reported causes (median 1; range 0–10 causes per incident) 48,055 Number of causes per category: mistake/forgotten 9,611 SOP not followed 6,535 other 31, 909 Total number of SOP-related causes: 10,543 SOP not followed 6,535 SOP not known 2,116 SOP not available, incomplete or unclear 1,684 SOP not accessible 208 Number of incidents with SOP cause 8,789 Table 3 Explanation of risk matrix Table 5 Hospital-wide key figures, July 2009-July 2012 Risk matrix based on the estimated patient consequences and the estimated risk of recurrence of the incident. Patient consequences and risk of recurrence of reported perioperative incidents Patient consequences and risk of recurrence of reported perioperative incidents Patient consequences and risk of recurrence of reported perioperative incidents HIMS characterized 1,822 (71%) incidents as ‘medium risk incidents’ which is shown in Table 6. Table 7 pre- sents a specification of the estimated patient conse- quences and risk of recurrence of incidents. Patient consequences were estimated to have been inflicted 414 (32%) of 1,300 adverse events: 273 events were consid- ered to have caused minimal patient harm and/or pain, 105 temporary patient harm and/or severe pain, and 34 permanent patient harm and/or needing major intervention Table 4 Explanation of reporting requirments based on the classified risk Extreme risk incident The reporter/ORIRC contacts the involved head of the department and checks whether the catastrophe is handled according to the standard procedures, meaning that the Board of Hospital Directors reports the catastrophe to the Health Care Inspectorate. High risk incident The ORIRC gathers further information, analyzes the incident, discusses the incident in a meeting, formulates conclusions and/or improvement actions. Medium risk incident The ORIRC gathers further information, discusses the incident in a meeting, formulates conclusions and/or improvement actions. Low risk incident The ORIRC formulates conclusions and/or improvement actions. ORIRC = Operating Room Incident Reporting Committee. Reporting requirements based on the classified risk. Characteristics of the voluntarily reported perioperative incidents Perioperatively 2,563 incidents were voluntarily reported in HIMS: 1,300 adverse events and 1,263 ‘near-miss’ events. The reporters were all professionals involved in perioperative patient care: anesthesia, operating room and recovery nurses (37%), ward nurses (31%), physi- cians (17%), administrative personnel (5%), and others (6%). Of 85 (3%) incidents the appointment of the re- porter was not mentioned. Figure 1 provides an over- view of the types of incidents; communication failures (27%) and equipment failures (23%) were the most fre- quently reported type of voluntarily reported periopera- tive incidents. Risk classification of the 2,563 voluntarily reported perioperative incidents. Reported causes Table 10 shows the reported predefined causes of peri- operative incidents and their classification. A total of 4,346 causes were reported (median 1, range 0–10 per incident). In total 2,966 (68%) incident causes were related to human factors, 1,004 (23%) to organizational factors, 89 (2%) to technical failure, 128 (3%) were patient-related and 159 (4%) were related to other factors. Most frequently repor- ted causes were SOP not followed (16,2%), human mistake or having forgotten (15,4%) and communication problems (11,5%). In total 1194 (27,5%) SOP related causes were noted, as summarized in Table 10 part b. The estimated patient consequences and risk of recur- rence of reported perioperative ‘near-miss’ events are presented in Table 8. In total 233 (18%) of these 1263 ‘near-misses’ were estimated as potentially harmful, which was classified as marginally serious in 107 near-incidents, serious in 81, and very serious in 44. One potential cata- strophic ‘near-miss’ event concerned mechanical problems with a part of the operating table and is described as an example in Table 9. Table 4 Explanation of reporting requirments based on the classified risk The reporter/ORIRC contacts the involved head of the department and checks whether the catastrophe is handled according to the standard procedures, meaning that the Board of Hospital Directors reports the catastrophe to the Health Care Inspectorate. Table 6 Risk classification of the 2,563 voluntarily reported perioperative incidents Table 6 Risk classification of the 2,563 voluntarily reported perioperative incidents Risk Total incidents n % Extreme risk 3 (0.1%) High risk 349 (13.6%) Medium risk 1822 (71.1%) Low risk 389 (15.2%) Total 2563 Risk classification of the 2,563 voluntarily reported perioperative incidents. Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Page 5 of 10 Table 7 Estimated patient consequences and risk of recurrence of the 1,300 voluntarily reported perioperative adverse events Estimated patient consequences Total Catastrophe 0 0 0 1 1 2 Very serious 4 6 16 7 1 34 Serious 4 18 58 18 7 105 Marginally serious 22 47 146 44 14 273 None 134 228 335 138 51 886 Total 164 299 555 208 74 1300 Estimated risk of recurrence Almost inevitable Probable Possible Small Negligible Estimated patient consequences and risk of recurrence of the 1,300 voluntarily reported perioperative adverse events. Table 7 Estimated patient consequences and risk of recurrence of the 1,300 voluntarily reported perioperative adverse events ble 7 Estimated patient consequences and risk of recurrence of the 1,300 voluntarily reported peri patient consequences and risk of recurrence of the 1,300 voluntarily reported perioperative advers like (re)operation and/or extended hospitalization or treat- ment. Two catastrophic adverse events, with one mortal- ity, were reported to both the hospital board and the Dutch Health Care Inspectorate. The risk of recurrence of the previously mentioned 414 adverse events was esti- mated as follows: possible recurrence within a day (n = 30), within a week (n = 71), within a few weeks (n = 220), within a few months (n = 70), and of 23 adverse events it was estimated that the event would occur not more frequently than once a year. Reported causes Reported causes of procedure non-compliance Adverse event Communication Recovery nurse at the holding of the OR SOP not followed Medium risk During surgery the following happened: Adverse event Other Anesthetic nurse - Other organization-related problem, namely: “delay because of shortage of staff”; - 30 minutes waiting because the patient arrived too late in the OR; - For this operation there was no blood typing performed; - Human error or forgotten. - During the time out it appeared that the right size implant was not available. High risk Surgery was performed without recent available imaging. During surgery, it appeared that metastases were increased in size necessitating adjustment of the surgical procedure. Adverse event Diagnostics Radiologist - SOP not known - SOP not available/ incomplete/unclear - Incorrect performance Extreme risk The headrest of the surgical table suddenly went loose, which could have caused the head of the patient to bend downwards uncontrollably but the head of the patient was stabilized in time by the anesthesiologist. ‘Near-miss’ event Equipment OR nurse - Broken material; - Wrong design; - Other human error, namely: “part of the table not correctly fixated”. Table 9 Examples of reported perioperative incidents in HIMS forgotten’, appeared to be frequently reported incident causes. About one third of the reported perioperative incidents was associated with SOP non-compliance; 79% of these SOP-related causes were related to human failure. The SOP-related incidents were not associated with more patient consequences than other incidents. It is noteworthy that the percentage voluntarily reported incidents associated with SOP non-compliance within the operating department did not differ from the hospital- wide incidence. SOP related incidents were associated with patient harm (OR 1.13 (95% CL 0.90-1.40), p = 0.291). Most SOP related causes (n = 992) were reported by non-physicians, 170 by physicians and 32 by reporters who did not mention their function in the organization. Non-physicians reported less frequently SOP causes of incidents than physicians (52% versus 68%, p < 0.0001), but non-physicians reported more often SOP causes of near-incidents (48% versus 32%, p < 0.0001). There was no statistically significant difference between both groups in reporting human or organization related factors of SOP non-compliance. Both groups most frequently reported SOP causes with incidents that were classified as medium risk incidents. There is increasing information that better guideline compliance is associated with improved perioperative outcomes [15,16]. Reported causes of procedure non-compliance A more detailed analysis of the 1,194 SOP related causes showed that 79% was related to human failure: a SOP was known but not followed in 702 cases and not known in 245 cases. Organization related factors were: unavail- able, inaccessible, incomplete and unclear SOPs in 247 (21%) of cases. Procedure non-compliance was reported with 877 (34%) of incidents; 648 SOP causes were repor- ted with 471 adverse events, and 546 with 406 ‘near- miss’events. A total of 2,149 (84%) of the voluntarily reported peri- operative incidents were considered to have caused no pa- tient harm, or delay of treatment which caused no harm, as shown in the Tables 7 and 8. The risk of recurrence in 381 of these 2,149 incidents were estimated to reoccur within a day, 505 within a week, 861 within a few weeks, 296 within a few months, and of 106 incidents it was estimated that the event would occur no more than once a year. Table 11 summarize the patient consequences and risk of recurrence of SOP associated perioperative incidents. In 151 of the 877 SOP related incidents, the events were associated with patient harm, while 263 of 1,686 non Table 8 Estimated potential patient consequences and risk of recurrence of the 1,263 voluntarily reported perioperative ‘near-miss’ events Patient consequences could have been Total Catastrophe 0 0 1 0 0 1 Very serious 10 7 15 6 6 44 Serious 13 37 27 3 1 81 Marginally serious 19 26 49 11 2 107 None 205 207 434 138 46 1030 Total 247 277 526 158 55 1263 Estimated risk of recurrence Almost inevitable Probable Possible Small Negligible Estimated potential patient consequences and risk of recurrence of the 1,263 voluntarily reported perioperative ‘near-miss’ events. Table 8 Estimated potential patient consequences and risk of recurrence of the 1,263 voluntarily reported perioperative patient consequences and risk of recurrence of the 1,263 voluntarily reported perioperative Estimated potential patient consequences and risk of recurrence of the 1,263 voluntarily reported perioperative ‘near-miss’ events. Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Page 6 of 10 Table 9 Examples of reported perioperative incidents in HIMS Examples of reported perioperative incidents in HIMS HIMS risk classification Description Event type Incident type Function of reporter Reported cause Low risk Two patients did not have correct marking signs although the surgeon had signed the checklist. Reported causes of procedure non-compliance A study on the implementation of a bundle of care to reduce postoperative surgical site in- fections showed that increased bundle compliance from 10% to 60% was associated with a significant 36% reduc- tion in infection rate [16]. Another study in a Dutch uni- versity hospital on the effect of the use of a perioperative safety checklist showed a significant 56% reduction of the in-hospital 30-day mortality after surgery in patients with completed checklists whereas the mortality rate remained unchanged in patients with partially completed or non- completed checklists [15]. The results of our study clearly show that a thorough analysis of the barriers that hinder adequate communication and compliance with SOPs is essential to further improve perioperative safety [18-20]. To illustrate the characteristics of voluntarily reported perioperative incidents, examples are described in Table 9. Discussion We studied the characteristics of voluntarily reported perioperative incidents at our operating department in the period July 2009-July 2012. Reported incidents inclu- ded ‘near-miss’ events as they can be seen as ‘free lessons to be learned’ [17]. Overall, 67,360 operations were per- formed in the three-year study period and 2,563 peri- operative incidents were voluntarily reported. Most (84%) of these incidents were not considered as potentially harmful for patients, but 16% were, which comprised 0.6% of all surgery patients. SOP non-compliance, short- comings in communication, and mistakes or just ‘having Incident reporting and investigation was first used in the 1940s to improve safety and performance of military aviation [21] and some decades later incident reporting Page 7 of 10 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Page 7 of 10 Table 10 Causes of perioperative ‘near-misses’ and adverse events A: Reported causes (n = 4,346) of the perioperative incidents (n = 2,563) HIMS predefined causes N % Human SOP not followed 702 16.2% Mistake/forgotten 669 15.4% Communication problem 498 11.5% Other human acting, namely*) 449 10.3% SOP not known 245 5.6% Professional not capable for task 161 3.7% Distracted 105 2.4% Unqualified or incorrect performance 77 1.8% Incorrect use 40 0.9% Wrong record filing 20 0.5% Total human 2,966 68.2% Organizational Other organizational, namely*) 315 7.2% SOP not available, incomplete, or unclear 217 5.0% Culture at workplace 114 2.6% High workload 115 2.6% Equipment/supply related, namely*) 67 1.5% Inadequately trained professional 67 1.5% Medical devices not available 62 1.4% SOP not accessible 30 0.7% Unclear instructions 17 0.4% Total organizational 1,004 23.1% Technical Broken material 61 1.4% Wrong design 28 0.6% Total technical 89 2.0% Patient-related Other patient related, namely*) 91 2.1% Patient condition 19 0.4% Patient behaviour 18 0.4% Total patient-related 128 2.9% Other, namely*) 159 3.7% Total 4,346 100% B: Summary of SOP releated causes SOP not followed 702 16.2% SOP not known 245 5.6% SOP not available, incomplete, or unclear 217 5.0% SOP not accessible 30 0.7% Total of SOP related causes 1,194 27,5% *)Further described by the reporter in open text field. SOP = Standard Operative Procedure, including instructions, regulations, protocols, and guidelines. Table 10 Causes of perioperative ‘near-misses’ and adverse events was introduced in anesthesiology [22]. Meanwhile, inci- dent reporting has become a widely recommended me- thod to gather information about AEs in hospital care [18] and several methods have been developed [13,23-25]. Discussion Much information about AEs in hospitals comes from the retrospective study of medical records [2,4,26,27]. How- ever, retrospective record review has the well-known disadvantage that AEs may not have been identified or re- ported because they were not recorded in the medical file. These retrospective studies also rarely give information about ‘near-miss’events. Patient’s information is also a reli- able source for the identification of care-related AEs [28]. Monitoring the performance of professionals by trained observers may provide the most reliable picture of peri- operative practice [13,29]. However, these studies may un- derreport the actual rate of AEs because the researchers only observed during daytime of weekdays [29]. Smith at al. witnessed that around 20% of the incidents reported were the result of violation from existing protocols [13]. To further improve patient safety it is essential not only to get insight into the number, type, risk and causes of voluntarily reported incidents, but also to reach agree- ment on definitions and reproducible ways of reporting and scoring. The Netherlands Technical Agreement aims to contribute to the uniformity of the safety management system in hospitals and to create openness about patient safety towards patients and public. In order to improve the effectiveness of the national incident reporting system, we suggest further standardization of incident reporting data, specifically of the categorization of the types and causes of reported incidents. This has the potential to pro- vide us with a system to compare hospital performance and to benchmark performance using a validated system. p g y The five basic elements essential for the successful translation from incident reporting to learning are 1) an open reporting culture allowing independent non-punitive data input, 2) the opportunity to freely narrate one’s own version of the event, 3) an analysis that turns the incident report into a lesson, 4) adequate feedback [23], and 5) def- initions clear enough to be used in other centres in order to be able to compare hospital performances. Investigating and analyzing incidents requires optimal engagement of physicians to get insight into the root cause and preven- tion of these events [23]. The use of a standardized frame- work for analysis of events has been recommended and introduced in several centers around the world including our center [23,30]. A positive safety culture is associated with increased willingness to report errors [31,32], with increased compliance with SOPs [33] and with fewer AEs [34]. Discussion Apparently professionals at our department felt safe enough to report communication failures and non- compliance with SOPs. They knew that the information will not be used to blame or undertake actions against the reporter and that after analysis of an incident the Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 Page 8 of 10 Table 11 Patient consequences and risk of recurrence of SOP related incidents A. Reported SOP-related perioperative adverse events and ‘near-miss’events (n = 877) Estimated Patient consequences Total Catastrophe 0 0 0 0 0 0 Very serious 6 2 4 6 1 19 Serious 6 12 39 4 0 61 Marginally serious 15 27 79 17 4 142 None 139 164 254 72 26 655 Total 166 205 376 99 31 877 Estimated risk of recurrence Almost inevitable Probable Possible Small Negligible B. Reported SOP-related perioperative adverse events (n = 471) Catastrophe 0 0 0 0 0 0 Very serious 1 1 4 3 1 10 Serious 2 9 25 3 0 39 Marginally serious 8 16 62 13 3 102 None 59 91 117 39 14 320 Total 70 117 208 58 18 471 Estimated risk of recurrence Almost inevitable Probable Possible Small Negligible Table 11 Patient consequences and risk of recurrence of SOP related incidents A. Reported SOP-related perioperative adverse events and ‘near-miss’events (n = 877) occurred incidents. A second point of attention is the fact that a substantial part of perioperative care is delivered outside the operating department. Therefore, our results, collected in the operating department, do not represent the full scope of perioperative incidents, as an unknown proportion will have been reported to other incident reporting committees within the hospital. Finally, this single center study may only reflect the cul- ture and customs of our hospital. Since non-compliance with guidelines is a well-known phenomenon, our re- sults are most likely not specific for our hospital. How- ever, there is no information about the contribution of non-compliance with SOPs as cause of perioperative incidents in other hospitals. information was anonymized to be used for training purposes and improving the quality of care, if deemed useful for this purpose. A major weakness of incident reporting in all studies is under-reporting. Incident reporting may capture only 4% to 50% of AEs [25,27,32-38]. The reasons for not reporting are numerous: clinical factors (e.g. Conclusions l l Voluntarily incident reporting provide important and detailed information about perioperative patient safety problems. The most important finding of the present study is that professionals themselves report non- compliance with SOPs associated with human failure is an important area for improvement. Furthermore shortcom- ings in communication, mistakes, and forgetting were identified as important targets for improvement to reduce perioperative incidents in our hospital. This finding re- quires acknowledgement of the risk of human attitude, behaviour and failure. Moreover these findings challenge for the development of tools to improve guideline adher- ence and effective communication, in order to improve perioperative patient safety. Discussion emergency scenario), time constraints, unfamiliarity with the sys- tem, problems with the definitions of what constitutes a reportable incident or near-incident, lack of a hospital policy of ‘no disciplinary action’ on incident reporting, lack of anonymity, lack of feedback and confusing aims of the reporting system as such [13,18]. However, the best policy to improve reporting behaviour is currently unknown [39]. Unfortunately, because of the risk of under-reporting, voluntary incident reporting is not a reliable instrument to monitor performance in e.g. the plan-do-study-act cycle. However, it may be used as qualitative monitor to identify areas that require further efforts to improve perioperative patient safety. Author details 1 1Department of Operating Theatres, Radboud University Medical Center, Geert Grooteplein-Zuid 10, Internal postal code 738, 6525, GA, Nijmegen, The Netherlands. 2Department of IQ Healthcare, Radboud University Medical Center, Nijmegen, The Netherlands. 3Department of Anesthesiology, Radboud University Medical Center, Nijmegen, The Netherlands. 21. Flanagan JC: The critical incident technique. Psychol Bull 1954, 51:327–358. 22. Cooper JB, Newbower RS, Long CD, McPeek B: Preventable anesthesia mishaps: a study of human factors. Anesthesiology 1978, 49:399–406. 23. Mahajan RP: Critical incident reporting and learning. Br J Anaesth 2010, 105:69–75. Received: 24 October 2014 Accepted: 27 November 2014 24. Barach P, Small SD: Reporting and preventing medical mishaps: lessons from non-medical near miss reporting systems. BMJ 2000, 320:759–763. Competing interests 14. Boelle PY, Garnerin P, Sicard JF, Clergue F, Bonnet F: Voluntary reporting system in anaesthesia: is there a link between undesirable and critical events? Qual Health Care 2000, 9:203–209. 15. van Klei WA, Hoff RG, van Aarnhem EE, Simmermacher RK, Regli LP, Kappen TH, van Wolfswinkel L, Kalkman CJ, Buhre WF, Peelen LM: Effects of the introduction of the WHO “Surgical Safety Checklist” on in-hospital mortality: a cohort study. Ann Surg 2012, 255:44–49. Authors’ contribution AH wrote the article and contributed substantially to the acquisition, analysis and interpretation of data. HC participated in drafting the article and contributed substantially to the interpretation of data. HG contributed substantially to the conception and design of the study, to the interpretation of data, and critically revised the article. AW contributed substantially to the conception and design of the study, to the analysis and interpretation of data, and critically revised the article. JD contributed substantially to the conception and design of the study, to the analysis and interpretation of data, and participated in drafting and critically revising the article. All authors approve this final version to be published. All authors agree to be accountable for all aspects of the work. 16. Crolla RM, van der Laan L, Veen EJ, Hendriks Y, van Schendel C, Kluytmans J: Reduction of surgical site infections after implementation of a bundle of care. PLoS One 2012, 7:e44599. 17. Cooke DL, Dunscombe PB, Lee RC: Using a survey of incident reporting and learning practices to improve organisational learning at a cancer care centre. Qual Saf Health Care 2007, 16:342–348. 18. Haller G, Courvoisier DS, Anderson H, Myles PS: Clinical factors associated with the non-utilization of an anaesthesia incident reporting system. Br J Anaesth 2011, 107:171–179. Acknowledgements W f l f h 19. Grol RWM, Eccles M, Davis D: Improving patient care. The implementation of change in health care. 2013:40–63 We are grateful for the advice and hospital data provided by Silvia van Gils, Process Improvement and Innovation Consultant, Radboud university medical center. 20. Fourcade A, Blache JL, Grenier C, Bourgain JL, Minvielle E: Barriers to staff adoption of a surgical safety checklist. BMJ Qual Saf 2012, 21:191–197. Strength and limitations of the study We have used voluntarily reporting of incidents as an important source of information and hypothesized that this would make us capable to contribute to understand- ing and identifying clues for improving perioperative safety [23,40]. The present study highlights the areas where further efforts are required to improve patient safety. Because of the likelihood of under-reporting, our dataset cannot be considered a reproduction of all actually Page 9 of 10 Page 9 of 10 Heideveld-Chevalking et al. Patient Safety in Surgery (2014) 8:46 References 25. Anderson JE, Kodate N, Walters R, Dodds A: Can incident reporting improve safety? Healthcare practitioners’ views of the effectiveness of incident reporting. Int J Qual Health Care 2013, 25:141–150. 1. Wagner C, Van der Wal G: Voor een goed begrip, bevordering 1. Wagner C, Van der Wal G: Voor een goed begrip, bevordering patiëntveiligheid vraagt om heldere definities. Medisch Contact 2005, 60:1888–1891. 26. Vincent C, Neale G, Woloshynowych M: Adverse events in British hospitals: preliminary retrospective record review. BMJ 2001, 322:517–519. 2. 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BMJ 2000, 320:768–770. 9. de Bruijne MC: ZM, Hoonhout LHF, Wagner C: Onbedoelde schade in Nederlandse ziekenhuizen, dossieronderzoek van ziekenhuisopnames in 2004. Amsterdam/Utrecht: EMGO/NIVEL; 2007. 33. Aaa N: The impact of organizational climate on safety culture and individual behavior. Saf Sci 2000, 34:99–110. 10. LangelaanM BRJ, Broekens MA, Siemerink KM, Steeg L, van de Asscheman H, Bruijne MC, de Wagner C: Monitor Zorggerelateerde schade 2008, Dossieronderzoek in Nederlandse ziekenhuizen. NIVEL/EMGO+: Amsterdam/ Utrecht; 2010. 34. Mardon RE, Khanna K, Sorra J, Dyer N, Famolaro T: Exploring relationships between hospital patient safety culture and adverse events. J Patient Saf 2010, 6:226–232. 35. Lingard L, Espin S, Whyte S, Regehr G, Baker GR, Reznick R, Bohnen J, Orser B, Doran D, Grober E: Communication failures in the operating room: an observational classification of recurrent types and effects. Qual Saf Health Care 2004, 13:330–334. 11. 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Runciman WB, Merry A: A tragic death: a time to blame or a time to learn? Qual Saf Health Care 2003, 12:321–322. References Patient Safety in Surgery (2014) 8:46 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit
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Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula
Frontiers in plant science
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ETH Library ETH Library Journal Article Author(s): Ribeiro, Bianca; Erffelinck, Marie-Laure; Lacchini, Elia; Ceulemans, Evi; Colinas, Maite; Williams, Clara; Van Hamme, Evelien; De Clercq, Rebecca; Perassolo, Maria; Goossens, Alain Publication date: 2022-09-30 Rights / license: Creative Commons Attribution 4.0 International Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula Kanellis, Aristotle University of Thessaloniki, Greece REVIEWED BY Chenggang Liu, University of North Texas, United States Barunava Patra, University of Kentucky, United States Shasha Li, Northwest A&F University, China *CORRESPONDENCE Alain Goossens alain.goossens@psb.vib-ugent.be †PRESENT ADDRESS Bianca Ribeiro, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium Maite Colinas, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland ‡These authors have contributed equally to this work Bianca Ribeiro 1,2†‡, Marie-Laure Erffelinck 1,2‡, Elia Lacchini 1,2‡, Evi Ceulemans 1,2, Maite Colinas 1,2†, Clara Williams 1,2, Evelien Van Hamme 3, Rebecca De Clercq 1,2, Maria Perassolo 1,2,4,5 and Alain Goossens 1,2*§ Bianca Ribeiro 1,2†‡, Marie-Laure Erffelinck 1,2‡, Elia Lacchini 1,2‡, Evi Ceulemans 1,2, Maite Colinas 1,2†, Clara Williams 1,2, Evelien Van Hamme 3, Rebecca De Clercq 1,2, Maria Perassolo 1,2,4,5 and Alain Goossens 1,2*§ Bianca Ribeiro 1,2†‡, Marie-Laure Erffelinck 1,2‡, Elia Lacchini 1,2‡, Evi Ceulemans 1,2, Maite Colinas 1,2†, Clara Williams 1,2, Evelien Van Hamme 3, Rebecca De Clercq 1,2, Maria Perassolo 1,2,4,5 and Alain Goossens 1,2*§ 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, 2VIB Center for Plant Systems Biology, Ghent, Belgium, 3VIB Bio Imaging Core, Ghent, Belgium, 4Cátedra de Biotecnología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina, 5Instituto de Nanobiotecnologı´a (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad de Buenos Aires, Buenos Aires, Argentina SPECIALTY SECTION This article was submitted to Plant Metabolism and Chemodiversity, a section of the journal Frontiers in Plant Science RECEIVED 24 March 2022 ACCEPTED 07 September 2022 PUBLISHED 30 September 2022 CITATION Ribeiro B, Erffelinck M-L, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M and Goossens A (2022) Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. Front. Plant Sci. 13:903793. doi: 10.3389/fpls.2022.903793 Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA- modulated basic helix-loop-helix (bHLH) transcription factors (TFs), triterpene saponin biosynthesis activating regulator 1 (TSAR1) and TSAR2, have previously been identified as direct activators of TS biosynthesis in the model legume Medicago truncatula. Originally published in: Originally published in: Frontiers in Plant Science 13, https://doi.org/10.3389/fpls.2022.903793 This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. TYPE Original Research PUBLISHED 30 September 2022 DOI 10.3389/fpls.2022.903793 Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula OPEN ACCESS EDITED BY Angelos K. Kanellis, Aristotle University of Thessaloniki, Greece REVIEWED BY Chenggang Liu, University of North Texas, United States Barunava Patra, University of Kentucky, United States Shasha Li, Northwest A&F University, China *CORRESPONDENCE Alain Goossens alain.goossens@psb.vib-ugent.be †PRESENT ADDRESS Bianca Ribeiro, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium Maite Colinas, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland ‡These authors have contributed equally to this work §Senior author SPECIALTY SECTION This article was submitted to Plant Metabolism and Chemodiversity, a section of the journal Frontiers in Plant Science RECEIVED 24 March 2022 ACCEPTED 07 September 2022 PUBLISHED 30 September 2022 CITATION Ribeiro B, Erffelinck M-L, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M and Goossens A (2022) Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. Front. Plant Sci. 13:903793. doi: 10.3389/fpls.2022.903793 OPEN ACCESS EDITED BY Angelos K. Introduction moieties, additionally diversifying the TS compendium (Seki et al., 2015) (Supplementary Figure 1). The past decades, great progress has been made in the quest for transcription factors (TFs) that are modulated by JA or other cues and that control the production of specialized metabolites in plants (De Geyter et al., 2012; Zhou and Memelink, 2016; Goossens et al., 2017; Colinas and Goossens, 2018; Shoji, 2019). Particularly relevant are the basic helix-loop-helix (bHLH) TFs (Goossens et al., 2017). MYC2 was the first bHLH TF reported to control different branches of terpene biosynthesis in Arabidopsis thaliana, Solanum lycopersicum and Artemisia annua, among others (Hong et al., 2012; Kazan and Manners, 2013; Spyropoulou et al., 2014; Goossens et al., 2017). Later, in the medicinal plant Catharanthus roseus, source of the anti-cancer drugs vinblastine and vincristine, both MYC2 as well as MYC2- unrelated bHLH TFs, such as bHLH iridoid synthesis 1 (BIS1) and BIS2, were found to elicit the monoterpenoid branch of the monoterpenoid indole alkaloid (MIA) pathway (Zhang et al., 2011; Van Moerkercke et al., 2015; Van Moerkercke et al., 2016; Goossens et al., 2017; Schweizer et al., 2018; Liu et al., 2021). Likewise, the M. truncatula orthologs of the BIS TFs, i.e. triterpene saponin biosynthesis activating regulator 1 (TSAR1) and TSAR2, were reported to transcriptionally regulate the non- haemolytic and haemolytic branch of TS biosynthesis, respectively (Mertens et al., 2016a). Plants are continuously challenged with biotic and abiotic stresses. To cope specifically with biotic stresses, such as herbivore feeding or pathogen attack, plants can trigger the biosynthesis of various classes of specialized defense metabolites. A well-known class is that of the structurally and functionally diverse triterpene saponins (TS), which are produced in distinct plant species, including legumes such as Medicago truncatula, and which are particularly valuable for pharmaceutical and agrochemical purposes (Chang and Keasling, 2006; Ajikumar et al., 2008; Kumari et al., 2013; Moses et al., 2014a; Netala et al., 2015). Phytohormones play an essential role in the stress- induced elicitation of these compounds, again illustrated by the fact that M. truncatula TS production is transcriptionally controlled by a JA signaling cascade (Suzuki et al., 2002; De Geyter et al., 2012; Pollier et al., 2013a; Mertens et al., 2016a; Goossens et al., 2017). The early committed steps in TS biosynthesis occur mainly at the endoplasmic reticulum (ER) membrane and start from 2,3-oxidosqualene, which is the last common precursor with the phytosterols. Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula Here, we report on the involvement of the core endoplasmic reticulum (ER) stress-related basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing of M. truncatula bZIP17 and bZIP60 proteins were altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure. M. truncatula bZIP17 and bZIP60 proteins were shown to localize in the nucleus and appeared to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes. Furthermore, interference between ER stress-related bZIP and JA-modulated bHLH TFs in the regulation of JA-dependent terpene biosynthetic pathways may be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus. Frontiers in Plant Science 01 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 KEYWORDS triterpene, saponin, Medicago catharanthus, catharanthus, jasmonate, endoplasmic reticulum, bZIP, basic helix-loop-helix Introduction Subsequent cyclization of 2,3-oxidosqualene by saponin-specific 2,3-oxidosqualene cyclases (OSC)s, more specifically b-amyrin synthase (BAS) in M. truncatula, yields the pentacyclic oleanane-type triterpene backbone b-amyrin (Supplementary Figure 1). Subsequent competitive action of two cytochrome P450-dependent monooxygenases (P450s) results in branching of the M. truncatula TS biosynthetic pathway, resulting in the production of two specific classes: the haemolytic and non-haemolytic TS (Gholami et al., 2014). The haemolytic TS branch is defined by three consecutive oxidations at position C-28 of b-amyrin by the P450 CYP716A12, thereby yielding oleanolic acid (Carelli et al., 2011; Fukushima et al., 2011). Positions C-2 and C-23 can be further oxidized by respectively CYP72A67 and CYP72A68v2 (Fukushima et al., 2013; Biazzi et al., 2015). The non-haemolytic branch starts with an oxidation reaction at position C-24 of b- amyrin, catalyzed by CYP93E2, and thereby precluding oxidation at position C-28 (Fukushima et al., 2013; Moses et al., 2014b). Subsequent oxidation at position C-22 by CYP72A61v2 yields soyasapogenol B (Fukushima et al., 2013). UDP-dependent glycosyltransferases (UGTs) can further decorate the triterpene aglycones through attachment of sugar Posttranslational regulatory mechanisms of TS biosynthesis have also been described (Hemmerlin, 2013; Erffelinck and Goossens, 2018). Particularly, the JA-inducible really interesting new gene (RING) membrane-anchor (RMA) E3 ubiquitin ligase makibishi 1 (MKB1) has been reported to control TS biosynthesis in M. truncatula by targeting 3- hydroxy-3-methylglutaryl-CoA reductase (HMGR), a rate- limiting enzyme in sterol and TS precursor biosynthesis, for degradation by the 26S proteasome (Pollier et al., 2013a). MKB1 forms part of the ER-associated degradation (ERAD) machinery, which monitors the correct folding of membrane and secretory proteins whose biogenesis takes place in the ER. Recently, we also identified a heat shock protein 40 that interacts with MKB1 to support its activity (Erffelinck et al., 2021).When plants are evoked with environmental stresses, a programed defense response is launched, in which the ERAD, the unfolded protein response (UPR) and other ER stress responses play an important role (Malhotra and Kaufman, 2007; Liu and Howell, 2010b). Frontiers in Plant Science 02 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 10.3389/fpls.2022.903793 The coding sequences of C. roseus bZIP17 and bZIP60 were amplified from C. roseus var. “Little bright eyes” cDNA with Q5® High-Fidelity DNA Polymerase (New England BioLabs®) and recombined into the entry vector pDONR221 (Gateway®). After sequence verification, the entry clones were recombined with the destination vector p2GW7 (Karimi et al., 2002) for N. tabacum protoplast assays (Vanden Bossche et al., 2013). Introduction The promoter regions of GES, G10H and IS recombined with the vector pGWL7 (Karimi et al., 2002) and the full-length coding sequence for BIS1 recombined with the destination vector p2GW7 (Karimi et al., 2002) had previously been obtained by Van Moerkercke et al. (2015). For expression in flower petals under control of the CaMV35S promoter, entry clones were recombined with pK7WG2D (Karimi et al., 2002), using LR Clonase™enzyme mix (ThermoFisher). Eukaryotic cells have developed signaling networks in response to ER stress, through ER stress sensors that are tethered at the ER membrane. In the model plant A. thaliana, several ER stress- specific sensors, including the RNase inositol-requiring enzyme 1 (IRE1), the basic leucine zipper (bZIP) TFs bZIP17 and bZIP28, and the NAC TFs NAC062 and NAC089, have been reported (Liu et al.,2007a;Iwataet al.,2008;LiuandHowell,2010a;Morenoetal., 2012; Yang et al., 2014a; Yang et al., 2014b; Henriquez-Valencia et al., 2015; Kim et al., 2018; Howell, 2021). The primary target of IRE1 in response to ER stress is bZIP60 mRNA, which is spliced, causing a frame shift and thereby the elimination of the transmembrane domain of the bZIP60 TF at translation. This truncated version is consequently translocated to the nucleus, where it can install a specific ER stress response. An analogous ER-to-nucleus translocation occurs with bZIP17 and bZIP28, but through proteolytic cleavage (Liu et al., 2007a; Liu et al., 2007b; Howell, 2021). Flower petals of C. roseus var. “Little bright eyes” plants (grown under greenhouse conditions) were infiltrated with Agrobacterium tumefaciens C58C1 harboring the constructs for overexpression as previously described (Schweizer et al., 2018). Here, we explored the regulatory interplay between JA and ER stress signaling in the model legume M. truncatula. We demonstrate that M. truncatula bZIP17 and bZIP60 can interfere with the transactivation of TS-specific gene promoters by the JA- responsive TSAR1 and TSAR2 TFs and thereby modulate the output of the JA response. We also provide evidence that the interplay between these two TF sets may be conserved in the plant kingdom by demonstrating that it also occurs in the regulation of terpene biosynthesis in the distinct plant C. roseus. DNA constructs For the elicitation of TS pathway gene expression, 100 µM methyl jasmonate (MeJA) was added to the medium. For the induction of ER stress, 300 mM NaCl, 0.5 mM SA, or 2 mM DTT was added to the medium. Given that we anticipated that the MeJA concentration that we typically employ to elicit TS biosynthesis may be too strong and possibly mimic antagonistic effects of the ER stress agents, we first determined the minimal MeJA concentration with which TS pathway gene expression could still be induced. qRT-PCR analysis of control (CTR) M. truncatula hairy root lines indicated that at a concentration of 5 µM MeJA, a pronounced and significant induction of TS pathway gene expression could still be observed (Supplementary Figure 2). This concentration was used for all further experimentation, except for SA, which, as a reported potent JA antagonist of the JA signaling pathway in A. thaliana (Van Der Does et al., 2013), was still combined with a MeJA concentration of 100 µM. Sequences of the full-length ORFs of bZIP17 (Medtr7g088890) and bZIP60 (Medtr1g050502) were obtained from the M. truncatula genome version 4.0 (Tang et al., 2014) and were cloned using Gateway® technology (Invitrogen). Full-length and spliced coding sequences for bZIP17 and bZIP60 were PCR amplified (for primers, see Supplementary Table 1) and recombined into the donor vector pDONR221. After sequence verification, the entry clones were recombined with the destination vector p2GW7 for Nicotiana tabacum protoplast assays (Vanden Bossche et al., 2013). The promoter regions of HMGR1, CYP93E2, HMGR4, CYP72A67, UGT73F3 and BAS recombined with the vector pGWL7 and the full-length coding sequences for TSAR1 and TSAR2 recombined with the destination vector p2GW7 had previously been obtained (Mertens et al., 2016a). For the generation of M. truncatula hairy roots, sequence-verified entry clones were recombined with the destination vector pK7WG2D for overexpression and pK7GWIWG2(II) for silencing (Karimi et al., 2007). Primers used for cloning of overexpression and silencing constructs and for quantitative reverse transcription PCR (qRT-PCR) analysis are reported in Supplementary Table 1. Generation and cultivation of Medicago truncatula hairy roots Sterilization of M. truncatula seeds (ecotype Jemalong J5), transformation of seedlings by A. rhizogenes (strain LBA 9402/ 12), and the subsequent generation of hairy roots were carried out as described previously (Pollier et al., 2011). Hairy roots were cultivated for 21 d in liquid medium to provide proper amounts for RNA extraction. frontiersin.org Confocal microscopy Control and MKB1KD (knock-down line of MKB1) (Pollier et al., 2013a) hairy roots were cultivated in nutritive liquid medium (Murashige and Skoog with vitamins supplemented Frontiers in Plant Science 03 frontiersin.org 10.3389/fpls.2022.903793 Ribeiro et al. with 1% sucrose) for 2 w and treated with 100 µM MeJA or ethanol (mock treatment) for 24 h. Confocal images (16-bit) were captured with an LSM880 confocal microscope equipped with an Airyscan detector (Zeiss, Jena, Germany). Images were taken in super-resolution, FAST mode by using a Plan-Apochromat 63x/ 1.4 oil objective (1584 × 1584, pixel size: 43 nm × 43 nm). EGFP was excited using the 488-nm line of an Argon laser (30%) and emission was captured between 495 and 550 nm. Z-sections were made every 185 nm. Images were calculated through pixel reassignment and Wiener filtering by using the built-in “Airyscan Processing” command in the Zen software. Leuven) for Illumina NextSeq500 RNA sequencing (75 nt, single-end read). As described (Pollier et al., 2013b) and using default parameters, the raw RNA-Seq reads were quality- trimmed and mapped on the M. truncatula genome v4.0 (Tang et al., 2014) with TOPHAT v2.0.6. Uniquely mapped reads were counted and FPKM values were determined with CUFFLINKS version v2.2.1 (Trapnell, 2013). Differential expression analyses were performed using Cuffdiff (Trapnell, 2013). RNA-Seq data have been deposited in the ArrayExpress database (accession E-MTAB-11668). Leuven) for Illumina NextSeq500 RNA sequencing (75 nt, single-end read). As described (Pollier et al., 2013b) and using default parameters, the raw RNA-Seq reads were quality- trimmed and mapped on the M. truncatula genome v4.0 (Tang et al., 2014) with TOPHAT v2.0.6. Uniquely mapped reads were counted and FPKM values were determined with CUFFLINKS version v2.2.1 (Trapnell, 2013). Differential expression analyses were performed using Cuffdiff (Trapnell, 2013). RNA-Seq data have been deposited in the ArrayExpress database (accession E-MTAB-11668). Subcellular localization of the bZIP proteins was determined via Agrobacterium-mediated transient expression in N. benthamiana epidermal cells. bZIP proteins, either full length or truncated, were fused at the C-terminus of eGFP using the Gateway® vector pB7WGF2. To verify subcellular localization, target proteins were co-transformed together with fluorescent markers for nucleus and ER using pB7m34GW:p35S::NLS-3XCERULEAN and pH7WG2:: KDEL-RFP637, respectively. Each vector used was transformed in the A. tumefaciens strain C58C1 and a bacterial absorbance A600 nm of 0.8 was used for infiltrating each construct. Phylogenetic analysis M. truncatula hairy root samples were extracted as described (Pollier et al., 2011; Ribeiro et al., 2020) and subjected to Ultra Performance Liquid Chromatography High Resolution Mass Spectrometry (UPLC-HRMS) at the VIB Metabolomics Core Ghent (VIB-MCG). 10 µl was injected on a Waters Acquity UHPLC device connected to a Vion HDMS Q-TOF mass spectrometer (Waters, Manchester, UK). Chromatographic separation was carried out on an ACQUITY UPLC BEH C18 (150 × 2.1 mm, 1.7 mm) column (Waters, USA); column temperature was maintained at 40°C. A gradient of two buffers was used for separation: buffer A (99:1:0.1 water:acetonitrile: formic acid, pH 3) and buffer B (99:1:0.1 acetonitrile:water: formic acid, pH 3), as follows: 99% A buffer decreased to 50% A from 0 to 30 min, decreased to 30% from 30 to 35 min, and decreased to 0% from 0 to 37 min. The flow rate was set to 0.35 mL min−1. Electrospray ionization (ESI) was applied, LockSpray ion source was operated in negative ionization mode under the following specific conditions: capillary voltage, 2.5 kV; reference capillary voltage, 3 kV; source temperature, 120°C; desolvation gas temperature, 550°C; desolvation gas flow, 800 L h−1; and cone gas flow, 50 L h−1. The collision energy for full MS scan The bZIP proteins from A. thaliana and M. truncatula were selected based on Dröge-Laser et al. (2018) and Wang et al. (2015), respectively. The amino acid sequences of all selected bZIP proteins were obtained through PLAZA (Van Bel et al., 2018) and the Catharanthus roseus Functional Genomics Database (croFGD; http://bioinformatics.cau.edu.cn/croFGD/) (She et al., 2019). These were aligned using MAFFT. The conserved blocks were determined using GBlocks 0.91b and manual curation. IQTREE was used for model selection (Kalyaanamoorthy et al., 2017), after which the best substitution model was selected; the maximum likelihood phylogenetic tree was generated using 1000 bootstrap replicates (Nguyen et al., 2015). The tree figure was made using FigTree software. Confocal microscopy 72 h after infiltration, leaf sections were collected and fluorescence analyzed by confocal microscopy using a Zeiss LSM710 laser scanner microscope with Plan-Apochromat 20x/0.8 M27. The nuclear marker CFP was excited using a 405-nm laser, while 518-nm and 488-nm Argon lasers were adopted for excitation of the ER RFP marker and GFP::bZIPs fusions, respectively. Z-sections were taken every 2 um. Hairy roots and N. benthamiana infiltration images were processed generating maximum intensity projections and adding scale bars using Fiji software. Semi-quantitative qRT-PCR analysis Frozen hairy roots were ground and the material was used to prepare total RNA and first-strand complementary DNA using the RNeasy Mini Kit (Qiagen) and the iScript cDNA Synthesis Kit (Bio-Rad), respectively, according to each manufacturer’s instructions. qRT-PCR primers for bZIP17 and bZIP60 were designed using Beacon Designer 4 (Premier Biosoft International) (Supplementary Table 1). The M. truncatula 40S ribosomal protein S8 and translation elongation factor 1a were used as reference genes. The qRT-PCRs were carried out with a LightCycler 480 (Roche) and the LightCycler 480 SYBR Green I Master Kit (Roche) according to the manufacturer’s guidelines. Three replicates were made for each reaction and the relative expression levels using multiple reference genes were calculated using qBase (Hellemans et al., 2007). Frontiers in Plant Science RNA-Seq analysis Total RNA of three independent transformant lines per construct was submitted to VIB Nucleomics Core (VIB, Frontiers in Plant Science 04 frontiersin.org 10.3389/fpls.2022.903793 Ribeiro et al. with caltrop-like structures and a perturbed TS profile, accompanied by a TS-specific negative transcriptional feedback (Pollier et al., 2013a). We hypothesized that perturbed ER functionality could trigger an ER-inherent mechanism to manage ER capacity and integrity, and thereby (in)directly modulate TS metabolism. Therefore, we performed confocal imaging to monitor the ER network structure of M. truncatula MKB1KD and CTR hairy roots. Hereby, we exploited the fact that the MKB1KD hairy roots also ectopically express ER-targeted GFP (GFP-KDEL) under the control of a rolD promoter, which is used as a visual marker for transformation. The ER network structure was notably altered in MKB1KD hairy roots when compared to CTR lines, for instance exhibiting less of the characteristic three-way junctions (Figure 1). These phenotypical features were even more pronounced in MKB1KD hairy roots that were elicited with MeJA compared to mock- treated MKB1KD hairy roots. Interestingly, MeJA treatment of CTR roots also led to a visual alteration of the ER network structure, but the effect was distinct from or far less pronounced than the effect caused by loss of MKB1 function (Figure 1). was set at 6 eV for low energy settings, for high energy settings (HDMSe) it was ramped from 20 to 70 eV. Mass range was set from 120 to 2000 Da, scan time was set at 0.1 s. Nitrogen (greater than 99.5%) was employed as desolvation and cone gas. Leucine- enkephalin (100 pg mL−1 solubilized in water:acetonitrile 1:1 [v/ v], with 0.1% formic acid) was used for the lock mass calibration, with scanning every 2 min at a scan time of 0.1 s. Profile data was recorded through UnifiWorkstation v2.0 (Waters). Data processing was done with Progenesis QI v2.4 (Waters). Data were pre-processed by removing features with constant or infinity values across samples. Zero values were replaced by 1.0e-10 for statistical processing. Subsequently, data were transformed using the Arch-sinh function and scaled using the Pareto method. Each condition was analyzed in triplicate on three independent biological replicates for both CTR and bZIP17KD lines. Data were analyzed by two-way ANOVA considering only features with a p value ≤0.01 across samples. RNA-Seq analysis Ontology for selected candidate TS was determined by comparison with in-house metabolites databases integrated with ChEBI features (Chemical Entities of Biological Interest - EMBL-EBI) as well as by matching features against previously identified TS (Pollier et al., 2011; Ribeiro et al., 2020). Transient expression assays in protoplasts Given that MKB1KD hairy roots display an altered morphology with irregular cell shapes and the absence of intercellular spaces (Pollier et al., 2013a), the differences in ER network structure may not necessarily reflect ER stress caused by the perturbed ERAD machinery but rather an intracellular reorganization following the modifications in the cellular structure. Therefore, a transcript profiling study by RNA-sequencing (RNA-Seq) was performed on three independent M. truncatula CTR and MKB1KD hairy root lines, either mock- or MeJA-treated. A total of 415,338,234 single-end reads of 50 nt were obtained and mapped on the M. truncatula genome version 4.0 (Mt4.0) (Tang et al., 2014). The resulting differential expression profiles were then mined for the closest M. truncatula orthologs of a list of known A. thaliana ER stress marker genes (Howell, 2013). As such, a set of genes encoding luminal-binding protein 1/2 (BiP1/2; Medtr8g099945), BiP3 (Medtr8g099795), stromal cell derived factor 2 (SDF2; Medtr3g106130), sorbitol dehydrogenase (SDH; Medtr1g025430), calnexin (CNX; Medtr3g098430), UDP-glucose:glycoprotein glucosyltransferase (UGGT; Medtr2g006960), heat-shock protein 70 (HSP70; Medtr3g081170), and protein disulfide isomerase-like 1-1 (PDIL1-1; Medtr3g088220) were found to be significantly upregulated in MKB1KD roots compared to CTR roots, both upon mock and MeJA treatment (Figure 2A). Notably, MeJA elicitation itself was also sufficient to trigger an ER stress response in CTR roots, albeit less pronounced (Figure 2A), in accordance with the moderately altered ER network structure (Figure 1). Together, these data suggest that a transcriptome reminiscent of Transient expression assays in N. tabacum BY-2 protoplasts were carried out as described by Vanden Bossche et al. (2013). Protoplasts were transfected with a reporter, an effector, and a normalizer plasmid. The effector plasmids contained the TSAR, BIS, or bZIP ORFs driven by the CaMV35S promoter; the reporter plasmids contained the FIREFLY LUCIFERASE (fLUC) ORF under control of the target promoters. The normalization plasmid contained the Renilla luciferase (rLUC) under control of the CaMV35S promoter. Protoplasts were incubated overnight and lysed. fLUC and rLUC readouts were collected using the Dual-Luciferase® Reporter Assay System (Promega). Each assay incorporated eight biological repeats. Promoter activities were normalized by dividing the fLUC values with the corresponding rLUC values and the average of the normalized fLUC values was calculated and set out relatively to the control fLUC values, i.e. measured in protoplasts transfected with an effector plasmid carrying a GUS control gene. Frontiers in Plant Science Confocal imaging exposes an altered ER network structure in Medicago truncatula MKB1KD hairy roots Previously, we have shown that silencing of MKB1 in M. truncatula hairy roots (MKB1KD) results in dissociated roots Frontiers in Plant Science 05 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 FIGURE 1 Silencing of MKB1 and MeJA elicitation alters the ER network structure. Shown are maximum intensity projections of images obtained by Airyscan microscopy of ER-targeted GFP in stably transformed CTR and MKB1KD M. truncatula hairy roots. Left, CTR roots elicited (24 h) with ethanol (mock) or 100 µM MeJA. Right, mock- and MeJA-treated MKB1KD roots. Scale bars = 20 mm. FIGURE 1 Silencing of MKB1 and MeJA elicitation alters the ER network structure. Shown are maximum intensity projections of images obtained by Airyscan microscopy of ER-targeted GFP in stably transformed CTR and MKB1KD M. truncatula hairy roots. Left, CTR roots elicited (24 h) with ethanol (mock) or 100 µM MeJA. Right, mock- and MeJA-treated MKB1KD roots. Scale bars = 20 mm. AtbZIP28 and AtbZIP49, whereas AtbZIP60 is part of the group K as a unique gene. In the M. truncatula genome, the bZIP TFs groups B and K are respectively and solely represented by Medtr7g088890 and Medtr1g050502 (Supplementary Figures 3, 4). It therefore appears that M. truncatula might not have other paralogs for the bZIP TF genes in either group B and K, or, alternatively, they are not annotated yet by the Mt4.0 genome, as for instance is also the case for the MKB1 gene. However, our results are in accordance with a genome-wide analysis of the bZIP TF gene family previously carried out for six legume genomes (Glycine max, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, Lotus japonicas, and M. truncatula), where also only a single ortholog for both group B and K bZIP TFs was encountered in five of the legumes studied (Wang et al., 2015). G. max formed a notable exception, with two paralogs in each an ER stress response is not only triggered by loss of MKB1 function but also by JA elicitation. We further assessed the transcript levels of the putative M. truncatula orthologs of the core A. thaliana ER stress-related bZIP TFs, AtbZIP17, AtbZIP28 and AtbZIP60. Because the bZIP TF gene family is well represented in the M. truncatula genome, with at least 81 potential members (Tang et al., 2014), first a phylogenetic analysis for all potential M. truncatula bZIP TF genes that were annotated by Wang et al. Confocal imaging exposes an altered ER network structure in Medicago truncatula MKB1KD hairy roots (2015) was carried out to define the putative M. truncatula bZIP17, bZIP28 and bZIP60 orthologs. Amino acid sequences of all M. truncatula bZIP gene entries, as well as the previously reported A. thaliana bZIP TF genes (Dröge-Laser et al., 2018), were retrieved from PLAZA (Van Bel et al., 2018). As previously reported by Dröge-Laser et al. (2018), AtbZIP17 is part of the group B that also comprises Frontiers in Plant Science 06 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 B C A FIGURE 2 Silencing of MKB1 and MeJA elicitation both trigger an ER stress response in M. truncatula. (A, B) RNA-Seq analysis of M. truncatula orthologs of A. thaliana ER stress marker (A) and bZIP TF (B) genes in CTR and MKB1KD roots, mock- or MeJA-treated for 4 h. The Y-axis represents the normalized fragments per kb of exon per million fragments mapped (FPKM) values. Error bars designate SE (n = 3, except for MeJA-elicited CTR where n = 2). (C) qRT-PCR analysis for the detection of spliced bZIP60 transcripts in CTR and MKB1KD roots, mock- or MeJA-treated for 4 h. The error bars designate SE (n = 3). Different letters indicate statistically significant differences at P < 0.05 as determined by ANOVA, post hoc Tukey analysis. A B C RE 2 C B Silencing of MKB1 and MeJA elicitation both trigger an ER stress response in M. truncatula. (A, B) RNA-Seq analysis of M. truncatula orthologs of A. thaliana ER stress marker (A) and bZIP TF (B) genes in CTR and MKB1KD roots, mock- or MeJA-treated for 4 h. The Y-axis represents the normalized fragments per kb of exon per million fragments mapped (FPKM) values. Error bars designate SE (n = 3, except for MeJA-elicited CTR where n = 2). (C) qRT-PCR analysis for the detection of spliced bZIP60 transcripts in CTR and MKB1KD roots, mock- or MeJA-treated for 4 h. The error bars designate SE (n = 3). Different letters indicate statistically significant differences at P < 0.05 as determined by ANOVA, post hoc Tukey analysis. group, which may be the consequence of a recent whole-genome duplication that G. max experienced (Wang et al., 2015). investigated, given that this would demand extensive additional experimentation and that the results for bZIP60 were more indicative of the activation of an ER stress response. Frontiers in Plant Science Medicago truncatula bZIP17 and bZIP60 can counteract transactivation of TS biosynthesis promoters by TSAR1 and TSAR2 Next, we hypothesized that the two bZIP17 and bZIP60 TFs could negatively regulate TS biosynthesis, hence explaining the TS-specific negative feedback observed in MKB1KD hairy roots (Pollier et al., 2013a). Localization of some form of the bZIPs in the nucleus is expected in this hypothesis. In silico analysis of the full-length M. truncatula bZIP60 and bZIP17 sequences confirmed the presence of the expected evolutionary splicing (for bZIP60) or protease cleavage (for bZIP17) sites and the respective ER-anchoring transmembrane domains and nuclear localization signals (Supplementary Figures 5, 6), which is in line with the evolutionary conservation of the UPR pathway (Howell, 2021). We designed N-terminal GFP-tagged versions of the full- length and truncated bZIP17 and bZIP60 proteins and expressed those transiently via Agroinfiltration of N. benthamiana leaves. Though we could not unambiguously determine a single subcellular localization of either the full-length or truncated variants, nuclear localization of both truncated M. truncatula bZIP17 and bZIP60 variants was clearly observed (Supplementary Figure 7). Next, we tested whether bZIP17 and bZIP60 were able to modulate the previously reported transactivation of a set of TS biosynthesis reporter constructs (promoter-fLUC) by TSAR1 or TSAR2 in a transient expression assay in N. tabacum Bright Yellow-2 (BY-2) protoplasts (Mertens et al., 2016a). For any of the tested reporter constructs, no effect of both the full-length bZIP17 and bZIP60 or the truncated versions lacking the transmembrane domain, bZIP17D and bZIP60D, on reporter fLUC activity was observed (exemplified with proCYP93E2 in Supplementary Figure 8). However, the high transactivation of proHMGR1, proHMGR4, probAS, and proCYP93E2 by TSAR1, as compared to the GUS control, was significantly repressed when combined with the truncated bZIP17D or bZIP60D, but not with full-length bZIP17 or bZIP60 (Figure 3A). A similar trend was observed for the transactivation of proHMGR1, proCYP72A67 and proUGT73F3 by TSAR2 (Figure 3B). Taken together, these data suggest that the truncated M. truncatula ER stress regulatory TFs bZIP17D and bZIP60D can counteract the transactivation of TS biosynthesis genes in M. truncatula by TSAR1 and TSAR2 bHLH factors and may therefore be We also managed to generate three independent bZIP17 and two independent bZIP60 knock-down lines (bZIP17KD and bZIP60KD), all showing approximately a fourfold reduction in bZIP expression (Figure 4B and Supplementary Figure 11B). A notable growth phenotype with a callus-like morphology was observed, especially for bZIP60KD hairy root lines (Figure 4A and Supplementary Figure 11A), but which is distinct from the caltrop-like MKB1KD phenotype. Functional characterization of Medicago truncatula bZIP17 and bZIP60 in planta To further evaluate the in planta role of bZIP17/bZIP60 in M. truncatula, we generated gain- and loss-of-function hairy root lines for the bZIP17/bZIP60 genes. Three independently generated root lines expressing the GUS gene were used as the control. For bZIP17, we generated three independent M. truncatula hairy root lines overexpressing bZIP17D (bZIP17D- OE, Supplementary Figure 9A). Quantitative reverse transcription-PCR (qRT-PCR) analysis confirmed overexpression of bZIP17D, though this seemingly did not increase total bZIP17 transcript levels in an appreciable manner (Supplementary Figure 9B). An average fourfold increase of bZIP60 transcript levels was also observed in those lines. Accordingly, the expression level of the chaperone BiP1/2 was significantly increased in the bZIP17D-OE hairy root lines, in line with previous observations in other species such as A. thaliana (Li et al., 2017) and maize (Yang et al., 2013). Only two of the nine tested TS biosynthesis genes, i.e. CYP716A2 and UGT73F3, did show significant differential expression in the three bZIP17D-OE lines compared to the CTR (Supplementary Figure 9C). Likewise, constitutive ectopic bZIP17D overexpression did not appear to comprehensively affect MeJA induction of TS biosynthesis genes, because a significant decrease in the MeJA response was only observed for two of the eight tested TS biosynthesis genes, i.e. BAS and CYP716A2 (Supplementary Figure 10). Unfortunately, we did not manage to generate lines overexpressing bZIP60D, despite several transformation rounds. Confocal imaging exposes an altered ER network structure in Medicago truncatula MKB1KD hairy roots Indeed, bZIP60 transcripts accumulated to significantly higher levels in MKB1KD hairy roots as compared to CTR roots, both in mock (2.6 fold) and MeJA (3.9 fold) conditions (Figure 2B). Furthermore, also MeJA treatment could elicit upregulation of bZIP60 transcript levels particularly in the MKB1KD (2.5 fold) hairy roots (Figure 2B). Contrary to bZIP17, ‘activation’ of bZIP60 can be assessed at the transcript level, given that it is regulated by IRE1- mediated splicing (Nagashima et al., 2011). To assess the splicing status of bZIP60, qRT-PCR was performed using primers Subsequent mining of the RNA-Seq data indicated that bZIP17 gene transcript levels were only significantly upregulated in MKB1KD hairy roots when elicited with MeJA compared to mock treatment of CTR and MBK1KD (~3.2 fold) (Figure 2B). However, given that activation and translocation of AtbZIP17 occurs posttranslationally following proteolytic cleavage in the Golgi (Liu et al., 2007a; Zhou et al., 2015; Kim et al., 2018), the lack of transcriptional elicitation of bZIP17 does not exclude that its activity could be enhanced posttranslationally by loss of MKB1 function or by MeJA elicitation. This possibility was not further Frontiers in Plant Science 07 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 10.3389/fpls.2022.903793 accountable for the TS-specific transcriptional feedback observed in MKBKD hairy roots (Pollier et al., 2013a). designed to detect the predicted spliced bZIP60 amplicon. This analysis indicated that the level of spliced bZIP60 amplicons was increased, both in MKB1KD compared to CTR and following elicitation with MeJA treatment, both in CTR and MKB1KD hairy roots (Figure 2C). Together, our transcriptome analysis supports the occurrence of an increased ER stress response, caused by loss of MKB1 function, and to a minor extent also by MeJA elicitation. Medicago truncatula bZIP17 and bZIP60 can counteract transactivation of TS biosynthesis promoters by TSAR1 and TSAR2 Furthermore, bZIP60 transcript levels were significantly increased in the bZIP17KD lines (Figure 4B). Conversely, no feedback on bZIP17 expression was observed in the bZIP60KD hairy root lines (Supplementary Figure 11B). Importantly however, the transcript levels of all analyzed TS biosynthesis genes, except those of TSAR1, were slightly, but significantly, increased in the bZIP17KD lines (Figure 4C). These observations were corroborated with metabolite profiling by liquid chromatography – mass spectrometry (LC-MS) analysis, which demonstrated significantly increased accumulation levels of several of the measured TS in the bZIP17KD lines, both in mock- and MeJA- Frontiers in Plant Science 08 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 B A FIGURE 3 M. truncatula bZIP17D and bZIP60D repress transactivation of TS biosynthesis gene promoters by TSAR TFs. (A, B) Transient transactivation assays in BY-2 protoplasts using the indicated target promoters fused to the fLUC reporter gene and TSAR1 (A) or TSAR2 (B) as effectors combined with full-length or truncated bZIP17 and bZIP60. The Y-axis shows fold change in normalized fLUC activity relative to the control transfection with proCaMV35S:GUS. The error bars designate SE of the mean (n = 8 biological repeats). Different letters indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. B A FIGURE 3 M. truncatula bZIP17D and bZIP60D repress transactivation of TS biosynthesis gene promoters by TSAR TFs. (A, B) Transient transactivation FIGURE 3 M. truncatula bZIP17D and bZIP60D repress transactivation of TS biosynthesis gene promoters by TSAR TFs. (A, B) Transient transactivation assays in BY-2 protoplasts using the indicated target promoters fused to the fLUC reporter gene and TSAR1 (A) or TSAR2 (B) as effectors combined with full-length or truncated bZIP17 and bZIP60. The Y-axis shows fold change in normalized fLUC activity relative to the control transfection with proCaMV35S:GUS. The error bars designate SE of the mean (n = 8 biological repeats). Different letters indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. modulated pathways (Pauwels et al., 2009; De Geyter et al., 2012). In order to find plant growth or stress conditions in which M. truncatula bZIP17 and bZIP60 might show an opposite or correlative expression pattern to those of the TS pathway genes, we mined the M. truncatula Gene Expression Atlas (MtGEA; http://bioinfo.noble.org/gene-atlas/) (He et al., 2009). Medicago truncatula bZIP17 and bZIP60 can counteract transactivation of TS biosynthesis promoters by TSAR1 and TSAR2 We particularly looked for conditions in which increased bZIP17 and bZIP60 expression was observed, in combination with a modulated TS gene expression pattern. Such a situation was encountered for bZIP17 in roots of M. truncatula seedlings grown in the presence of 180 mM NaCl (Supplementary Figure 12). This was not unexpected, given that in A. thaliana, salt stress was reported to invoke ER stress, for which the action of bZIP17 is needed for the stress coping mechanism (Li et al., 2017). This observation suggested that in planta situations, in which altered bZIP60 and bZIP17 activity may modulate TS gene expression, can indeed be encountered. treated conditions (Figure 5). In the bZIP17KD hairy root lines, the effect was less consistent, with only a slight but significant increase in the expression level of CYP716A12 and UGT73F3 (Supplementary Figure 11C). Unfortunately, we did not manage to generate hairy root lines silencing both bZIP17 and bZIP60, despite several transformation attempts. It is plausible to assume that because of the crucial roles of these bZIP factors for plant physiology, simultaneous loss-of-function of both is not viable. Nonetheless, the data obtained with the M. truncatula bZIP17KD lines support the role of at least bZIP17 as a negative attenuator of the TS pathway. Frontiers in Plant Science frontiersin.org ER stress inducers repress transcript levels of TS pathway genes Often, TFs that regulate specialized metabolite biosynthetic pathways are coexpressed with the target genes that encode the enzymes of the pathways, particularly when it concerns JA- As far as we could judge, the MtGEA did not seem to contain transcriptome data of other stress or growth conditions with a Frontiers in Plant Science 09 frontiersin.org frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 B C A FIGURE 4 Silencing of bZIP17 slightly increases TS biosynthesis gene expression in M. truncatula hairy roots. (A) Morphology of control (CTR) and bZIP17KD hairy roots. (B, C) qRT-PCR analysis of bZIP17, bZIP60, BiP1/2 genes (B) and TS biosynthetic genes (C) in three independent CTR and bZIP17KD hairy root lines. Values in the y-axis represent the expression ratio relative to the normalized transcript levels of CTR lines. The error bars designate SE (n = 3, technical repeats). Statistical significance was determined by a Student’s t-test (*P < 0.05, **P < 0.01, ***P < 0.001). B C C FIGURE 4 Silencing of bZIP17 slightly increases TS biosynthesis gene expression in M. truncatula hairy roots. (A) Morphology of control (CTR) and bZIP17KD hairy roots. (B, C) qRT-PCR analysis of bZIP17, bZIP60, BiP1/2 genes (B) and TS biosynthetic genes (C) in three independent CTR and bZIP17KD hairy root lines. Values in the y-axis represent the expression ratio relative to the normalized transcript levels of CTR lines. The error bars designate SE (n = 3, technical repeats). Statistical significance was determined by a Student’s t-test (*P < 0.05, **P < 0.01, ***P < 0.001). levels (Supplementary Figure 13). Next, we assessed TS pathway gene expression in the CTR line upon different stress treatments. NaCl treatment did not affect the basal expression of TS pathway genes, nor did it interfere with the MeJA elicitation thereof (Figure 6A). Different and more interesting trends were observed with the DTT and SA treatments. First, SA had a pronounced inhibitory effect on the MeJA induction of all TS pathway genes tested (Figure 6B). Whether this is partly or entirely mediated by increased bZIP activity cannot be judged at this stage however, given that in A. thaliana other TFs such as ORA59 or the TF cofactor NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) have also been implicated in the SA- mediated suppression of JA signaling (Van Der Does et al., 2013; Nomoto et al., 2021). Frontiers in Plant Science Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 suppressive effect was specific for MeJA elicitation of TS pathway genes, we also assayed expression of known early response JA genes involved in the JA amplification loop (Pauwels et al., 2009). Notably, the transcript levels of JAZ1, LOX, MYC2a and MYC2b were significantly increased by DTT treatment (Supplementary Figure 14). Moreover, DTT boosted MeJA elicitation of those JA pathway genes. The latter observations can likely be explained by the reported need for a reducing environment for the JA-Ile-induced interaction between COI1 and JAZ1 (Yan et al., 2009). As such, overall, our qRT-PCR analyses indicated that the negative effect of DTT on MeJA elicitation is specific for TS pathway genes. Since the ER stress response is a conserved mechanism in plants and many specialized metabolite biosynthesis pathways are regulated by TFs that bind G-boxes or closely related boxes, we hypothesized that the action of ER stress bZIP factors on the control of specialized metabolite pathways could be conserved across plant species. An obvious model system to explore this is the medicinal plant C. roseus, in which different branches of the MIA pathway are controlled by bHLH factors such as the BISs, which are functional orthologs of the TSARs (Van Moerkercke et al., 2015; Van Moerkercke et al., 2016; Mertens et al., 2016b; Schweizer et al., 2018). Finally, we assessed the effect of combined DTT and MeJA application also in the bZIP17KD and bZIP60KD hairy root lines. However, no consistent or pronounced differences could be detected with regard to the antagonistic effect that was observed in the CTR line (Figures 6D, E). Only MeJA elicitation of CYP716A12 and TSAR2 was less pronounced in both knock-down lines, and the suppressive effect of DTT on MeJA elicitation was only attenuated for CYP716A12. We assume that either the MeJA effect is capable of overruling the ER stress, or alternatively that the remaining active bZIP gene in the knock-down lines can still account for the ER stress effect. Nonetheless, taken together, our data suggest that also in planta, ER stress can attenuate the JA response in M. truncatula roots, or at least part of it, such as the elicitation of the TS pathway. To determine the putative orthologs of the bZIP17 and bZIP60 genes in C. roseus, a BLAST analysis was performed using the AtbZIP17 and AtbZIP60 amino acid sequences as query in the C. ER stress inducers repress transcript levels of TS pathway genes In this regard, the results obtained with the more specific ER stress agent DTT may be considered more indicative. Indeed, also DTT application significantly suppressed the MeJA elicitation of half of the tested TS pathway genes (Figure 6C). To assess whether the DTT- pronounced effect on bZIP17/bZIP60 expression or a reported ER stress effect. Because in A. thaliana, the reducing agent dithiothreitol (DTT) and the stress hormone salicylic acid (SA) are known to evoke ER stress and to induce the upregulation and activation of bZIP17 and bZIP60 (Moreno et al., 2012; Henriquez- Valencia et al., 2015; Li et al., 2017), we decided to analyze bZIP, ER stress and TS pathway gene expression in the presence of NaCl, DTT, SA, all in combination or not with MeJA, in CTR M. truncatula hairy root lines. As expected, bZIP17 and bZIP60 transcript levels were increased upon NaCl and DTT treatment in the CTR M. truncatula hairy roots (Supplementary Figures 13A, B). Upon SA treatment, only bZIP60 transcript levels were significantly increased (Supplementary Figure 13C). In all cases, increased BiP1/2 transcript levels were further indicative of successful ER stress induction by all three stress agents. In most cases, combined application with MeJA aggravated the ER stress as reflected by a further increase in the ER stress gene transcript Frontiers in Plant Science 10 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 FIGURE 5 Silencing of bZIP17 enhances the accumulation of TS in M. truncatula hairy roots. Relative accumulation of TS in mock- and MeJA-treated control (CTR) and bZIP17KD hairy roots. Values on the y axis correspond to fold changes relative to the average of the mock-treated control lines. Intensity values were transformed, scaled and analyzed by two-way ANOVA (p ≤0.01), categories refer to Tukey’s post-hoc test (p < 0.05). For each of the TS, the identity, retention time and m/z value is indicated on top. The small letters represent the categories that refer to Tukey’s post-hoc test (p < 0.05). They indicate significant differences between treatments. FIGURE 5 Silencing of bZIP17 enhances the accumulation of TS in M. truncatula hairy roots. Relative accumulation of TS in mock- and MeJA-treated control (CTR) and bZIP17KD hairy roots. Values on the y axis correspond to fold changes relative to the average of the mock-treated control lines. Intensity values were transformed, scaled and analyzed by two-way ANOVA (p ≤0.01), categories refer to Tukey’s post-hoc test (p < 0.05). ER stress inducers repress transcript levels of TS pathway genes For each of the TS, the identity, retention time and m/z value is indicated on top. The small letters represent the categories that refer to Tukey’s post-hoc test (p < 0.05). They indicate significant differences between treatments. Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 Frontiers in Plant Science Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 roseus Functional Genomics Database (croFGD; http://bioinformatics.cau.edu.cn/croFGD/) and Medicinal Plant Genomics Resource (http://medicinalplantgenomics.msu.edu/). The highest significant hits were CROT021933 and CROT026761, respectively, which were confirmed to belong to the bZIP TFs group B and K, respectively, by phylogenetic analysis (Supplementary Figure 15). Moreover, CROT021933 Frontiers in Plant Science 11 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 B C D E A FIGURE 6 Effects of ER stress on the expression of TS pathway genes in M. truncatula hairy roots. (A-E) qRT-PCR analysis of TS pathway genes in control (CTR) (A-C), bZIP17KD (D) and bZIP60KD (E) hairy root lines. Hairy roots were treated with 300 mM NaCl (A), 0.5 mM SA (B) or 2 mM DTT (C-E) for 4 h prior to the 4-h MeJA treatment (5 µM for (A, C-E) and 100 µM for (B)). Expression ratios were plotted relative to the normalized mock- treated line. The error bars designate SE (n = 3 for (A-D) and n = 2 for (E), corresponding to the independent transformed CTR, bZIP17KD and bZIP60KD lines generated). Different letters sample indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. B E E E FIGURE 6 Effects of ER stress on the expression of TS pathway genes in M. truncatula hairy roots. (A-E) qRT-PCR analysis of TS pathway genes in control (CTR) (A-C), bZIP17KD (D) and bZIP60KD (E) hairy root lines. Hairy roots were treated with 300 mM NaCl (A), 0.5 mM SA (B) or 2 mM DTT (C-E) for 4 h prior to the 4-h MeJA treatment (5 µM for (A, C-E) and 100 µM for (B)). Expression ratios were plotted relative to the normalized mock- treated line. The error bars designate SE (n = 3 for (A-D) and n = 2 for (E), corresponding to the independent transformed CTR, bZIP17KD and bZIP60KD lines generated). Different letters sample indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. truncated CrbZIP17D and CrbZIP60D, but not of the intact CrbZIP17 and CrbZIP60 (Figure 7A). In the case of proGES, counteraction of BIS1-mediated transactivation was only observed with CrbZIP17D (Figure 7A). Together, these data suggest that translocated ER stress response bZIP TFs can counteract the BIS1-mediated transcriptional activation of MIA biosynthesis genes in C. roseus. and CROT026761 shared the same conserved protein sequence motifs with their bZIP TF group members (Supplementary Figures 15, 16). Frontiers in Plant Science Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 Next, a transient expression assay was performed in BY2 protoplasts to assess transactivation of a set of promoters from the genes encoding enzymes of the C. roseus MIA biosynthesis pathway that are known to be controlled by the BIS TFs (Van Moerkercke et al., 2015; Mertens et al., 2016b; Van Moerkercke et al., 2016; Schweizer et al., 2018), including geraniol 8-oxidase (G8O), geraniol synthase (GES) and iridoid synthase (IS), by the C. roseus BIS1 TF in combination with C. roseus CrbZIP17, CrbZIP60 or the truncated versions thereof (CrbZIP17D and CrbZIP60D). And indeed, the transactivation mediated by BIS1 of proG8O and proIS was compromised in the presence of the To further corroborate this, we also assessed the effect of the C. roseus bZIPs in C. roseus in planta, in particular through an A. tumefaciens-assisted C. roseus flower infiltration platform that was previously successfully used as an expression system to (co-) express TF(s) and thereby screen for novel MIA biosynthesis regulators (Schweizer et al., 2018). Here, we transiently transformed C. roseus flowers with overexpression cassettes for Frontiers in Plant Science 12 frontiersin.org frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 B C A B C A FIGURE 7 C. roseus bZIP17D and bZIP60D can repress the transactivation of MIA biosynthesis genes by BIS1. (A) Transient transactivation assays in BY-2 protoplasts using the indicated target promoters fused to the fLUC reporter gene and BIS1 as effector combined with full-length or truncated C. roseus bZIP17 and bZIP60. The Y-axis shows fold change in normalized fLUC activity relative to the control transfection with proCaMV35S:GUS. The error bars designate SE of the mean (n = 4). Different letters indicate statistically significant differences at P < 0.05 as determined by ANOVA, post hoc Tukey analysis. (B, C) qRT-PCR analysis of CrBIS1, CrbZIP17, CrbZIP60 and CrBiP1 genes (B) and of MIA pathway genes (C) in C. roseus flower petals transiently overexpressing CrBIS1, CrbZIP17D, CrbZIP60D, CrBIS1/CrbZIP17D or CrBIS1/CrbZIP60D under control of the CaMV35S promoter. Control samples were infiltrated with the pCaMV35S:GUS construct. The error bars designate SE of the mean (n = 4). Different letters indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. A B C FIGURE 7 C. roseus bZIP17D and bZIP60D can repress the transactivation of MIA biosynthesis genes by BIS1. Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 Finally, as anticipated, the combinatorial overexpression of CrbZIP17D or CrbZIP60D could significantly counteract the BIS1-mediated transcriptional activation of all MIA pathway genes tested (Figure 7C). Taken together, our findings suggest that interference by ER stress bZIP TFs in the attenuation of JA-dependent terpene biosynthetic pathways might be widespread in the plant kingdom. Catharanthus roseus bZIP17 and bZIP60 counteract transactivation of monoterpenoid indole alkaloid biosynthesis gene promoters by BIS1 (A) Transient transactivation assays in BY-2 protoplasts using the indicated target promoters fused to the fLUC reporter gene and BIS1 as effector combined with full-length or truncated C. roseus bZIP17 and bZIP60. The Y-axis shows fold change in normalized fLUC activity relative to the control transfection with proCaMV35S:GUS. The error bars designate SE of the mean (n = 4). Different letters indicate statistically significant differences at P < 0.05 as determined by ANOVA, post hoc Tukey analysis. (B, C) qRT-PCR analysis of CrBIS1, CrbZIP17, CrbZIP60 and CrBiP1 genes (B) and of MIA pathway genes (C) in C. roseus flower petals transiently overexpressing CrBIS1, CrbZIP17D, CrbZIP60D, CrBIS1/CrbZIP17D or CrBIS1/CrbZIP60D under control of the CaMV35S promoter. Control samples were infiltrated with the pCaMV35S:GUS construct. The error bars designate SE of the mean (n = 4). Different letters indicate statistically significant differences at P < 0.05, as determined by ANOVA, post hoc Tukey analysis. BIS1, CrbZIP17D, and CrbZIP60D, as well as the double combinations BIS1/CrbZIP17D and BIS1/CrbZIP60D. qRT-PCR analysis confirmed overexpression of all TF genes (Figure 7B). In support of the functionality of the bZIP TFs, the expression level of the chaperone BiP1 was significantly increased in all the bZIP17D- OE and bZIP60D-OE samples (Figure 7B). Likewise, in line with previous observations (Van Moerkercke et al., 2015; Van Moerkercke et al., 2016; Schweizer et al., 2018), overexpression of BIS1 strongly upregulated all known BIS targets of the MIA pathway genes tested (Figure 7C). Finally, as anticipated, the combinatorial overexpression of CrbZIP17D or CrbZIP60D could significantly counteract the BIS1-mediated transcriptional activation of all MIA pathway genes tested (Figure 7C). Taken together, our findings suggest that interference by ER stress bZIP TFs in the attenuation of JA-dependent terpene biosynthetic pathways might be widespread in the plant kingdom. BIS1, CrbZIP17D, and CrbZIP60D, as well as the double combinations BIS1/CrbZIP17D and BIS1/CrbZIP60D. qRT-PCR analysis confirmed overexpression of all TF genes (Figure 7B). In support of the functionality of the bZIP TFs, the expression level of the chaperone BiP1 was significantly increased in all the bZIP17D- OE and bZIP60D-OE samples (Figure 7B). Likewise, in line with previous observations (Van Moerkercke et al., 2015; Van Moerkercke et al., 2016; Schweizer et al., 2018), overexpression of BIS1 strongly upregulated all known BIS targets of the MIA pathway genes tested (Figure 7C). Frontiers in Plant Science frontiersin.org Discussion The ERAD-type E3 ubiquitin ligase MKB1 has previously been reported to manage TS biosynthesis in M. truncatula by controlling HMGR stability (Pollier et al., 2013a). Silencing of MKB1 in M. truncatula MKB1KD hairy roots results in an aberrant caltrop-like morphology, increased accumulation of monoglycosylated TS, decreased accumulation of higher glycosylated TS, and a specific downregulation of TS biosynthesis gene expression. Pollier et al. (2013a) speculated that this TS-specific transcriptional response might constitute a negative feedback loop to cope with the ectopic accumulation of bioactive monoglycosylated saponins. Intrigued by this anomaly, we explored the MKB1KD hairy root phenotype by additional microscopic and transcriptomic analyses. These combined analyses pointed to an ER stress response, reflected Frontiers in Plant Science 13 frontiersin.org frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 10.3389/fpls.2022.903793 by an altered ER network structure and increased transcript levels of M. truncatula orthologs of known A. thaliana ER stress marker genes. Because in A. thaliana, and conceivably plants in general, the ER stress response can be mediated by two signaling branches, both depending on bZIP TFs, AtbZIP17/AtbZIP28 and AtbZIP60, respectively, that translocate from the ER to the nucleus in ER stress conditions, we speculated that the TS-specific feedback in MKB1KD hairy roots may be mediated by the action of the M. truncatula orthologs of these bZIP TFs. Indeed, subsequent functional analysis confirmed that the truncated versions of M. truncatula bZIP60 and bZIP17 can localize to the nucleus and interfere with TSAR1/TSAR2-mediated transactivation of TS gene promoters. We therefore speculate that this mechanism could be imposed by plants to attenuate or fine-tune the biosynthesis of TS under particular stress conditions. ERSE-like cis-elements, the targets of the ER stress response bZIPs, are present in several of the TS gene promoters. Notably, in the minimal CYP93E2 promoter region that contains N-box motifs (5´-CACGAG-3´) that are necessary and sufficient for TSAR-mediated transactivation (Mertens et al., 2016a), this ERSE-like box (5´-ATTCGACCACG-3´) overlaps with one of the N-boxes, making this promoter a plausible target for inhibitory crosstalk. However, given that partial substitution of the ERSE-like motif would also affect the N-box, and that the latter reduces the capacity of TSAR1 to transactivate this promoter fragment (Mertens et al., 2016a), we could not unambiguously assess this hypothesis. Likewise, we pursued several protein–DNA and protein–protein interaction methods, including yeast one-hybrid to investigate interactions of bZIPs with TS gene promoters, and yeast two-hybrid and bimolecular fluorescence complementation in agro-infiltrated N. Discussion benthamiana leaves, to assess possible TSAR–bZIP protein interactions, but none of these assays yielded conclusive results. Hence, our model on how ER stress-related bZIPs hinder TSAR1 transcriptional activity, and, by consequence, transactivation of TS biosynthesis genes (Figure 8), remains speculative with regard to the exact modus operandi. What is the molecular mode of action by which the bZIP TFs repress TSAR- induced TS gene expression? It remains to be determined how the bZIP and TSAR TFs interact to modulate TS biosynthesis. It has been demonstrated in A. thaliana that under non-stressed conditions, the activity of bZIP28 is inhibited by elongated hypocotyl 5 (HY5), another bZIP TF (Nawkar et al., 2017), by competition for binding to the G-box element (CACGTG) displayed within the ER stress response element (ERSE) motifs in the promoters of the UPR genes. Under ER stress conditions, HY5 undergoes proteasomal degradation, releasing the competition and enabling bZIP28 to bind to the ERSE motifs and activate the UPR (Nawkar et al., 2017). A similar scenario has been reported for JA-inducible genes by Van Der Does et al. (2013) in A. thaliana, where SA can suppress JA signaling downstream of the JA receptor by targeting GCC promoter motifs via the TF octadecanoid-responsive Arabidopsis AP2/ERF domain protein 59 (ORA 59). In C. roseus, the production of MIAs is regulated by the bHLH TF CrMYC2 (Zhang et al., 2011; Paul et al., 2017; Schweizer et al., 2018). Overexpression of CrMYC2 induces expression of the genes encoding bZIP G-box binding factors (GBFs), resulting in a reduced alkaloid accumulation in C. roseus hairy roots (Sui et al., 2018). Given that CrGBF1 can bind the same cis-element (T/G- box) as CrMYC2 in MIA biosynthesis gene promoters and that CrGBFs can dimerize with CrMYC2, it has been suggested that CrGBF TFs can antagonize CrMYC2 by competitive binding to the T/G-box, and/or by forming a heterodimeric complex, preventing CrMYC2 from binding its target promoters (Sui et al., 2018). Accordingly, we hypothesize a mechanism in M. truncatula, in which induction of TS biosynthesis genes by the bHLH TFs TSAR1 and TSAR2 could be antagonized by bZIP17 and bZIP60, plausibly either by competitive binding to the promoters or by the formation of a protein complex that would impede TSAR TF transcriptional activity. Physiological relevance and evolutionary conservation of the suppressive effect of ER stress-induced bZIP factors on JA-inducible and bHLH TF-mediated elicitation of terpene biosynthesis in plants Physiological relevance and evolutionary conservation of the suppressive effect of ER stress-induced bZIP factors on JA-inducible and bHLH TF-mediated elicitation of terpene biosynthesis in plants FIGURE 8 Hypothetical model of action of bZIP17 and bZIP60 and TSAR under normal and ER stress conditions. Under non-ER stress conditions, TSAR can bind to the N-box present in the promoters of TS biosynthesis genes and activate their expression. This can occur both in the absence and presence of JAs. Under ER stress conditions, unfolded proteins accumulate and bind to BiP in the ER. This triggers IRE1 to perform unconventional splicing of bZIP60 mRNA as well as the release of bZIP17 from the ER and its cleavage by proteases in the Golgi apparatus. The resulting active forms of bZIP17 and bZIP60 translocate to the nucleus, where they can transactivate the expression of ER stress-responsive genes but also hinder the TSARs and thereby repress the transactivation of TS biosynthesis gene expression. TSAR, triterpene saponin biosynthesis activating regulator; bZIP, basic leucine zipper TF; BiP, binding protein chaperone; IRE1, inositol-requiring enzyme 1; S1P, site-1 protease; S2P, site-2 protease. antagonize JA action is through the targeting of GCC promoter motifs via the TF ORA59 in A. thaliana (Van Der Does et al., 2013). More recently, the immune cofactor NPR1 was found to be recruited to JA-responsive promoter regions that are co-occupied by a transcription complex consisting of MYC2 and the MED25 Mediator subunit. In the presence of SA, NPR1 physically associates with MYC2 and inhibits transcriptional activation by disrupting MYC2’s interaction with MED25 (Nomoto et al., 2021). Our study suggests that another mechanism of SA–JA antagonism could involve ER stress and the bZIP factors involved therein, but this hypothesis still needs further support with additional experimentation. Nonetheless, such an additional mechanism involving the ER stress machinery could offer plants a means to activate stress response or defense pathways in a stress- specific manner, allowing plants to distinguish between biotic and abiotic stress, or between different pathogens and other attackers. An SA-induced ER stress response could be a mechanism to restrain JA signaling, or at least one of its outputs, namely the elicitation of terpene and/or other specialized metabolite pathways. Given the fact that we observed an antagonism between ER stress-inducible bZIP TFs and JA-inducible bHLH factors in two distinct species, M. truncatula and C. roseus, which each produce a species-specific compendium of JA-inducible terpene metabolites, this mechanism may be widespread in the plant kingdom. Physiological relevance and evolutionary conservation of the suppressive effect of ER stress-induced bZIP factors on JA-inducible and bHLH TF-mediated elicitation of terpene biosynthesis in plants The molecular mechanisms of ER stress signaling have been well studied over the last years, at least in A. thaliana. Many studies made use of compounds such as tunicamycin, which blocks N-linked glycosylation, or the reducing agent DTT, as artificial ER stress inducers. Exploiting such ER stress agents, in particular DTT, we could further support the inverse correlation between TS expression and levels of ER stress, as DTT treatment repressed the expression, particularly in mock conditions and to a lesser extent in the presence of MeJA, of several TS genes encoding both pathway enzymes and the regulatory TSARs themselves in M. truncatula hairy root lines. There is also increasing knowledge of the physiological conditions upon which ER stress is induced ‘naturally’ in plants. For instance, salt and heat stress have been shown to activate an overall ER stress response in A. thaliana (Gao et al., 2008; Deng et al., 2011; Tang et al., 2012; Li et al., 2017). Furthermore, also SA was reported to induce both IRE1/bZIP60 and bZIP17/bZIP28 branches of ER stress signaling in A. thaliana (Nagashima et al., 2014), although how is still under debate. It has been reported that SA treatment activates phosphatidylinositol 4-kinase (PI4K), thereby increasing PI phosphates (PIPs) in the Golgi membrane (Krinke et al., 2007). Contrarily, inhibition of PI4K activity leads Frontiers in Plant Science 14 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 FIGURE 8 Hypothetical model of action of bZIP17 and bZIP60 and TSAR under normal and ER stress conditions. Under non-ER stress conditions, TSAR can bind to the N-box present in the promoters of TS biosynthesis genes and activate their expression. This can occur both in the absence and presence of JAs. Under ER stress conditions, unfolded proteins accumulate and bind to BiP in the ER. This triggers IRE1 to perform unconventional splicing of bZIP60 mRNA as well as the release of bZIP17 from the ER and its cleavage by proteases in the Golgi apparatus. The resulting active forms of bZIP17 and bZIP60 translocate to the nucleus, where they can transactivate the expression of ER stress-responsive genes but also hinder the TSARs and thereby repress the transactivation of TS biosynthesis gene expression. TSAR, triterpene saponin biosynthesis activating regulator; bZIP, basic leucine zipper TF; BiP, binding protein chaperone; IRE1, inositol-requiring enzyme 1; S1P, site-1 protease; S2P, site-2 protease. Author contributions AG conceived the project, original screening and research plans. AG supervised the experiments. BR, M-LE, MC, EL, EC, CW, EVH, RC and MP performed the experiments. BR, M-LE, MC, EL, EC, CW, EVH and AG designed the experiments and analyzed the data. BR, M-LE and AG wrote the article with contributions of all the authors. AG agrees to serve as the author responsible for contact and ensures communication. All scientists who have contributed substantially to the conception, design or execution of the work described in the manuscript are included as authors, in accordance with the guidelines from the Committee on Publication Ethics (COPE) (http://publicationethics.org/resources/guidelines). All authors agree to the list of authors and the identified contributions. All authors contributed to the article and approved the submitted version. Physiological relevance and evolutionary conservation of the suppressive effect of ER stress-induced bZIP factors on JA-inducible and bHLH TF-mediated elicitation of terpene biosynthesis in plants University (project O1J14813), the Swiss National Science Foundation for a postdoctoral fellowship to MC (P300PA_177831) and the BEC.AR program for overseas training of Argentine professionals in the fields of science, technology and productive innovation for a scholarship to MP. Funding This work was supported by the Research Foundation Flanders by research project grants to AG (G004515N and G005915N) and a predoctoral fellowship to EC, the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 825730 (Endoscape) to AG, the Program Ciências Sem Fronteiras for a predoctoral fellowship to BR (Grant 201135/2014-0), the Special Research Fund from Ghent Acknowledgments The data presented in the study are deposited in the ArrayExpress database, accession number E-MTAB-11668. The authors thank Deniz Malat and Robin Vandenbossche for excellent technical assistance, and Steven Vandersyppe, Keylla Bicalho, and Geert Goeminne for the LC-MS service; Saskia Lippens for discussions and access to the imaging facilities, and Annick Bleys for the critical reading and help in preparing the manuscript. 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. Supplementary material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/ fpls.2022.903793/full#supplementary-material 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. Chang, M. C. Y., and Keasling, J. D. (2006). Production of isoprenoid pharmaceuticals by engineered microbes. Nat. Chem. Biol. 2, 674–681. doi: 10.1038/nchembio836 Carelli, M., Biazzi, E., Panara, F., Tava, A., Scaramelli, L., Porceddu, A., et al. (2011). MedicagotruncatulaCYP716A12isamultifunctionaloxidaseinvolvedinthebiosynthesis of hemolytic saponins. Plant Cell 23, 3070–3081. doi: 10.1105/tpc.111.087312 Physiological relevance and evolutionary conservation of the suppressive effect of ER stress-induced bZIP factors on JA-inducible and bHLH TF-mediated elicitation of terpene biosynthesis in plants Notably, activation of ER stress and the UPR by JA treatment was recently demonstrated in tomato (Czékus et al., to a decrease in PIPs and inhibition of BIP3 induction upon SA treatment (Krinke et al., 2007). Krinke et al. (2007) speculated that upon SA treatment, the phospholipid content in the ER membrane system and traffic within is changed, thereby activating ER-localized ER stress sensors in A. thaliana. During SA defense, the transcriptional cofactor NPR1 is converted from an oligomer into a monomer, which leads to the expression of pathogenesis-related protein 1 (PR1) gene family members (Wang et al., 2005). Recently, NPR1 has also been shown to be able to interact with bZIP28 and bZIP60 and to suppress the UPR, independently from SA (Lai et al., 2018). Furthermore, Meng et al. (2017) showed that the constitutive expresser of pathogenesis‐related genes 5 (CPR5), a negative modulator of SA, inhibits both the SA-dependent IRE1/bZIP60 and the ER stress‐induced bZIP28/IRE1–bZIP60 branches, favoring the growth of plants. Many studies reported both on antagonistic (Rojo et al., 2003; Bostock, 2005; Beckers and Spoel, 2006) and synergistic interactions between SA and JA in plants (Schenk et al., 2000; Van Wees et al., 2000; Mur et al., 2006). SA appears to confer resistance to biotrophic pathogens, whereas JA to insect herbivory and necrotrophic pathogens (Pieterse et al., 2001; Bostock, 2005; Stout et al., 2006). This regulatory mechanism could offer the plant a way to activate specific stress response pathways, while repressing others, and, thus contribute to the homeostasis of the cell and/or the appropriate defense response. As indicated above, one mechanism by which SA could Frontiers in Plant Science 15 frontiersin.org Ribeiro et al. 10.3389/fpls.2022.903793 2020), indicating that (complex) interplay between ER stress and JA signaling may be common in the plant kingdom. As such, the latter as well as our study may open an avenue for new research on how plants fine-tune their interaction with an ever-changing and often hostile environment. University (project O1J14813), the Swiss National Science Foundation for a postdoctoral fellowship to MC (P300PA_177831) and the BEC.AR program for overseas training of Argentine professionals in the fields of science, technology and productive innovation for a scholarship to MP. Bostock, R. M. (2005). Signal crosstalk and induced resistance: straddling the line between cost and benefit. Annu. Rev. Phytopathol. 43, 545–580. doi: 10.1146/ annurev.phyto.41.052002.095505 Biazzi, E., Carelli, M., Tava, A., Abbruscato, P., Losini, I., Avato, P., et al. (2015). CYP72A67 catalyzes a key oxidative step in Medicago truncatula hemolytic saponin biosynthesis. Mol. Plant 8, 1493–1506. doi: 10.1016/j.molp.2015.06.003 Bostock, R. M. (2005). Signal crosstalk and induced resistance: straddling the line between cost and benefit. Annu. Rev. Phytopathol. 43, 545–580. doi: 10.1146/ annurev.phyto.41.052002.095505 Carelli, M., Biazzi, E., Panara, F., Tava, A., Scaramelli, L., Porceddu, A., et al. (2011). MedicagotruncatulaCYP716A12isamultifunctionaloxidaseinvolvedinthebiosynthesis of hemolytic saponins. Plant Cell 23, 3070–3081. doi: 10.1105/tpc.111.087312 Chang, M. C. Y., and Keasling, J. D. (2006). Production of isoprenoid pharmaceuticals by engineered microbes. Nat. Chem. 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To cite this version: Karoliina Parhiala, Mehmet Yalcinkaya, Vishal Singh. Maintenance of Facilities and Aircrafts: A Comparison of IT-Driven Solutions. 11th IFIP International Conference on Product Lifecycle Manage- ment (PLM), Jul 2014, Yokohama, Japan. pp.11-20, ￿10.1007/978-3-662-45937-9_2￿. ￿hal-01386471￿ Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-01386471 https://inria.hal.science/hal-01386471v1 Submitted on 24 Oct 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 MAINTENANCE OF FACILITIES AND AIRCRAFTS: A COMPARISON OF IT-DRIVEN SOLUTIONS Karoliina Parhiala1, Mehmet Yalcinkaya2 and Vishal Singh3 1 Aalto Design Factory, Aalto University, Finland 2, 3 Department of Civil and Structural Engineering, Aalto University, Finland {karoliina.parhiala, mehmet.yalcinkaya, vishal.singh}@aalto.fi Abstract. Building Information Modeling (BIM) can significantly impact both new as well as existing architecture/engineering/construction (AEC) projects. It can provide a virtually simulated and large integrated database that can be leveraged not only in design and engineering, but also in planning and management operations, and facilities maintenance. Although most of the BIM tools are now mature enough to use in various phases of project lifecycle, they have been primitive and under-developed for many years. The concepts underpinning BIM have been around since the 1960s through various manufacturing industries such as automotive, ship building or aerospace. In the aerospace industry, especially in aircraft design and manufacturing, the concept similar to BIM is a Digital Mock-Up (DMU). It is both a tool and a product of engineering. As in BIM, aircraft’s DMU is also a comprehensive digital product representation that is used to simulate the use, behavior and performance of a finished aircraft. While BIM and DMU are used for different industries and products, they do share similarities and differences. This paper briefly describes BIM and DMU technologies and their context, specifically focusing on implementation of these two technologies for operation and maintenance (O&M). Keywords: Building Information Modeling, BIM, Digital Mockup, DMU, Configured Digital Mockup, cDMU, Maintenance 1. Introduction From the phases of the lifecycle of any type of manufacturing project, the operations and maintenance (O&M) phase is the longest one and is expected to cover previous costs of its lifecycle phases and to produce profits for its owner. O&M can be defined as “all actions that have the objective of retaining or restoring an item in or to a state in which it can perform its required function to ensure related business operations are efficient in terms of using the optimum resource as needed, and meeting customer requirements. These actions include the combination of all technical and corresponding administrative, managerial and supervision activities” [1]. O&M services include different activities with respect to the nature of the related 1 1 industry. The critical aspect to achieve the objectives of O&M services is information management and application of state-of-art technologies to the related industry. This paper presents two state-of-art IT-driven approaches towards product lifecycle management (PLM); Building Information Modeling (BIM), specifically developed for architectural/engineering/construction (AEC) and Digital Mock-Up (DMU) applied in mechanical engineering, especially in aviation industry. The paper describes BIM and DMU technologies and presents logical and functional similarities between them in product development and finally focuses on implementation of these two systems for O&M phase of the associated products’ lifecycle. a. Digital Mockup (DMU) Definition of the Configured Digital Mock-Up at Airbus [4] Figure 2. Different disciplines extract their views from the Aircraft [3] Figure 1. Definition of the Configured Digital Mock-Up at Airbus [4] Figure 1. Definition of the Configured Digital Mock-Up at Airbus [4] Figure 2. Different disciplines extract their views from the Aircraft [3] Figure 2. Different disciplines extract their views from the Aircraft [3] For each product configuration, hence each aircraft configuration, the DMU is called Configured Digital Mock-Up (cDMU). As customers are usually ordering more than one aircraft with the same configuration, the first configured and manufactured aircraft of the order is called Head of Version (HoV). Aircraft manufactured later with the same configuration are copies of the HoV. The cDMU is designed only for HoV, but then copied and linked to all aircrafts with the same configuration. As a result every manufactured aircraft has its own cDMU [4]. a. Digital Mockup (DMU) Digital Mock-Up is a terminology used for 3D representation of a product. It is composed of 3D Models, Computer Aided Design (CAD) native files and/or visualization data, and Configuration Metadata. The metadata is Product Structure with parent-child relations and positioning information, and Attributes for lifecycle management. Attributes are all the business and technical information of the product. This means that besides including the data of products’ parts, it holds information at least on work sharing, industrial flow, regulations of authorities, change process and configuration management. DMU is more than a CAD file. DMU integrates data from engineering, manufacturing and maintenance, and uses the data to simulate various industrial processes, uses, behavior and performance of the finished product [2]. Barring a few exceptions, e.g. [2], there are limited academic studies on DMU, and nearly all of the knowledge on DMU comes from aviation industry. Most outspoken on using DMU in their product development process has been the aircraft manufacturer Airbus S.A.S [3]. Therefore, the concept of DMU is presented through an example of DMU at Airbus. For Airbus, DMU is the source of all the original product information and the binding reference in all Airbus’s operations. But first of all, it was created to service the design and engineering processes. Everybody, inside and outside Airbus, subcontractors and suppliers are expected to work with the same DMU, from the same, shared database and access the latest information possible [4]. DMU at Airbus is presented in figure 1. The DMU can be accessed through several different views. This way, the user can not only access the data that is relevant to his/her work, but the connection of the data still remains within the product structure. [5] Different views are represented in Figure 2. DMU starts at the design phase from where on, the whole lifecycle of the aircraft can be envisioned [5]. It is used for aircraft representation, assist the communication and decision making throughout whole lifecycle of the aircraft. With the DMU, different kinds of scenarios to visualize and test various design solutions, for example cockpit ergonomics, are created. For aircraft performance and structural analysis, the DMU provides behavior simulations already in the early stages of the development. To reduce physical prototypes to minimum, the DMU is utilized to simulate and 2 optimize the work in manufacturing factories, validate the transport concept and plan the final assembly line. [4] Figure 1. b. Building Information Modeling (BIM) BIM represents both the technology as well as the process of digital representation of a facility through the use of object-oriented, data-rich, models potentially across the planning, design, construction and operation phases of the facility. In that sense, unlike DMU with its clear meaning, the terminology BIM is interchangeably used to represent the digital model (Building Information Model), the process (Building Information Modelling), and increasingly the approach to managing the technology and the process (Building Information Management). Nonetheless, the BIM model can be viewed, extracted and analyzed by different stakeholders and user groups to manage, simulate and analyze various aspects of the project for improved decision making, operations and maintenance of the facility [6, 7]. 3 BIM is also composed of 3D Models, native CAD files and/or visualization data, and Configuration Metadata. The metadata is Product Structure with parent-child relations, and Attributes that are the main identifiers for model management such as object types, ownership and history. BIM also allows additional Attributes to be added, which can include information about the business and technical information of the objects. This means that besides including the geometry and specifications of the objects in the model, it is possible to add information that can be intelligently used for workflow management, procurement and regulations by defining relationships between such attributes. However, unlike DMU such attributes and information on work sharing, industrial flow, regulations of authorities, change process and configuration management are rarely included in current BIM models. Thus, BIM can be configured and modified regarding the project/task requirements with the potential support of external software and hardware. Similar to DMU, BIM is expected to be the source of all the project information linked through a shared database. It is expected that in an ideal BIM project the different stakeholders such as the designers, client, contractors, subcontractors and suppliers can work with a shared BIM and access the latest information [8]. The use of a shared database in BIM can ensure that the different model views and data can be checked and updated for consistency and conflict resolution [9].The model can be used to demonstrate the entire building lifecycle from conceptual design to demolition (Figure 3) [10]. Thus, materials’ quantity takeoff can be extracted, work definitions and sequences can be defined, so the actual construction progress can be simulated in a virtual environment [11]. Figure 3. BIM implementation through building lifecycle [10] Figure 3. b. Building Information Modeling (BIM) BIM implementation through building lifecycle [10] However, unlike the Airbus example, where Airbus is clearly the client, manager and coordinator of the DMU through the development stages, the fragmented nature of the construction industry means that the handling of BIM is much more fragmented and complex in the construction sector. The issues of ownership and management of BIM across the different phases remain unclear to most players in the industry. As a result, when compared to the role of Airbus in the development DMU, the following 4 4 generic points can be stated about BIM: (1) BIM discussion has exploded as much in academic research as it has gained the attention of the industry, (2) The role of clients as champions of BIM is critical to the implementation of BIM in practice [12], (3) Unlike, the aerospace industry that has very few, but dominant global players, in the fragmented construction sector the government agencies, regulatory authorities and public clients across different regions have also had to play an important role in binding the use of BIM across different phases of construction projects in the corresponding regions [13]. The discussion on versioning aspect of DMU and cDMU also highlights the following key differences in the context and scope of BIM in construction sector, vis- à-vis the use of DMU in the aerospace sector: (1) Unlike the aerospace sector, designs in construction projects are typically unique and rarely re-used for multiple instances. This means the concepts of Model Versions in BIM are entirely different to Model Versions in DMU. Instead, versioning in BIM is typically associated with aspects such as levels of detail (LOD), solution alternatives and different stages of model development [8], (2) Since versioning in BIM is more about model coordination within the same project rather than across different instances of the product, instead of the concept of Head of Versions, typically the concepts of Reference Models is used in BIM development. b. Building Information Modeling (BIM) Typically the Reference Model from one discipline is used to coordinate the models of all the other disciplines to ensure version compatibility, and (3) Unlike the aerospace industry where the DMU can be directly used for fabrication, the lack of automation from design to fabrication in construction industry means that the Reference Models typically vary across the different phases of the construction projects, because the as-built facility typically varies from the as-designed model resulting from the changes and inaccuracies in the construction phase. In the design phase, the architecture model is typically the Reference Model, while in the construction phase, the construction model may become the Reference Model. Similarly, it is expected that the as-built model of a facility should become the Reference Model in the maintenance phase. However, the use of as-built models is rare in practice. The lack of automation between design and fabrication also explains why the LOD is an important aspect of BIM models [14]. In summary, both DMU and BIM are identical in their object-oriented approach, but the differences between them result from their context and the products they create, which have their own metadata requirements. In general, the benefits of both IT-solutions in product development are similar, fundamentally derived from the way in which the user groups can contribute to the shared data model, and use the information [3, 10]. The most common benefits of DMU [3, 5] and BIM [11] include: • Improved coordination in design through visualized object-oriented data which enables improved design management and change control • Ability to perform simulation and optimization products’ performance • Ability to perform cost performance analysis and cost impact of any change in design and manufacturing process • Reduction in manufacturing risks through identification of manufacturability issues, clash detection, schedule and cost simulations, etc in design process. • Creation of operation and maintenance information database 5 5 a. Aircraft Continuing Airworthiness Management Aircraft continuing airworthiness is managed by Continuing Airworthiness Management Organization (CAMO). As stated in European Aviation Safety Agency’s directives for maintenance organizations [15], “Continuing Airworthiness means all of the processes ensuring that, at any time in its operating life, the aircraft complies with the airworthiness requirements in force and is in a condition for safe operation”. CAMO usually is the operator of the aircraft, whether the aircraft is owned or leased. The organization itself is not responsible for the actual maintenance work, but ensures that all needed maintenance and repairs are performed as demanded. Actual maintenance work is done by authority approved maintenance organization [16]. Aircraft maintenance consists of scheduled and unscheduled maintenance. Unscheduled maintenance is corrective maintenance; repairs of defects. Scheduled maintenance aims to prevent decline of the aircrafts airworthiness. Scheduling is based on aircraft’s flight hours, flight cycles and overall time in service [17]. To have the ability to execute the maintenance to secure aircraft’s airworthiness, a wide set of data on aircraft and its maintenance procedures is needed. This data can be divided to maintenance data, and aircraft configuration and condition data. Maintenance data is the collection of documents to regulate and guide the aircraft maintenance. It includes aviation authority issued requirements, airworthiness directives and technical data provided by OEM. Aircraft configuration and condition data is general identification information on aircraft and components installed on it. It describes the status of airworthiness directives and history of defects, maintenances and modifications. Records of operational data are also part of aircraft’s condition information [5]. a. Aircraft Continuing Airworthiness Management Regulated by the authorities [18], the OEM provided technical data should be followed, as shown in Table 1: Table 1: OEM Technical data to be provided, as per the regulations [18] Aircraft Description Instructions for maintenance Operation Table 1: OEM Technical data to be provided, as per the regulations [18] 6 6 Aircrafts operation and control instructions with procedures in special situations Instructions for ground operations, weighting and balancing Aircrafts operation and control instructions with procedures in special situations Instructions for ground operations, weighting and balancing Aircraft specifications to that detailed level that the maintenance can be carried out properly Aircraft servicing information, including access points, tools and materials Information for maintenance scheduling for each part of the aircraft, with frequency and extent of the maintenance activities Information for maintenance scheduling for each part of the aircraft, with frequency and extent of the maintenance activities Airworthiness limitations for damage- tolerance and fatigue evaluation Descriptions and installations of aircrafts products and systems Airworthiness limitations for damage- tolerance and fatigue evaluation Dissembling and assembling information of parts in the aircraft Dissembling and assembling information of parts in the aircraft Troubleshooting instructions for malfunctions Structural pictures of aircraft with allowable working areas and access plates Troubleshooting instructions for malfunctions Detailed instructions for special inspection methods, like non-destructive testing Detailed instructions for special inspection methods, like non-destructive testing Protective treatments after inspections Protective treatments after inspections Electrical wiring interconnection systems continued airworthiness instructions Electrical wiring interconnection systems continued airworthiness instructions Information for structural fasteners List of tools needed DMU in Aircraft Maintenance The subject of utilizing the DMU in aircraft maintenance, or any product maintenance, has not been widely addressed. To open a discussion on how the DMU could be deployed in aircraft continuing airworthiness management, a master’s thesis was written on the topic. The thesis approaches the topic from user’s point of view by conducting interviews with two CAMOs [5]. Results of that thesis are presented here. Data management to secure aircraft continuing airworthiness is not a new subject; it is a mandatory requirement from aviation authorities. For that reason, sophisticated maintenance management software have been developed and used to manage aircraft configuration and condition, and maintenance data. However, current challenge with those data, especially OEM provided technical data, is that it represents aircrafts in parts. Having a full 3D-model of the whole aircraft would enable the aircraft parts to be examined in their actual context, the aircraft. This visual and spatial information gives better view on the part locations and access to them. Better visualization improves accuracy of maintenance planning and troubleshooting by facilitating the location of components, estimation of man-hours for maintenance tasks, and analysis of potential defects. This would reduce Aircraft on Ground (AOG) -time and make CAMO’s operations more efficient. The key challenges to the deployment of DMU in aircraft airworthiness management are limited resources, competence, time and money. To be able to use DMU as a reliable reference, it should be kept updated so as to correspond to the aircraft configuration and condition at any given point of the aircraft’s lifecycle. Another challenge arises from the ownership of the DMU and that the DMU is the core competence and intellectual property of the OEM. b. Facilities Maintenance Facilities maintenance is the continuous process of service provision required to maintain a facility and its environment through its service life. These services 7 7 encompass the entire activities required to assure that a built environment will perform the functions for which the facility was designed and constructed [19]. O&M phase of a construction project typically includes scheduled, and preventive and emergency maintenance activities of major building systems. Managing the maintenance of facilities can be difficult on the O&M phase owing to various types of equipment and facilities. Furthermore, it is inconvenient for maintenance staff to maintain those facilities by relying on paper-based documents. In contrast to the aviation industry, which has the legal obligation to regulate the maintenance of both private and passenger aircrafts and their lifecycle information, such practices and regulations are not common in construction industry. Although many governmental organizations have the responsibility to maintain their buildings, there is no obligation to maintain private buildings. Nonetheless, manuals and strategic maintenance guidelines may be agreed upon through contractual agreement between the owner and contractor. These manuals and guides typically describe the basic information requirements for effective maintenance activities such as: basic information requirements for effective maintenance activities, such as: • Architectural and structural components of the facility like ceiling surfaces, floor coverings, roofing, and walls. • Design details, floor plans, spaces and zones, and as-built drawings. • Environmental considerations, required tools and equipment for safety issues, safety instructions of building systems. • Equipment lists, descriptions, maintenance and repair guides, operation manuals. • Preventive maintenance schedules, procedures, logs, troubleshooting guides, removal and replacement instructions of building systems, warranty information. • Operation instructions of building systems, operation logbooks, start-up and shut-down procedures, emergency operating instructions. • Descriptions of all systems in buildings, assembly and components diagram, utility connections and cutoff plans. The listed information requirements are rarely applied to that extent, because of the difficulties to structure and digitally hand them over to a centralized source. As reported by National Institute of Standards and Technology (NIST), “an inordinate amount of time is spent locating and verifying specific facility information from previous activities. Much valuable data associated with the design, construction and operation of a facility is lost during its lifecycle” [20]. BIM in Facilities Maintenance BIM can provide a shared resource and information sets about a facility’s structure, functions and technical systems (mechanical, electrical, plumbing, lighting, etc.), including product manufacturers, if available and added to the model. However, construction contracts rarely stipulate providing or using these potential information in BIM models for maintenance activities, and hence, there are very few cases on the actual use of BIM for facilities management. Instead, there are many other technologies that can also exchange the facility data. Building automation systems 8 (BAS) or Building Management Systems (BMS) most often handle the operation of building mechanical, electrical, plumbing (MEP) and lightening systems. Integrated Work Management Systems (IWMS) or Computerized Maintenance Management Systems (CMMS) support maintenance activities, work orders, space management, personnel management, etc. However, the exchange and re-usability of the data in these systems and the fragmented nature of AEC industry make the information transfer among project stakeholders challenging, especially through BIM [21]. (BAS) or Building Management Systems (BMS) most often handle the operation of building mechanical, electrical, plumbing (MEP) and lightening systems. Integrated Work Management Systems (IWMS) or Computerized Maintenance Management Systems (CMMS) support maintenance activities, work orders, space management, personnel management, etc. However, the exchange and re-usability of the data in these systems and the fragmented nature of AEC industry make the information transfer among project stakeholders challenging, especially through BIM [21]. Therefore, an important point for the success of BIM for facilities maintenance activities is an accurate and structured specification of the BIM data and interoperability of BIM and maintenance software. Construction Operations Building Information Exchange (COBie) has been developed for O&M data handover [22]. COBie is a rapidly evolving standard to capture information, such as zones, rooms (spaces), equipment and components, tests and certificates, safety and emergency plans, start-up and shut-down procedures, etc. in BIM electronically during design and construction, to provide it to facility managers in a spreadsheet format. It can potentially eliminate the inefficient process of transferring large amounts of paper based documents or electronic data within facility management systems (CMMS, BAS, etc.). To establish the common practice and adoption of BIM-based maintenance management, contractual agreements are needed to stipulate the use and update of COBie data by the project stakeholders. In addition, the COBie standards and templates need further maturity and integration with different BIM applications. References [1] European Federation of National Maintenance Societies. URL: http://www.efnms.org/ [ ] p p g [2] DOLEZAL, W. R. Success Factors for Digital Mock-ups (DMU) in complex Aerospace Product Development. TU München, Genehmigten Dissertation, Munich, Germany, 2008. p , g , , [3] Airbus SAS, Setting new standards with the A350 XWB Digital Mock-Up. http://videos airbus com/video/dc6bd25e7f3s html Accessed: 11 Jan 2014 [3] Airbus SAS, Setting new standards with the A350 XWB Digital Mock-Up. http://videos.airbus.com/video/dc6bd25e7f3s.html. Accessed: 11 Jan 2014 s.airbus.com/video/dc6bd25e7f3s.html. Accessed: 11 Jan 2 [4] Parhiala, K. M Utilising Configured Digital Mock-Up in Aircraft Continuing Airworthiness Management. Aalto University School of Engineering, Master’s Thesis, Finland, 2014. [5] Garbade, R., and Dolezal, W. R. "DMU@ Airbus—Evolution of the Digital Mock-up (DMU) at Airbus to the Centre of Aircraft Development." The Future of Product Development. Springer Berlin Heidelberg, 2007. 3-12. [6] Associated General Contractors of America. The Contractor’s Guide to BIM, 1st ed. http://www.engr.psu.edu/ae/thesis/portfolios/2008/tjs288/Research/AGC_GuideToBIM.pdf [6] Associated General Contractors of America. The Contractor’s Guide to BIM, 1st ed. http://www.engr.psu.edu/ae/thesis/portfolios/2008/tjs288/Research/AGC_GuideToBIM.pdf p g p p j p [7] Mitchell, J et al. Adopting BIM for facilities management: Solutions for managing the Sydney Opera House. CRC-Construction Innovation, Brisbane, Australia (2007). p g p p j p [7] Mitchell, J et al. Adopting BIM for facilities management: Solutions for managing the Sydney Opera House. CRC-Construction Innovation, Brisbane, Australia (2007). y y p [8] Gu, N, Singh, V, London, K, Brankovic, L and Taylor, C. BIM : Expectations and a reality check. In: Ren, A, Ma, Z and Lu, X (Eds.), "ICCCBE-XII & INCITE 2008", Tsinghua University. Tsinghua University Press, 1-6, (2008). [8] Gu, N, Singh, V, London, K, Brankovic, L and Taylor, C. BIM : Expectations and a reality check. In: Ren, A, Ma, Z and Lu, X (Eds.), "ICCCBE-XII & INCITE 2008", Tsinghua University. Tsinghua University Press, 1-6, (2008). [9] Singh, V. Gu, N. Wang, X. A theoretical framework of a BIM-based multi-disciplinary collaboration platform, Automation in Construction 20(2), (2011) 134-144. [9] Singh, V. Gu, N. Wang, X. A theoretical framework of a BIM-based multi-disciplinary collaboration platform, Automation in Construction 20(2), (2011) 134-144. [10] Dispenza, K. The daily life of building information modeling (BIM). URL: http://buildipedia.com/aec-pros/design-news/the-daily-life-of-building-information- modeling-bim. Accessed: 25 Jan 2014 [10] Dispenza, K. The daily life of building information modeling (BIM). URL: http://buildipedia.com/aec-pros/design-news/the-daily-life-of-building-information- modeling-bim. Accessed: 25 Jan 2014 [11] Khemlani, L. Top criteria for BIM solutions. 4. Conclusion This paper presents a comparison of BIM and DMU, two different IT-driven solutions applied in AEC and aviation industry respectively. In this paper O&M phase of the specified industries’ products (buildings and aircrafts) are reviewed, and BIM and DMU’s value adding functions are discussed. It is proposed that even if the industries and their related domains/products are different, both BIM and DMU apply similar functions for their individual products. However, it is important to understand and analyze the specific circumstances during each domain’s lifecycle to figure out the specific needs, strategies to apply related IT-driven solutions. For both solutions, number of issues and potential improvements arise in data management features of related software applications. Potential improvements by means of visualization, data collection/updating and information transfer may ease the BIM/DMU based activities during lifecycle, and make it more efficient. Future work should include the application of both BIM and DMU for different phases of the lifecycle by highlighting specific workflow issues. Since O&M phase of both industries include various types of data coming from design and production/construction phases, the specific information requirements for O&M should be clarified and data/information transfer between these phases may also be a potential area to search. 9 9 References http://www.aecbytes.com/feature/2007/BIMSu [12] Coates, P, Arayici, Y, Koskela, K, Kagioglou, M, Usher, C and O'Reilly, K 2010, The key performance indicators of the BIM implementation process , in: The Int’l Conf. on Computing in Civil and Building Engineering , June 30 - July 2 2010, Nothingham, UK. [13] Gu, N, Singh, V, Taylor, C, London, K, Ljiljana, B. BIM adoption: expectations across disciplines, (in) Handbook of Research on Building Info. Model’g and Constr. Info.: Concepts and Technologies. Ed Underwood, J. & Isikdag, U, 501-520, (2010). [14] Singh, V (2013) Challenges for integrated design and delivery teams in AEC, Proceedings of International Conference on Product Lfecycle Management, Nantes, France 8-10 July. [15] Maintenance Organisation Approvals – PART-145. Acceptable Means of Compliance and Guidance Material. Luxembourg: European Aviation Safety Agency, 2012, ISBN ISBN [14] Singh, V (2013) Challenges for integrated design and delivery teams in AEC, Proceedings of International Conference on Product Lfecycle Management, Nantes, France 8-10 July. [ ] g ( ) g g g y g of International Conference on Product Lfecycle Management, Nantes, France 8-10 July. [15] Maintenance Organisation Approvals – PART-145. Acceptable Means of Compliance and Guidance Material. Luxembourg: European Aviation Safety Agency, 2012, ISBN ISBN 978-92-9210-121-3. [16] Continuing Airworthiness Requirements – PART-M. Acceptable Means of Compliance and Guidance Material. Luxembourg: Eu. Av. Saf. Ag., 2012, ISBN-13 978-92-9210-123-7 [16] Continuing Airworthiness Requirements – PART-M. Acceptable Means of Compliance and Guidance Material. Luxembourg: Eu. Av. Saf. Ag., 2012, ISBN-13 978-92-9210-123-7 [17] Aubin, B. R. (2004). Aircraft Maintenance: The art and science of keeping aircraft safe, Society of Automotive Engineers, Warrendale, PA. 2004. [17] Aubin, B. R. (2004). Aircraft Maintenance: The art and science of keeping aircraft safe, Society of Automotive Engineers, Warrendale, PA. 2004. [18] Certification Specifications and Acceptable Means of Compliance for Large Aeroplanes. CS-25. Luxembourg: European Aviation Safety Agency, 14.6.2012, 2013. [19] Whole Building Design Guide, Facilities operation&maintenance. http://www.wbdg.org/om/om.php Accessed: 19 Jan 2014. p g g p p [20] NIST, Cost analysis of inadequate interoperability in the U.S capital and facilities industry, http://fire.nist.gov/bfrlpubs/build04/art022.html. Accessed 23 Dec 2013. [21] Madritsch, T. May, M. Successful IT implementation in facility management, Facilities 27 (11/12) (2009) 429-444. [22] East, W. bSa Construction Operations Building Information Exchange (COBIE): Means and Methods, The National Institute of Building Sciences, 2012. 10
https://openalex.org/W1990876016
https://europepmc.org/articles/pmc3565232?pdf=render
English
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Experimental evidence of nitrogen control on pCO2 in phosphorus-enriched humic and clear coastal lagoon waters
Frontiers in microbiology
2,013
cc-by
5,580
INTRODUCTION organic matter is produced and destroyed (Cole et al., 2000). Indeed, high terrestrial organic inputs may explain the positive general trend reported between dissolved organic carbon (DOC) and the partial pressure of CO2 (pCO2) in lake waters (Jonsson et al., 2003). Several studies have showed positive relationships in DOC and pCO2 in lakes in high latitudes and even globally (Sobek et al., 2005) supporting the idea that lakes are an important source of CO2 globally (Cole et al., 1994, 2007; Duarte and Prairie, 2005; Tranviket al.,2009). Meanarealratesof CO2 evasionfromlakesare higher at low latitudes, probably by the potential positive effect of warmer conditions on the organic decomposition (Marotta et al., 2009; Kosten et al., 2010). In this way, the degradation of organic matter to CO2 by bacteria shows important fluxes in the carbon cycling in natural aquatic ecosystems (Azam, 1998). Carbon dioxide (CO2) is one of most important greenhouse gas in terms of global warming (IPCC, 2007; Royer et al., 2007; Solomon et al., 2010). The terrestrial biomass represents a relevant global stock of carbon (C), which is removed from the atmosphere by primary production (Gough et al., 2008). However, a significant part of this terrestrial organic matter leaches into aquatic ecosys- tems, where it may be buried in bottom sediments (Downing et al., 2008) or remineralized to CO2 by aquatic biological decomposi- tion (Aufdenkampe et al., 2011). In the watershed, most natural inland waters are relatively small, but their wide geographic dis- tribution, high abundance, and common location at low altitudes make them a typical fate for the water inflow from broad areas, playing a crucial role on the global C cycle (Cole et al., 2007). Additionally, the expansion of the human activities has intensi- fied substantially the nitrogen (N) and phosphorus (P) input into ecosystems, often resulting in the eutrophication of natural waters (Vitousek and Mooney, 1997). These nutrients regulate aquatic primary production and respiration (Cole et al., 2000; Biddanda et al., 2001). Experimental evidence of nitrogen control on pCO2 in phosphorus-enriched humic and clear coastal lagoon waters Experimental evidence of nitrogen control on pCO2 in phosphorus-enriched humic and clear coastal lagoon waters Roberta B. Peixoto1, Humberto Marotta 2 and Alex Enrich-Prast1* 1 Laboratory of Biogeochemistry, Department of Ecology, Institute of Biology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 2 Sedimentary and Environmental Processes Laboratory (LAPSA/UFF), Department of Geography, Institute of Geosciences, Universidade Federal Fluminense, Niterói, Brazil Natural and human-induced controls on carbon dioxide (CO2) in tropical waters may be very dynamic (over time and among or within ecosystems) considering the potential role of warmer temperatures intensifying metabolic responses and playing a direct role on the balance between photosynthesis and respiration. The high magnitude of biological processes at low latitudes following eutrophication by nitrogen (N) and phosphorus (P) inputs into coastal lagoons waters may be a relevant component of the carbon cycle, showing controls on partial pressure of CO2 (pCO2) that are still poorly understood. Here we assessed the strength of N control on pCO2 in P-enriched humic and clear coastal lagoons waters, using four experimental treatments in microcosms: control (no additional nutrients) and three levels of N additions coupled to P enrichments. In humic coastal lagoons waters, a persistent CO2 supersaturation was reported in controls and all nutrient-enriched treatments, ranging from 24- to 4-fold the atmospheric equilibrium value. However, both humic and clear coastal lagoons waters only showed significant decreases in pCO2 in relation to the controlled microcosms in the two treatments with higher N addition levels. Additionally, clear coastal lagoons water microcosms showed a shift from CO2 sources to CO2 sinks, in relation to the atmosphere. Only in the two more N-enriched treatments did pCO2 substantially decrease, from 650 μatm in controls and less N-enriched treatments to 10 μatm in more N-enriched microcosms. Humic substrates and N inputs can modulate pCO2 even in P-enriched coastal lagoons waters, thereby being important drivers on CO2 outgassing from inland waters. *Correspondence: Alex Enrich-Prast, Laboratory of Biogeochemistry, Department of Ecology, Institute of Biology, Universidade Federal do Rio de Janeiro, Cidade Universitária s/n, Rio de Janeiro 68020, Brazil. e-mail: aenrichprast@gmail.com Reviewed by: Reviewed by: James Cotner, University of Minnesota, USA Luciana De Oliveira Vidal, Federal University of Juiz de Fora, Brazil Reviewed by: James Cotner, University of Minnesota, USA Luciana De Oliveira Vidal, Federal University of Juiz de Fora, Brazil Edited by: André Megali Amado, Universidade Federal do Rio Grande do Norte, Brazil Keywords: eutrophication, pCO2, nitrogen, humic coastal lagoons, clear water coastal lagoons www.frontiersin.org INTRODUCTION Highly productive waters due to external inputs of inorganic nutrients tend to be net autotrophic, acting as a net sink for CO2 (Duarte and Agusti, 1998), while, those waters are Coastal lagoons are ecosystems often altered by the human land use (Marotta et al., 2010b), which show intense C fluxes (Duarte et al.,2008; Marotta et al.,2010b) The terrestrial inputs from leach- ing and groundwaters enhance CO2 in lakes by the contribution of inorganic C (Raymond et al., 1997; Marotta et al., 2010b), or organic substrates supporting the aquatic respiration (del Giorgio et al., 1997; Jonsson et al., 2003). Photosynthesis and respiration are the major metabolic pathways determining whether what level February 2013 | Volume 4 | Article 11 | 1 www.frontiersin.org Nitrogen control on pCO2 in coastal lagoons Peixoto et al. highly enriched in organic substrates may show persistent CO2 supersaturation (Carpenter et al., 2001; Marotta et al., 2012). highly enriched in organic substrates may show persistent CO2 supersaturation (Carpenter et al., 2001; Marotta et al., 2012). at the sampling time was different between both, almost threefold above in Comprida lagoon than in Carapebus lagoon (1.6 and 0.5 m, respectively). No rainfall had been recorded during the incubations and the water temperature inside the microcosms var- ied between 25 and 30◦C during the experiment. The evaporation contributedtonegligencewaterlevelreductioninsidemicrocosms, which was compensated by adding filtered waters from the same lake during the experiment. Despite consistent evidences supporting the role of the limi- tation by either P (Schindler et al., 2008) or N (Camacho et al., 2003), N and P co-limitation may be also crucial on the bio- logical metabolism in natural waters (Conley et al., 2009; Paerl, 2009). The biological N fixation can contribute to reduce the role of N inputs to stimulate biological activity in P-enriched waters, although more evidences is still needed for a better understanding on N limitation in coastal lagoons waters, where P is commonly enriched by domestic discharges. The experiment was carried out over 15 days in highly P- enriched treatments in which different amounts of N were added, and the control (i.e., no N addition) per coastal lagoon. Three replicates were used in each experimental treatment and the con- trol totalizing 24 microcosms. ANALYTICAL METHODS pH was measured with a precision of 0.01 pH units using aAnalion PM 608 pH meter and the total alkalinity following the Gran’s titration (APHA, 1992). Temperature and salinity were measured with a calibrated Thermosalinometer YSI-30. CO2 concentra- tions in waters were determined using the pH-alkalinity method (Mackereth et al., 1978) with appropriate corrections for temper- ature, altitude, and ionic strength as Cole et al. (1994). pCO2 was calculated from Henry’s law with appropriate corrections for temperature and salinity (Cole and Caraco, 1998) as in Marotta et al. (2010a). Carapebus coastal lagoon (22◦13′21.29′′S and 41◦36′53.22′′W) has clear waters, while Comprida coastal lagoon (22◦16′44.55′′S and 41◦39′24.76′′W) has highly humic and dark waters. The dark color and high Color:DOC ratio in coastal lagoons waters of this region commonly reflects a higher contribution of terrestrial organic compounds from Restinga vegetation (Marotta et al., 2010a). STUDY AREA The experiment was conducted using surface waters from two tropical coastal lagoons situated at the same conservation area (Restinga de Jurubatiba National Park) in the north of Rio de Janeiro State (Brazil). Both coastal lagoons are elongated, with their main axis perpendicular to the shoreline (maximum depth<4.5m; area<6.5km2),oligotrophic(nutrientsandchloro- phyll a in the Table 1) and relatively close to each other (distant 6.8 km). The mean daily temperature in this area ranges from 20.7◦C in July to 26.2◦C in February. Despite high inter-annual variability, the minimum and maximum monthly rainfall are typ- ically observed in August (38 mm) and December (182 mm; INMET, 1992). The tropical climate reflects in warm coastal lagoons waters (>20◦C). February 2013 | Volume 4 | Article 11 | 2 INTRODUCTION 1.4 μM of P as KH2PO4 and K2HPO4 (1:1 mass ratio to attenuate changes in pH) and 2.8, 28, and 120 μM of N as KNO3 were daily added to +N+P, ++N+P and +++N+P treatments, respectively. Nutrients were carefully added during the morning. Total additions were 20 μM P and 40, 400, and 1600 μM N in +N+P, ++N+P and +++N+P treatments, respectively, during the experiment. These concentra- tions and the corresponding N:P ratio were chosen to simulate the nutrient levels typically observed in urban coastal lagoons at the same region outside the Restinga de Jurubatiba National Park. The control microcosms showed only the low nutrient levels observed in both environments (0.4 and 0.9 μM P and 58.1 and 45.2 μM N, respectively in Carapebus and Comprida lagoons). All mea- surements were performed by the end of the experimental time (day 15). In this study, we assessed the short-term effect of N additions on pCO2 in P-enriched humic and clear coastal lagoons waters. We tested the hypotheses that lake pCO2 is controlled by N availability in P-enriched waters. EXPERIMENTAL DESIGN Water samples for total P and N analyses were previously frozen. Total P concentrations were measured by the molybdenum blue method with pre-digestion and total N concentrations by the sum of Kjeldahl N and NOx forms (APHA, 1992). Chlorophyll a con- centrations (a proxy for phytoplankton biomass) in water samples filtered through Whatman GF/F filters (0.7 μm pore size) were extracted with ethanol in the dark for 24 h before fluorimetric determination, using an excitation wavelength of 433 nm and Surface waters from both coastal lagoons were incubated in open- air 3.0-l glass bottles (microcosms) directly exposed to sunlight and other weather changes next to the studied coastal lagoons in June 2003. Solar incidence was the same for all microcosms, as they were placed close to each other, representing common light conditions for surface waters near to the interface with the atmo- sphere. However, the light attenuation indicated by Secchi depth Table 1 | Nutrients, chlorophyll a, color, DOC, Color:DOC ratio, salinity (PSU – practical salinity unity), and pH in surface waters of Carapebus and Comprida coastal lagoons used in experimental microcosms. Values are means and units of each variable are described below. Lagoon Total N (μmol l−1) Total P (μmol l−1) Chlorophyll a (μg l−1) Color (430 nm) DOC (mg l−1) Color:DOC ratio (abs at 430 nm:mg l−1) Salinity (PSU) pH Carapebus 45.3 1.0 13.8 0.014 9.84 0.0014 5.1 7.84 Comprida 58.1 0.4 2.5 0.102 17.43 0.0058 0.1 5.66 Frontiers in Microbiology | Aquatic Microbiology February 2013 | Volume 4 | Article 11 | 2 color, DOC, Color:DOC ratio, salinity (PSU – practical salinity unity), and pH in surface waters of Carapebus and n experimental microcosms. Values are means and units of each variable are described below. le 1 | Nutrients, chlorophyll a, color, DOC, Color:DOC ratio, salinity (PSU – practical salinity unity), and pH in sur mprida coastal lagoons used in experimental microcosms. Values are means and units of each variable are desc Frontiers in Microbiology | Aquatic Microbiology Nitrogen control on pCO2 in coastal lagoons Peixoto et al. FIGURE 1 | Daily mean pCO2 after different N additions for humic and clear waters, respectively from Lake Comprida and Lake Carapebus at the last day of the experiment. Each solid circle indicates one microcosm and the horizontal line the average. EXPERIMENTAL DESIGN The four treatments are control (no additional nutrients) and three N levels (+N, ++N, and +++N, respectively 40, 400, and 1600 μM N – KNO3) +P addition (+P 20 μM P – KH2PO4 and K2HPO4). No significant differences among treatments and lake waters were represented by equal lower case letters (Tukey–Kramer, p > 0.05).The dashed line represents the pCO2 value at equilibrium with the overlying atmosphere (380 μatm). Note that values are in log scale. FIGURE 1 | Daily mean pCO2 after different N additions for humic and clear waters, respectively from Lake Comprida and Lake Carapebus at the last da of the e periment Each solid circle indicates one microcosm FIGURE 1 | Daily mean pCO2 after different N additions for humic and clear waters, respectively from Lake Comprida and Lake Carapebus at the last day of the experiment. Each solid circle indicates one microcosm and the horizontal line the average. The four treatments are control (no additional nutrients) and three N levels (+N, ++N, and +++N, respectively 40, 400, and 1600 μM N – KNO3) +P addition (+P 20 μM P – KH2PO4 and K2HPO4). No significant differences among treatments and lake waters were represented by equal lower case letters (Tukey–Kramer, p > 0.05).The dashed line represents the pCO2 value at equilibrium with the overlying atmosphere (380 μatm). Note that values are in log scale. t e ast day o t e e pe e t ac so d c c e d cates o e c ocos and the horizontal line the average. The four treatments are control (no additional nutrients) and three N levels (+N, ++N, and +++N, respectively 40, 400, and 1600 μM N – KNO3) +P addition (+P 20 μM P – KH2PO4 and K2HPO4). No significant differences among treatments and lake waters were represented by equal lower case letters (Tukey–Kramer, p > 0.05).The dashed line represents the pCO2 value at equilibrium with the overlying atmosphere (380 μatm). Note that values are in log scale. RESULTS Humic water microcosms from Comprida coastal lagoon showed average pCO2 values 10-fold higher than clear waters from Carape- bus coastal lagoon in the controls and treatments +N+P,++N+P, +++N+P (Tukey–Kramer, p < 0.05; Figure 1). A compari- son between control and the less N-enriched treatment (+N+P) showed no significant difference in pCO2 among them, both in clear and humic waters (one-way ANOVA, p > 0.05; Figure 1). In contrast, these pCO2 values in control and +N+P treatments were significantly higher (Tukey–Kramer, p < 0.05; Figure 1) than those respective humic or clear water with higher N-additions (++N+P and +++N+P), which were also not significantly dif- ferent between them (one-way ANOVA, p > 0.05; Figure 1). CO2 supersaturation was persistent in all humic treatments but not in clear water microcosms. The clear water microcosms presented a shift from being a source of CO2 in the controls and +N+P treat- ment to becoming a sink in ++N+P and +++N+P treatments in relation to the atmosphere (Figure 1). Bacterial production increased with the amount of N added in both humic and clear water lake microcosms. However, this increase was significantly higher and more evident at the ++N+P and +++N+P humic lake water microcosms (Tukey–Kramer, p < 0.05; Figure 4). STATISTICAL ANALYSIS The data were log-transformed (except pH) to meet the assump- tions of parametric tests, including significant Gaussian distri- bution (Kolmogorov–Smirnov, p > 0.05) and homogeneity of variances (Bartlett, p > 0.05). Hence, differences among exper- imental treatments and the control were tested with one-way ANOVA (significance p < 0.05) followed by the Tukey–Kramer post hoc test (significance p < 0.05). All statistics were performed using GraphPad Prism 5.01 for Windows. less N-enriched humic treatments (control and +N+P) showed chlorophyll a significantly lower than ++N+P or +++N+P, and TSS significantly lower only than +++N+P (Tukey–Kramer, p < 0.05; Figures 2 and 3). However, the clear water microcosms showed no differences between treatments when chlorophyll a and TSS were all compared (one-way ANOVA, p > 0.05; Figures 2 and 3, respectively). Farther, humic water microcosms did not show any periphytic biomass on the microcosm wall, while a thick green periphytic biomass (non-pelagic microalgae) was observed at the edges of the ++N+P and +++N+P treatments microcosms. EXPERIMENTAL DESIGN The four treatments are control (no additional nutrients) and three N levels (+N, ++N, and +++N, respectively 40, 400, and 1600 μM N – KNO3) +P addition (+P 20 μM P – KH2PO4 and K2HPO4). No significant differences among treatments and lake waters were represented by equal lower case letters (Tukey–Kramer, p > 0.05).The dashed line represents the pCO2 value at equilibrium with the overlying atmosphere (380 μatm). Note that values are in log scale. an emission wavelength of 673 nm (Varian Eclipse). Total sus- pended solids (TSS) were analyzed by the difference of weight before and after filtering and drying GF/F filters. Water sam- ples filtered in these Whatman GF/F filters were also analyzed for color at 430 nm (Strome and Miller, 1978) using a Beck- man DU 80 spectrophotometer (Fullerton, CA, USA) in a 1-cm quartz cuvette, and acidified to pH < 2.0 to determine DOC by the high-temperature catalytic oxidation method using a TOC-5000 Shimadzu Analyzer. The bacterial production was estimated from the rate of incorporation of 3H-leucine (Smith and Azam, 1992), assuming a 3H-leucine dilution factor of 2 and a carbon:protein ratio of 0.86 (Wetzel and Likens, 1991). A volume of 1.3 ml of water from the microcosms and placed in an eppendorf (1.5 ml). In all tubes, rejoinders were added 20 μl of 3H-leucine (5× diluted standard solution, 159 mCi mol−1, Amersham), reach- ing a final concentration of 20 nM and incubated for 45 min in the dark. After the incubation period, were added in rejoinders, 90 μl of 100% trichloroacetic acid (TCA) stopping and starting the reaction extraction. Each tube was washed sequentially with 5% TCA and 80% ethanol and 500 μl of scintillation cocktail (Aquasol and Dupont) was added to each tube and the radioac- tivity measured in a liquid scintillator. Bacterial production was calculated by assuming a dilution factor of intracellular leucine equal to 2, and a protein rate of carbon equal to 0.86 (Wetzel and Likens, 1991). FIGURE 1 | Daily mean pCO2 after different N additions for humic and clear waters, respectively from Lake Comprida and Lake Carapebus at the last day of the experiment. Each solid circle indicates one microcosm and the horizontal line the average. www.frontiersin.org DISCUSSION ll h h Overall, the humic waters from Comprida coastal lagoon showed a persistent CO2 supersaturation reaching higher pCO2 values than the controls or respective treatments with clear waters from Cara- pebus coastal lagoon. The humic nature of waters in Comprida coastal lagoon reflects the terrestrial DOC supply to heterotrophic bacteria in these ecosystems (Farjalla et al., 2009). Allochthonous organic resources contribute to high respiration rates and subse- quently pCO2 within most lake waters (Duarte and Prairie, 2005; Cole et al.,2007). These results support the conclusion that, in that humic coastal lagoons waters have higher pCO2 values than the clear coastal lagoons, probably due to the more intense respiration of organic substrates (Marotta et al., 2010a). The humic water microcosms also showed no significant dif- ference (one-way ANOVA, p > 0.05) for pelagic chlorophyll a and TSS comparing controls and +N+P. Additionally, these February 2013 | Volume 4 | Article 11 | 3 www.frontiersin.org Nitrogen control on pCO2 in coastal lagoons Peixoto et al. FIGURE 2 | Pelagic chlorophyll a after different N addition for humic and clear waters. Note that values are in log scale. Legend as described in Figure 1. FIGURE 3 |Total suspended solids (TSS) after different N addition for humic and clear waters. Legend as described in Figure 1. Furthermore, P-enriched microcosms with higher N addi- tions showed higher bacterial production rates and algal biomass FIGURE 4 | Bacterial production after different N addition for humic and clear waters. Legend as described in Figure 1. FIGURE 2 | Pelagic chlorophyll a after different N addition for humic and clear waters. Note that values are in log scale. Legend as described in Figure 1. FIGURE 2 | Pelagic chlorophyll a after different N addition for humic and clear waters. Note that values are in log scale. Legend as described in Figure 1. FIGURE 4 | Bacterial production after different N addition for humic and clear waters. Legend as described in Figure 1. The CO2 balance was determined by higher N inputs, as higher N treatments showed strong net decreases in pCO2, supporting the potential role of aquatic primary producers on CO2 uptake (Carig- nan et al., 2000). Both heterotrophs and autotrophs are stimulated by the nutrient additions (Biddanda et al., 2001), although the net autotrophy may be favored in the balance, a general trend often reported for natural waters (Duarte and Agusti, 1998). Frontiers in Microbiology | Aquatic Microbiology REFERENCES Marotta, H., Duarte, C. M., Guimaraes- Souza, B. A., and Enrich-Prast, A. (2012). Synergistic control of CO2 emissions by fish and nutrients in a humic tropical lake. Oecologia 168, 839–847. in highly humic aquatic ecosystems. Environ. Sci. Pollut. Res. Int. 16, 531–538. Cole, J. J., Pace, M. L., Carpenter, S. R., and Kitchell, J. F. (2000). Persistence of net heterotrophy in lakes dur- ing nutrient addition and food web manipulations. Limnol. Oceanogr. 45, 1718–1730. APHA. (1992). Standard Methods for the Examination of Water and Wastewa- ter. Washington, DC: American Pub- lic Health Association. Gough, C. M., Vogel, C. S., Schmid, H. P., and Curtis, P. S. (2008). Con- trols on annual forest carbon storage: lessons from the past and predic- tions for the future. Bioscience 58, 609–622. ter. Washington, DC: American Pub- lic Health Association. Aufdenkampe, A. K., Mayorga, E., Ray- mond, P. A., Melack, J. M., Doney, S. C., Alin, S. R., et al. (2011). Riverine coupling of biogeochemi- cal cycles between land, oceans, and atmosphere. Front. Ecol. Environ. 9, 53–60. Marotta, H., Duarte, C. M., Meirelles- Pereira, F., Bento, L., Esteves, F. A., and Enrich-Prast, A. (2010a). Long-term variability of CO2 in two shallow tropical lakes experi- encing episodic eutrophication and acidification events. Ecosystems 13, 382–392. Cole, J. J., Prairie, Y. T., Caraco, N. F., Mcdowell, W. H., Tranvik, L. J., Striegl, R. G., et al. (2007). Plumb- ing the global carbon cycle: inte- grating inland waters into the terres- trial carbon budget. Ecosystems 10, 171–184. Guariento, R. D., Carneiro, L. S., Cal- iman, A., Bozelli, R. L., Leal, J. J. F., and Esteves, F. D. A. (2010). Interactive effects of omnivorous fish and nutrient loading on net pro- ductivity regulation of phytoplank- ton and periphyton. Aquat. Biol. 10, 273–282. Azam, F. (1998). Microbial control of oceanic carbon flux: the plot thick- ens. Science 280, 694–696. Conley, D. J., Paerl, H. W., Howarth, R. W., Boesch, D. F., Seitzinger, S. P., Havens, K. E., et al. (2009). Controlling eutrophication: nitrogen and phosphorus. Science 323, 1014– 1015. Marotta, H., Duarte, C. M., Pinho, L., and Enrich-Prast, A. (2010b). Rainfall leads to increased pCO2 in Brazilian coastal lakes. Biogeosciences 7, 1607–1614. Biddanda, B., Ogdahl, M., and Cot- ner, J. (2001). Dominance of bacterial metabolisminoligotrophicrelativeto eutrophic waters. Limnol. Oceanogr. 46, 730–739. Guariento, R. D., Carneiro, L. S., Cal- iman, A., Leal, J. J. F., Bozelli, R. L., and Esteves, F. A. REFERENCES (2011). Food web architecture and basal resources interact to determine biomass and stoichiometric cascades along a ben- thic food web. PLoS ONE 6:e22205. doi: 10.1371/journal.pone.0022205. del Giorgio, P. A., Cole, J. J., and Cimb- leris, A. (1997). Respiration rates in bacteria exceed phytoplankton pro- duction in unproductive aquatic sys- tems. Nature 385, 148–151. Marotta, H., Duarte, C. M., Sobek, S., and Enrich-Prast, A. (2009). Large CO2 disequilibria in tropical lakes. Glob. Biogeochem. Cycles 23. Camacho, A., Wurtsbaugh, W. A., Mir- acle, M. R., Armengol, X., and Vicente, E. (2003). Nitrogen limita- tion of phytoplankton in a Spanish karst lake with a deep chlorophyll maximum: a nutrient enrichment bioassay approach. J. Plankton Res. 25, 397–404. Paerl, H. W. (2009). Controlling eutrophication along the freshwater– marine continuum: dual nutrient (N and P) reductions are essential. Estu- aries Coasts 32, 593–601. Downing, J. A., Cole, J. J., Middelburg, J. J., Striegl, R. G., Duarte, C. M., Korte- lainen, P., et al. (2008). Sediment organic carbon burial in agricultur- ally eutrophic impoundments over the last century. Glob. Biogeochem. Cycles 22, GB1018. INMET. (1992). Relatório Anual do Instituto Nacional de Meteorologia - 1991. Rio de Janeiro: INMET. IPCC. (2007). Climate Change 2007: The Physical Science Basis. Paris: IPCC. Carignan, R., Planas, D., and Vis, C. (2000). Planktonic produc- tion and respiration in oligotrophic Shield lakes. Limnol. Oceanogr. 45, 189–199. Raymond, P. A., Caraco, N. F., and Cole, J. J. (1997). Carbon dioxide concen- tration and atmospheric flux in the Hudson River. Estuaries 20, 381–390. Duarte, C. M., and Agusti, S. (1998). The CO2 balance of unproduc- tive aquatic ecosystems. Science 281, 234–236. Jonsson, A., Karlsson, J., and Jans- son, M. (2003). Sources of carbon dioxide supersaturation in clearwater and humic lakes in northern Sweden. Ecosystems 6, 224–235. Royer, D. L., Berner, R. A., and Park, J. (2007). Climate sensitivity con- strained by CO2 concentrations over the past 420 million years. Nature 446, 530–532. Carpenter, S. R., Cole, J. J., Hodg- son, J. R., Kitchell, J. F., Pace, M. L., Bade, D., et al. (2001). Trophic cascades, nutrients, and lake produc- tivity: whole-lake experiments. Ecol. Monogr. 71, 163–186. Duarte, C. M., and Prairie, Y. T. (2005). Prevalence of heterotro- phy and atmospheric CO2 emissions from aquatic ecosystems. Ecosystems 8, 862–870. Kosten, S., Roland, F., da Motta Marques, D. M. L., Van Nes, E. H., Mazzeo, N., Sternberg, L. S. L., et al. (2010). DISCUSSION ll h h Our results contrasted with the persistence of CO2 supersaturation in highly organic-enriched waters from whole-lake (Cole et al., 2000) or mesocosm studies (Marotta et al.,2012) also assessing the effects of experimental nutrient additions. One plausible explanation for this discrepancy would be the absence of the bottom sediment as an additional source of organic substrates to CO2 production within the microcosms. FIGURE 3 |Total suspended solids (TSS) after different N addition for humic and clear waters. Legend as described in Figure 1. Increases in the phytoplankton biomass (pelagic chlorophyll a) contributed to net CO2 decreases in highly N- and P-enriched microcosms with humic waters of the Comprida coastal lagoon, but not in those with clear waters of the Carapebus coastal lagoon, where no significant differences in pelagic chlorophyll a were reported among all experimental treatments or con- trols. Indeed, the CO2 decrease observed in more N- and P-enriched clear water microcosms was mainly related to the presence of periphyton biomass on the walls, which was absent in the humic water microcosms likely due to light attenua- tion to primary production in their dark waters (Thomaz et al., 2001). In humic waters, TSS increase might be related to the phytoplankton growth, as the pCO2 decreased without any peri- phyton growth on the microcosm walls. On the other hand, higher concentrations of non-algal solids in suspension (TSS not related to changes in chlorophyll a or any external partic- ulate input) are a proxy for large-bodied zooplankton, which can be strongly stimulated under eutrophic conditions by the availability of algae (Cole et al., 2000). Despite the source of FIGURE 3 |Total suspended solids (TSS) after different N addition for humic and clear waters. Legend as described in Figure 1. Furthermore, P-enriched microcosms with higher N addi- tions showed higher bacterial production rates and algal biomass (pelagic or periphytic chlorophyll a), suggesting that the N supply might limit the heterotrophic and autotrophic metabolic activity in P-enriched tropical coastal lagoon. Despite N2 fixation may be sufficient to allow biomass to continue to be produced even with extreme reductions in N inputs into lakes (Schindler et al., 2008; Smith and Schindler, 2009), our experimental evidences confirm that N might be a relevant control on eutrophication in coastal waters as previously pointed out (Conley et al., 2009; Paerl, 2009). DISCUSSION ll h h February 2013 | Volume 4 | Article 11 | 4 Frontiers in Microbiology | Aquatic Microbiology Nitrogen control on pCO2 in coastal lagoons Peixoto et al. experimental bias related to any extrapolation from the periphy- ton response on the microcosm walls to whole ecosystem scale, our results support a potential relevance of N control under P- enriched conditions on algae community. The strength of this zooplankton control on phytoplankton, but not on periphyton biomass in highly nutrient-enriched lake waters was previously reported using experimental mesocosms in another lake at the same studied region as in this work (Guariento et al., 2011). Thus, the absence of common grazers on zooplankton in tropical coastal lagoons, i.e., snails and fishes (Guariento et al., 2010), might have contributed to the increase of the periphyton biomass in clear water nutrient-enriched microcosms. decrease in both humic and clear coastal lagoons waters. The N inputs even under P-enriched conditions might lead to intense net decreases in CO2 in coastal lagoons waters. Both inorganic N and organic substrates inputs modulate the CO2 balance in freshwater and brackish coastal lagoons. ACKNOWLEDGMENTS We thank the students of the Limnology postgraduate course (Federal University of Rio de Janeiro) by the help during the experiment: Alexandre Lopes, Bruna Braun, Carla G. Pozer, Jayme Santangelo, Maja Kajin, Marcelo F. G. Brito, Marcio R. Miranda, Luciana O.Vidal, Luciana S. da Costa, and Fatima Locca. We are also thankful to Vinicius Farjalla, Claudio C. Marinho, Frederico Meirelles, and Thais Laque for logistical support and analyses. In conclusion, our hypothesis was confirmed as N is an important driver on pCO2 in P-enriched coastal lagoons waters. Higher experimental N enrichments promoted a significant pCO2 REFERENCES Climate-dependent CO2 emissions from lakes. Glob. Bio- geochem. Cycles 24, GB2007. Schindler, D. W., Hecky, R. E., Findlay, D. L., Stainton, M. P., Parker, B. R., Paterson, M. J., et al. (2008). Eutrophication of lakes cannot be controlled by reducing nitrogen input: results of a 37-year whole-ecosystem experiment. Proc. Natl. Acad. Sci. U.S.A. 105, 11254– 11258. Schindler, D. W., Hecky, R. E., Findlay, D. L., Stainton, M. P., Cole, J. J., and Caraco, N. F. (1998). Atmospheric exchange of carbon dioxide in a low-wind oligotrophic lake measured by the addition of SF6. Limnol. Oceanogr. 43, 647–656. Duarte, C. M., Prairie, Y. T., Montes, C., Cole, J. J., Striegl, R., Melack, J., et al. (2008). CO2 emissions from saline lakes: a global estimate of a surpris- ingly large flux. J. Geophys. Res. 113, G04041. Mackereth, F. J. H., Heron, J., and Talling, J. F. (1978). Water Analysis: Some Revised Methods for Limnolo- gists. Freshwater BiologicalAssociation Scientific Publication n. 36. Winder- mere: Freshwater Biological Associa- tion. Cole, J. J., Caraco, N. F., Kling, G. W., and Kratz, T. K. (1994). Carbon- dioxidesupersaturationinthesurface waters of lakes. Science 265, 1568– 1570. Smith, D. C., and Azam, A. (1992). A simple, economical method for measuring bacterial protein synthesis Farjalla, V. F., Amado, A. M., Suhett, A. L., and Meirelles-Pereira, F. (2009). DOC removal paradigms February 2013 | Volume 4 | Article 11 | 5 www.frontiersin.org | 5 Nitrogen control on pCO2 in coastal lagoons Peixoto et al. rates in seawater using 3H-leucine 1. Mar. Microb. Food Webs 6, 107–114. Vitousek, P. M., and Mooney, H. A. (1997). Estimates of coastal popula- tions – response. Science 278, 1212– 1212. Strome, D. J., and Miller, M. C. (1978). Photolytic changes in dis- solved humic substances. Verh. Int. Ver. Theor. Angew. Limnol. 20, 1248– 1254. rates in seawater using 3H-leucine 1. Mar. Microb. Food Webs 6, 107–114. Citation: Peixoto RB, Marotta H and Enrich-Prast A (2013) Experimental evi- dence of nitrogen control on pCO2 in phosphorus-enriched humic and clear coastal lagoon waters. Front. Microbio. 4:11. doi: 10.3389/fmicb.2013.00011 Smith, V. H., and Schindler, D. W. (2009). Eutrophication science: where do we go from here? Trends Ecol. Evol. 24, 201–207. Wetzel, R. G., and Likens, G. E. (1991). Limnological Analyses, 2nd Edn. New York: Springer-Verlag, 391 p. Thomaz, S. M., Enrich-Prast, A., Gonçalves, J. F., dos Santos, A. M., and Esteves, F. A. (2001). Received: 30 July 2012; accepted: 12 Jan- uary 2013; published online: 06 February 2013. Frontiers in Microbiology | Aquatic Microbiology February 2013 | Volume 4 | Article 11 | 6 REFERENCES Metabolism and gaseous exchanges in two coastal lagoons from Rio de Janeiro with distinct limnological characteristics. Braz. Arch. Biol. Technol. 44, 433–438. This article was submitted to Frontiers in Aquatic Microbiology, a specialty of Frontiers in Microbiology. This article was submitted to Frontiers in Aquatic Microbiology, a specialty of Frontiers in Microbiology. Sobek, S., Tranvik, L. J., and Cole, J. J. (2005). Temperature independence of carbon dioxide supersaturation in global lakes. Glob. Biogeochem. Cycles 19, 1–10. Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any com- mercial or financial relationships that could be construed as a potential con- flict of interest. Copyright © 2013 Peixoto, Marotta and Enrich-Prast. This is an open-access arti- cle distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are cred- ited and subject to any copyright notices concerning any third-party graphics etc. Solomon, S., Daniel, J. S., Sanford, T. J., Murphy, D. M., Plattner, G. K., Knutti, R., et al. (2010). Per- sistence of climate changes due to a range of greenhouse gases. Proc. Natl. Acad. Sci. U.S.A. 107, 18354– 18359. Tranvik, L. J., Downing, J. A., Cot- ner, J. B., Loiselle, S. A., Striegl, R. G., Ballatore, T. J., et al. (2009). Lakes and reservoirs as regulators of carbon cycling and climate. Limnol. Oceanogr. 54, 2298–2314. Received: 30 July 2012; accepted: 12 Jan- uary 2013; published online: 06 February 2013. February 2013 | Volume 4 | Article 11 | 6 Frontiers in Microbiology | Aquatic Microbiology
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Ziviler Ungehorsam in modernen Demokratien. Eine Nachlese in demokratietheoretischer Absicht
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s u b \ u r b a n . zeitschrift für kritische stadtforschung Magazin 2014, Band 2, Heft 2 Seiten 137-142 zeitschrift-suburban.de Ziviler Ungehorsam in modernen Demokratien Eine Nachlese in demokratietheoretischer Absicht Christian Volk Dass politischer Protest zu ‚Rechtsverstößen‘ führen kann, ist nichts Neues. Protestierende besetzen mitunter Plätze und Häuser, leisten Wider­stand gegen die Staatsgewalt oder verstoßen gegen ein polizeilich verhäng­tes Auf­ent­­halts­verbot. Auch bei den diversen Protesten, die in der jüngsten Vergangenheit die mediale Aufmerksamkeit auf sich zogen – ob im Gezi-Park, auf dem Kiewer Maidan-Platz, in Sarajevo oder rund um die Rote Flora in Hamburg –, ist es zu solchen ‚Rechtsverstößen‘ gekommen. Der Grund, warum man das Wort ‚Rechtsverstöße‘ dabei besser in An­ füh­ rungs­ zeich­ en setzt, hängt – ganz abgesehen von der sozialen Konstruiertheit des Begriffs – eng mit der öffentlichen Deutung und Wahrnehmung des Pro­tests selbst zusammen. Denn in der medialen Rezeption hierzulande wurden beispielsweise die Proteste in Istanbul, Kiew oder Sarajevo nicht genuin als ‚Rechtsverstöße‘ bewertet, sondern als Akte des zivilen Unge­hor­sams, die im Geiste einer demokratischen Verfassung stehen, zur Demo­kra­ti­sie­rung der Demokratie beitragen oder gar Teil des Kampfes zur Durchsetzung der Demokratie sind. Auf der anderen Seite hingegen standen die Proteste in Hamburg. Den ‚Rechtsverstößen‘ dort sprach man eine sinnvolle politische beziehungsweise demokratische Bedeutung ab und deutete sie vorrangig als ‚linke Kra­wall­mache­rei‘. Richard Wagner (2014) ging in der Frankfurter Allgemeinen Zei­tung gar so weit, zu behaupten, dass die in Hamburg zeitweise zum Symbol gewordene Klobürste[1] in der Tat die geeignetste Versinnbild­lich­ung der hiesigen Polizeiarbeit sei. Und im konservativen parteipolitischen Lager stand unter anderem ein ‚Abiturverbot‘ für Protestierende als dis­ zi­ pli­ narische Maßnahme und ‚Lösungsstrategie‘ hoch im Kurs (Hamburger Morgenpost, 22.12.2013). Gegen eine solche Einteilung und Lesart versuche ich im Folgenden die These zu erläutern, dass auch radikalere Formen von Protest und Kri­ tik an der bestehenden Gesellschaft und herrschenden Politik not­wen­­di­ ger Be­stand­­teil des demokratischen Miteinanders sind. Radikale Formen von Pro­­test sind als Akte des zivilen Ungehorsams zu interpretieren, weil sie mo­ der­ ne Demokratien repolitisieren. Eine liberal-demokratische 138 sub\urban Sichtweise auf Protest und zivilen Ungehorsam, wie sie in der medialen Rezeption an­zu­tref­fen ist, greift hier zu kurz. Wie ist das zu verstehen? Sieht man von Wagners extremer Position und semantisch höchst fragwürdiger Ausdrucksweise einmal ab, so lassen sich zwei Kriterien benennen, die die gängige Einschätzung in den Medien, die hier kurz skizziert worden ist, anzuleiten scheinen: zum einen die Form des Protestes – in­wie­fern diese angemessen ist und sich an bestehende Regeln und Gesetze hält; zum anderen die Ziele des Protestes – inwiefern er dazu dient, demokratische und verfassungsmäßig verbriefte Rechte, die von der Regierung nicht ausreichend beachtet oder gar gebrochen werden, einzuklagen. Mit dieser Einschätzung findet man sich in guter Gesellschaft. Kein geringerer als John Rawls, der große US-amerikanische Philosoph des 20. Jahrhunderts, legt in seinen Überlegungen zum zivilen Ungehorsam exakt diese Maßstäbe an (vgl. Rawls 1998: 421). Diese Maßstäbe erwachsen aus einer liberalen Grundhaltung und gehen entsprechend davon aus, dass je gerechter eine Gesellschaftsordnung ist (das heißt: je mehr sie an demokratischen Werten realisiert hat und an justiziellen Einspruchsmöglichkeiten bereithält), desto weniger gerechtfertigt sind kollektive politische ‚Rechtsverstöße‘. In einer vollends gerechten Gesellschaft verliere der zivile Ungehorsam seine Rechtfertigbarkeit (ebd.: 399). Mit dieser liberalen Grundüberzeugung lassen sich dann auch die unterschiedlichen Einschätzungen von Protesten in den Medien erklären: Denn was in ‚defizitären‘ Demokratien der Türkei, der Ukraine oder Bosnien-Herzegowinas wohlwollend betrachtet wird, ist in Deutschland noch lange nicht erlaubt. Doch so einfach ist es nicht. Politischer Protest in modernen Demokratien lässt sich mit einer solch liberalen Sichtweise nur schwer entschlüs­seln und mit einer demokratischen Grundordnung in Einklang bringen. Ein ge­nauerer Blick auf aktuelle politische Protestbewegungen in Deutsch­land macht zum einen deutlich, dass es vielen dieser Bewegungen mit ihren Pro­test­prak­tiken weniger um das Einklagen von Rechten oder um Korrekturen an der Regierungspolitik geht. So stellen die Proteste von Blockupy etwa die neoliberale Grundorientierung des europäischen Finanzsystems infrage, während es Aktivist_innen des Flüchtlingscamps in Berlin mit ihren For­de­rungen um eine grundsätzliche Reformierung des Konzepts der nationa­ len Zugehörigkeit und eine grundlegende Staatskritik ging. Viele Grup­pie­rung­en rund um die Rote Flora vertreten ähnliche Positionen und Forderungen und kombinieren diese häufig noch mit einer grundlegenden Kapitalismuskritik. Kurzum: Diese Bewegungen stehen für tiefgreifende politische Veränderungen und alternative Lebensweisen. Man mag diese grund­le­gen­de Kritik vielleicht inhaltlich nicht teilen; um diesen Protest jedoch verstehen und demokratietheoretisch einordnen zu können, ist es von zentraler Bedeutung, seine genuin politische Dimension zu erfassen. Tut man dies nicht und kriminalisiert stattdessen kurzerhand radikalere Formen von Protest, entpolitisiert man die Demokratie. Ein erster Hinweis auf eine solche politische Dimension ist, dass es sich bei diesen Protesten um kollektive Akte des politischen Widerspruchs handelt, die im öffentlichen Raum stattfinden und sich an eine politische 2014, Band 2, Heft 2 Volk 139 Öffentlichkeit richten. Dass dafür die Form des zivilen Ungehorsams gewählt wird, ist nicht unerheblich. Denn dies kann als Indiz dafür betrachtet werden, dass eine bedeutende Anzahl von (zumeist jungen) Personen von den Beteiligungsangeboten moderner Demokratien nicht erreicht wird, oder mehr noch: sich von dem existierenden Spektrum öffentlichpoli­tisch­er Meinungen nicht wirklich repräsentiert fühlt oder gar an der Leben­dig­keit der politisch-demokratischen Institutionen und Verfahren zweifelt. Aus dieser Perspektive erscheinen gemeinschaftlich begangenen ‚Rechtsverstöße‘ oder besser: Protestpraktiken in einem anderen Licht. Man erkennt in ihnen auch einen Beitrag zur Repolitisierung moderner demokratischer Ordnungen – also auch der bundesrepublikanischen. Inwiefern Repolitisierung? Aus demokratietheoretischer Sicht sind meiner Ansicht nach drei Aspekte ausschlaggebend: Zuallererst wird mittels des Protestes der Versuch unternommen, neu zu bestimmen, wer, wann, wo und wie sprechen darf. Auf diese Weise realisiert man das „Beteiligungsversprechen“ (Buchstein/Jörke 2003: 488) von demokratischen Gesellschaften. Dass man dabei, wie im Fall der Hamburger Proteste, ein Übereinkommen mit der Regierung ablehnt, hat Gründe. Ein ganz wesentlicher Grund ist sicherlich, dass es den Protestierenden nicht um die Verwirklichung irgendeines konkreten Rechts geht. Ihnen geht es um ihren direkten Ausdruck, um politische Expressivität.[2] Wenn beispielsweise die Bewegung rund um die Rote Flora fordert, dass diese besetzt bleiben soll, dann heißt das, dass man das Haus nicht geschenkt oder rechtlich übertragen haben will. Es geht um den Akt des Besetzens und die Praktik des Besetzthaltens. In diesem Akt und in dieser Praktik wird der grundlegende Widerspruch zur kapitalistischen Logik und den liberalen Eigentumsvorstellungen zum Ausdruck gebracht. Mit einem liberalen Politikverständnis – man betreibt Politik, um Interessen zu realisieren und Rechte durchzusetzen – lässt sich diese politische Praktik kaum entschlüsseln. Denn sie mündet nicht in einer Forderung, der innerhalb der politisch-rechtlichen Grundordnung einfach nachgekommen werden kann. Die Forderung lebt und entfaltet ihre politische Symbolik überhaupt erst im Widerspruch zur bürgerlich-liberalen Grundordnung. Indem man sich mittels des Protests als ‚politische Mitsprecher_innen‘ etabliert, verweist man – zweitens – auch auf die Möglichkeit, den Sta­tus quo anders zu beschreiben. Das heißt, man wendet sich gegen eine Gegen­warts­ beschrei­bung, die festlegen möchte, was als politisches Problem zu gelten hat und was dementsprechend eine praktikable oder nicht praktikable Antwort auf ‚dieses Problem‘ ist. Gegen den Trend in modernen Demokratien, politische Meinungs- und Entscheidungsfindung aus dem Parlament heraus auf für die Öffentlichkeit schwer zugängliche ‚Expertengremien‘ oder Institutionen zu übertragen, trägt der Protest hier den Streit auf die Straße und macht ihn sichtbar. Wenn der Kern der Demokratie die öffent­liche Re­ prä­sen­ta­tion politischer Konflikte ist, dann gilt es die Sichtbarmachung dieses Streites auch ein Stück weit anzuerkennen. Denn dadurch wird öffentliche Aufmerksamkeit erzeugt, werden Themen mit politischer Bedeutung versehen und Bürger_innen zum politischen Nachdenken herausgefordert. Es werden nicht berücksichtigte Optionen deutlich gemacht, es wird ‚das Gemachte‘ an der Politik aufgedeckt und herausgestellt, wer mögliche 140 sub\urban Ge­win­ner und Verlierer von politischen Entscheidungen sind. Damit betont der Protest einen zentralen Charakterzug politischer Gemeinwesen, der im Alltag moderner Demokratien aus dem Bewusstsein zu schwinden droht: die Alternativität politischer Entscheidungen. Drittens handelt es sich beim Protest um eine gemeinschaftliche politische Praxis. Das ist insofern besonders hervorzuheben, als Protest jene seltenen Räume und Arenen in modernen Demokratien etabliert und bewahrt, in denen Menschen noch politische Fragen diskutieren, sich organisieren, Mo­men­te von Gemeinsamkeit und Solidarität erfahren können. Dadurch wenden sich Protestbewegungen explizit und auf der Grundlage lebensweltlicher sozialer Praktiken auch gegen die Transformation von demokratischer Politik in Verwaltung, Beratung und Management. Allerdings erschöpft sich demokratische Politik nicht allein in der Sicht­ bar­machung des politischen Konflikts. Demokratische Politik verlangt auch eine Verständigung (nicht Konsensfindung oder Problemlösung) über den Konflikt. Exakt aus diesem Grund darf eine politische Protestbewegung das Postulat der Verständigung nicht auf Dauer aufkündigen, wenn sie ihren freiheitlich-emanzipatorischen Gehalt behalten will. Mit ‚auf Dauer‘ meine ich, dass Protestbewegungen stets eine konfrontative, mitunter auch gewaltsame Seite haben, denn – darauf hat Robin Celikates (2013: 225) zurecht hingewiesen: Ohne faktische Konfrontation kann Protest seine symbolische Bedeutung häufig gar nicht ausbilden. Wenn man auf einem öffentlichen Platz ein Camp errichten oder in einem Gebäude ein autonomes Zentrum erhalten will, von dem eine gewisse politische Symbolik ausgehen soll, dann muss man diesen Platz und dieses Gebäude auch verteidigen. Anderenfalls bleibt es bei einer leeren und wirkungslosen Willensbekundung. Damit rechtfertigt man nicht den militanten Irrglauben, der uns aus Pamphleten wie „Irgendwann werden wir schießen müssen“ entgegenschlägt und wo für den Einsatz von „Handund Schnellfeuerwaffen“ plädiert wird – ein Pamphlet, das nach den Ausschreitungen in Hamburg im Dezember von einer Gruppe mit dem Namen „Das unverbesserliche Kollektiv“ (2013) veröffentlicht wurde. Die Überzeugung, dass Protest mitunter nicht ohne faktische Konfrontation auskommt, speist sich lediglich aus dem Zweifel am Goodwill und an der unmittelbaren Kooperationsbereitschaft der Regierenden. Wenn jedoch die Konfrontation das alleinige Moment der Bewe­gung dar­stellt und der verständigungsorientierte Umgang mit dem poli­tisch­ en Gegner nicht zum politischen Repertoire gehört, dann wird sie über kurz oder lang einen guten Teil ihres emanzipatorischen Gehalts verlieren. Aus welchem Grund? Ohne Austausch und Irritationen tendieren die diskursiven Praktiken im Inneren der Protestbewegung dazu, eine absolute Gegnerschaft zum politischen Establishment herauszubilden und zu zementieren. Aus einem agonistischen Antagonismus droht eine FreundFeind-Beziehung zu werden (vgl. Mouffe 2007: 30ff.).[3] Dabei werden die reflexiven demokratischen Praktiken im Inneren von Protestbewegungen unterminiert; aus Diskussion und Debatte wird angewandte Ideologie; es dominieren Platti­tü­den, Ste­reo­typen und ‚Halbwissen‘, die im Dienste der Selbstvergewisserung stehen, anstatt zur Ausbildung politischer Urteilskraft beizutragen. Hinzu kommt, dass so eine politische Haltung 2014, Band 2, Heft 2 Volk 141 zustande kommt, die möglicherweise berechtigte Einwände, Kompromisse oder Alternativvorschläge der Gegenseite gar nicht mehr zur Kenntnis nehmen kann. Streit, Diskurs und Debatte werden dann nicht nur unnötig, sondern auch unmöglich. Statt durch Protest zu einem öffentlichen Diskurs und zur politischen Bewusstseinsbildung beizutragen, droht weit eher die Eskalation des Konflikts. Auch Protestbewegungen in modernen Demokratien haben eine gewisse politische Verantwortung zu übernehmen – nicht zuletzt auch deshalb, weil die ihnen zugrunde liegenden Praktiken sich der demokratischen Erfahrung verdanken. Eine wahrlich demokratische politische Ordnung zeichnet sich nämlich nicht zuletzt durch ihren ‚Ermöglichungscharakter‘ aus, das heißt, dass sie radikalen Protest als Akte der Repolitisierung und damit des zi­vi­len Un­ge­hor­sam deuten kann und zulässt. Dies ist insofern von fun­da­men­ta­ler Bedeutung, als in Demokratien politischer Protest nicht prinzi­piell zur großen Heldentat werden muss, nicht prinzipiell zu einer Frage von Leben oder Tod. Genau unter diesem Vorzeichen aber steht Protest meist in Diktaturen, autoritären oder gar totalitären Regimen. Hier steht zu befürchten, dass jeder politische Protest mit Gewalt und Terror erstickt wird. Dass dem so ist, macht den radikalen Protest in Demokratien jedoch nicht weniger legitim. Die beschriebene Repolitisierung durch radikalen Protest bestätigt nur den spezifischen Unterschied zwischen autoritären und demokratischen Gesellschaften. Gerade weil radikaler politischer Protest in vielerlei Hinsicht moderne Demokratien repolitisiert und ein Bestandteil des demokratischen Zusammenlebens ist, ist er im Geiste einer demokratischen Verfassung und folglich auch als ziviler Ungehorsam zu verstehen. Endnoten [1] Um ihren Protest gegen die Proklamation des Gefahrengebiets in der Hamburger Innenstadt durch die Polizei Ausdruck zu verleihen, führten einige Hamburger Bürger_innen bei ihrem Gang durch das ‚Gefahrengebiet‘ absichtlich eine Reihe an skurrilen Gegenständen mit sich (z. B. eine Gurke, versehen mit einer Zündschnur), die dann bei der zu erwartenden Leibesvisitation im Zuge der Polizeikontrollen zum Vorschein kamen. Bei einer dieser Polizeikontrollen zog ein Polizist einem jungen Mann eine Klobürste aus dem Hosenbund. Das entsprechende Video machte sehr schnell die Runde und die Klobürste wurde so zum Symbol des Hamburger Protestes. [2] Hinzu kommt noch, dass sie es ablehnen, mit konkreten Forderungen an die politi­ sch­en Macht­­haber heranzutreten, weil sie dadurch deren Legitimität anerkennen und die hie­­rarch­ische politische Ordnungsstruktur reproduzieren würden. [3] Im Unterschied zu Mouffe sehe ich sowohl auf der Seite der Medien und politischen Eliten als auch aufseiten der Protestbewegungen die Gefahr, dass sich diskursive Praktiken ausbilden, die eine antagonistische Austragung demokratischer Politik verhindern. Für eine ausführliche Kritik an und Auseinandersetzung mit Mouffe und der Tradition der radikalen Demokratie vgl. Volk 2013. Autor_innen Christian Volk; Politische Theorie und Ideengeschichte (Politikwissenschaft) volkch@uni-trier.de 142 sub\urban Literatur Buchstein, Hubertus / Jörke, Dirk (2003): Das Unbehagen an der Demokratietheorie. In: Leviathan 31, 470-495. Celikates, Robin (2013): Ziviler Ungehorsam zwischen Gewaltfreiheit und Gewalt. In: Franziska Martinsen / Oliver Flügel-Martinsen (Hg.), Gewaltbefragungen. Beiträge zur Politischen Philosophie der Gewalt. Bielefeld: Transcript Verlag, 215-229. Das unverbesserliche Kollektiv (2013): Irgendwann werden wir schießen müssen. https:// linksunten.indymedia.org/node/102039 (letzter Zugriff am 10.8.2014). Heinemann, Christoph / Iksanov, Anastasia / Bromberg, Wiebke (2013): Die Schlacht um die Schanze. http://www.mopo.de/polizei/4700-randalierer--3168-polizisten-dieschlacht-um-die-schanze,7730198,25708136,item,2.html (letzter Zugriff am 10.8.2014). Mouffe, Chantal (2007): Über das Politische. Wider die kosmopolitische Illusion. Frankfurt a. M.: Suhrkamp Verlag. Rawls, John (1998): Eine Theorie der Gerechtigkeit. Frankfurt a. M.: Suhrkamp Verlag. Volk, Christian (2013): Zwischen Entpolitisierung und Radikalisierung. Zur Theorie von Demokratie & Politik in Zeiten des Widerstands. In: Politische Vierteljahresschrift 1/2013, 75-110. Wagner, Richard (2014): Mit der Klobürste. In: Frankfurter Allgemeine Zeitung, 13.1.2014. http://www.faz.net/aktuell/politik/inland/hamburg-mit-der-klobuerste-12748725.html (letzter Zugriff am 16.6.2014). 2014, Band 2, Heft 2
https://openalex.org/W2060149234
https://bmcneurosci.biomedcentral.com/counter/pdf/10.1186/1471-2202-11-52
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Intravenous administration of mesenchymal stem cells exerts therapeutic effects on parkinsonian model of rats: Focusing on neuroprotective effects of stromal cell-derived factor-1α
BMC neuroscience
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BioMed Central © 2010 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Mesenchymal stem cells (MSCs) are pluripotent stem cells derived from bone marrow with secretory functions of various neurotrophic factors. Stromal cell-derived factor-1α (SDF-1α) is also reported as one of chemokines released from MSCs. In this research, the therapeutic effects of MSCs through SDF-1α were explored. 6- hydroxydopamine (6-OHDA, 20 μg) was injected into the right striatum of female SD rats with subsequent administration of GFP-labeled MSCs, fibroblasts, (i.v., 1 × 107 cells, respectively) or PBS at 2 hours after 6-OHDA injection. All rats were evaluated behaviorally with cylinder test and amphetamine-induced rotation test for 1 month with consequent euthanasia for immunohistochemical evaluations. Additionally, to explore the underlying mechanisms, neuroprotective effects of SDF-1α were explored using 6-OHDA-exposed PC12 cells by using dopamine (DA) assay and TdT-mediated dUTP-biotin nick-end labeling (TUNEL) staining. Results: Rats receiving MSC transplantation significantly ameliorated behaviorally both in cylinder test and amphetamine-induced rotation test compared with the control groups. Correspondingly, rats with MSCs displayed significant preservation in the density of tyrosine hydroxylase (TH)-positive fibers in the striatum and the number of TH-positive neurons in the substantia nigra pars compacta (SNc) compared to that of control rats. In the in vitro study, SDF-1α treatment increased DA release and suppressed cell death induced by 6-OHDA administration compared with the control groups. Conclusions: Consequently, MSC transplantation might exert neuroprotection on 6-OHDA-exposed dopaminergic neurons at least partly through anti-apoptotic effects of SDF-1α. The results demonstrate the potentials of intravenous MSC administration for clinical applications, although further explorations are required. might not repair the dopaminergic pathway or prevent its degeneration [4-6]. Research article Intravenous administration of mesenchymal stem cells exerts therapeutic effects on parkinsonian model of rats: Focusing on neuroprotective effects of stromal cell-derived factor-1α Feifei Wang, Takao Yasuhara*, Tetsuro Shingo, Masahiro Kameda, Naoki Tajiri, Wen Ji Yuan, Akihiko Kondo, Tomohito Kadota, Tanefumi Baba, Judith Thomas Tayra, Yoichiro Kikuchi, Yasuyuki Miyoshi and Isao Date * Correspondence: tyasu37@cc.okayama-u.ac.jp 1 Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan Full list of author information is available at the end of the article Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Open Access Background Parkinson's disease (PD) is a common neurological disor- der characterized by degeneration of nigrostriatal dop- aminergic neurons [1]. The neuronal loss leads to deficiency of DA in the striatum, which is responsible for characteristic motor symptoms such as akinesia, rigidity and tremor [2,3]. The medication using L-DOPA and sur- gical treatment such as deep brain stimulation are estab- lished as effective therapies, although those treatments Cell therapy was developed as a hopeful therapeutic tool for PD. Neural stem cells [7,8], neural precursor cells [9], fetal cells [10,11] and embryonic stem cells [12] have been studied for treatment on PD model of rats. How- ever, there are ethical problems about the usage of embryonic and fetal tissues. These cells are limited in availability and relatively difficult to be prepared. Adult mesenchymal stem cells (MSCs) have many advantages for cell therapy because of the easy availability and pluri- potency without ethical problems [13,14]. * Correspondence: tyasu37@cc.okayama-u.ac.jp 1 Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan Full list of author information is available at the end of the article Page 2 of 9 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Several cytokines are known to secrete from MSCs. SDF-1α is one of the chemotactic cytokines (chemokines) and the unique ligand for a CXC chemokine receptor (CXCR4) [15]. The chemokines induced by inflammation in the central nervous system (CNS) usually play a role in the local immune response. Meanwhile, recent studies showed that the central functions of chemokines are not restricted to neuroinflammation, as originally thought, but extend to novel functions [16-19]. SDF-1α was found to exert neuroprotective effects [20]. It suppressed cell loss of primary cortical cultures induced by H2O2 neuro- toxicity with the modulation of neurotrophic factor- expression. Rats receiving intracerebral administration of SDF-1α reduced infarct volumes with functional amelio- ration through up-regulation of anti-apoptotic proteins [20]. Figure 1 Improvement in forelimb akinesia and amphetamine- induced rotations by MSC transplantation. A: Cylinder test revealed the amelioration of forelimb akinesia in rats receiving MSC transplanta- tion, compared with control groups at 3 and 4 weeks after transplanta- tion. *p < 0.05 versus the control groups. Behavioral tests TH staining revealed the significant preservation of TH- positive fibers in the striatum (49.8 ± 14.5%, relative to the intact side, p values > 0.05, Figure 2A-D, I) and TH- positive cells in the SNc (57.3 ± 10.3%, relative to the intact side; p values > 0.01, Figure 2E-H, J) of MSC group, compared to those of fibroblast group (striatum: 25.2 ± 13.1%, SNc: 25.2 ± 13.1%) and PBS group (striatum: 25.3 ± 12.5%, SNc: 25.3 ± 12.5%). In cylinder test (Figure 1A), MSC group significantly ameliorated forelimb akinesia over time, compared to PBS and fibroblast group (PBS: 44.2 ± 11.3, 46.9 ± 16.6, 53.1 ± 13.3 and 64.7 ± 17.3%; fibroblast: 44.9 ± 14.8, 51.9 ± 6.3, 55.0 ± 12.4 and 60.2 ± 16.1%; MSC: 37.1 ± 12.5, 38.5 ± 12.6, 33.0 ± 8.9 and 29.3 ± 13.7% at 1, 2, 3 and 4 weeks after transplantation, respectively. One-way measures of ANOVA, F2, 16 = 16.2, p < 0.0001 and post-hoc t-test of p's value < 0.01 vs. other control groups). Background B: The number of rotations was significantly less in rats receiving MSC transplantation, compared with that in control groups at 2, 3 and 4 weeks after transplantation. *p < 0.05 versus the control groups. Figure 1 Improvement in forelimb akinesia and amphetamine- ally, compared to fibroblast and PBS group with signifi- cant differences. Background B: The number of rotations was significantly less in rats receiving MSC transplantation, compared with that in control groups at 2, 3 and 4 weeks after transplantation. *p < 0.05 versus the control groups.       1 2 3 4 Contralateral bias (%) Weeks after transplantation Cylinder test PBS Fibroblast MSC * * 0 5 10 2 3 4 Turns / minutes Weeks after transplantation Amphetamine-induced rotations PBS Fibroblast MSC * * * Worse Worse Better Better A B       1 2 3 4 Contralateral bias (%) Weeks after transplantation Cylinder test PBS Fibroblast MSC * * Worse Better A A Weeks after transplantation 0 5 10 2 3 4 Turns / minutes Weeks after transplantation Amphetamine-induced rotations PBS Fibroblast MSC * * * Worse Better B Amphetamine-induced rotations B Recent studies reported that intrastriatal transplanta- tion of MSCs restored the function of nigrostriatal dop- aminergic systems, leading to the early improvement of behavioral deterioration in PD model of rats [21-24]. However, there is no study that demonstrated therapeutic effects of intravenous MSC administration for PD model of rats. Furthermore, the mechanisms of functional recovery achieved by MSCs transplantation have not been revealed completely so far. In this study, we explored whether intravenous administration of MSCs exerted therapeutic effects on PD model of rats in vivo. Then, neuroprotective effects of SDF-1α secreted from trans- planted MSCs were explored using 6-OHDA-exposed PC12 cells in vitro. Weeks after transplantation Figure 1 Improvement in forelimb akinesia and amphetamine- induced rotations by MSC transplantation. A: Cylinder test revealed the amelioration of forelimb akinesia in rats receiving MSC transplanta- tion, compared with control groups at 3 and 4 weeks after transplanta- tion. *p < 0.05 versus the control groups. B: The number of rotations was significantly less in rats receiving MSC transplantation, compared with that in control groups at 2, 3 and 4 weeks after transplantation. *p < 0.05 versus the control groups. Figure 1 Improvement in forelimb akinesia and amphetamine- induced rotations by MSC transplantation. A: Cylinder test revealed the amelioration of forelimb akinesia in rats receiving MSC transplanta- tion, compared with control groups at 3 and 4 weeks after transplanta- tion. *p < 0.05 versus the control groups. Detection of transplanted MSCs At 2 days, 1 week and 4 weeks after cell transplantation, lungs, kidneys and brains were removed. We found that the majority of cells were localized to the pulmonary tis- sue and a few cells actually reached the brain and remained there at 2 days after transplantation (Figure 3A, C, E). Some cells were also observed in the pulmonary tis- sue and the brain at 1 week after transplantation (Figure 3B, D, F), there were significantly fewer than those seen at 2 days after transplantation. There were no detectable GFP-positive cells in the brain at 4 weeks after transplan- tation. In amphetamine-induced rotation test (Figure 1B), MSC group significantly reduced the number of rotations over time, compared to PBS and fibroblast group (PBS: 7.5 ± 1.2, 8.8 ± 3.1 and 8.5 ± 3.5 turns/minute; fibroblast: 6.8 ± 1.2, 7.8 ± 2.7 and 8.2 ± 3.3 turns/minute; MSC: 4.2 ± 1.8, 1.6 ± 1.1 and 1.2 ± 0.7 turns/minute at 2, 3 and 4 weeks after transplantation, respectively. One-way mea- sures of ANOVA, F2, 16 = 15.8, p < 0.0001 and post-hoc t- test of p's value < 0.01 vs. other control groups). Thus, in the behavioral tests, MSC group ameliorated behavior- In amphetamine-induced rotation test (Figure 1B), MSC group significantly reduced the number of rotations over time, compared to PBS and fibroblast group (PBS: 7.5 ± 1.2, 8.8 ± 3.1 and 8.5 ± 3.5 turns/minute; fibroblast: 6.8 ± 1.2, 7.8 ± 2.7 and 8.2 ± 3.3 turns/minute; MSC: 4.2 ± 1.8, 1.6 ± 1.1 and 1.2 ± 0.7 turns/minute at 2, 3 and 4 weeks after transplantation, respectively. One-way mea- sures of ANOVA, F2, 16 = 15.8, p < 0.0001 and post-hoc t- test of p's value < 0.01 vs. other control groups). Thus, in the behavioral tests, MSC group ameliorated behavior- Page 3 of 9 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Figure 2 Preservation of dopaminergic systems of 6-OHDA-lesioned rats by MSC transplantation. A-H: TH-positive fibers in the striatum and neurons in the SNc of rats that received MSC transplantation were markedly preserved (D, H), compared with rats receiving PBS injection (B, F) and fibroblast transplantation (C, G). Normal TH-positive fibers and neurons were recognized in the intact striatum (A) and SNc (E). Scale bar: 100 μm in (A)-(D), 200 μm in (E)-(H). Detection of transplanted MSCs I: The density of TH-positive fibers in the striatum was analyzed with a computerized image analysis system. Rats receiving MSC transplantation showed a significant preservation in the density of TH-positive fibers in the striatum compared with the control rats. *p < 0.05 versus the control groups. J: The number of TH-positive neurons in the SNc was counted. The number of TH-positive neurons in the SNc was also significantly high, compared with the control rats. *p < 0.05 versus the control groups. A B C D E H G F 0 20 40 60 80 PBS Fibroblast MSC % relative to the intact side TH-positive neurons in the SNc * J 0 20 40 60 80 PBS Fibroblast MSC % relative to the intact side Density of TH-positive fibers in the striatum * I A B C D A B C D 0 20 40 60 80 PBS Fibroblast MSC % relative to the intact side Density of TH-positive fibers in the striatum * I 0 20 40 60 80 PBS Fibroblast MSC % relative to the intact side Density of TH-positive fibers in the striatum * I B C D E H G F 0 20 40 60 80 PBS Fibroblast MSC % relative to the intact side TH-positive neurons in the SNc * J J J E G H Figure 2 Preservation of dopaminergic systems of 6-OHDA-lesioned rats by MSC transplantation. A-H: TH-positive Figure 2 Preservation of dopaminergic systems of 6-OHDA-lesioned rats by MSC transplantation. A-H: TH-positive fibers in the striatum and neurons in the SNc of rats that received MSC transplantation were markedly preserved (D, H), compared with rats receiving PBS injection (B, F) and fibroblast transplantation (C, G). Normal TH-positive fibers and neurons were recognized in the intact striatum (A) and SNc (E). Scale bar: 100 μm in (A)-(D), 200 μm in (E)-(H). I: The density of TH-positive fibers in the striatum was analyzed with a computerized image analysis system. Rats receiving MSC transplantation showed a significant preservation in the density of TH-positive fibers in the striatum compared with the control rats. *p < 0.05 versus the control groups. J: The number of TH-positive neurons in the SNc was counted. The number of TH-positive neurons in the SNc was also significantly high, compared with the control rats. *p < 0.05 versus the control groups. Characterization of MSCs We characterized MSCs by immunocytochemical investi- gations. MSCs were positive for matrix receptors, CD44 (93.2 ± 2.1%, Figure 4A) and negative for leukocyte com- mon antigen, CD45 (3.8 ± 0.52%, Figure 4B). Nuclear fragmentation was observed in 6-OHDA- exposed PC12 cells at 12 hours after 6-OHDA exposure. The cell viability of PC12 cells was significantly increased by SDF-1α treatment (Figure 5D-H). Treatment with PBS showed many TUNEL-positive apoptotic cells (72.5 ± 8.2% relative to the whole cells). Treatment with 1, 10 and 50 ng/ml of SDF-1α significantly reduced apoptotic cell death (45.3 ± 2.6, 38.5 ± 8.8 and 42.6 ± 7.6%, respectively, p < 0.05, Figure 5I) compared to treatment with PBS. There were no significant differences among the different concentrations of SDF-1α, that is, 1, 10 and 50 ng/ml. Detection of transplanted MSCs OHDA exposure, the expression of CXCR4 was remark- ably up-regulated on 6-OHDA-exposed PC12 cells com- pared with PBS-exposed PC12 cells (Figure 5B-C). TUNEL staining g Secretion of SDF-1α from MSCs We used ELISA to determine whether SDF-1α was secreted from the MSCs. Over 6 and 24 hours period in culture, MSCs secreted 72.0 ± 16 pg/1 × 104 cells/6 hours and 183.5 ± 142 pg/1 × 104 cells/24 hours of SDF-1α. CXCR4 staining CXCR4 staining CXCR4 staining revealed that normal PC12 cells expressed CXCR4 (Figure 5A). The expression of CXCR4 was also observed in 6-OHDA-exposed PC12 cells at 1, 6 and 12 hours after 6-OHDA exposure. At 6 hours after 6- Page 4 of 9 Wang et al. BMC Neuroscience 2010, 11:52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 http://www.biomedcentral.com/1471-2202/11/52 with anti-SDF-1α antibody, only anti-SDF-1α antibody, MSC supernatant combined with anti-SDF-1α antibody and PBS (43.4 ± 8.5, 45.3 ± 12.5, 33.5 ± 2.7 and 40.5 ± 4.7%, respectively, Figure 7). These results suggested that MSC supernatant exerted anti-apoptotic effects on 6- OHDA-exposed PC12 cells and SDF-1α antibody blocked the anti-apoptotic effect of SDF-1α. Figure 3 Detection of transplanted MSCs. Transplanted MSCs were observed in lung (A), kidney (C) and brain (E) at 2 days after transplan- tation. Some MSCs were also observed in lung (B), kidney (D) and brain (F) at 1 week after transplantation. The insets of panels E and F demon- strated the highly magnified images of GFP-positive MSCs. Green: GFP- positive MSCs, Blue: DAPI-positive nuclei. White arrows show trans- planted GFP-MSCs. Scale bar: 50 μm. A C B E 2 days 1 week Lung Kidney Brain D F A C B E 2 days 1 week Lung Kidney Brain D F D Discussion We carried out intravenous administration of MSCs on PD model of rats and evaluated its therapeutic effects focusing on SDF-1α. Rats with MSC transplantation sig- nificantly ameliorated both in cylinder test and amphet- amine-induced rotation test, compared with fibroblasts and PBS group. Correspondingly, rats with MSCs showed better preservation in the density of TH-positive fibers in the striatum and the number of TH-positive neurons in the SNc. To explore the underlying mechanisms, focusing on SDF-1α, we then proceeded to in vitro studies. In the in vitro studies, SDF-1α treatment suppressed apoptotic cell death of 6-OHDA-exposed PC12 cells with conse- quent increase of DA release from the cells, compared with the control. Furthermore, anti-SDF-1α antibody reduced the anti-apoptotic effects of SDF-1α. Figure 3 Detection of transplanted MSCs. Transplanted MSCs were observed in lung (A), kidney (C) and brain (E) at 2 days after transplan- tation. Some MSCs were also observed in lung (B), kidney (D) and brain (F) at 1 week after transplantation. The insets of panels E and F demon- strated the highly magnified images of GFP-positive MSCs. Green: GFP- positive MSCs, Blue: DAPI-positive nuclei. White arrows show trans- planted GFP-MSCs. Scale bar: 50 μm. Anti-apoptotic effects of SDF-1α In our present study, we demonstrated SDF-1α had anti- apoptotic effects against 6-OHDA-exposed PC12 cells in vitro. PC12 cells expressed CXCR4, an exclusive receptor of SDF-1α. CXCR4 is a member of G protein-coupled receptor (GPCR) family. Many studies have shown that SDF-1α/CXCR4 interaction causes activation of multiple signal transduction pathways, including phosphati- dylinositol 3-kinase (PI3K)/Akt signaling pathway which provides enhanced survival signal and extracellular sig- nal-regulated kinase (ERK 1/2) signaling pathway which provides enhanced cell proliferation [29]. A recent report also demonstrated that SDF-1α treatment reduced apop- totic cell death of endothelial progenitor cells under serum deprivation through PI3K/Akt pathway and decreased caspase-3-activity, an important apoptotic molecule [30]. HPLC analysis The supernatant containing DA from 6-OHDA-exposed PC12 cells were analyzed with HPLC. DA release from 6- OHDA-exposed PC12 cells significantly increased by treatment with 1, 10 ng/ml of SDF-1α (1056 ± 126 ng/2 × 105 cells, 958 ± 114 ng/2 × 105 cells, respectively) com- pared to treatment with PBS (518 ± 150 ng/2 × 105 cells, Figure 6). There were no significant differences between the concentrations of 1 and 10 ng/ml of SDF-1α. Neutralization assay for anti-apoptotic effect of SDF-1α 6-OHDA-exposed PC12 cells treated with SDF-1α or MSC supernatant showed significant suppression of apoptosis (26.6 ± 7.9 and 29.4 ± 3.7%, respectively) com- pared with PC12 cells treated with SDF-1α combined The supernatant containing DA from 6-OHDA-exposed PC12 cells were analyzed with HPLC. DA release from 6- OHDA-exposed PC12 cells significantly increased by treatment with 1, 10 ng/ml of SDF-1α (1056 ± 126 ng/2 × 105 cells, 958 ± 114 ng/2 × 105 cells, respectively) com- pared to treatment with PBS (518 ± 150 ng/2 × 105 cells, Figure 6). There were no significant differences between the concentrations of 1 and 10 ng/ml of SDF-1α. Neutralization assay for anti-apoptotic effect of SDF-1α 6-OHDA-exposed PC12 cells treated with SDF-1α or MSC supernatant showed significant suppression of apoptosis (26.6 ± 7.9 and 29.4 ± 3.7%, respectively) com- pared with PC12 cells treated with SDF-1α combined In the CNS diseases, intracerebral administration of SDF-1α (1 μg/μl) exerted neuroprotection on stroke model of rats with reduced infarct volumes and improve- ment in neural plasticity. The report showed that SDF-1α disrupted the downstream of caspase-3 apoptotic signal in the ischemic penumbra of stroke model of rats with subsequent cortical neuronal protection [20]. In PD model of rats, caspase-3 activity is deeply involved in the apoptosis of dopaminergic neurons induced by 6-OHDA [31,32]. Therefore SDF-1α might enhance the survival of dopaminergic neurons through CXCR4, inducing down- regulation of caspase-3 and activation of PI3/Akt path- way. Figure 4 Characterization of MSCs. MSCs were positive for CD44 (CD44: red; GFP: green, A) and negative for CD45 (CD45: red; GFP: green, B). Scale bar: 50 μm. A B A B A Figure 4 Characterization of MSCs. MSCs were positive for CD44 (CD44: red; GFP: green, A) and negative for CD45 (CD45: red; GFP: green, B). Scale bar: 50 μm. Wang et al. HPLC analysis BMC Neuroscience 2010, 11:52 Page 5 of 9 http://www.biomedcentral.com/1471-2202/11/52 0 20 40 60 80 100 0 0.1 1 10 50 % of TUNEL-positive cells 6')˞ QJPO * * * I A E F B D G H C A E F B D G H C D B E G 0 20 40 60 80 0 0.1 1 10 50 % of TUNEL-positive cells 6')˞ QJPO * * * 0 Figure 5 Anti-apoptotic effects of SDF-1α on 6-OHDA-exposed PC12 cells. A: CXCR4 was expressed in PBS-exposed PC12 cells. Scale bar: 20 μm. B, C: At 6 hours after 6-OHDA exposure, the expression of CXCR4 was remarkably up-regulated on 6-OHDA-exposed PC12 cells (C) compared with PBS-exposed PC12 cells (B). Scale bar: 100 μm. D-H: TUNEL/DAPI staining revealed that the number of apoptotic cells with green-colored, fragmented TUNEL-positive nuclei were reduced in SDF-1α treatment cells (D: 0.1 ng/ml, E: 1 ng/ml, F: 10 ng/ml, G: 50 ng/ml) compared with that of the control cells (H). Scale bar: 100 μm. I: SDF-1α treatment significantly reduced the number of TUNEL-positive 6-OHDA-exposed PC12 cells. *p < 0.05 versus the control with PBS. Figure 6 Enhanced DA secretion from PC12 cells by SDF-1α. PC12 cells treated with SDF-1α significantly increased DA secretion. *p < 0.05 versus the control with PBS. 0 500 1000 1500 0 0.1 1 10 50 '$ QJ™ FHOOV  SDF-1˞ (ng / ml) * * The activation of DA release by SDF-1α treatment y We showed that SDF-1α promoted DA release from 6- OHDA-exposed PC12 cells. A recent report demon- strated that CXCR4 was constitutively expressed on dop- aminergic neurons in the SNc of normal rats and that SDF-1α could increase secretion of DA from dopaminer- gic neurons [33]. Thus, the results suggest that SDF-1α might activate nigrostriatal DA transmission. In our study, DA release might be increased by the functional preservation of 6-OHDA-exposed PC12 cells, as well as the enhanced survival of PC12 cells by SDF-1α, although the increasing effects on DA release might not depend on the dose of SDF-1α. Meanwhile, high dose of SDF-1α might have proapoptotic effects on the cells. Studies on neuroblastoma cells demonstrated that 10 nM of SDF-1α induced neuronal apoptosis after 24 hours-incubation by the activation of signaling pathways involving Src phos- Figure 6 Enhanced DA secretion from PC12 cells by SDF-1α. PC12 cells treated with SDF-1α significantly increased DA secretion. Conclusions The present data provided evidences that MSCs might exert neuroprotection for 6-OHDA-exposed dopaminer- gic neurons both in vitro and in vivo through possibly with anti-apoptotic mechanisms. The results suggest the potentials of intravenous MSC administration for PD. SDF-1α might be at least partly involved in the neuropro- tective effects. Clinical application of MSC transplanta- tion for PD patients might be considered, although further explorations are required. phorylation [34]. The discrepancy might lie on the differ- ences of the used dosage, cells and experiment design, although we should know the fact that SDF-1α has neuro- protective effects with possible neuronal toxicity at high dose. HPLC analysis *p < 0.05 versus the control with PBS. Wang et al. BMC Neuroscience 2010, 11:52 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Page 6 of 9 g http://www.biomedcentral.com/1471-2202/11/52 Figure 7 Blockade of SDF-1α cancelled neuroprotective effects of SDF-1α on 6-OHDA-exposed PC12 cells. SDF-1α antibody blocked the anti-apoptotic effect of SDF-1α and MSC supernatant exerted neu- roprotective effects on 6-OHDA-exposed PC12 cells. *p < 0.05 versus all the control groups.     RI781(/SRVLWLYHFHOOV * * transplantation. This fact might be supposed from previ- ous studies demonstrating that there were scant cells in the brain after intravenous transplantation of MSCs [39,40], although in our study, transplanted MSCs might die during the disease progression or lose green fluores- cence before euthanasia. Nevertheless, MSC transplanta- tion exerted strong therapeutic effects, which might be the proof that secreted trophic factors from MSC grafts might play a key role in the neuroprotective effects in our study. Additionally, MSCs were transplanted intrave- nously at 2 hours after 6-OHDA injection. The early transplantation of MSCs might be the reason of the strong therapeutic effects with the possibility to counter- act 6-OHDA toxicity. As shown in the in vitro study, SDF- 1α from MSCs probably contributed to the functional recovery as well as other trophic factors. Figure 7 Blockade of SDF-1α cancelled neuroprotective effects of SDF-1α on 6-OHDA-exposed PC12 cells. SDF-1α antibody blocked the anti-apoptotic effect of SDF-1α and MSC supernatant exerted neu- roprotective effects on 6-OHDA-exposed PC12 cells. *p < 0.05 versus all the control groups. Methods In vivo study Recently the therapeutic potentials of MSC transplanta- tion have been studied in various pathological conditions of the CNS [35,36]. It have been demonstrated that intra- venous administration of MSCs increased the expression of basic fibroblast growth factor (bFGF), suppressed apoptotic cell death, promoted endogenous cell prolifera- tion and subsequently achieved functional recovery after stroke [37]. Additionally, MSCs produce neurotrophic factors, including vascular endothelial growth factor (VEGF), glial cell line-derived neurotrophic factor (GDNF) and brain-derived neurotrophic factor (BDNF), which are also well known as strong neuroprotectants [38]. The mechanisms of therapeutic effects of MSCs in the ischemic brain might include neuroprotective effects through the secreted neurotrophic factors, effective angiogenesis for amelioration in the microenvironment of ischemic penumbra and enhanced neurogenesis with possible neuronal differentiation of transplanted MSCs for synapse formation, although the number might be very low, especially with intravenous administration [39,40]. MSC transplantation might also exert neuropro- tective effects on PD model of rats at least partly through the secreted trophic factors [41]. Behavioral tests The level of SDF-1α secreted from MSCs was quantified using ELISA kits (R&D Systems, Minneapolis, MN). 1 × 104 MSCs were plated in 12-well culture plate (Thermo Fisher Scientific, Roskilde, Denmark). At 24 hours after plating for attachment, cells were incubated with Hanks' Balanced Salt Solutions (HBSS). Each 50 μl of the super- natant was obtained 6 and 24 hours later. This ELISA sys- tem can detect a minimum of 14 pg/ml of SDF-1α. Culture of PC12 Cells All rats were evaluated behaviorally with cylinder test and amphetamine-induced rotation test for 1 month. Forelimb akinesia was analyzed with cylinder test at 1, 2, 3 and 4 weeks after transplantation. Contacts made by each forepaw with the wall of a clear cylinder (diameter: 20 cm) were counted. The asymmetry score of forelimb use in wall exploration was calculated as a contralateral bias, where contralateral bias = [(the number of contacts with contralateral limb) - (the number of contacts with ipsilateral limb)]/[(the number of contacts with contralat- eral limb) + (the number of contacts with ipsilateral limb)] × 100 [27,28]. PC12 cells were obtained from Dainippon Sumitomo Pharma Biomedical (Osaka, Japan) and used for in vitro studies. Cells were plated in DMEM supplemented with 5% horse serum (Gibco, Cergy Pontoise, France), 5% new- born calf serum (Gibco, Cergy Pontoise, France), 1% (v/v) penicillin/streptomycin (Gibco, Cergy Pontoise, France) a density of 1 × 105 cells/well on poly-D-ornitin-coated glass slides in 24-well culture plate (Thermo Fisher Scien- tific, Roskilde, Denmark). Cells were cultured at 37°C in a fully humidified atmosphere with 5% CO2. At 24 hours after the initial plating, the medium was exchanged for fresh medium. Amphetamine-induced rotational behavior was per- formed at 2, 3 and 4 weeks after transplantation. Rats were monitored for 90 minutes with a video camera after intraperitoneal injection of D-amphetamine (3.0 mg/kg, Dainippon Sumitomo Pharma, Osaka, Japan). Data are expressed as the number of complete body turns per min- ute. Preparation of brain sections At 4 weeks after transplantation, rats were euthanized and brains were removed. Coronal sections were cut at 40 μm-thickness with a freezing microtome (-20°C). Immu- nohistochemical investigations were performed with consecutive sections of the striatum and SNc. Addition of SDF-1α and 6-OHDA to PC12 cells del by intrastriatal injection of 6-hydroxydopamine Adult female Sprague-Dawley rats weighing 220-250 g (n = 25, Charles River, kanagawa, Japan) were used for the experiments. All the rats were anesthetized by intraperi- toneal injection of sodium pentobarbital (30 mg/kg) and placed on a stereotaxic apparatus (Narishige, Tokyo, Japan). The skull was exposed and a burr hole was drilled. A total of 20 μg of 6-OHDA (4 μl of 6-OHDA dissolved in saline containing 0.2 mg/ml ascorbic acid; Sigma-Aldrich, Tokyo, Japan) was administered in the right striatum with a Hamilton syringe (26 gauge, Hamilton, Massy, France) at a flow rate of 1 μl/min. Coordinates from the bregma were: AP = +1.0 mm, ML = +3.0 mm, DV = -5.0 mm. The syringe was left in place for 5 minutes after injection and then removed slowly to optimize toxin diffusion. At 2 days (n = 2), 1 week (n = 2) and 4 weeks (n = 2) after cell transplantation, rats were euthanized and brains, lungs and kidneys were removed in order to find where transplanted MSCs resided. Coronal sections were cut at 40 μm-thickness with a freezing microtome (-20°C). The sections were incubated with DAPI solution (Sigma- Aldrich, Tokyo, Japan) for 30 minutes. Finally, stained sections were analyzed with fluorescence microscopy (Keyence, Osaka, Japan). Intravenous administration of MSCs, fibroblasts or PBS Isolation, characterization and labeling of MSCs Isolation, characterization and labeling of MSCs We used adult female Sprague-Dawley rats (n = 6, 220- 250 g, Charles River, Japan) according to the approved Guidelines of the Institutional Animal Care and Use Committee of Okayama University. Rats were euthanized by sodium pentobarbital (200 mg/kg) with subsequent removal of the femoral bones. After flushing of femoral bone marrow, total nucleated cells were cultured at 2 × 104 cells/cm2 in DMEM (Gibco, Cergy Pontoise, France) supplemented with 10% fetal calf serum (Gibco, Cergy Pontoise, France), 1% (v/v) penicillin/streptomycin (Gibco, Cergy Pontoise, France). Fibroblasts were also obtained from rat skin and cultured in same medium. Cells were cultured at 37°C in a fully humidified atmo- sphere with 10% CO2. Medium was changed twice a week until confluence. The MSCs were isolated on the basis of their ability to adhere to the culture plates. After the sec- ond passage, expanded MSCs and fibroblast were used for infection with a fiber-mutant F/RGD adenovirus vec- tor containing enhanced green fluorescent protein (EGFP) genes (AxCA-EGFP-F/RGD). Characterization of MSCs was assessed by immunocytochemical staining. MSCs were stained with antibodies against CD44, a rep- resentative marker of mesenchymal stem cells or CD45, a In our study, fluorescence microscopy revealed no detectable GFP-positive cells in the brain at 4 weeks after Page 7 of 9 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 peroxidase activity. After washing in PBS, sections were incubated in rabbit anti-TH antibody solution (Chemi- con, CA, 1:1000) with 10% normal goat serum for 18 hours at 4°C. After rinses in PBS, the sections were incu- bated for 30 minutes in biotin-conjugated donkey anti- rabbit IgG (Jackson Laboratories, CA, 1:1000) and subse- quently avidin-peroxidase complex (Vector Laboratories, CA, 1:200) for 30 minutes. The sections were then treated with 3,4-diaminobenzidine (Sigma-Aldrich, Tokyo, Japan) and H2O2, mounted on albumin-coated slides, and sealed. Stained sections were analyzed with standard bright field microscopy (Olympus, Tokyo, Japan). D i f l d MSC leukocyte common antigen [25,26]. All the stained cells were finally double stained with DAPI (4',6-diamino-2- phenylindole, Sigma-Aldrich, Tokyo, Japan). g y p ntrastriatal injection of 6-hydroxydopamine ntravenous administration of MSCs, fibroblasts or PBS At 2 hours after 6-OHDA lesion, rats were anesthetized with 1.5% halothane with oxygen/nitrogen. GFP-labeled MSCs (n = 6), GFP-labeled fibroblasts (n = 6), (1 × 107 cells, respectively) or PBS (n = 7) were administered to PD model of rats by injection into the femoral vein. Behavioral tests Addition of SDF-1α and 6-OHDA to PC12 cells Human recombinant SDF-1α (Peprotech, NJ) was dis- solved in PBS. PC12 cells were treated with each concen- tration of SDF-1α (0, 0.1, 1, 10, 50 ng/ml). At 30 minutes after SDF-1α treatment, cells were exposed to 50 μM 6- OHDA or PBS for 12 hours at 37°C. Then cells were fixed with 4% paraformaldehyde for immunocytochemical investigations. For HPLC analyses, at 12 hours after 6- TH Immunohistochemical staining in the striatum and SNc TH Immunohistochemical staining in the striatum and SNc TH staining was performed by free-floating methods. Sections were washed in PBS and incubated in 3% H2O2 i 70% th l f 10 i t t bl k th d TH Immunohistochemical staining in the striatum and SNc TH staining was performed by free-floating methods. S ti h d i PBS d i b t d i 3% H O g TH staining was performed by free-floating methods. Sections were washed in PBS and incubated in 3% H2O2 in 70% methanol for 10 minutes to block the endogenous Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Page 8 of 9 body (Peprotech, NJ, 0.5 μg/ml) were dissolved in PBS, respectively. Culture supernatant was prepared by har- vesting MSCs (2 × 105 cells) in HBSS for 24 hours and diluted 33% to make the dose of SDF-1α appropriate for the results of previous reports. At 24 hours after plating, PC12 cells were treated with SDF-1α, SDF-1α combined with anti-SDF-1α antibody, only anti-SDF-1α antibody, MSC supernatant, MSC supernatant combined with anti- SDF-1α antibody and PBS. At 30 minutes after treatment, cells were exposed to 50 μM 6-OHDA or PBS for 12 hours at 37°C. After exposure, cells were washed 3 times in PBS and fixed for TUNEL assay. OHDA exposure, cells were washed by HBSS twice. 500 μl of HBSS were put on each well for 1 hour. The super- natant was collected, filtered and stored at -80°C. CXCR4 staining To confirm the expression of CXCR4 in PC12 cells, we performed immunocytochemical investigations. At 24 hours after plating for attachment, cells were exposed to 50 μM of 6-OHDA or PBS for 1, 6 and 12 hours at 37°C. After exposure, cells were fixed with 4% paraformalde- hyde and incubated in rabbit anti-CXCR4 antibody solu- tion (Chemicon, MA, 1:1000) with 10% normal goat serum for 18 hours at 4°C. References 1. Hornykiewicz O: Parkinson's disease: from brain homogenate to treatment. Fed Proc 1973, 32(2):183-90. 1. Hornykiewicz O: Parkinson's disease: from brain homogenate to treatment. Fed Proc 1973, 32(2):183-90. 1. Hornykiewicz O: Parkinson's disease: from brain homogenate to treatment. Fed Proc 1973, 32(2):183-90. 2. Treciokas LJ, Ansel RD, Markham CH: One to two year treatment of Parkinson's disease with levodopa. Calif Med 1971, 114(5):7-14. 2. Treciokas LJ, Ansel RD, Markham CH: One to two year treatment of Parkinson's disease with levodopa. Calif Med 1971, 114(5):7-14. 3. Péchadre JC, Larochelle L, Poirier LJ: Parkinsonian akinesia, rigidity and tremor in the monkey. Histopathological and neuropharmacological study. J Neurol Sci 1976, 28(2):147-57. 3. Péchadre JC, Larochelle L, Poirier LJ: Parkinsonian akinesia, rigidity and tremor in the monkey. Histopathological and neuropharmacological study. J Neurol Sci 1976, 28(2):147-57. DA release from PC12 cells was analyzed by high perfor- mance liquid chromatography with electrochemical detection (HPLC-ECD, Shiseido Fine Chemicals, Tokyo, Japan). Aliquots (200 μl of HBSS) of the supernatant was injected into HPLC and interphased with an electro- chemical detector with a glossy carbon flow-through detector cell. The analytes were separated on a C18, that is, 5 μm base deactivated reverse-phase column (Shiseido Fine Chemicals, Tokyo, Japan). The mobile phase with final pH of 2.5, consisted of 0.1 M NaH2PO4, 150 mg/L octyl sodium sulfate, 10 mg/L ethylenediamine tetraa- cetic acid (EDTA) disodium salt, and 5% acetonitrile. Neutralization of anti-apoptotic effects by SDF-1α using anti- DA release from PC12 cells was analyzed by high perfor- mance liquid chromatography with electrochemical detection (HPLC-ECD, Shiseido Fine Chemicals, Tokyo, Japan). Aliquots (200 μl of HBSS) of the supernatant was injected into HPLC and interphased with an electro- chemical detector with a glossy carbon flow-through detector cell. The analytes were separated on a C18, that is, 5 μm base deactivated reverse-phase column (Shiseido Fine Chemicals, Tokyo, Japan). The mobile phase with final pH of 2.5, consisted of 0.1 M NaH2PO4, 150 mg/L octyl sodium sulfate, 10 mg/L ethylenediamine tetraa- cetic acid (EDTA) disodium salt, and 5% acetonitrile. Neutralization of anti-apoptotic effects by SDF-1α using anti- 4. Yahr MD, Duvoisin RC, Hoehn MM, Schear MJ, Barrett RE: L-Dopa (L-3,4- dihydroxyphenylanine)--its clinical effects in parkinsonism. Am Neurol Assoc 1968, 93:56-63. 5. Cotzias GC: L-Dopa for Parkinsonism. N Engl J Med 1968, 278(11):630. d b h f f h b l l d h 6. Statistical analysis All values were expressed as mean ± standard deviation. Data were statistically analyzed by one-way measures of ANOVA. Statistical significance was present at p < 0.05. Addition of SDF-1α and 6-OHDA to PC12 cells After rinses in PBS, the sec- tions were incubated for 30 minutes in FITC-conjugated donkey anti-rabbit IgG (Jackson Laboratories, CA, 1:1000). Cells were mounted on the slides with GEL/ MOUNT (Biomeda Corporation, CA) and analyzed with fluorescence microscopy (Olympus, Tokyo, Japan). TUNEL staining Authors' contributions DNA fragmentation of apoptotic cells were identified by TUNEL method. The procedure was conducted accord- ing to the manufacturer's instruction (Roche, Basel, Swit- zerland). Briefly, PC12 cells were fixed with 4% paraformaldehyde for 30 minutes and washed in PBS 3 times. Then the cells were incubated with 3% H2O2 in 70% methanol for 10 minutes and washed with PBS twice. After that, the cells were incubated with 0.1% Triton X- 100 in 0.1% sodium citrate for 2 minutes on ice. The slides were washed twice with PBS and the areas around samples were dried. TUNEL reaction mixture (50 μl) was added to each sample. Subsequently, slides were incu- bated for 60 minutes at 37°C in a humidified atmosphere in the dark. After washing with PBS, slides were mounted by GEL/MOUNT. Stained sections were analyzed with fluorescence microscopy (Olympus, Tokyo, Japan). HPLC analysis FW is involved in acquisition of all data and drafting/revising the manuscript. TS, TY, YM and ID designed the study, analyzed the data and revised the manu- script. NT and TK helped in vivo experiments including surgeries and animal care. WJY and AK helped in vitro experiments including immunocytochemical investigations. TB and YK helped immunohistochemical investigations. TJT and MK helped additional experiments in the revised manuscript. All authors read and approved the final manuscript. Author Details f Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan Received: 28 September 2009 Accepted: 26 April 2010 Published: 26 April 2010 This article is available from: http://www.biomedcentral.com/1471-2202/11/52 © 2010 Wang et al; licensee BioMed Central Ltd. 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BMC Neuroscience 2010, 11:52 doi: 10.1186/1471-2202-11-52 Cite this article as: Wang et al., Intravenous administration of mesenchymal stem cells exerts therapeutic effects on parkinsonian model of rats: Focusing on neuroprotective effects of stromal cell-derived factor-1? BMC Neuroscience 2010, 11:52 25. Pittenger MF, Mackay AM, Beck SC, Jaiswal RK, Douglas R, Mosca JD, Moorman MA, Simonetti DW, Craig S, Marshak DR: Multilineage potential of adult human mesenchymal stem cells. Science 1999, 284(5411):143-7. 26. Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Zhang M, Mal N, Kiedrowski M, Chacko M, Askari AT, Popovic ZB, Koc ON, Penn MS: SDF-1 expression by mesenchymal stem cells results in trophic support of cardiac myocytes after myocardial infarction. FASEB J 2007, 21(12):3197-207. 34. Geeraerts T, Deiva K, M'sika I, Salim H, Héry C, Tardieu M: Effects of SDF- 1alpha and gp120IIIB on apoptotic pathways in SK-N-SH neuroblastoma cells. 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We explored whether the neutralization of SDF-1α might inhibit the anti-apoptotic effects of SDF-1α and superna- tant of MSC culture might have anti-apoptotic effects on 6-OHDA-exposed PC12 cells. Human recombinant SDF- 1α (Peprotech, NJ, 10 ng/ml) and rabbit anti-SDF-1α anti- Page 9 of 9 Wang et al. BMC Neuroscience 2010, 11:52 http://www.biomedcentral.com/1471-2202/11/52 Kotobuki N, Hirose M, Takakura Y, Ohgushi H: Cultured autologous human cells for hard tissue regeneration: preparation and characterization of mesenchymal stem cells from bone marrow. Artif Organs 2004, 28(1):33-9. 27. Hovakimyan M, Haas SJ, Schmitt O, Gerber B, Wree A, Andressen C: Mesencephalic human neural progenitor cells transplanted into the neonatal hemiparkinsonian rat striatum differentiate into neurons and improve motor behaviour. J Anat 2006, 209(6):721-32. 28. 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From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain
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Abstract The gut microbiome has been implicated in the pathogenesis of a wide array of immune-related neurological disorders, including psychiatric and neurological disorders. This fascinating journey from the gut to the gray matter reveals an astonishing dimension of scientific exploration. The intricate interconnectedness of the gut-brain axis and the microbiota's impact on brain function carries substantial implications for mental well-being. This burgeoning field not only holds great promise for insights into the prevention and treatment of neurological conditions but also underscores the significance of maintaining a well-balanced and nurtured microbiomes for overall cognitive health. CC License CC-BY-NC-SA 4.0 Keywords: Gut microbiome, Brain, Therapeutic nutrition From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain Swagata Mukhopadhyay1, Debanjana Bhattacharyya2, Jagannath Ghosh3* 1Senior Research Fellow, Department of Physiology, WBSU, Barasat, W.B., India. 2Temporary Assistant Professor, Department of Food and Nutrition, The Maharaja Sayajirao University of Baroda, India. *3Assistant Professor, Department of Food and Nutrition, School of Allied Health Sciences, Swami Vivekananda University, Barrackpore, Kolkata-700121, India. *Corresponding author’s E-mail: jagannathg@svu.ac.in Article History Received: 28 Sept 2023 Revised: 21 Oct 2023 Accepted: 02 Nov 2023 CC License CC-BY-NC-SA 4.0 Abstract The gut microbiome has been implicated in the pathogenesis of a wide array of immune-related neurological disorders, including psychiatric and neurological disorders. This fascinating journey from the gut to the gray matter reveals an astonishing dimension of scientific exploration. The intricate interconnectedness of the gut-brain axis and the microbiota's impact on brain function carries substantial implications for mental well-being. This burgeoning field not only holds great promise for insights into the prevention and treatment of neurological conditions but also underscores the significance of maintaining a well-balanced and nurtured microbiomes for overall cognitive health. Keywords: Gut microbiome, Brain, Therapeutic nutrition *Corresponding author’s E-mail: jagannathg@svu.ac.in Journal of Advanced Zoology Introduction In recent times, there has been an upward trend of fascination with investigating the interplay between the microbiome and the brain. Researchers have made fascinating discoveries indicating that th trillions of microorganisms constituting our microbiome can remarkably influence brain development behavior, and even mental health (Appleton, 2018; Galland, 2014; Smith, 2015). A pivotal revelation from these investigations is that gut microbes possess the ability to communicate with the brain through various intricate mechanisms. They can produce hormones, immune molecules, and specialized metabolites that can shape brain function and behavior (Appleton, 2018). This intricate communication network between the gut and the brain is commonly denoted as the "gut-brain axis." It encompasses complex system involving millions of nerves, including the pivotal vagus nerve, which assumes critical role in transmitting signals between the gut and the brain (Galland, 2014). Extensive research has confirmed that the gut microbiome can exert a profound impact on both brain development and behavior, a phenomenon observed in both animals and humans (Smith, 2015). For instance, research studies have revealed that manipulating the gut microbiota in mice can result in alterations in gen expression within various regions of the brain, subsequently influencing neurophysiology and behavio (Galland, 2014). Moreover, the concept of dysbiosis, signifying an imbalance in the bacteria composition of the microbiome, has been associated with mental health conditions such as anxiety and depression (Cryan et al., 2020). The profound interconnectedness of the gut-brain axis and th microbiome's impact on brain function carries substantial implications for mental well-being Unraveling these intricate connections may potentially pave the way for innovative treatments fo mental health disorders and offer insights into strategies for maintaining optimal brain health Enhancing gut health and fostering a diverse and harmonious microbiome makes it conceivable t positively influence mental wellness (Galland, 2014). Nonetheless, it's imperative to acknowledge tha the field of microbiome research is relatively nascent, and there remains much to uncover regarding th intricate interplay between the microbiome and the brain. Establishing causality in microbiome studie poses a significant challenge, and researchers are diligently working to decipher the precise mechanism while elucidating the significance of these processes in human development and overall health (Appleton, 2018; Galland, 2014). ISSN: 0253-7214 Volume 44 Issue S-6 Year 2023 Page 1598:1604 Journal of Advanced Zoology Journal of Advanced Zoology ISSN: 0253-7214 Volume 44 Issue S-6 Year 2023 Page 1598:1604 ________________________________________________________________________________________________________ From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain Swagata Mukhopadhyay1, Debanjana Bhattacharyya2, Jagannath Ghosh3* 1Senior Research Fellow, Department of Physiology, WBSU, Barasat, W.B., India. 2Temporary Assistant Professor, Department of Food and Nutrition, The Maharaja Sayajirao University of Baroda, India. *3Assistant Professor, Department of Food and Nutrition, School of Allied Health Sciences, Swami Vivekananda University, Barrackpore, Kolkata-700121, India. *Corresponding author’s E-mail: jagannathg@svu.ac.in Article History Received: 28 Sept 2023 Revised: 21 Oct 2023 Accepted: 02 Nov 2023 CC License CC-BY-NC-SA 4.0 Abstract The gut microbiome has been implicated in the pathogenesis of a wide array of immune-related neurological disorders, including psychiatric and neurological disorders. This fascinating journey from the gut to the gray matter reveals an astonishing dimension of scientific exploration. The intricate interconnectedness of the gut-brain axis and the microbiota's impact on brain function carries substantial implications for mental well-being. This burgeoning field not only holds great promise for insights into the prevention and treatment of neurological conditions but also underscores the significance of maintaining a well-balanced and nurtured microbiomes for overall cognitive health. Keywords: Gut microbiome, Brain, Therapeutic nutrition J gy ISSN: 0253-7214 Volume 44 Issue S-6 Year 2023 Page 1598:1604 ________________________________________________________________________________________________________ - 1598 - From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain Swagata Mukhopadhyay1, Debanjana Bhattacharyya2, Jagannath Ghosh3* 1Senior Research Fellow, Department of Physiology, WBSU, Barasat, W.B., India. 2Temporary Assistant Professor, Department of Food and Nutrition, The Maharaja Sayajirao University of Baroda, India. *3Assistant Professor, Department of Food and Nutrition, School of Allied Health Sciences, Swami Vivekananda University, Barrackpore, Kolkata-700121, India. *Corresponding author’s E-mail: jagannathg@svu.ac.in Article History Received: 28 Sept 2023 Revised: 21 Oct 2023 Accepted: 02 Nov 2023 CC License CC-BY-NC-SA 4.0 Abstract The gut microbiome has been implicated in the pathogenesis of a wide array of immune-related neurological disorders, including psychiatric and neurological disorders. This fascinating journey from the gut to the gray matter reveals an astonishing dimension of scientific exploration. The intricate interconnectedness of the gut-brain axis and the microbiota's impact on brain function carries substantial implications for mental well-being. This burgeoning field not only holds great promise for insights into the prevention and treatment of neurological conditions but also underscores the significance of maintaining a well-balanced and nurtured microbiomes for overall cognitive health. Keywords: Gut microbiome, Brain, Therapeutic nutrition 1. Relationship between gut microbes and neurological illness: Recent research has sparked growing interest in the intricate link between gut microorganisms and neurological diseases (Faruqui et al., 2021). This correlation extends across a wide range of neurological disorders linked to the immune system. These encompass developmental disorders, neurodegenerative conditions, and emotional disorders, all of which have shown associations with alterations in gut microbiota and the creation of microbial metabolites (Faruqui et al., 2021; Sittipo et al., 2022). Imbalances in the gut microbiota can result in a condition known as gut dysbiosis, potentially facilitating the emergence of neurological disorders through the proliferation of pathogenic bacteria (Faruqui et al., 2021). Notably, both the gut and the brain's immune systems can become activated by microbial triggers, potentially leading to neuro-inflammation and the onset of neurological disorders (Tiwari et al., 2023). The gut microbiome has surfaced as a potential influential factor in predisposition to various neurological conditions (Cryan et al., 2020). This is because gut bacteria wield substantial influence over brain development, behavior, and the host immune system (Suganya & Koo, 2020). Disruptions in the gut-brain axis have been implicated in the etiology of psychological and neurological diseases (Suganya & Koo, 2020). Dysbiosis, characterized by an imbalance in the gut microflora, has been linked to the initiation and progression of neurological disorders (Sorboni et al., 2022). This multifaceted relationship between gut microorganisms and neurological health underscores the significance of ongoing research in this field. Emerging research underscores the pivotal role of the gut microbiome in both neurological health and disease. Central to this connection is the intricate gut-brain axis, an elaborate communication system encompassing millions of nerves, prominently featuring the vagus nerve (Suganya & Koo, 2020). The gut microbiome wields its influence over the brain through a diverse array of mechanisms, including the production of hormones, immune molecules, specialized metabolites, modulation of RNAs, interactions with the vagus nerve, and engagement with both the immune and nervous systems (Faruqui et al., 2021; Cryan et al., 2020; Tiwari et al., 2023; Suganya & Koo, 2020; Sittipo et al., 2022). These discoveries have connected the gut microbiota to a variety of neurological illnesses, including multiple sclerosis, Parkinson's disease, Alzheimer's disease, autism spectrum disorder, and depression (Faruqui et al., 2021; Cryan et al., 2020; Sittipo et al., 2022). For instance, individuals with autism spectrum disorder have exhibited distinct differences in gut microbiome composition compared to their healthy counterparts (Faruqui et al., 2021). Relationship between gut microbes and neurological illness: Similarly, patients diagnosed with multiple sclerosis have displayed a gut microbiome composition distinct from that of healthy individuals (Sittipo et al., 2022). In the realm of mental health, depression and anxiety disorders have also been associated with alterations in gut microbiome composition, further highlighting the intricate interplay between gut microbes and neurological health (Cryan et al., 2020; Suganya & Koo, 2020). Consequently, the relationship between gut microbes and neurological conditions represents a burgeoning area of investigation. Disruptions in the gut microbiota and the production of microbial metabolites have been identified as potential contributors to a wide array of immune-related neurological disorders. Furthermore, disruptions in the gut-brain axis have been linked to the pathogenesis of both psychiatric and neurological illnesses, suggesting that gut microbiota may play a role in the development of these neurological problems. 1. Introduction 1. Introduction In recent times, there has been an upward trend of fascination with investigating the interplay between the microbiome and the brain. Researchers have made fascinating discoveries indicating that the trillions of microorganisms constituting our microbiome can remarkably influence brain development, behavior, and even mental health (Appleton, 2018; Galland, 2014; Smith, 2015). A pivotal revelation from these investigations is that gut microbes possess the ability to communicate with the brain through various intricate mechanisms. They can produce hormones, immune molecules, and specialized metabolites that can shape brain function and behavior (Appleton, 2018). This intricate communication network between the gut and the brain is commonly denoted as the "gut-brain axis." It encompasses a complex system involving millions of nerves, including the pivotal vagus nerve, which assumes a critical role in transmitting signals between the gut and the brain (Galland, 2014). Extensive research has confirmed that the gut microbiome can exert a profound impact on both brain development and behavior, a phenomenon observed in both animals and humans (Smith, 2015). For instance, research studies have revealed that manipulating the gut microbiota in mice can result in alterations in gene expression within various regions of the brain, subsequently influencing neurophysiology and behavior (Galland, 2014). Moreover, the concept of dysbiosis, signifying an imbalance in the bacterial composition of the microbiome, has been associated with mental health conditions such as anxiety and depression (Cryan et al., 2020). The profound interconnectedness of the gut-brain axis and the microbiome's impact on brain function carries substantial implications for mental well-being. Unraveling these intricate connections may potentially pave the way for innovative treatments for mental health disorders and offer insights into strategies for maintaining optimal brain health. Enhancing gut health and fostering a diverse and harmonious microbiome makes it conceivable to positively influence mental wellness (Galland, 2014). Nonetheless, it's imperative to acknowledge that the field of microbiome research is relatively nascent, and there remains much to uncover regarding the intricate interplay between the microbiome and the brain. Establishing causality in microbiome studies poses a significant challenge, and researchers are diligently working to decipher the precise mechanisms while elucidating the significance of these processes in human development and overall health (Appleton, 2018; Galland, 2014). - 1598 - - 1599 - Understanding of the gut-brain axis and how it relates to neurological disorders: The gut-brain axis plays a pivotal role as a communication bridge that links the gut and the brain, encompassing an extensive network of nerves, with a particular emphasis on the essential vagus nerve (Morkel et al., 2020). This intricate system allows the gut microbiome to exert its influence on the brain through a myriad of mechanisms, encompassing the production of hormones, immune molecules, specialized metabolites, modulation of RNAs, engagement of the vagus nerve, and interactions with both the immune and nervous systems (Barbosa & Barbosa, 2020; Bhatia et al., 2023; Morkel et al., 2020; Vakili et al., 2022; Maiuolo et al., 2021). The disruption of the gut-brain axis may emerge as a significant contributor to various diseases of the nervous system (Barbosa & Barbosa, 2020). Altered gut microbiota and the production of microbial metabolites have been correlated with a broad spectrum of immune-related neurological disorders, encompassing developmental disorders, neurodegenerative conditions, and emotional disorders (Barbosa & Barbosa, 2020; Maiuolo et al., 2021). The perturbation of the gut microbiota balance, often referred to as gut dysbiosis, can potentially pave the way for neurological disorders through the proliferation of pathogenic bacteria (Barbosa & Barbosa, 2020). Neuro-inflammation or the onset of neurological problems brought on by bacteria may result from immune system activation, both in the gut and the brain (Morkel et al., 2020). The gut microbiome has been implicated as a plausible key susceptibility factor in the development of neurological disorders (Bhatia et al., 2023). Furthermore, gut bacteria wield substantial influence over brain development, behavior, and the host immune system (Vakili et al., 2022). Dysbiosis, characterized by an imbalance in the gut microflora, has been associated with the initiation and progression of neurological disorders (Socała et al., 2021). Current research endeavors are also investigating how prebiotics and probiotics affect neurological diseases (Bhatia et al., 2023). Scientists are delving into the bidirectional communication pathways between the gut and brain, aiming to identify potential therapeutic targets for managing neurological disorders and enhancing our comprehension of the gut-brain axis (Bhatia et al., 2023). Nonetheless, it's crucial to recognize that for this knowledge to be effectively applied in clinical settings, we need a more comprehensive dataset to firmly establish causal connections between dysfunction in the gut-brain axis and neurological diseases (Barbosa & Barbosa, 2020). Thus, the gut-brain axis plays a pivotal role in the realm of neurological health and disease. Deconstructing the gut-brain axis: mechanisms and operations The gut-brain axis is a dynamic, two-way communication mechanism that connects the central nervous system (CNS) with the gastrointestinal tract (GI tract) (Appleton, 2018; Rege & Graham, 2017). This intricate network comprises both direct and indirect pathways connecting cognitive and emotional centers in the brain with various functions in the intestinal realm (Rege & Graham, 2017). Regulated by the central and enteric nervous systems, as well as the neural, endocrine, and immune systems (Sudo et al., 2004), the gut-brain axis is significantly influenced by the gut microbiota. In fact, the term "microbiota-gut-brain (MGB or BGM) axis" explicitly acknowledges the role of gut microbiota in the biochemical signaling events that transpire between the GI tract and the CNS (Sudo et al., 2004). The enteric neural system, the vagus nerve, the hypothalamic-pituitary-adrenal axis (HPA axis), the sympathetic and parasympathetic branches of the autonomic nervous system, and the gut bacteria are all parts of the gut-brain axis (Sudo et al., 2004). Functioning through diverse mechanisms, the gut- brain axis operates as follows: Direct Signaling: The enteric nervous system's afferent neurons, which send signals to the brain via the vagus nerve, may be directly stimulated by gut bacteria. Furthermore, the gut microbiota breaks https://jazindia. nline at: le o b ila Ava - 1599 - https://jazindia.com nline at: le o b ila Ava https://jazindia.com nline at: le o b ila Ava From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain down the available substrates to produce a variety of metabolites, such as short-chain fatty acids and neuroactive substances. These molecular signals go across several axes, eventually affecting how distant tissues operate (Appleton, 2018; Carabotti et al., 2015; Rutsch et al., 2020). down the available substrates to produce a variety of metabolites, such as short-chain fatty acids and neuroactive substances. These molecular signals go across several axes, eventually affecting how distant tissues operate (Appleton, 2018; Carabotti et al., 2015; Rutsch et al., 2020). Neurotransmitters: The gut microbiome exerts its influence on brain function by regulating the production, metabolism, and transmission of neurotransmitters (Rutsch et al., 2020). For example, gut bacteria play a role in the metabolism of the amino acid tryptophan, a precursor to serotonin—a neurotransmitter pivotal in mood regulation, appetite, and sleep (Rutsch et al., 2020). Immune System: Immune signaling and immune cells are involved in the gut-brain axis. Deconstructing the gut-brain axis: mechanisms and operations By affecting intestinal permeability, which allows bacterial antigens to penetrate the epithelium and trigger an immune response in the gut, the brain has the potential to affect the make-up and function of the gut microbiota (Rege & Graham, 2017; Sudo et al., 2004). Metabolites: Metabolites generated by the gut microbiome possess the capacity to elicit neurochemical and behavioral effects (Sudo et al., 2004). These metabolites can regulate gene expression and influence cellular processes in distant tissues, including the brain (Rutsch et al., 2020). In summation, the gut-brain axis constitutes a multifaceted and bidirectional communication channel connecting the microbiome and the brain. This intricate interplay allows the microbiome to exert its influence on brain function through mechanisms involving direct signaling via the vagus nerve, neurotransmitter production, immune interactions, and the release of metabolites (Appleton, 2018; Rege & Graham, 2017; Rutsch et al., 2020; Sudo et al., 2004). Understanding of the gut-brain axis and how it relates to neurological disorders: Emerging research has highlighted the profound influence of the gut microbiome on the brain and its potential involvement in various neurological disorders. Specific neurological conditions that have been linked to gut microbes include: Depression: Individuals with depression often exhibit alterations in their gut microbiome compared to their healthy counterparts. Some gut microbes, like Lactobacillus and Bifidobacterium, have shown positive effects on mood and behavior (de la Fuente-Nunez et al., 2018). Autism Spectrum Disorder (ASD): The gut microbiome has been implicated in the development of ASD, with studies revealing differences in the gut microbiome of children with ASD compared to healthy children (de la Fuente-Nunez et al., 2018). Autism Spectrum Disorder (ASD): The gut microbiome has been implicated in the development of ASD, with studies revealing differences in the gut microbiome of children with ASD compared to healthy children (de la Fuente-Nunez et al., 2018). Schizophrenia: The gut microbiome has also been associated with schizophrenia, with individuals diagnosed with the condition exhibiting alterations in their gut microbiome composition (de la Fuente- Nunez et al., 2018). Schizophrenia: The gut microbiome has also been associated with schizophrenia, with individuals diagnosed with the condition exhibiting alterations in their gut microbiome composition (de la Fuente- Nunez et al., 2018). Parkinson's Disease: Emerging evidence suggests a link between the gut microbiome and Parkinson's disease, with individuals affected by the disease displaying differences in their gut microbiome compared to those without the condition (de la Fuente-Nunez et al., 2018). Parkinson's Disease: Emerging evidence suggests a link between the gut microbiome and Parkinson's disease, with individuals affected by the disease displaying differences in their gut microbiome compared to those without the condition (de la Fuente-Nunez et al., 2018). Multiple Sclerosis (MS): The gut microbiome has been implicated in the development and progression of MS, with individuals with MS showing distinct differences in their gut microbiome composition (Sittipo et al., 2022). Alzheimer's Disease: The gut microbiome has been connected to Alzheimer's disease, with individuals diagnosed with the condition displaying alterations in their gut microbiome compared to healthy individuals (Cryan et al., 2020). Understanding of the gut-brain axis and how it relates to neurological disorders: Alterations in the gut microbiota and the production of microbial metabolites have been closely associated with a wide array of immune-related neurological disorders. The perturbation of the gut-brain axis has been implicated in the development of both psychological and neurological diseases. Ongoing research efforts aim to elucidate the intricate mechanisms through which gut microbes influence the brain, potentially leading to the development of innovative treatments for neurological disorders. Strategies for cultivating a flourishing gut-brain connection Strategies for cultivating a flourishing gut-brain connection Available online at: https://jazindia.com - 1600 - Numerous successful approaches exist for nurturing a robust gut-brain axis, a critical two-way communication system connecting the gastrointestinal tract to the central nervous system. Here are some strategies to promote a robust gut-brain axis: Dietary Choices: Diet plays a significant role in shaping the composition of the gut microbiome. Incorporating foods rich in beneficial elements such as omega-3 fatty acids from oily fish, fermented foods, high-fiber foods, and polyphenol-rich foods can positively impact the gut-brain axis (Oriach et al., 2016). A diet abundant in prebiotic and probiotic foods, like yogurt, kimchi, kefir, and kombucha, can enhance beneficial gut bacteria and support brain health (Chakrabarti et al., 2022). Mindfulness Practices: Engaging in mindfulness practices can strengthen the connection between the gut and brain, potentially improving mood and overall well-being. Mindful eating, in particular, can contribute to a healthier gut-brain axis. Regular Exercise: Physical activity not only enriches and promotes beneficial gut bacteria but also helps reduce stress, which can negatively affect the gut-brain axis. Probiotics: Incorporating foods naturally containing beneficial bacteria, such as fermented foods like yogurt, kimchi, kefir, and kombucha, can contribute to a healthier gut-brain axis (Chakrabarti et al., 2022). "Good Mood" Foods: Certain foods like dark chocolate, coffee, and tea containing flavanols have been associated with improved cognitive function and mood (Anderson et al., 2017). "Good Mood" Foods: Certain foods like dark chocolate, coffee, and tea containing flavano been associated with improved cognitive function and mood (Anderson et al., 2017). In summary, promoting a thriving gut-brain axis involves a combination of dietary and lifestyle adjustments. Consuming a diet rich in prebiotic and probiotic foods, practicing mindfulness, engaging in regular physical activity, and consuming flavonol-containing foods can all play a role in nurturing a healthy gut-brain axis (Oriach et al., 2016; Anderson et al., 2017; Chakrabarti et al., 2022; Post et al., 2023). Understanding of the gut-brain axis and how it relates to neurological disorders: While more research is needed to fully comprehend the mechanisms through which gut microbes influence neurological disorders, these findings suggest that cultivating a healthy gut microbiome through dietary choices, exercise, and lifestyle modifications may support a robust gut-brain axis and potentially reduce the risk of neurological disorders (Faruqui et al., 2021; de la Fuente-Nunez et al., 2018; Tiwari et al., 2023; Sittipo et al., 2022; Cryan et al., 2020; Willyard, 2021). Process through which microbiome affects the brain https://jazindia.com nline at: le o b ila Ava - 1601 - The gut-brain axis serves as a vital communication link between the enteric microbiota residing in the gut and the central nervous system (CNS) (Carabotti et al., 2015). This communication primarily occurs through the vagus nerve, which acts as the conduit, transmitting information from the gut's luminal From Gut to Gray Matter: The Surprising Links Between The Microbiome and Brain environment to the CNS (Carabotti et al., 2015; Galland, 2014). Notably, experiments in vagotomized mice revealed that neurochemical and behavioral effects were absent, emphasizing the critical role of the vagus nerve as the primary modulatory pathway between the microbiota and the brain (Carabotti et al., 2015). environment to the CNS (Carabotti et al., 2015; Galland, 2014). Notably, experiments in vagotomized mice revealed that neurochemical and behavioral effects were absent, emphasizing the critical role of the vagus nerve as the primary modulatory pathway between the microbiota and the brain (Carabotti et al., 2015). The influence of the microbiota on the brain is multifaceted. It involves the secretion of signaling molecules by neurons, immune cells, and enterochromaffin cells, which are regulated by the brain and can, in turn, impact the microbiota (Carabotti et al., 2015). This communication is further facilitated by the presence of neurotransmitter receptors in bacteria, enabling a direct interaction between CNS effectors and gut bacteria (Carabotti et al., 2015). On the other hand, the microbiota's makeup and activity may be influenced by the brain. Altering intestinal permeability is one way to do this. This enables bacterial antigens to get through the epithelium and start an immune reaction in the gut mucosa. Additionally, enteric nervous system afferent neurons can be directly activated by gut bacteria, causing the vagus nerve to transmit signals to the brain (Carabotti et al., 2015). The gut microbiome significantly contributes to this bidirectional communication by metabolizing available substrates and releasing various metabolites, including short-chain fatty acids (SCFA) and neuroactive compounds. These biochemical signals traverse different axes and play a role in modulating functions in distant tissues (Carabotti et al., 2015). Neurologically active compounds generated by the gut microbiome also influence brain function by regulating the production, metabolism, and transmission of neurotransmitters. For instance, the microbiota metabolizes the amino acid tryptophan, a precursor to serotonin—a neurotransmitter that plays a pivotal role in mood regulation, appetite, and sleep (Carabotti et al., 2015). Examples of gut microbes that can influence the brain Some examples of gut microbes that can influence the brain include: Bacteroides fragilis: This gut bacterium has been found to produce a molecule called polysaccharide A (PSA), which can modulate the immune system and reduce inflammation in the brain (Willyard, 2021). Lactobacillus and Bifidobacterium: These probiotic bacteria have been shown to have positive effects on mood and behavior. They can produce neurotransmitters like serotonin and gamma-aminobutyric acid (GABA), which play a role in regulating mood and anxiety (Galland, 2014). Akkermansia muciniphila: This gut bacterium is associated with a healthy gut lining and has been linked to improved brain function. It can produce molecules that help maintain the integrity of the intestinal barrier, which may have indirect effects on brain health (Martin et al., 2018). Faecalibacterium prausnitzii: This gut bacterium is known for its anti-inflammatory properties. It produces butyrate, a short-chain fatty acid that can reduce inflammation in the gut and potentially have positive effects on brain function (Carabotti et al., 2015). Escherichia coli: While typically associated with infections, certain strains of Escherichia coli have been found to produce a metabolite called N-acylphosphatidylethanolamine (NAPE), which can have neuroprotective effects and influence brain function. Process through which microbiome affects the brain Furthermore, the gut microbiota has been found to regulate myelination, a critical process involving the formation of the myelin sheath around nerve fibers. This regulation occurs by influencing the expression of myelination-related genes in oligodendrocytes (Willyard, 2021; Dash et al., 2022). References: Anderson, S. C., Cryan, J. F., &Dinan, T. (2017). The psychobiotic revolution: mood, food, and the new science of the gut-brain connection. National Geographic Books. Appleton, J. (2018). The gut-brain axis: Influence of microbiota on mood and mental health. Integrative Medicine: A Clinician's Journal, 17(4), 28. Barbosa, P. M., & Barbosa, E. R. (2020). The gut brain-axis in neurological diseases. International Journal of Cardiovascular Sciences, 33, 528-536. Berding, K., &Cryan, J. F. (2022). Microbiota-targeted interventions for mental health. Current opinion in psychiatry, 35(1), 3. Bhatia, N. Y., Jalgaonkar, M. P., Hargude, A. B., Sherje, A. P., Oza, M. J., & Doshi, G. M. (2023). Gut-brain axis and neurological disorders-how microbiomes affect our mental health. CNS &Neurological Disorders- Drug Targets (Formerly Current Drug Targets-CNS & Neurological Disorders), 22(7), 1008-1030. Butler, M. I., Mörkl, S., Sandhu, K. V., Cryan, J. F., &Dinan, T. G. (2019). The gut microbiome and mental health: what should we tell our patients?: le microbiote intestinal et la santémentale: que devrions-nous dire à nos patients?. The Canadian Journal of Psychiatry, 64(11), 747-760. p f Carabotti, M., Scirocco, A., Maselli, M. A., &Severi, C. (2015). The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of gastroenterology: quarterly publication of the Hellenic Society of Gastroenterology, 28(2), 203. Carabotti, M., Scirocco, A., Maselli, M. A., &Severi, C. (2015). The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of gastroenterology: quarterly publication of the Hellenic Society of Gastroenterology, 28(2), 203. Chakrabarti, A., Geurts, L., Hoyles, L., Iozzo, P., Kraneveld, A. D., La Fata, G., ... &Vauzour, D. (2022). The microbiota–gut–brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice. Cellular and Molecular Life Sciences, 79(2), 80. Cryan, J. F., O'Riordan, K. J., Sandhu, K., Peterson, V., &Dinan, T. G. (2020). The gut microbiome in neurological disorders. The Lancet Neurology, 19(2), 179-194. Cryan, J. F., O'Riordan, K. J., Sandhu, K., Peterson, V., &Dinan, T. G. (2020). The gut microbiome in neurological disorders. The Lancet Neurology, 19(2), 179-194. gy Dash, S., Syed, Y. A., & Khan, M. R. (2022). Understanding the role of the gut microbiome in brain development and its association with neurodevelopmental psychiatric disorders. Frontiers in Cell and Developmental Biology, 10, 880544. p gy de la Fuente-Nunez, C., Meneguetti, B. T., Franco, O. L., & Lu, T. K. (2018). 4. Conclusion In conclusion, the intricate link between the microbiome and the brain, as explored in this captivating journey from the gut to the gray matter, reveals an astonishing dimension of scientific exploration. As our comprehension of this intricate connection continues to advance, it becomes increasingly apparent that the well-being of our brain is intricately tied to the health of our gut. This burgeoning field not only holds great promise for insights into the prevention and treatment of neurological conditions but also underscores the significance of maintaining a well-balanced and nurtured microbiome for overall cognitive health. The profound interplay between our gut and gray matter serves as a reminder that our bodies function as complex ecosystems, and the keys to a healthier, more agile mind may well be found within the depths of our digestive system. Postbiotics and microbial metabolites: These have attracted interest as another potential gut-targeted intervention. Postbiotics and microbial metabolites: These have attracted interest as another potential gut-targeted intervention. Collectively, the exogenous factors whose benefit to mental health is partially mediated by the gut microbiota are referred to as psychobiotics. While these interventions show promise, more research is needed to fully understand their effectiveness and mechanisms of action (Berding & Cryan, 2022; Butler et al., 2019; Fu et al., 2021). Potential treatments for mental health conditions that target the microbiome The gut microbiome has emerged as a promising target for interventions in mental health conditions (Berding & Cryan, 2022; Butler et al., 2019). Numerous interventions that focus on targeting the microbiota have been investigated as potential strategies to address mental health issues, including mood and anxiety disorders. These interventions encompass: Probiotics: Live microorganisms that, when given in sufficient quantities, boost the host's health. Prebiotics: Substances that selectively stimulate the growth and/or activity of beneficial microorganisms in the gut. Synbiotics: An amalgamation of probiotics and prebiotics that enhance gut health (Appleton, 2018). Available online at: https://jazindia.com - 1602 - Fecal microbiota transplant (FMT): The transfer of fecal matter from a healthy donor to a recipient to restore the recipient's gut microbiome. Diet: Certain dietary patterns, such as the Mediterranean diet, have been associated with improved mental health outcomes. https://jazindia.com nline at: le o b ila Ava References: Neuromicrobiology: how microbes influence the brain. ACS chemical neuroscience, 9(2), 141-150. Faruqui, N. A., Prium, D. H., Mowna, S. A., Ullah, M. A., Araf, Y., Sarkar, B., ... & Rahman, M. S. (2021). Gut microorganisms and neurological disease perspectives. Future Neurology, 16(1), FNL53. Faruqui, N. A., Prium, D. H., Mowna, S. A., Ullah, M. A., Araf, Y., Sarkar, B., ... & Rahman, M. S. (2 microorganisms and neurological disease perspectives. Future Neurology, 16(1), FNL53. Fu, X., Chen, T., Cai, J., Liu, B., Zeng, Y., & Zhang, X. (2021). 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The gut-brain axis: how microbiota and host inflammasome influence brain physiology and pathology. References: Frontiers in immunology, 11, 604179. Sittipo, P., Choi, J., Lee, S., & Lee, Y. K. (2022). The function of gut microbiota in immune-related neu disorders: A review. Journal of Neuroinflammation, 19(1), 1-17. f f , ( ), Sittipo, P., Choi, J., Lee, S., & Lee, Y. K. (2022). The function of gut microbiota in immune-related neurological disorders: A review. Journal of Neuroinflammation, 19(1), 1-17. Smith, P. A. (2015). The tantalizing links between gut microbes and the brain. Nature, 526(7573), 312-314. Socała, K., Doboszewska, U., Szopa, A., Serefko, A., Włodarczyk, M., Zielińska, A., ... &Wlaź, P. (2021). The role of microbiota-gut-brain axis in neuropsychiatric and neurological disorders. Pharmacological Research, 172, 105840. Sorboni, S. G., Moghaddam, H. S., Jafarzadeh-Esfehani, R., &Soleimanpour, S. (2022). A comprehensive review on the role of the gut microbiome in human neurological disorders. Clinical Microbiology Reviews, 35(1), e00338-20. Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X. N., ... & Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. The Journal of physiology, 558(1), 263-275. Suganya, K., & Koo, B. S. (2020). Gut–brain axis: role of gut microbiota on neurological disorders and how probiotics/prebiotics beneficially modulate microbial and immune pathways to improve brain functions. International journal of molecular sciences, 21(20), 7551. Tiwari, P., Dwivedi, R., Bansal, M., Tripathi, M., & Dada, R. (2023). Role of gut microbiota in neur disorders and its therapeutic significance. Journal of Clinical Medicine, 12(4), 1650. Tiwari, P., Dwivedi, R., Bansal, M., Tripathi, M., & Dada, R. (2023). Role of gut microbiota in neurological disorders and its therapeutic significance. Journal of Clinical Medicine, 12(4), 1650. Vakili, K., Fathi, M., Yaghoobpoor, S., Sayehmiri, F., Nazerian, Y., Nazerian, A., ... & Rezaei-Tavirani, M. (2022). The contribution of gut-brain axis to development of neurological symptoms in COVID-19 recovered patients: A hypothesis and review of literature. Frontiers in Cellular and Infection Microbiology, 12, 983089. gy Willyard, C. (2021). How gut microbes could drive brain disorders. Nature, 590(7844), 22-25. Willyard, C. (2021). How gut microbes could drive brain disorders. Nature, 590(7844), 22-25. Willyard, C. (2021). How gut microbes could drive brain disorders. Nature, 590(7844), 22-25. Willyard, C. (2021). How gut microbes could drive brain disorders. Nature, 590(7844), 22-25. - 1604 - Available online at: https://jazindia.com
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New Physics II: Spin Picture, Particle Structure, and Fundamental Interactions
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"No great discovery was ever made without a bold guess," Sir Isaac Newton. "No great discovery was ever made without a bold guess," Sir Isaac Newton. "The pursuit of science demands particular courage," Galileo Galilei. ⋆Contact e-mail: kangstudy@outlook.com CONTENTS rising in the east and setting in the west every day does not signify that the sun revolves around the earth, and the high-speed bullet smashing into pieces on a water surface cannot attest that the water is hard. Considering that nature enjoys simplicity shown in Newton’s second law of motion and the inverse-square law, it is critical to start with the extensively applicable basic theory when illuminating experimental phenomena. Otherwise, the geocentric model would persistently perfect its accuracy and scope in depicting observed phenomena by introducing more than 13 free parameters. 1 Introduction 2 The Classical Counterpart of Spin 3 Spin-related Concepts 3.1 Spin magnetic moments and magnetic charges 3.2 Electron structure 3.3 Muon structure and time dilation 3.4 Neutrino chirality, beta decay, and virtual electrons 3.5 Mass, nucleons, and quarks 3.6 Vacuum quantization and fundamental interactions 4 Conclusions 1 Introduction 2 The Classical Counterpart of Spin 3 Spin-related Concepts 3 Spin related Concepts 3.1 Spin magnetic moments and magnetic charges 3.2 Electron structure 3.3 Muon structure and time dilation 3.4 Neutrino chirality, beta decay, and virtual electrons 3.5 Mass, nucleons, and quarks 3.6 Vacuum quantization and fundamental interactions 4 Conclusions In this paper, the classical counterpart of spin is ascertained based on the correspondence principle and relevant experimental data. Be- sides enabling almost all quantum puzzles to be clarified, it also opens the door to unifying quantum mechanics and classical me- chanics (formulating the theory of everything [TOE]). New Physics II: Spin Picture, Particle Structure, and Fundamental Interactions China Kang⋆ ABSTRACT Experimental data sometimes fails to render the expected truth, such as high-speed bullets smashing into pieces on a water surface cannot verify the water’s hardness. By re-examining the essence underneath quantum phenomena and analyzing their relevance to universal classical theory, this study has thoroughly revealed the classical counterpart of spin. Subsequently, the equivalence between spin angular momentum (of energy or charge) and vorticity flux (of energy or charge) has also been unveiled, thus intuitively clarifying many abstruse physical concepts, like spin magnetic moment, virtual electron, relativistic time dilation, neutrino chirality, quark origin, and fundamental interactions (including gravitons). From now on, almost all quantum puzzles (e.g., wave-particle duality, quantum entanglement, Schrödinger’s cat) can be understood classically, just as prominent physicists such as Planck, Einstein, and Schrödinger longed for back then. This paper can be considered a blueprint for the theory of everything (TOE). Key words: spin; virtual electrons; neutrinos; gravitons; fundamental interactions; the theory of ev n; virtual electrons; neutrinos; gravitons; fundamental interactions; the theory of everything (TOE) 1 INTRODUCTION Richard Feynman famously quipped, "I think I can safely say that nobody understands quantum mechanics." Until now, quantum concepts such as Schrödinger’s cat and quantum entanglement still baffle the public. Moreover, quantum mechanics continues using the nuclear magneton µN = eℏ 2mp , although it is only predicted by imitating the electron spin magnetic moment (Bohr magneton) µB = e(αc/n) 2π(na0)  π(na0)2 = e[a0me(αc)] 2me = eℏ 2me resulting from an electron in a circular motion. Seemingly, we have yet to grasp quantum mechanics from the ground up. Beyond limited and one-sided experimental data, from the universality of nature rules, it can be deduced that the key to clarifying quantum mechanics and unifying fundamental physical theories should be to figure out the classical counterpart of spin. © 2022 The Authors China Kang China Kang 2 lence between spin circulation and spin-vorticity flux, reflecting the continuum properties of space and the one-way nature of time. The constant h = mΩAT is equivalent to the energy-vorticity flux (mc2ΩAT > 0), closely related to the unipolar directivity of the same fundamental interaction (energy flowing). For example, apples fall from trees to the ground, chicks hatch from eggs, and boiling water cools spontaneously in a low-temperature environment; such sequence can never be reversed. and linear polarization is a cycloidal motion with spin angular momentum perpendicular to translational momentum. Furthermore, the photon’s energy Eγ = hνγ = pγc = mγc2 = 2Eγ k is purely kinetic, contributed jointly by its light-speed spin and light-speed translation. In fact, 300 years ago, Newton conjectured "it consists in a circulating or a vibrating motion of the Ray, or of the Medium, or something else" when he discussed the reflection and refraction of photons (Newton, 1717). Since the electron spin obeys rmev = ℏ, its spin quantum number 1 2 should be caused by the spin-vortex-surface polarization tension or spin magnetic moment nullifying half of its mass-spin angular momentum: |Se| = rmev −me e µB = 1 2rmev = 1 2ℏ. For an electron moving at a near-light speed in a vacuum, if its De Broglie wavelength (λ = 2πr) is shorter, the mass me in formula rmev = ℏ needs to be replaced by a mass-like variable derived from its moving system energy. (Which can be verified by double-slit interference of near-light-speed electrons.) Indeed, the vacuum regarded as a non-dispersive medium (the ether) is a critical mechanical model in Fresnel optics and Maxwell electromagnetism. Moreover, Einstein never outright denied the existence of the ether, and experiments have long proven that the vacuum is non-empty. Accordingly, the superfluid properties of vacuum (see 3.6) and the circular spin of elementary particles (even if bound inside composite particles) inevitably lead to particles exhibiting wave-particle duality. By now, we can already elucidate both single-particle two-slit interference and delayed-choice quan- tum eraser experiments through the same unified wave theory. When an electron is in an external magnetic field, its spin-angular- momentum orientation tends toward the parallel or antiparallel di- rection relative to the magnetic field due to the magnetic torque. China Kang Indeed, the spin-orientation change of the electron is caused by the classical collision between it and a vacuum particle (their spins are not in the same plane; see 3.6). Assuming that the angle between an electron’s initial spin and a new external magnetic field is a random θ (0 ⩽θ ⩽π), the spin-projection changed amount Se (1 ± cos θ) of the electron determines its spin-orientation statistical probability Considering the spin-vortex tension of electrons and the stereo- scopic structure of atoms, we can infer that hydrogen atoms’ dis- crete energy-level orbitals (ring bands) have a stratified equipotential spherical-shell structure (Stodolna et al. , 2013). Thus, the magnetic quantum number m should follow |m| = (l + 1) (1 −cos θ) ⩽l  m ∈Z, −π 2 < θ < π 2  , rnlm ≈(l + 1)rns cos θ  rnsme αc n = ℏ, rns = na0  .      (3) (3) P↕= 1 ± cos θ (1 + cos θ) + (1 −cos θ) ⇒      P↑= cos2 θ 2 P↓= sin2 θ 2 (0 ⩽θ ⩽π). (1) Note that the electron’s revolution on an s-shell (l = 0; orbital angular momentum is zero) is just the spin. Additionally, the electron cloud essentially consists of a continuous trail of electrons. (1) For helium atoms and helium-like ions, the ground-state Bohr energy EZ approximates the potential energy of the two electrons revolving around a nucleus at the same spin-orbit: This statistical probability mirrors, in essence, nothing more than the classical distribution of the classical measurements resulting from classical collisions. This statistical probability mirrors, in essence, nothing more than the classical distribution of the classical measurements resulting from classical collisions. EZ = −r1  Ze2 4πε0r2 1 − e2 4πε0 (2r1)2  = −mev2 1 ≈−  Z −1 4 2 me (αc)2 . (4) Constrained by energy conservation and angular momentum conservation, a single particle cannot be simultaneously in a space-position-pervading or spin-orientation-superposition state. At every point of the one-way timeline, any particle has a definite, sole, classical space position and spin orientation in an observer’s reference frame. Naturally, the quantum tunneling of electrons is closely related to the transition, transmission, diffraction, Newtonian pendulum model, and electrons’ identity, which can also be considered a phenomenon in line with classical theory. 2 THE CLASSICAL COUNTERPART OF SPIN It is known that Bohr magneton µB = e(αc/n) 2π(na0)  π(na0)2 = 1 2 na0 × e αc n is akin to the coil-current magnetic moment and charge-revolving angular momentum (disregarding electron clouds for now). Moreover, at different energy levels of hydrogen atoms, the electron spin following na0me αc n = ℏ⇒|r × mev| = ℏ also implies that the spin of electrons is most likely to be a circular motion. For a photon, considering that both its wavelength and its diffractive ability are negatively correlated to its frequency, and that its circular polarization appears like spiral motion, we can express the Planck constant as h = 2πℏ= EγTγ = pγcTγ = λpγ = 2πrmγc (r = λ 2π; mγ = Eγ c2 is not a rest mass but an energy factor). Note that limited experiments can sometimes generalize locally correct patterns but fail to provide the truth. For example, the sun Now, we can infer that the classical counterpart of spin is none other than circular motion (disregarding composite particles temporarily). Naturally, circular polarization is a spiral motion with spin angular momentum parallel to translational momentum, © 2022 The Authors 3.2 Electron structure (5) When one electron and one positron annihilate, their energy is released in the form of photons. Where do their electric charges go, and how are the emitted photons created? indicating that the spin magnetic moment is the charge-spin angular momentum and is equivalent to the charge-speed circulation or the charge-vorticity flux. Therefore, spin magnetic moments totally can be articulated by the regular motion of charges, without bothering too much about the mass of particles (especially hadrons). As we know, the annihilation of particle-antiparticle pairs necessarily releases photons, and the mass loss ∆m0 in nuclear reactions certainly will convert into energy ∆m0c2. Further, considering the mass-energy equation E = m0c2 and the decay of neutral mesons (e.g., π0 →2γ, or π0 →γ + e−+ e+, or even π0 →e−+ e+ + e−+ e+, . . . ), it can be inferred that the electric charge itself has no energy, and that bound-state photons furnish the energy of non-photon particles (see 3.4 for neutrinos). However, for a near-light-speed electron in a vacuum, if its spin radius reaches r ≪ ℏ mec, and then there is 1 2rec ≪µB? In this case, the electron spin magnetic moment remaining constant should permit its charge spin not to coincide with its near-light-speed centroid spin. More likely, the spin-vortex of a near-light-speed electron can pairwise induce negative-positive polarization charges (see 3.6) that spin contrarily to maintain the spin magnetic moment. Since near-light-speed electron collisions can produce the hadrons generated in high-energy proton collisions (Briere, Harris & Mitchell, 2016) (which will eventually be fully verified), measuring the magnetostatic fields around polar particles has the equivalent experimental value as large collider experiments. Essentially, a pair of negative and positive charges released from the annihilation of an electron and a positron are bound to pair up (transforming into a negative-positive virtual electron pair) and fuse into the vacuum medium. Moreover, electrons and positrons can be considered ions of the vacuum electromagnetic medium: For example, collisions of near-light-speed electrons’ magnetic fields (induced by the vortex of vacuum electromagnetic media) can pairwise produce the electron and positron (symmetrical monopole ionized-state virtual electrons) from the vacuum. Experiments have long proved that electricity and magnetism are two kinds of kinematic properties of the identical thing – the mo- tion state of electric charges relative to an observer’s static vacuum dielectric determines its observable electromagnetic manifestations. 3.1 Spin magnetic moments and magnetic charges As an example of the spin magnetic moment, the Bohr magneton can be expressed as µB = 1 2 |r × ev| = 1 4π ˛ 2πr 0 ev · dl = er2 4 |∇× v| = 1 4π ¨ πr2 0 eΩ· dA (rmev = ℏ) , (5) China Kang (4) Substituting the relevant experimental data (Kramida et al., 2021) gives E2−Eexp 2 Eexp 2 ≈5.4%, E20−Eexp 20 Eexp 20 ≈0.14%, and E30−Eexp 30 Eexp 30 ≈0.70%... Therefore, the motion of the electron outside nuclei can entirely be investigated from a particle viewpoint. Substituting the relevant experimental data (Kramida et al., 2021) gives E2−Eexp 2 Eexp 2 ≈5.4%, E20−Eexp 20 Eexp 20 ≈0.14%, and E30−Eexp 30 Eexp 30 ≈0.70%... Therefore, the motion of the electron outside nuclei can entirely be investigated from a particle viewpoint. 2021) gives 2021) gives Notably, the vacuum electromagnetic medium is an essential ele- ment that participates in expressing many properties of macroscopic matter such as shapes, colors, temperature, and binding energy. For a free electron (rmev = ℏ), h e = ¸ 2πr 0 me e vdl = ˜ πr2 0 me e ΩdA depicts both spin-speed circulation and spin-vorticity flux. Corre- spondingly, Cooper pair magnetic flux can be expressed as Φ0 = 2 ˜ π( r 4) 2 0 ∇× me e v dA = 2 ¸ 2π r 4 0 me e vdl = 2πrmev 2e = h 2e, (where |∇× v| = 2v r/4,) implying that the Cooper pair is probably the electron pair composed of two counter-spinning electrons paired into two-body orbital motion with r 4 as the radius. As for so-called quantum entanglement, its essence is nothing more than the correlation of independent measurement results between particles whose spin angular momenta before measure- ment have strong symmetries (e.g., parallel or antiparallel). For example, the spins of spin-symmetric electrons tend to remain spin-symmetric when crossing the same magnetic field, which is substantially as classical as the left-right symmetry of a pair of gloves. Essentially, the Planck constant depicts the periodic action (mv2T) and vortex of elementary particles spinning in a space fluid: h = ˆ λ/v 0 mv2dt = ˛ 2πr 0 mvdl = ¨ πr2 0 mΩdA, (2) (2) As mentioned above, numerous quantum puzzles are viable to understand intuitively after identifying the classical counterpart of elementary particle spin. where Ω= |∇× v| = 2v r . This equation manifests the equiva- where Ω= |∇× v| = 2v r . This equation manifests the equiva- China Kang, New Classical Physics II, 1–8 China Kang, New Classical Physics II, 1–8 Spin, Particles, and Interactions Spin, Particles, and Interactions 3 3 SPIN-RELATED CONCEPTS observer) induced by moving charges, the magnetic pole is nothing but the characteristic direction of the charge-vorticity flux (magnetic moment or charge angle momentum). Thus, the so-called magnetic monopole is redundant to the universe and cannot exist in nature. Spin has no genesis, which is the basic form of energy timelessly existing and the intrinsic motion of energy carriers (elementary par- ticles). Now, from spin corresponding to circular motion, let’s re- examine some spin-related phenomena. We will discuss the follow- ing six aspects: 3.1 spin magnetic moments and magnetic charges; 3.2 electron structure; 3.3 Muon structure and time dilation; 3.4 neu- trino chirality, beta decay, and virtual electrons; 3.5 mass, nucleons, and quarks; 3.6 vacuum quantization and fundamental interactions. The so-called anomaly of spin magnetic moments is the anomaly relative to an inaccurate theoretical prediction; actually, it is precisely the most normal phenomenon governed by the laws of nature. Con- ceivably, the cyclical spin of charges is accompanied by other regular motions, thus causing the magnetic moment anomaly of polar parti- cles to approximate constants. Moreover, the scattering cross-section and charge radius of particles with nonzero magnetic moments in- dicate that the elementary charge necessarily has a well-regulated composition, which is also the experimental fact that re-examines the structure and constituent of particles. China Kang 4 different accelerated states (including spin centripetal acceleration). As shown in the Hafele-Keating experiment and the timing period of the atomic clock on satellites, it is not the relative speed but the centripetal acceleration that determines time dilation (period dilation, in essence). is just the charge-radius re at which the electron’s electromagnetic energy converges to mec2 = 1 2 e2 4πε0re + 1 2 (µ0ec)2 4πµ0re = e2 4πε0re . (Such a direct relation applies mainly to charged leptons; the elementary charge is a basic, extraordinary, indivisible, and indestructible spherical shell that is far more exquisite than the cell wall.) For high-speed muons (where gravity can be neglected because v2 0 ≫R⊕g0), their average life can be expressed as The contribution of the electron self-energy oscillation to its spin magnetic moment is µ′ e = −1 2 |rc × ec| = −1 2 reec 2π = −1 2π eremec 2me = −α 2πµB, (8) Tv ≈ p c2 −v2 0 √ c2 −v2 T0 0 < v2 0 ≪c2, 0 < v2 < c2 , (9) (9) which is precisely the self-energy correction term for electron spin magnetic moment in quantum electrodynamics. Note that |rc × mec| = α 2πℏshows that the bound-state spin of an elemen- tary particle bound inside the charge-shell does not necessarily obey rmv = ℏ(usually follows rmv ≪ℏ). where v and v0 are the eddying speed of the vorticity field induced by the motion of the muon relative to the stationary centroid of the where v and v0 are the eddying speed of the vorticity field induced by the motion of the muon relative to the stationary centroid of the earth. Note cT √ c2−v2 c = cT0 √ c2−v2 0 c suggests that the bound-state energy particle (neutrinos) of muons moves a changeless projection distance cTicosβi (the actual path is a curve including reflec- tion and coordinate-system rotation) relative to the charge-shell exit before being released. It is thus conceivable that a photon entering water from the air still travels at the speed of light, but its original straight wavelength is bent into an undulating or helical curve. The measured value of the electron magnetic moment anomaly is less than α 2π. Theoretically, the charge-shell of electrons should keep rotating. 3.3 Muon structure and time dilation Muons possess electromagnetic properties remarkably akin to electrons. However, the muon is extremely unstable (with an average lifetime of only 2-µs), which will spontaneously decay into an electron and release energy in the form of neutrinos. Accordingly, the muon can be considered a composite electron with a higher-energy magnitude (the muon transitions to the electron without releasing photons). Another difference from the electron is that the muon magnetic moment anomaly exceeds α 2π; hence its charge shell should rotate in the same direction as its spin. It is worth mentioning that, just as an observer at rest relative to a point charge can only observe its electrostatic field (since the vacuum remains static with the observer), the measurable light speed in the vacuum is only the light speed in a static vacuum. By considering the star in stellar aberration phenomena as a moving light source, we can infer that the ray (whose radiation direction is at an angle α to the moving direction of the source) will be additionally deflected by an angle of β ≈arcsin vsinα c towards the moving direction after enter- ing (and interacting with) the vacuum of a stationary reference frame. Additionally, Fizeau’s empirical formula cn = c n + 1 − 1 n2  v = c−v/n n + v totally can illuminate the constancy of the light speed in the vacuum from the perspective of Galilean transformation, showing that the vacuum medium (refractive index n = 1) dragged by moving objects does not influence the measurement of the light speed. Consequently, the mechanism of the constancy of the light speed in a vacuum is unified with that of the invariance of the speed of mechanical waves in isotropic and homogeneous media. See Eq. (25) for the dynamic system of photons moving at the light speed. As for other phenomena explained by relativity, such as the gravitational deflection of starlight and the perihelion precession of Mercury, a more intuitive and natural interpretation will be given in a separate article (entitled "The Dynamic System of Photons and the Large-scale Structure of Universe"). The average lifetime of muons influenced by speed is considered to confirm time dilation, but why is the timing period of pendulum clocks affected by gravitational acceleration not regarded as evidence of time dilation? China Kang Thus, it must be the charge-shell rotating in the opposite di- rection to the electron spin that causes the electron magnetic moment anomaly to be less than α 2π. From the classical mechanical perspec- tive, the electron magnetic moment anomaly can be expressed as ae ≈ 1 a0αc |rc × c| −2 3 |re × v|  – the relevant correction term also needs to consider only the regular motion of the charge (includ- ing polarized charges) in a vacuum electromagnetic medium. As shown by the periodic variation of atomic clock timing in the Hafele-Keating experiment, the spontaneous transition (from higher to lower energy levels) of electrons outside the nucleus is akin to muon decay, reflecting a certain internal structure possessed by leptons and the kinematic model for the so-called time dilation of polar subatomic particles with discrete energy levels. 3.2 Electron structure Considering qm = µ0qv as a magnetic charge, then the line current induces a magnetic field Up to now, the precise charge radius of electrons (sensitive to measuring parameter, in fact) has not been pinpointed. Is this because the electron has no charge radius or possesses an elastic charge-outer-shell? Experimentally, an electron possesses a low-energy-state scattering cross-section, and its electrostatic self-energy converges to a constant, meaning that the electron must have an elastic spherical charge-shell that can be distorted and pierced but not fragmented. Naturally, while the charge of an electron is furnished by its shell carrying an elementary charge, its mass me = 1 c2 GM2 P ňC = 1 c2 e2 4πε0re is contributed by a bound-state photon inside the shell as an energy standing wave in a gravitational field. In addition, the root reason why an electron does not decay should be that its bound-state photon is totally reflected back and forth inside the charge-shell and cannot spontaneously scatter out. dH = dqm 4πµ0r2 ⃗e = µ0vdq 4πµ0r2 ⃗e = vIdt 4πr2 ⃗e = Idl × r 4πr3 (∇· H = 0) , (6) (6) which is precisely Biot-Savard’s law. Ignoring the retarded potential ( v2 c2 ≪1), a moving charge will engender a circumferential magnetic field B⊥v = qm 4πr2 ⃗e = µ0qv 4πr2 ⃗e = µ0q 4πr · 1 2∇× v (r > re) , (7) (7) (7) where ∇× v = 2v r ⃗e is the vorticity of negative-positive virtual electron pairs induced by the moving charge (observed in the observer’s stationary reference frame). Inside an electron, the bound-state photon spins at the speed of light (orbiting the spin-vortex-core) and reflects back and forth at the speed of light, thereby behaving as cycloidal oscillation. Meanwhile, the charge-shell will delay by one period and move in the selfsame cycloidal motion. Conceivably, one arch span 2πrc of the cycloid Because the magnetic field arises from the directional eddying of the stationary vacuum dielectric (which is always dragged by any China Kang, New Classical Physics II, 1–8 4 China Kang China Kang China Kang, New Classical Physics II, 1–8 3.4 Neutrino chirality, beta decay, and virtual electrons Similarly, the stimu- lated reaction path for 58 27CoI=2 −→ 58 26FeI=2 is most likely [p1/2 + γ−1] + γ1 →n−1/2 + e+ 1/2 + ν1/2 (where [p1/2 + γ−1] denotes that the photon γ−1 comes from the nucleus). where the nuclear spin I ̸= 0 of the even-even nuclei 60 28Ni and 58 26Fe means excited states. Since the number of nucleons remains unchanged and the nuclear spin loses ℏwhen 60 27CoI=5 decays into 60 28NiI=4 (∆I = −1), the spontaneous decay path must be n1/2 →p−1/2 + e− 1/2 + ν1/2. Similarly, the stimu- lated reaction path for 58 27CoI=2 −→ 58 26FeI=2 is most likely [p1/2 + γ−1] + γ1 →n−1/2 + e+ 1/2 + ν1/2 (where [p1/2 + γ−1] denotes that the photon γ−1 comes from the nucleus). e± v + e± v →ν1/2 + ν−1/2. (13) (13) Of course, as shown in e± v →e−+ e+, a single e± v can also be ionized in an ultra-strong magnetic field (this has actually been con- firmed by hight-energy electron collision experiments). Moreover, multiple e± v can be combined into great-mass (especially unstable) composite particles when subjected to high-energy collisions, which is the root reason why high-speed electron collisions can create other particles. Corresponding to that more than 1000 types of nuclides (most of them extremely unstable) can be synthesized by electrons and nucleons, it must also be one of the most natural laws of the universe that photons and charges (e+ v , e− v ) compose hundreds of subatomic particles (most of them extremely unstable). In the decay of 60 27CoI=5 −→ 60 28NiI=4, that e−tends toward emitting along the direction of the parent-neutron magnetic moment, while the νe tends toward radiating in the opposite direction and is right-handed. In the decay of 58 27CoI=2 −→ 58 26FeI=2, that e+ tends toward emitting along the direction of the parent-proton magnetic moment, while the νe tends toward radiating in the opposite direction and is left-handed. Are the characteristic emission directions of the released e+ and e−from beta decay genuinely caused by the parity breaking of neutrinos? If a proton can become a neutron whether it absorbs νe or νe, can it be established that νe and νe with the same energy are identical particles? The electroweak theory depicts neutron decay as d−1 3 →u 2 3 + W −1 →u 2 3 + e−1 + ν. Spin, Particles, and Interactions Spin, Particles, and Interactions 5 magnetic moment that leads to the emitting direction of the e+ and e−released from decay. Logically, the radiation direction of neu- trinos in beta decay is entirely passively determined by momentum conservation. And for orbital electron capture reactions that do not emit charged particles, take one example (Goldhaber, Grodzins & Sunyar, 1958), the electron capture in 3.4 Neutrino chirality, beta decay, and virtual electrons Undoubtedly, neutrinos that cannot be accelerated by gravitational or electromagnetic forces certainly will travel at the speed of light (see below for neutrino os- cillation). Even if the average speed of neutrinos across a large-scale medium (including various lighttight liquids and solids) is marginally lower than the speed of light in a vacuum, is it not supremely natural? Technically speaking, neutrinos are not so-called chiral particles, but neutral energy particles with zero magnetic moments and traveling at the speed of light. Moreover, there is no experimental proof that annihilation can occur between neutrinos and antineu- trinos; therefore, it is entirely feasible to consider neutrinos and antineutrinos as identical particles. Free neutrinos have no mass since they have zero charges and magnetic moments and cannot exhibit standing wave effects in the gravitational field (and undoubtedly cannot be accelerated or decelerated). The so-called neutrino oscillation should be primarily caused by the neutrino scattering or absorbing energy during its journey. Because neutrinos are involved in the fission and fusion of many polar particles and have a spin quantum number of 1/2, it can be inferred that the neutrino should have a neutral spherical-shell structure composed of a pair of superposing negative and positive charge-shells. Naturally, the non-constant energy of a neutrino is furnished by the bound-state photon inside its shell. Neutrinos are viewed as chiral particles that violate the law of conservation of parity. For example, the two beta decay types are as follows (disregarding parity tentatively): 60 27CoI=5 → 60 28NiI=4 + e−+ νe, ⇒n1/2 →p−1/2 + e− 1/2 + ν1/2; (11a) 58 27CoI=2 → 58 26FeI=2 + e+ + νe, ⇒  p1/2 + γ−1  + γ1 →n−1/2 + e+ 1/2 + ν1/2, (11b) (11a) Now, denoting the virtual electron pair (e+ v + e− v ) constituting the vacuum electromagnetic medium as e± v (spin 0; see 3.6 for details), one primary way of generating neutrinos (in ultra-strong magnetic fields – energy-matter circulating fields, such as a proton surface and the eyewall of a black-hole vortex) can be expressed as where the nuclear spin I ̸= 0 of the even-even nuclei 60 28Ni and 58 26Fe means excited states. Since the number of nucleons remains unchanged and the nuclear spin loses ℏwhen 60 27CoI=5 decays into 60 28NiI=4 (∆I = −1), the spontaneous decay path must be n1/2 →p−1/2 + e− 1/2 + ν1/2. 3.4 Neutrino chirality, beta decay, and virtual electrons As shown in µ−→e−+ νe + νµ and µ+ →e+ + νe + νµ, both muon and anti-muon decay release one charged particle and two neutral neutrinos. Why does the released charged particle (e−or e+) tend toward emitting in the direction of the muon or anti-muon magnetic moment? Is this really caused by the parity breaking of neutrinos? (Don’t forget Lenz’s law in electromagnetic interactions and the equivalence between magnetic moments and charge vorticity flux.) Furthermore, what is the essential difference between different neutrinos (if parity can be ignored as disregarded in Dirac’s "The Principles of Quantum Mechanics")? 152 63 EuI=0 + e−→ 152 62 SmI=1 + νe, ⇒∆I = 1 ⇒↓p−1/2 + ↑e− 1/2 →↓n1/2 + ↑ν−1/2 ) (12) (12) is also closely related to the nucleon magnetic moment. Conceivably, one proton (magnetic moment) induces one electron to approach it against its magnetic moment direction, and angular momentum conservation and linear momentum conservation collectively determine the spin and radiation direction of the created neutrino. Neutron decay likewise releases the neutrino νe: Neutron decay likewise releases the neutrino νe: (10) n1/2 →p1/2 + e−+ νe, or n1/2 →p−1/2 + e−+ νe, (10) where the subscript of the nucleon denotes the spin quantum number and spin direction. Experiments demonstrate that the energy spec- trum of β−(e−) rays is continuous, while the corresponding energy of neutrino νe is a variable within the interval 0, mnc2 −mec2 . Accordingly, neutrinos are photon-like neutral energy carriers, and carrying different magnitudes of energy is one of the essential distinctions between diverse neutrinos. Undoubtedly, neutrinos that cannot be accelerated by gravitational or electromagnetic forces certainly will travel at the speed of light (see below for neutrino os- cillation). Even if the average speed of neutrinos across a large-scale medium (including various lighttight liquids and solids) is marginally lower than the speed of light in a vacuum, is it not supremely natural? where the subscript of the nucleon denotes the spin quantum number and spin direction. Experiments demonstrate that the energy spec- trum of β−(e−) rays is continuous, while the corresponding energy of neutrino νe is a variable within the interval 0, mnc2 −mec2 . Accordingly, neutrinos are photon-like neutral energy carriers, and carrying different magnitudes of energy is one of the essential distinctions between diverse neutrinos. 3.3 Muon structure and time dilation Even in the Hafele-Keating experiment, why is time dilation independent of the relative velocity between the aircraft and the ground but dependent on the centripetal acceleration of the aircraft with respect to the earth’s center? Observed within the earth’s Hill sphere, if two reference frames have the same centripetal acceleration relative to the earth’s center, why is there no time dilation between them no matter how large the relative speed between them is? Moreover, for the atomic clock on GPS satellites, why can its timing period be expressed as the acceleration relation T q c2−2R⊕g0−R⊕a0 T ( h √R 465 1 )? In fact, high-speed muons with extended lifetimes have higher spin frequencies (quicker non-decay changes) and greater spin-vectorial acceleration. Besides, photons that constantly fluctuate (spin) in space and continuously frequency-shift in gravitational fields (keep changing) are also experiencing the uniform elapse of cosmic background time (absolute, true, and mathematical Newtonian time). Consequently, the so-called time dilation is nothing more than the period variation of particles’ characteristic motion (e.g., decay and transition; but why unfairly disregard spins and fluctuations?) in At this point, it can be judged that special relativity (which alone cannot calculate the timing-period variations of satellite clocks) dis- torted space and time. Its partial correctness is nothing more than a mathematical coincidence (since Lorentz transformation is a rotation related to the vorticity field of the particle with non-zero magnetic moments), just like the one-sided validity of the geocentric model. Indeed, discussions such as the twin paradox and time travel are more like logical games or artistic imagination than physics. China Kang, New Classical Physics II, 1–8 China Kang 6 is different from that of electrons. ignoring chirality) should be p−1/2 + e− 1/2 + ν1/2 →n1/2. More precisely, the prime pathways (reversible) for synthesizing neutrons from protons are as follows: Now we know that collisions of near-light-speed electrons and positrons can generate leptons, mesons, and baryons but no quarks that are essential constituents of mesons and baryons. Furthermore, all the mesons and baryons (except nucleons) generated in high- energy collision experiments will inevitably decay swiftly into two or more kinds of (final-state) stable particles—including neutral particles (i.e., neutrinos, photons, and virtual electron pairs) and charged particles (i.e., electrons and protons, but no quarks). Indeed, apart from being impossible to form composite particles with fractional charges under any circumstances, the so-called quarks also have no sensible theoretical source or experimental evidence. Neutrino absorption : h p−1/2 + ν1/2 i + e± v →[p−1/2 + ν1/2 + e− 1/2] + e+ −1/2 →n1/2 + e+ −1/2; (14a) Electron capture : h p−1/2 + e− 1/2 i + 2e± v →[p−1/2 + ν1/2 + e− 1/2] + ν−1/2 →n1/2 + ν−1/2; (14b) β+ decay : h p−1/2 + γ1 + γ−1 i + 3e± v →[p−1/2 + ν1/2 + e− 1/2] + e+ −1/2 + ν−1/2 →n1/2 + ... (14c) (14c) Of course, experiments have partly verified and will completely con- firm that the reversible reactions in these equations mirror the nature of protons and neutrons converting to each other. Logically, the fractional charges of elementary particles are redundant to nature. It is perfectly reasonable to correct valence quarks to high-energy unipolar virtual electrons and correct quark- antiquark pairs to bound-state negative-positive virtual electron pairs. Naturally, gluons can be considered bound-state photons, and all non-photon particles necessarily consist of electric charges and bound-state photons. (As early as in "Opticks" [Ques. 30], Newton reasoned that the changing of matter into light and light into matter "is very conformable to the Course of Nature".) 3.4 Neutrino chirality, beta decay, and virtual electrons In this case, quantum mechanics cannot essentially clarify nucleons’ spin and spin magnetic moments, and the data fitting of mW ≈17000md ≈34000mu ≈85mn is not much more elegant than the geocentric model. Corresponding to the reversibility of electrons absorbing photons to transition and hydrogen combining with oxygen to form water (2H + O ⇌H2O), the reverse reaction of neutron decay (n1/2 →p−1/2 + e− 1/2 + ν1/2; In fact, neutrinos are immune to electromagnetic fields, while the magnetic moment is equivalent to the charge-vorticity flux. Conse- quently, it must be the parent-particle (e.g., nucleons and muons) China Kang, New Classical Physics II, 1–8 China Kang, New Classical Physics II, 1–8 3.5 Mass, nucleons, and quarks The mass of an object is, in essence, nothing more than the (electromagnetic) standing wave effect of its inherent bound-state energy E0 spinning at the speed of light in a gravitational field, as shown in the mass-energy equation m0 = 1 c2 E0 (independent of space coordinates or time passing). When a particle with nonzero magnetic moment travels (meanwhile spins) at a higher speed, its spin-vorticity field certainly will carry more temporary bound-state energy, thus showing the kinematic phenomenon of mass increase. The charge-mass ratio of electrons has long verified this point. As we know, high-speed objects will be subjected to strong impact forces when dashing into a high-density incompressible fluid, and near-light-speed electrons colliding can produce composite particles. Thus, it can be inferred that the neutron’s spontaneous decay n1/2 →p−1/2 +e−+νe should reflect the natural constituent of neutrons more factually than high-energy collision experiments. Moreover, re is greater than 3rp, the outer charges of protons and neutrons have opposite polarities (Miller, 2007), and the charge is an elastic spherical shell that can be penetrated. Hence, the proton is most likely to convert into a neutron by occupying an electron’s interior rather than swallowing the electron whole. Nucleons are composite particles possessing a complex and stable structure that can steadily imprison constant energy (equivalent to mass in gravitational fields). The electric charge radius of protons is rp ≈4 ℏ mpc (ignoring measurement bias influenced by experimental conditions), and its average internal pressure (energy density) is Pp ≈ mpc2 4πr3p/3 =  MP 8me 2 wU (15) (15) It is conceivable that a neutron consists of a negative-charge shell, an internal proton, and a certain amount of bound-state energy. The charge stratification of neutrons is negative-positive-negative from the outside to the inside (Miller, 2007) (ignoring experimental biases and the distortion affected by the internal proton), implying that the positive charge layer inside the neutron is furnished by its inner proton. The charged outer shells have opposite polarities, fundamentally determining that a proton and a neutron can be glued together at close distances less than re. Note that the spin of a nucleon is primarily furnished by its internal constituents—moving nucleons do not have to follow rmv = ℏ, which is one of the main reasons why macroscopic matter can stay still. China Kang, New Classical Physics II, 1–8 3.5 Mass, nucleons, and quarks ≈3.76 × 1053 eV · m−3 ≈6 × 1034 Pa ≈6 × 1029 atm, ≈3.76 × 1053 eV · m−3 ≈6 × 1034 Pa ≈6 × 1029 atm, where wU = ρUc2 =  mp MP 4 3c4 4πGň2 C is the average energy density of the universe. This value is consistent with experimental data (Shanahan & Detmold, 2019), confirming the fluid characteristics of energy space. Furthermore, the experiment demonstrates that the proton’s central pressure is outward and that its surrounding region generates inward pressure, indicating that the proton must have a charge-stratified-nested spherical-shell structure. where wU = ρUc2 =  mp MP 4 3c4 4πGň2 C is the average energy density where wU = ρUc2 =  mp MP 4 3c4 4πGň2 C is the average energy density C of the universe. This value is consistent with experimental data (Shanahan & Detmold, 2019), confirming the fluid characteristics of energy space. Furthermore, the experiment demonstrates that the proton’s central pressure is outward and that its surrounding region generates inward pressure, indicating that the proton must have a charge-stratified-nested spherical-shell structure. In fact, the charge stratification of nucleons has roughly been experimentally verified (Miller, 2007). Note that the polarization effect of charges in highly dense dielectrics is not negligible and that the spherical-shell charge shape is sensitive to the experimental energy of magnitude. Can the charge-shell without high-energy collisional distortion inside protons be considered the natural-state valence quark with a well-regulated structure? From electrodynamics (no strong interactions), it can be derived that the neutron’s charged outer shell has the electromagnetic energy (mn −mp) c2, and its charge radius is rn ≈ me mn−mp re. Thus, the outer charge and the inner proton jointly contribute to the neutron magnetic moment µn ≈− µp −1 2 2 3krnec  (16) ≈µp −4 9rnec ≈−1.91293 µN ≈0.99994 µexp n . (16) Since the magnetic moment is equivalent to the angular mo- mentum of electric charges, the proton spin magnetic moment naturally arises from the regular motion of its charged constituents. Accordingly, the so-called nuclear magneton µN = eℏ 2mp is just a mathematical imitation of the Bohr magneton induced by the circular spin of electrons; after all, the charge-spin form of protons Of course, there is also a theoretical possibility of µn ≈−µp + 1 3krnec. 3.6 Vacuum quantization and fundamental interactions The vacuum is a ground-state space. Moreover, the vacuum is an electromagnetic medium composed of virtual electrons and pos- sesses constant permittivity and permeability. All virtual electrons are paired in a negative-positive combination (unless ionized). Any two paired virtual electrons spin in reverse at the speed of light, thus forming a vortex-like LC circuit rather than the superstring (permittivity is closely related to the oscillating frequency of media). Theoretically, this LC circuit, which has no discrete energy levels and can store energy, should be one of the main components of dark matter (including superfluid-state hydrogen atoms). Additionally, virtual electrons are precisely the charge source and energy shell (akin to cell walls) of all non-photon particles. (19c) where A is the total stressed area apportioned among all elementary particles of a force-bearing object. Of course, countless elementary particles inside the macroscopic object are combined together through the vacuum dielectric, providing a much more extensive stress area than A to share the space stress. As we know, the electric field lines of a point charge are akin to ray-family streamlines, and the magnetic induction lines around a line current are comparable to the concentric-circles vortex filaments with the wire as the axis. Comparing the force direction between point charges and the force direction between parallel currents, we can infer that the electrostatic force results from the tangential stress of electromagnetic media, and the magnetic force arises from the normal stress of electromagnetic media. Similarly, the strong interaction (including asymptotic freedom) can also be understood more intuitively from the perspective of continuum mechanics (note that the circular spin of elementary particles and the pairing of quark-antiquark with spherical charges). Simultaneously, the vacuum is also a gravitational medium composed of gravitons. Since gravitation always points to the object’s centroid and the energy density wG = − 1 8πG(E2 G + B2 G) of gravitational fields obtained by imitating the formula for the electromagnetic field’s energy density is negative, the energy density of the gravitational medium should be a negative extremum. From GMm r = mc2 = rmc2 r = −ℏc r ⇒mg = −M = − q ℏc G = −MP, we can derive that the energy of a graviton that can neither annihilate nor dissipate is −MPc2. Spin, Particles, and Interactions of the neutron, the neutron magnetic moment should contain the contribution of induced charges. As for the exact charge distribution of neutrons, it is indispensable to measure the magnetostatic field around neutrons, besides continuing various collision experiments. Logically, gravitons distributed homogeneously should be in pairs, and the two paired gravitons spin at the speed of light in the same direction to form a vortex rather than the superstring. Gravitons have the minimum dimension rg = lP = q Gℏ c3 and are densely distributed, thus constituting an incompressible, isotropic, and ho- mogeneous three-dimensional space (absolute Newtonian space; the coordinate-independent spin frequency of gravitons can be consid- ered the elapsing speed of the cosmic background time–Newtonian time). In a vacuum, the zero-point energy density is approximately The proton magnetic moment can be fitted as µp ≈1 2 2 3 (rpec) + 2 3  3 64rpec  +  α 8πrp  ec  (17) = 8 3 + 1 8 + α 2π  eℏ 2mp ≈2.792 828 µN ≈0.999 993 µexp p , (17) w0 ≈mgc2 4πl3 P/3 = −M 6 P m2em4 p wU ≈−6.9 × 10131 eV · m−3, (18) (18) where 2 3 (rpec) + 2 3 2 64rpec  is contributed by the rotation of the spherical-shell charges, while α 8πrp  ec = α 2πµN is furnished by the spin of the core charge or the proton’s centroid (self-energy). Considering the stable pressure distribution and regular polarization effect inside a proton (disregarding charge-shell deformation in high-energy experiments), we can infer that the charge stratification of protons from outside to inside is probably positive (outer +e) – negative (middle layer −e near the core) – positive (core +e). Read- ily, the charge structure could be roughly ascertained by measuring the magnetostatic field around a proton (about 2 3 r3 p R3 µ0ec 4πr2p (1 + k) at its polar axis and half that on the equatorial plane). Although quantum theory calculates the magnitude of the zero-point energy (Wheeler & Misner, 1962) agreed with w0, it omits the minus sign; hence it cannot elucidate gravitation, either. Spin, Particles, and Interactions As shown in Newton’s second law F = dp dt = d(ρV c) dt ⃗e = d[ρ(Act)c] dt ⃗e = ρc2A = ˝ ∇PdV , fundamental interactions arise from the energy-density gradient of the space medium and are trans- ferred by the momentum of medium particles excited by interacting objects. Accordingly, gravitational force FG, Coulomb force FC, and Lorentz force FL can be expressed as FG = ρc2A = − Mc2 4πr2(Gm/c2) " 4π Gm c2 2# ⃗e = −GMm r2 ⃗e  r ≫Gm c2  , (19a) FC = ρc2A = q1 e mec2 4πr2  q2 e αℏ mec  " 4π q2 e αℏ mec 2# ⃗e = q1q2 4πε0r2 ⃗e (r ≫re) , (19b) FL = ρc2A = µ0H2 qm/(4πµ0r2) H 4πr2 ⃗e = qmH⃗e = µ0qv × H = qv × B, (19c) FG = ρc2A = − Mc2 4πr2(Gm/c2) " 4π Gm c2 2# ⃗e = −GMm r2 ⃗e  r ≫Gm c2  , (19a) The truth is that the Standard Model of particles has not radi- cally clarified the essential structure and elementary constituents of composite particles, nor has it elucidated the nature of mass, charge, or gravitation. More likely, the root of this dilemma is that many theoretical physicists are keen on high-energy collision experiments or mathematical tricks while neglecting to probe a few fundamental issues such as spin pictures and vacuum fluids. (19a) (19a) (19b) 3.5 Mass, nucleons, and quarks Since the proton inside a neutron can produce induced charges on the outer spherical equipotential surface China Kang, New Classical Physics II, 1–8 7 REFERENCES ≈1.380 650 × 10−23 J · K−1 1 J · K−1 = 1 Wb · s · m−1 . Isaac Newton, 1717, Opticks or, a Treatise of the Reflections, Refractions, Inflections, and Colours of Light (2nd), 278-281, the Project Gutenberg eBook #33504 Up to this point, all physical units can already be expressed by different combinations of three base units in the energy unit. Briere Roy A. , Harris Frederick A. , and Mitchell Ryan E. , 2016, Physics Accomplishments and Future Prospects of the BES Experiments at the Beijing Electron – Positron Collider, Annu. Rev. Nucl. Part. S. 66, 143- 170, DOI: 10.1146/annurev-nucl-102115-044802 Additionally, the vacuum is a non-dispersive, homogeneous, isotropic linear medium composed of invisible particles (gravitons and virtual electrons) that move at the speed of light ( c2 = dx dt 2 = ∂x2 ∂t2 ). Thus, the vacuum wave follows Goldhaber M. , Grodzins L. , and Sunyar A. W. , 1958, Helicity of Neutrinos, Phys. Rev. 109, 1015-1017, DOI: 10.1103/PhysRev.109.1015 ∂x2 ∂t2 ). Thus, the vacuum wave follows Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2021). NIST Atomic Spectra Database (ver. 5.9), [Online]. Avail- able: https://physics.nist.gov/asd [2021, December 9]. National In- stitute of Standards and Technology, Gaithersburg, MD. DOI: doi.org/10.18434/T4W30F ∂2f(x, t) ∂x2 = 1 c2 ∂2f(x, t) ∂t2 . (24) (24) Naturally, both gravitational and electromagnetic fields in the vacuum obey this formula when transporting energy. Naturally, both gravitational and electromagnetic fields in the vacuum obey this formula when transporting energy. Miller Gerald A. , 2007, Charge Densities of the Neutron and Proton, Phys. Rev. Lett. 99, 112001, DOI: 10.1103/PhysRevLett.99.112001 Again and again, such as the equations of fundamental interactions, the equations of magnetic moments and angular momentum, and the equations of electromagnetic and mechanical waves, the unification of natural laws is likewise fully reflected in the wave speed equations of various media. The vacuum wave speed complies with Shanahan, P. E. and Detmold, W. , 2019, Pressure Distribution and Shear Forces inside the Proton, Phys. Rev. Lett. 122, 072003, DOI: 10.1103/PhysRevLett.122.072003 Stodolna A. S. , Rouzée A. , Lépine F. , Cohen S. , Robicheaux F. , Gijs- bertsen A. , Jungmann J. H. , Bordas C. , and M. Vrakking J. J. , 2013, Hydrogen Atoms under Magnification: Direct Observation of the Nodal Structure of Stark States, Phys. Rev. Lett. 110, 213001 (2013). ACKNOWLEDGMENTS I am thankful that Newton’s physics thoughts still resonate with me today. In addition, I have been inspired by Planck’s efforts to incorporate quantum theory into classical mechanics, and I have been motivated by the dissatisfaction of some top physicists (e.g., Einstein, Schrödinger, Dirac, and Weinberg) with quantum mechanics. kB ≈h ec  1 + 1 2 r a0 αcε0  (23) 23 1 1 1 (23) China Kang Thus, vacuum permittivity ε0 should be the oscillating period of the vacuum LC circuit composed of virtual electron pairs: 4 CONCLUSIONS By analyzing the classical counterpart of the elementary particle spin, this study revealed the vortex properties of magnetic moments, the essence of beta decay, the structure of leptons and hadrons, the essential constituents of all particles, and the quantization of the vacuum. This paper can be considered a blueprint of the theory of everything (TOE), which will advance physicists to research particles, galaxies, and even black holes from the viewpoint of Newtonian particle dynamics and fluid mechanics (especially vortex theory). ε0 = 2π √ L0C0 = 2πC0 r L0 C0 = 2πC0RK  RK = h e2  . (21) According to e = p α (4πε0cℏ) and µ0ec = e ε0c, we can get 1 C = 1 m · p kg · m · s−1 and 1 Wb = 1 p kg · m · s−1. Moreover, the temperature of the vacuum medium is approximated as T vac 0 ≈1 kB 1 2 h ε0  ≈2.71015 K. (22) (22) Furthermore, this article has heralded the end or limits of theoret- ical physics. It is foreseeable that the development of physics-related disciplines will also be more efficient and meaningful. Note that the CMB should originate mainly from neutral hydrogen (T H 0 ≈ 2 3kB 1 2µBBa0 = 2 3kB 1 2h eBa0 4πme = 2 3kB 1 4 (µ0eαc)2 4πµ0a0 ≈2.80 K). Considering T vac 0 ≈ 1 kB  1 2 h ε0  ≈1 2 (µ0ec) c2 (ignoring dimen- sions) and that sensing temperature is closely related to electro- magnetic properties (high-energy neutrinos moving densely in all directions have no temperature), we can infer that the temperature should be the kinetic energy of the magnetic charge, and its unit is 1 K = 1 Wb · m s 2. Accordingly, the Boltzmann constant (CO- DATA recommended kB = 1.380 649×10−23 J·K−1) approximates 3.6 Vacuum quantization and fundamental interactions Conceivably, the energy density of a gravita- tional medium is partly neutralized by its resonance with an object’s energy carriers, thus inevitably presenting a centripetal gravitational field by the gradient of the negative energy density around the object. Of course, the gravitational medium will likewise exhibit strong grav- itational fields if its density can become marginally lower in galaxies. Imitating the electric flux ΦE = q ε0 , we have the magnetic flux ΦH = qm µ0 and the gravitational flux ΦG = −4πmG. Accordingly, long-range fundamental forces can be written as F = Φσ⃗e  σ = X 4πr2 , X ∈{Q, Qm, M}  . (20) (20) China Kang, New Classical Physics II, 1–8 8 China Kang China Kang For example, FL = ΦHσm⃗e = qm µ0 Qm 4πr2 ⃗e = µ0qv × H. For example, FL = ΦHσm⃗e = qm µ0 Qm 4πr2 ⃗e = µ0qv × H. where rU =  MP mp 2 ňC is the radius of a large-scale unit spherically- symmetric-space (2rU = RU is the observable radius of the universe; RU c is precisely the so-called universe age), gU is the gravitational acceleration on the surface of that unit sphere space, and Pvac = ρvacc2 is the energy density or pressure of vacuum media. Now, the dynamics of photons and the structure of the universe have also been elucidated naturally. (From 1 2hdν ≈−GρUV hν r2c2 √ R2 U−r2 RU dr, there is the cosmological redshift ZU ≈exp n 8 3  1 − cos3 ct RU o −1.) In physics, flux is defined as the amount of fluid, particles, or energy across a given surface per unit time. Considering ΦH = qm µ0 = qv = qdl dt (like an electric dipole moment flux) as the flux of virtual electron pairs and ΦG = −4πmG = −4π m MP 2πl2 Pc TP as the flux of gravitons, we can see that the electric flux ΦE = q ε0 should be the charge flux of virtual electrons. Subsequently, the unit of vacuum permittivity can be reduced to the time unit, which matches the definition of the flux and is consistent with the fact that the relative permittivity is closely related to the dielectric oscillation frequency. Thus, vacuum permittivity ε0 should be the oscillating period of the vacuum LC circuit composed of virtual electron pairs: In physics, flux is defined as the amount of fluid, particles, or energy across a given surface per unit time. Considering ΦH = qm µ0 = qv = qdl dt (like an electric dipole moment flux) as the flux of virtual electron pairs and ΦG = −4πmG = −4π m MP 2πl2 Pc TP as the flux of gravitons, we can see that the electric flux ΦE = q ε0 should be the charge flux of virtual electrons. Subsequently, the unit of vacuum permittivity can be reduced to the time unit, which matches the definition of the flux and is consistent with the fact that the relative permittivity is closely related to the dielectric oscillation frequency. REFERENCES DOI: 10.1103/PhysRevLett.110.213001 c = 1 √ε0µ0 = √gUrU = r Pvac ρvac = h/mγ 4π ˆ π 0 sinθdθ r  rmγc = h 2π  , (25) Wheeler J. A. and Misner C. , 1962, Geometrodynamics, Academic Press, New York. (25) China Kang, New Classical Physics II, 1–8 China Kang, New Classical Physics II, 1–8
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A genome-wide scan for candidate lethal variants in Thoroughbred horses
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A genome‑wide scan for candidate lethal variants in Thoroughbred horses OPEN Evelyn T. Todd1*, Peter C. Thomson1, Natasha A. Hamilton2, Rachel A. Ang1, Gabriella Lindgren3,4, Åsa Viklund3, Susanne Eriksson3, Sofia Mikko3, Eric Strand5 & Brandon D. Velie1 Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3′UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations. There is estimated to be a high rate of natural embryonic mortality in mammals. A large proportion of these embryonic losses occur soon after fertilisation, such that pregnancies often go undetected, with the only sign being reduced ­fertility1. Mutation screens in mice reveal that many genes are essential for development, with knockout of 29% of genes tested resulting in embryonic death by day ­142,3. Although mutations in these genes are expected to be under strong negative selection due to being completely deleterious, many species are estimated to carry between one and two recessive lethal mutations per ­genome4. However, single mutations are often uncom- mon in a population, such that unrelated individuals are unlikely to carry the same recessive lethal ­mutations5–7. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports A genome‑wide scan for candidate lethal variants in Thoroughbred horses OPEN The likelihood of an individual inheriting two copies of the same lethal mutation is dramatically increased by inbreeding events, whereby alleles that are identical by descent are inherited from a common ­ancestor8–10.i In recent years, a number of studies in livestock have identified embryonic lethal mutations at high frequen- cies due to intensive selective breeding ­practices11–18. This is often due to a limited number of sires with desirable characteristics making large genetic contributions to the ­population11,19. Moreover, population bottlenecks due to domestication and breed formation have also resulted in increased deleterious mutation loads and diminished gene pools in many domestic ­breeds20–23. These processes lead to a reduction in genetic diversity indices includ- ing effective population size, which is defined as the theoretical population size that shows the same rate of loss in genetic diversity as the study population (Ne)24,25. Reduced genetic diversity can increase the risk of drift and inbreeding events in future generations of a population. Lethal mutations that have reached high frequencies are often detected by deviations from the Hardy–Weinberg equilibrium with a lack of homozygotes for one ­allele12. Characterisation of such mutations can assist in improving breeding decisions to increase fertility rates in these populations and prevent these mutations from drifting to higher ­frequencies26,27. 1School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia. 2Racing Australia Equine Genetics Research Centre, Sydney, Australia. 3Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. 4Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium. 5Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway. *email: evelyn.todd@sydney.edu.au | https://doi.org/10.1038/s41598-020-68946-8 Scientific Reports | (2020) 10:13153 www.nature.com/scientificreports/ Table 1. The allele frequencies of two adjacent SNPs with an absence of minor homozygotes in genotype data from two Thoroughbred horse datasets. The expected number of minor homozygotes in each population was calculated under Hardy–Weinberg equilibrium. Observed genotype frequencies that significant deviate from Hardy–Weinberg equilibrium frequency expectations (p < 0.05) are denoted with an asterisk. A genome‑wide scan for candidate lethal variants in Thoroughbred horses OPEN Population Sample size Reference 6:38278097 6:38278874 Expected GG GG AG AA Expected CC CC AC AA Australian Thoroughbreds 156 Own data 7* 0 66 90 7* 0 66 90 Japanese Thoroughbreds 370 Fawcett et al.69 9* 0 117 253 9* 0 117 253 Swedish Warmblood 380 Privately pro- vided, Ablondi et al.70 4* 0 75 304 4* 0 74 306 Coldblooded Trotter 646 Privately provided, Velie et al.84 26* 0 258 388 28 22 226 393 Quarter Horse 137 Petersen et al.65 17* 0 97 40 17* 0 97 40 Exmoor Pony 285 Velie et al.71 0 0 1 279 0 0 1 282 Various breeds 582 Petersen et al.30 15 0 85 497 15 0 85 497 Table 1. The allele frequencies of two adjacent SNPs with an absence of minor homozygotes in genotype data from two Thoroughbred horse datasets. The expected number of minor homozygotes in each population was calculated under Hardy–Weinberg equilibrium. Observed genotype frequencies that significant deviate from Hardy–Weinberg equilibrium frequency expectations (p < 0.05) are denoted with an asterisk. The identification of high frequency lethal variants is of particular interest in domestic horse populations. Although a recent study has identified some candidate ­mutations28, to date there has been no published com- prehensive characterisation of common embryonic lethal alleles in horse populations. Despite the large variety of domestic horse breeds found throughout the world, many breeds suffer from low within-breed diversity and small Ne 29–31. Some horse breeds with large census population sizes also experience low genetic diversity due to intense artificial selective breeding practices and closed population ­structures30,31. Maintaining good fertil- ity rates is particularly important for horse populations due to the seasonal nature of breeding and the low individual fertility output, as mares produce only one foal from an eleven month gestation ­period32. Despite the extensive use of hormonal therapies to increase covering success in many domestic horse populations, per cycle pregnancy rates in some breeds only average around 65%, suggesting the presence of unknown variables that may reduce ­fertility33.h y y In this study, we aimed to characterise variants at high frequencies that may cause lethality in the Thorough- bred horse population. The Thoroughbred breed is of particular interest due to the closed population structure since the foundation of the studbook in the eighteenth ­century34. A genome‑wide scan for candidate lethal variants in Thoroughbred horses OPEN The population has since been intensely selected for the improvement of athletic ­abilities35,36, resulting in contemporary Thoroughbred horses being characterised by high levels of inbreeding and a small Ne 31, 37–39. Due to selective breeding practices, all Thoroughbred horses can trace their ancestry back to a small number of individuals from the foundation of the ­breed37,38. Genetic diversity in the Thoroughbred breed has been reduced in recent decades due to the increased commercialisa- tion of popular stallions providing large genetic contributions to the ­population40. Although such practices are in line with selective breeding ­principles41, they could also inadvertently increase the frequency of embryonic lethal variants in the population. Reproductive technologies such as artificial insemination are banned in the Thoroughbred population, making the maintenance of high levels of natural fertility imperative. Additionally, Thoroughbred horses have been used as foundation stock for other popular horse breeds including The Quarter Horse, Standardbred, and many Warmblood ­breeds30. Therefore, identification of lethal variants in Thorough- breds is also likely to assist in the breeding management of these populations. We also aimed to determine the frequency of any potentially lethal variants identified in the Thoroughbred population in other horse breeds and examine their transcriptomic profile in embryonic tissue. Results Id tif i Identifying candidate lethal SNPs at high frequencies in Thoroughbred horses. Analysis of genotype data from Thoroughbred horses (n = 156) identified only two adjacent, linked SNPs that significantly deviated from the Hardy–Weinberg equilibrium with an absence of homozygotes (Table 1). Under Hardy–Wein- berg equilibrium, seven minor allele homozygotes were expected for both of these SNPs in the dataset. Geno- type data from Japanese Thoroughbred horses (n = 370) also showed an absence of homozygotes for these SNPs (Table 1). In this dataset, the expected number of minor homozygotes for these SNPs under Hardy–Weinberg equilibrium was nine. Despite a complete absence of homozygotes, almost 35% of Thoroughbreds across both of these datasets were heterozygous for this two-SNP haplotype. These SNPs also showed an absence or reduction of minor homozygotes in genotype data for other domestic horse breeds (n = 2030, Table 1). yg g yp These two candidate SNPs mapped to the coordinates of 6:38278097 (rs68661802) and 6:38278874 (rs68663106), which are found in an intronic region of the LY49B gene on chromosome 6. This gene is part of the LY49 gene family, which plays an important role in innate immunity. There are five functional members of the LY49 gene family in Equus caballus, all of which closely grouped together on chromosome 6. Since both of the SNPs mapped to a non-coding region of the LY49B gene, the likelihood of either being a causal variant for lethality is low. Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 www.nature.com/scientificreports/ Figure 1. The equine LY49B gene structure and SNP positions. The two variants in the intronic region (6:38278097 and 6:38278874) were identified in preliminary analysis as showing a significant absence of homozygotes for one allele. The three variants marked with a * are in linkage disequilibrium to these SNPs and may cause a loss of function in homozygous state. The structure of the gene is based on the EquCab 2.0 reference genome where the LY49B gene is on the reverse strand. Figure 1. The equine LY49B gene structure and SNP positions. The two variants in the intronic region (6:38278097 and 6:38278874) were identified in preliminary analysis as showing a significant absence of homozygotes for one allele. The three variants marked with a * are in linkage disequilibrium to these SNPs and may cause a loss of function in homozygous state. Results Id tif i The structure of the gene is based on the EquCab 2.0 reference genome where the LY49B gene is on the reverse strand. Table 2. Amino acid residue sequence in a conserved area of the 3′UTR found in all Equus caballus LY49 h Gene Sequence LY49B AAA​GAC​TTT​CTC​AGGGCC​ATT​AAA​GAG​ATG​GGA​AAC​TGC​ TTT​CCA​AAGAC​ LY49C AGA​GAA​TTT​CCC​AGGGCC​ATT​AAA​GAG​AAG​AGC​AAC​TGA​ TTT​CCA​AAGAC​ LY49D AGA​GAA​TTT​CTC​AGGGCC​ATT​AAA​GAG​AAG​GGC​AAC​TGA​ TTT​CCA​AAGAC​ LY49E AGA​GAA​TTT​CTC​AGGGCC​ATT​AAA​GAG​AAG​GGC​AAC​TGA​ TTT​CCA​AAGAC​ LY49F AGA​GAA​TTT​TGC​AGGGTC​ATT​AAA​GAG​AGG​GGT​AAC​TGC​ TTT​CCA​AAGAC​ Phylogenetic origin of the candidate SNPs. According to the phylogenetic tree generated by Petersen et al.29,30, and their associated SNP data, the SNPs of interest were present in heterozygous state across most phy- logenetic branches of domestic horse breeds. Of the 32 breeds in this dataset, 23 had at least one heterozygote for both SNPs of interest. Notably, this two-SNP haplotype was not found in genotype data from one branch of the tree which contains the North Swedish Horse (n = 19), Norwegian Fjord Horse (n = 21) and Exmoor Pony (n = 24) (Table S1). A larger sample of Exmoor Pony data (n = 274, Table 1) found only one heterozygote for this haplotype. Frequency of the candidate SNPs in other breeds. Analysis of SNP data from other domestic breeds showed that heterozygotes for the SNPs of interest were at a particularly high frequency in the Quarter Horse population (71%, n = 137) (Table 1, Table S2). The proportion of heterozygotes was also high in Swedish Warm- bloods (n = 380) and Norwegian-Swedish Coldblooded Trotters (n = 641), being 20% and 40% respectively (Table 1). Smaller datasets also revealed that Belgian Draft (n = 19), French Trotter (n = 17), Paint (n = 15), Mor- gan (n = 19), Mongolian Paulista (n = 19) and Tuva (n = 15) breeds may also have a high proportion of heterozy- gotes for this haplotype in their populations (Table S1). Identifying candidate causal variants using whole genome sequence data. To further inves- tigate SNP frequencies in this region, variants were called from whole-genome sequence data of 90 domestic horses. The two SNPs identified in the preliminary analysis showed a complete absence of homozygotes for their minor alleles in these individuals (Table S3). Additionally, a number of variants closely linked to these SNPs were identified (Table S3, Figure S1). Annotation of these loci using ­SIFT42 identified three variants that may result in changes to protein structure or expression, so these represent the most likely candidates to cause lethality in homozygous state (Fig. Discussion Analysis of genotype data identified a two-SNP haplotype as a strong candidate for harbouring a variant that causes lethality in homozygous state. The SNPs identified in this preliminary analysis mapped to an intronic region in the LY49B gene on ECA6 (Table 1). The LY49B gene belongs to the LY49 (Killer cell lectin-like receptor subfamily A) family of receptors, which consists of five functional members in Equus caballus43. Other species (including humans) have a functionally similar, but structurally different gene family called KIR (Killer cell immunoglobin line receptors)44. The LY49/KIR gene family are expressed across various types of immune cells, and mediate their function through bindings to MHC-145. The LY49B gene is expressed in myeloid cells where it regulates their activity through an inhibitory effect, possibly to prevent their spontaneous ­activation46. Despite the important role that they play in immunity, the function of LY49 genes in development is currently unknown. In humans, incompatibilities between foetal KIR and maternal MHC (HLA) genotypes are associated with an increased risk of miscarriage and ­preeclampsia47–49. Additionally, knockdown of LY49 in mice showed a high rate of implantation ­failure50,51. These findings indicate that LY49B may play an important role in maternal/foetal compatibility and implantation success in horses.i p y p Analysis of transcriptomic data found that LY49B was first expressed in equine trophoblast tissue during the placental development stage. The first evidence of LY49B expression was found on day 23–24 of development (Table 3), during which the glycoprotein capsule surrounding the embryo is broken down and placental tissue starts to ­develop52. Measurable expression of LY49B was also found in chorion and chorionic girdle tissues between days 27 and 34 of development (Table S4). During this time, trophoblast cells rapidly proliferate to form the chorionic girdle, which then invades the endometrium to form epithelial ­cups53. It is possible that LY49B is important for successful implantation of the embryo by mediating the action of MHC-1 which is expressed during this ­time54,55. Further investigations into the role of LY49B in equine development would confirm whether impaired function causes lethality and the stage of development at which this occurs.i p y g p Variant calling in whole-genome sequence data from 90 domestic horses further confirmed an absence of minor homozygotes for the two SNPs of interest. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Table 3. Gene counts from RNA sequence data of three trophectoderm and three inner cell mass tissue samples from equine embryos. Transcript counts are in fragments per kilobase/million (FPKM). Tissue Gene count (FPKM) Trophectoderm Day 15 Day 22 Day 25 0.000 0.031 0.024 Inner cell mass Day 16 Day 23 Day 24 0.00 0.00 0.00 Tissue Gene count (FPKM) Trophectoderm Day 15 Day 22 Day 25 0.000 0.031 0.024 Inner cell mass Day 16 Day 23 Day 24 0.00 0.00 0.00 Table 3. Gene counts from RNA sequence data of three trophectoderm and three inner cell mass tissue samples from equine embryos. Transcript counts are in fragments per kilobase/million (FPKM). Table 3. Gene counts from RNA sequence data of three trophectoderm and three inner cell mass tissue samples from equine embryos. Transcript counts are in fragments per kilobase/million (FPKM). However, there is little conservation of the phenylalanine residue across taxa; some species have a phenylalan and others a serine at this position. This SNP is annotated as being “tolerated” in SIFT. h Two other variants that were closely linked to the candidate SNPs (6:38276742A > T and 6:38276955G > A) were found within the 3′UTR (3′untranslated region) of the LY49B gene. Alignment of the 3′UTR of the five func- tional LY49 genes in Equus caballus revealed that the region containing the SNP 6:38276955G > A (rs1139567427) is highly conserved in all members of the LY49 gene family (Table 2). This region may be important for mRNA stability and translation into a functional protein. The other variant 6:38276742A > T (rs1137325172) was found in an AU-rich region at the end of the LY49B mRNA transcript, which is often associated with polyadenylation and post translation stability. Transcriptomic analysis of RNA sequence data. Measurable levels of LY49B mRNA were not detected in equine trophectoderm tissue collected on day 16 of development. However, LY49B mRNA was observed in trophectoderm tissue collected on days 23 and 24 of development (Table 3). Additionally, LY49B mRNA tran- scripts were detected in microarray data from equine chorion and chorionic girdle tissue between days 27 and 34 of development (Table S4). Inner cell mass tissue collected on days 15, 22 and 25 of development did not show any measurable transcription of LY49B (Table 3). The genotypes of the candidate SNPs in the mRNA samples analysed were unknown. Results Id tif i 1).hi yg ( g ) The first of these variants, 6:38282610G > A (rs68663123), was located in an exonic region of the LY49B gene and resulted in an amino acid change from a phenylalanine to a serine residue. This substitution is located next to a tryptophan residue that appears to be highly conserved across members of the LY49 family and across species. Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 www.nature.com/scientificreports/ Rather, heterozygotes for this haplotype may have been present in pre-domesticated horses as a rare variant, and have become more frequent in some domestic breeds as the result of population bottlenecks due to breed formations and selective breeding practices. Domestication and breed formation events have been well documented to result in increased deleterious mutation loads in horses and other domestic ­species22,31,63,64. A high proportion of heterozygotes for this haplotype were found in some breeds closely related to the Thoroughbred including the Paint, French Trotter, Morgan and Quarter Horse. Notably, over 70% of Quarter Horse samples included in this study were heterozy- gous for these SNPs (Table 1). The Quarter Horse has an open stud book, and higher genetic diversity than the Thoroughbred ­population65, making the high frequency of a potentially lethal haplotype at first surprising. The Quarter Horse dataset reportedly did not contain full or half ­siblings65, but the collection of samples from one geographical area may not fully reflect the diversity of the worldwide population. An average relatedness analysis of these samples noted the large genetic influence of one particular Thoroughbred ­stallion65, which may explain the high frequency of heterozygotes observed in this population. However, the extremely high frequency of heterozygotes in this breed may be due to selective breeding favouring these individuals.ht yg y g g The Belgian Draft, Mangalarga Paulista and Tuva breeds also show a high proportion of heterozygotes, but are more distantly related to the Thoroughbred and to each other. Therefore, the high frequency of heterozygotes in these breeds may be due to independent genetic drift events. Heterozygotes for this haplotype were notably absent from one branch of the tree containing small heavy horses from Northern Europe, which are more distantly related to the Thoroughbred. A larger dataset of Exmoor Pony samples from this phylogenetic branch revealed one heterozygote for this haplotype (Table 1). This could be due to a calling error, but it is also possible that these SNPs exist at very low frequencies in these breeds. The small sample size of the genotype data for many individual breeds in this study means that heterozygote frequencies across all subpopulations found throughout the world may deviate from that reported here. However, these data provide an indication of breeds with high proportions of heterozygotes for this region. Analysis of SNP data from Northern-Swedish Coldblooded Trotters identified 22 homozygotes for the SNP at position 6:38278874. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Despite the importance of the 3′UTR for the mRNA stability and normal expression of a gene, little is known about how specific polymorphisms can affect post-transcriptional processing. This makes it difficult to identify how the 3′UTR variants identified in this study could affect the translation of LY49B mRNA into a functional pro- tein. The 3′UTR variant 6:38276955G > A was identified as a possible candidate for embryonic lethality because it is highly conserved between all members of the LY49B family (Table 2) in horses, so may play an important role in mRNA stability. The other 3′UTR variant (6:38276742A > T) is found in an AU-rich region at the end of the transcript, so may be important for the addition of the polyadenylation tail. Further examination of the effects that these variants have on post-transcriptional processing would determine if they impact the normal expression of LY49B in horses.i p Despite an absence of homozygotes, the two intronic SNPs identified in this study were found at high het- erozygote frequencies in the Thoroughbred population. Mares are often covered multiple times in a season, which may explain why a more discernible reduction in fertility has not been observed as a result of the high frequency of this variant. However, the presence of lethal variants at high frequencies may result in more coverings being required for each mare in a season. Currently, there is no evidence that variation in the LY49B gene is associated with phenotypic advantages in horses. However, it is possible that one of the variants linked to these SNPs results in a phenotypic advantage in heterozygotes, which could explain why they have reached such high frequencies in the breed. It is also possible that selective breeding practices favouring a limited number of stallion bloodlines are responsible for this potentially lethal haplotype drifting to high frequencies in the Thoroughbred population. This would be most likely to occur if a stallion that made a large genetic contribution to the population was a carrier. A similar instance has recently been documented in cattle, where a lethal variant at a high frequency was traced back to a sire with an extensive genetic influence on the ­population19.h gl p p The presence of this potentially lethal haplotype across many diverse breeds of domestic horses indicates that it may not be the result of a recent mutation present only in the Thoroughbred population. www.nature.com/scientificreports/ It is likely that there has been recombination between this SNP and the causal variant, and may appear more frequent in this population due to differences in breed history and recombination ­patterns66. However, additional analyses are required to explore this further. Overall, our findings suggest that this region shows evidence harbouring a homozygous lethal variant, yet a high proportion of heterozygotes are found across many domestic horse breeds.ih yg y In this study, we identified a haplotype at high heterozygote frequencies in the Thoroughbred horse popula- tion that is a strong candidate for harbouring a variant causing lethality in homozygous state. Similar analyses on larger datasets in other livestock populations have identified multiple lethal haplotypes, so it is likely that other such variants are present at high frequencies in the Thoroughbred population but were not captured in this study. Additionally, the use of commercial SNP arrays only allows for the identification of variants with high minor allele frequencies in populations. Analysis of larger sample sizes, and using higher density genotype data could allow for identification of other variants associated with lethality in domestic horses. The identification of this potentially lethal haplotype demonstrates the potential implications of heavily favouring a limited number of bloodlines in selective breeding practices. Further characterisation of lethal haplotypes in other breeds would also assist in breeding management to increase per covering fertility rates in domestic horse populations. Discussion Three variants closely linked to these SNPs were also identi- fied in these data as the most likely candidates to cause loss of function in the LY49B gene and result in lethality in homozygous state (Table S3). One SNP was a missense variant in the coding region of the LY49B gene that results in the substitution of a negatively charged serine for an aromatic phenylalanine residue. However, lack of conservation of this SNP in LY49 genes across taxa makes it seem unlikely to be a causative variant for embryonic lethality. Two other variants found in the 3′UTR of the LY49B gene were also closely linked to the SNPs identified in the preliminary analysis, and seemed more likely candidates to cause embryonic lethality in homozygous state.h p y y y y y yg The 3′UTR of a gene is responsible for transcriptional stability through the binding of miRNAs and RNA binding ­proteins56. The addition of the polyadenylation tail to the 3′UTR is also essential to ensure proper pro- cessing and translation of the mRNA ­strand57. Mutations in the 3′UTR can lead to degradation of the mRNA, resulting in reduced or inhibited translation even when the gene is ­transcribed58. Variation in the 3′UTR of genes are associated with a number of diseases including Huntington’s and breast cancer in ­humans59,60. Additionally, SNPs in the 3′UTR are associated with traits in livestock including milk production in cows, muscularity in sheep and obesity in ­horses58,61,62. Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 www.nature.com/scientificreports/ The whole genome datasets were downloaded from the European Nucleotide Archives (ENA, https​://www.ebi.ac.uk/ena) which included horses of different domestic breeds (PRJEB14779, n = 70) and additional Thoroughbred samples (PRJNA168142, n = 16 and PRJNA184688, n = 4) (Table S5).h h g p ( J , J , ) ( ) The SNP array used in the initial genotyping analysis was developed based on coordinates of the EquCab2.0 reference genome. For consistency, we used the EquCab2.0 assembly as a reference for the whole-genome sequence analysis. The EquCab2.0 assembly was also used because of an issue with resolution in the area of interest on the newer EquCab3.0 assembly. The raw reads were mapped to the EquCab2.0 reference genome using BWA-MEM algorithm from Burrows-Wheeler Alignment Tool (version 0.7.17)73. Duplicate reads were flagged using Samblaster (version 0.1.22)74, and base recalibration was performed using Genome Analysis Toolkit (GATK) (version 4.0.8.1)75. Variants (SNPs and INDELs (insertions and deletions)) were called using Haplotype Caller and then filtered using the standard hard filtering recommendations in ­GATK76. The individual SNPs were then filtered to only include high quality allele calls with an average filtered depth over 10 and a Phred score over 20.i Variants that were linked to the SNPs identified from the genotype data were produced using the LD function in PLINK (version 1.9) with a window size of 5 Mb67. Only SNPs with an r2 value of over 0.8 and a D′ value > 0.9 were shortlisted. The effects of each SNP on gene structure and function was characterised using SIFT (version 4G)42. The conservation of variants across taxa was analysed using the NCBI Conserved Domain Database ­Search77. Transcriptomic analysis. Publicly available RNA sequence data were used to examine expression lev- els of the genes of interest in embryonic tissue. The data included equine inner cell mass tissue (collected at day 15, 22 and 25, n = 3) and trophectoderm tissue (collected at day 16, 23 and 24, n = 3) from the Functional Annotation of ANimal Genomes (FAANG) equine biobank (available from ENA under the project name PRJNA223157)78. Adaptors were trimmed using bbduk from BBtools (version 37.98)79. Reads were aligned to the EquCab 2.0 genome using STAR (version 2.7.2b)80. Counts were generated using featurecounts from Sub- read package(version 1.5.1)81, then quantified in fragments per kilobase/million (FPKM) using the R package “edgeR”82 with the Equus_caballus_Ensembl_94 file used for annotation. www.nature.com/scientificreports/ www.nature.com/scientificreports/ pended in low TE (1 mM Tris, 0.1 mM EDTA). DNA was extracted from blood samples using the Qiasymphony DSP DNA mini kit (Qiagen, Hilden, Germany). pended in low TE (1 mM Tris, 0.1 mM EDTA). DNA was extracted from blood samples using the Qiasymphony DSP DNA mini kit (Qiagen, Hilden, Germany). Initial genotyping. Genotype data from a representative sample of Thoroughbreds were used to identify SNPs with a high proportion of heterozygotes, but an absence of homozygotes for one allele. Genome-wide SNP data were generated for 156 Australian Thoroughbred horses by genotyping samples on either the Illumina 70 K Chip (65,102 SNPs) (n = 102) or the Affymetrix 670 K Chip (670,796 SNPs) (n = 54). Common genotyped SNPs between the two arrays were scanned for deviations from the Hardy–Weinberg equilibrium with an absence of homozygotes for one allele using PLINK (version 1.9)67. The p values were adjusted using a false discovery rate correction with the R package “qvalue”68. Since SNPs with an absence of homozygotes could indicate a calling error, the search was narrowed to only include adjacent SNPs that fit such criteria.h y ji The frequencies of the candidate SNPs were then examined in publicly available genotype data from Japanese Thoroughbreds (n = 370) typed on the Affymetrix 670 K ­Chip69 and these were added the Thoroughbred sample. The SNP frequencies were then characterised from genotype data from Swedish Warmbloods (n = 380)70 and Norwegian-Swedish Coldblooded Trotters (n = 646)71 typed on the Affymetrix 670 K Chip. Publicly available data from Exmoor Ponies (n = 285, typed on the Affymetrix 670 K Chip)71, Quarter Horses (n = 137, typed on the Illumina 70 K Chip)72 and horses of 32 different domestic breeds (n = 582, typed on the Illumina 50 K Chip)29,30 were also included in this preliminary scan for SNP frequencies. In these data, raw intensities were plotted to check for calling errors. If potential calling errors were detected, SNPs were recalled using a mixture model fitted with an expectation–maximization algorithm in R. Variant discovery and mapping. Publicly available whole-genome sequence data were used to further examine the frequencies of the candidate SNPs identified in the initial genotype analysis, and to identify linked variants. Paired end whole-genome sequence data from 90 horses of different domestic breeds were used in this analysis (Table S5). www.nature.com/scientificreports/ Microarray data for chorion (n = 19) and chorionic girdle (n = 19) tissue collected from horse embryos between days 27–34 of ­development83 were also examined for gene expression levels. Ethics statement. Hair samples from Australian Thoroughbred horses were collected under approval from University of Sydney Ethics Committee (Number: N00-2009-3-5109.) Written informed consent to use the animals in this study was obtained from the owners of the animals. The hair samples from Swedish Warmblood horses were originally collected for parentage testing and stored in the biobank at the Animal Genetics Laboratory, SLU so ethics approval was not applicable. Hair and blood samples of Norwegian-Swedish Coldblooded Trotters were collected under approval from the Ethics Committee for Animal Experiments in Uppsala, Sweden (Number: C 121/14). All the methods were performed in accordance with the guidelines set out by the respective Animal Ethics Committees and the guidelines contained in the Guide for the Care and Use of Laboratory Animals. No experimen- tal procedure was performed on live animals. All other data was downloaded from publicly available repositories. Methods DNA e tra DNA extractions. DNA was extracted from the hair samples of Australian Thoroughbred horses using the Qiagen Gentra Puregene Tissue Kit (Qiagen, Redwood City, CA, USA). DNA was extracted from the hair sam- ples of Norwegian-Swedish Coldblooded Trotters and Swedish Warmbloods by incubating the samples for 2 h at 56 °C with Chelex 100 Resin (Bio-Rad Laboratories, Hercules, CA) and Proteinase K (20 mg/mL; Merck KgaA, Darmstadt, Germany). The Proteinase K was then inactivated by incubating for 10 min at 95 °C and DNA resus- Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 Data availabilityh y The whole-genome sequence data used in this study is publicly available for The European Nucleotide Archive. Genotype data for Japanese Thoroughbreds, Exmoor Ponies, Quarter Horses and other domestic horse breeds can be found in the supplementary information of their respective papers (https​://doi.org/10.1371/journ​ Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 www.nature.com/scientificreports/ al.pone.02184​07, 10.1371/journal.pone.0152966, 10.1093/jhered/est079 and 10.1371/journal.pone.0054997). The exceptions are genotype data from Australian Thoroughbred, Swedish Warmbloods and North Swedish Coldblooded Trotters, which are available on request but restrictions apply to the availability of these data which were used under license for the current study and so are not publicly available. al.pone.02184​07, 10.1371/journal.pone.0152966, 10.1093/jhered/est079 and 10.1371/journal.pone.0054997). The exceptions are genotype data from Australian Thoroughbred, Swedish Warmbloods and North Swedish Coldblooded Trotters, which are available on request but restrictions apply to the availability of these data which were used under license for the current study and so are not publicly available. Received: 13 May 2020; Accepted: 26 June 2020 References References 1. Spencer, T. E. Early pregnancy: concepts, challenges, and potential solutions. Anim. Front. 3, 48–55. https​://doi.org/10.2527/ af.2013-0033 (2013). 1. Spencer, T. E. 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Scientific Reports | (2020) 10:13153 | https://doi.org/10.1038/s41598-020-68946-8 © The Author(s) 2020 Additional information Supplementary information is available for this paper at https​://doi.org/10.1038/s4159​8-020-68946​-8. Correspondence and requests for materials should be addressed to E.T.T. Correspondence and requests for materials should be addressed to E.T.T. Correspondence and requests for materials should be addressed to E.T.T. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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CONSERVATION GENETIC ANALYSIS OF BLANDING’S TURTLES ACROSS OHIO, INDIANA, AND MICHIGAN by Dan Guinto A Thesis Submitted to the Faculty of Purdue University In Partial Fulfillment of the Requirements for the degree of Master of Science Department of Biology at Purdue Fort Wayne Fort Wayne, Indiana December 2021 Department of Biology at Purdue Fort Wayne Fort Wayne, Indiana December 2021 Dedicated to my friends, family, and many mentees who have guided and supported me along the THE PURDUE UNIVERSITY GRADUATE SCHOOL STATEMENT OF COMMITTEE APPROVAL Approved by: Dr. Jordan M. Marshall 2 2 way. 3 Hoffman, Liz King, Minh Lee, John Lynch, Carly Martenson, Jen Mayer, Andrew Metz, Chrissey Miller, Sophie Mills, Sean Obrochta, Elspeth Pierce, Zack Pitman, Shelby Priester, Trevor Proctor, Joseph Redinger, Mic Rohde, Courtney Ross, Dale Shank, Frank Schroyer, Jacob Schott, Tyler Scoville, Ayley Shortridge, Nick Smeenk, Hunter Smith, Jesse Sockman, Reine Sovey, Bria Spalding, Courtney Thompson, Jenny Swonger, Megan Wise. ACKNOWLEDGMENTS I would like to thank Dr. Mark Jordan for his constant guidance and support through each aspect of my graduate school journey. I would also like to thank my committee members Dr. Bruce Kingsbury, Dr. Rebecca Palu, Dr. Matt Cross, and Greg Lipps wisdom, guidance, and support. For Funding support for tissue collection and genotyping I’d like to thank the Indiana Department of Natural Resources, Toledo Zoo, and the U.S. Fish and Wildlife Service. Next I would like to thank our partners: (Ohio) from The Toledo Zoo, Matt Cross, ZooTeens; Terry Breymaier, Chris Otto, and Felicity Galavan from The Ohio State University, Greg Lipps; from The Ohio Division of Wildlife, Kate Parsons and Jim Schott; the Ohio Division of Natural Areas and Preserves, the Ohio Division of Parks and Watercraft; from Winous Point Marsh Conservancy, John Simpson and Brendan Shirkey; from Ottawa Shooting Club, Pete Ochs; Old Woman Creek National Estuarine Research Reserve; (Michigan), from the Michigan Natural Features Inventory; Yu Man Lee and Helen Enander; Michigan State University Extension, From the Michigan Department of Natural Resources, Amy Derosier; Michigan Nature Association, Huron-Clinton Metroparks, Seven Ponds Nature Center, Addison Township , (Indiana) Purdue University at Fort Wayne, the Kingsbury Lab, from Indiana Department of Natural Resources, Linnea Petercheff, Teresa Clark; from the Nature Conservancy, Nathan Herbert. Next I’d like to thank Tyler Scoville and Connor Dempsey for aid and assistance in conducting lab work. Finally I’d like to thank the many field leads, field technicians, and volunteers who contributed data collection and field sampling: Kailyn Atkinson, Chloe Bates, Julia Boldrick, Katie Brandewie, Charlotte Brennan, Morgan Boyer, Ian Chick, Elizabeth Cubberly, Connor Dempsey, Diana Digges, Dan Earl, Stephanie Emerine, Molly Fava, Nick Friedeman, Talia Greenblatt, Gia Haddock, Jessica Hinson, Beckie Hippensteel, Trevor 4 Hoffman, Liz King, Minh Lee, John Lynch, Carly Martenson, Jen Mayer, Andrew Metz, Chrissey Miller, Sophie Mills, Sean Obrochta, Elspeth Pierce, Zack Pitman, Shelby Priester, Trevor Proctor, Joseph Redinger, Mic Rohde, Courtney Ross, Dale Shank, Frank Schroyer, Jacob Schott, Tyler Scoville, Ayley Shortridge, Nick Smeenk, Hunter Smith, Jesse Sockman, Reine Sovey, Bria Spalding, Courtney Thompson, Jenny Swonger, Megan Wise. 5 5 TABLE OF CONTENTS LIST OF TABLES .......................................................................................................................... 8 LIST OF FIGURES ........................................................................................................................ 9 ABSTRACT .................................................................................................................................. 10 CONSERVATION GENETIC ANALYSIS ....................................................... 12 Introduction ....................................................................................................................... 12 Methods............................................................................................................................. 16 1.2.1 Ohio and Michigan Field Sampling ........................................................................... 16 1.2.2 Indiana Field Sampling .............................................................................................. 17 1.2.3 Lab Protocol ............................................................................................................... 17 Statistical Analyses ........................................................................................................... 19 1.3.1 Hardy Weinberg Equilibrium and Disequilibrium .................................................... 19 1.3.2 Descriptive Statistics ................................................................................................. 19 1.3.3 Structure Analysis, Genetic Clustering ...................................................................... 20 1.3.4 Migration ................................................................................................................... 23 1.3.5 Isolation by Distance and Geographic Isolation ........................................................ 24 1.3.6 Bottlenecking and Effective Population Size ............................................................ 25 Results ............................................................................................................................... 26 1.4.1 Hardy Weinberg Equilibrium and Disequilibrium .................................................... 26 1.4.2 Structure Analysis and Genetic Clustering ................................................................ 27 1.4.3 Migration ................................................................................................................... 29 1.4.4 Isolation By Distance and Watershed Isolation ......................................................... 29 1.4.5 Bottlenecking, Effective Population Size .................................................................. 30 Discussion ......................................................................................................................... 54 1.5.1 Population Structure .................................................................................................. 55 1.5.2 Genetic Status Within Populations ............................................................................ 58 1.5.3 Management Implications ......................................................................................... 60 Conclusions ....................................................................................................................... 63 LANDCSAPE RESISTANCE MODELING ...................................................... 65 Introduction ....................................................................................................................... 65 6 Methods............................................................................................................................. 68 2.2.1 Site Description ......................................................................................................... 68 2.2.2 Creating Resistance Surfaces ..................................................................................... 68 2.2.3 Genetic Distance ........................................................................................................ 70 2.2.4 Landscape Resistance Optimization .......................................................................... 70 Results ............................................................................................................................... 71 2.3.1 Genetic Distance ........................................................................................................ 71 2.3.2 Landscape Resistance Optimization .......................................................................... 71 2.3.3 Model Fit ................................................................................................................... 72 Discussion ......................................................................................................................... 75 Conclusion ........................................................................................................................ 77 REFERENCES ............................................................................................................................. 79 7 7 7 LIST OF TABLES Table 1.1 Summary of fifteen microsatellite loci run for all samples .......................................... 33 Table 1.2 Summary of descriptive statistics by locality ............................................................... 34 Table 1.3 Summary of pairwise FST and D (Jost D) differentiation scores. FST below and D above. Bold values do not include 0 in the 95% confidence intervals. .................................................... 37 Table 1.4 AMOVA results displaying variance for the HUC6 (bottom) and HUC8 (top) watershed levels. ............................................................................................................................................ 46 Table 1.5 Locality grouping based on TESS3r cluster assignment. ............................................. 47 Table 1.6 Mean historic migration calculated through Migrate, recent migration rate from BayesAss ....................................................................................................................................... 48 Table 1.7 Summary of Bottleneck tests and effective population size estimates with 95% confidence intervals. ..................................................................................................................... 51 Table 1.8 Comparison of effective population size estimates (Ne) for one site subsampled to different population sizes with 95% confidence intervals. ........................................................... 52 Table 1.9 Comparison of descriptive statistics for E. blandingii. * HO reported rather than HE. 53 Table 2.1 Summary of resistance model optimization. ................................................................. 74 8 8 LIST OF FIGURES Figure 1.1 Map of Blanding’s Turtle geographic range (USGS, 2018) ........................................ 31 Figure 1.2 Site Localities with greater than 10 turtles. ................................................................. 32 Figure 1.3 Number of alleles versus sample size by locality. ....................................................... 35 Figure 1.4 Observed alleles and observed heterozygosity over 200 years for three different bottleneck scenarios. ..................................................................................................................... 36 Figure 1.5 MedMeaK and MedMedK values reducing inclusion of extra clusters, estimated using the methods of Puechmaille (2016) .............................................................................................. 38 Figure 1.6 Bar graphs showing inferred clusters by individuals by site. K = 6 inferred from MedMeaK (top); K = 7 inferred from MedMedK (bottom). ........................................................ 39 Figure 1.7 Map displaying STRUCTURE results for K = 6 clusters over geographic space. ...... 40 Figure 1.8 Cross validation score for inferring number of clusters (top). TESS3r bar graphs showing inferred clusters by individuals by site for K=5 localities listed from west to east (bottom). ....................................................................................................................................................... 41 Figure 1.9 Values of BIC for inferring number of clusters (top). DAPC scatter chart of five inferred clusters (middle). Individual assignment from given populations to inferred clusters (bottom). . 43 Figure 1.10 Mantel test for isolation by distance (IBD) (top) and regression line for individual genetic distance (Dgen) vs geographic distance (GeoDis), r2 = 0.31, P <0.0001 (bottom). ........ 44 Figure 1.11 HUC 8 (left) and HUC 6 (right) watershed levels. .................................................... 45 Figure 1.12 Mean historic migration rate (top), mean recent migration rate (bottom) ................. 49 Figure 1.13 Mean historic and contemporary net immigration .................................................... 50 Figure 2.1 Resistance surfaces TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes).............................................................................................. 73 Figure 2.2 Monomolecular Transformation applied to TPI. ......................................................... 74 Figure 2.3 Optimized resistance surfaces, TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes) ......................................................................... 75 9 ABSTRACT The Blanding’s Turtle (Emydoidea blandingii) is considered a species of conservation need across much of its range. A key aspect to conserving a species is understanding the genetic diversity and population structure across the landscape. Several researchers have focused on E. blandingii genetic diversity in the northeastern United States, Canada, and the Midwest. However, little investigation has been done on localities within the Great Lakes region of Indiana, Michigan, and Ohio. Here 14 microsatellite loci are utilized to characterize the genetic diversity of E. blandingii in Indiana, Ohio, and Michigan. Understanding genetic trends within this region will allow for the defining of management units through genetic clustering, investigation of historic and recent migration between clusters, investigation of drivers of genetic differentiation, checks for bottlenecks, estimations of effective population size (Ne), and optimization of landscape resistance surfaces. Overall, little differentiation is observed between localities and within locality diversity tended to be high. A minimum of four clusters were identified and as many as seven clusters were detected in a hierarchical manner using three grouping methods (STRUCTURE, Tes3r, and DAPC). Historical migration between clusters was relatively low, and recent migration appears to be absent. Significant correlations between geographic distance and genetic differentiation (IBD), as well as watershed and genetic differentiation were observed. Optimized landscape resistance layers provided poor models and distance was maintained as the best driver of differentiation. No bottlenecking was detected, and Ne estimates were generally high, but likely biased by sample size. The long lifespan and delayed genetic differentiation of E. blandingii is likely responsible for the observed diversity and lack of differentiation between localities. This does not mean they are secure in the Great Lakes Region. Bottlesim analysis looking at the effects of population reduction and subsequent loss of genetic diversity indicates that many localities 10 within the study area are likely vulnerable to genetic loss in the next 200 years, which can be rapid and drastic in long-lived species. and drastic in long-lived species. 11 11 Introduction Turtles (Testudines) in general are one of the most imperiled groups of vertebrates [1]. Blanding’s Turtle (Emydoidea blandingii) is a species in decline that contributes to this trend, receiving protected status across much of its geographic range [2,3,9]. As a long-lived species with long generation times, large seasonal terrestrial movements, and low annual fecundity, the life history and spatial ecology of E. blandingii puts populations at a particular disadvantage in the face of habitat loss and degradation [2,4-6]. In addition, E. blandingii exhibit low haplotype and sequence diversity, which indicates potential for continued population decline due to lack of genetic adaptability [7]. E. blandingii populations in the Great Lakes region are reliant on shallow (~2.5 m deep) open marshes, ponds, and lakes with emergent herbaceous vegetation as well as a mix of forested ephemeral wetlands, prairies, and bare sands for upland movement/nesting [8]. A long-term (40+ years) study by Congdon and Gibbons (1996) demonstrates that E. blandingii populations can maintain stable population sizes with low recruitment in large (615 hectares), well protected preserves. Urban modification and conversion of such shallow wetland habitat complexes and uplands can lead to local extirpation and changes to the spatial ecology E. blandingii [10]. E. blandingii is reliant on large, contiguous wetlands and the destruction of this habitat is seen as a key threat to their persistence [6,8,11-16]. Of particular concern is the drastic reduction of wetlands in the Midwestern United States that have occurred since the 1700’s [17]. Reduction of movement corridors and exposure to roadways has been shown to increase the incidence of road mortality of E. blandingii [15,18]. Increased urbanization can also cause wetland degradation due to introductions of pesticides, herbicide, and fertilizers which may affect E. blandingii, as has been 12 shown for the common snapping turtle (Chelydra serpentina) [15]. Bioaccumulation and morphological impacts have been recorded in C. serpentina in wetland systems with chemical contamination [19,20]. Beyond physical alteration of the landscape, urbanization can also increase human and predator interaction with E. blandingii exposing them to increased poaching and mortality [8,10]. Collection can be particularly detrimental to small or isolated populations which may already be at risk of extirpation [15]. Removal of individuals can be particularly detrimental to small or isolated populations, especially due to the long reproductive lives that are required for population viability [4,21]. Introduction An important aspect of conservation planning beyond habitat protection is to understand the genetic composition and diversity of a species within localized populations as well as across their range. Understanding the local and range-wide genetic diversity of a species can help conservationists determine if and when it is appropriate to reintroduce individuals to a landscape or supplement remnant populations using translocation and/or head-starting. By examining the genetic composition prior to conservation actions, researchers can reduce the likelihood of inbreeding and outbreeding depression which could otherwise further imperil an already vulnerable long lived species such as E. blandingii [3]. Assessing the effects of such conservation actions for E. blandingii, and turtles in general, can be difficult as the effects may take decades to manifest due to the low genetic variability and reduced micro-evolutionary rates present in the order Testudines [22,23]. Small, isolated populations are expected to have lost genetic variation due to bottlenecks caused by range reduction and expansion [7]. However, turtles appear to retain higher than expected levels of genetic variation despite population decline, possibly due to their long generation times [24-30]. Prior studies examining within population genetic diversity of E. 13 13 blandingii have reported relatively high levels of observed and expected heterozygosity (HO & HE) across the range from 0.30 to 0.79 [24-30]. Relatively high levels of allelic richness (AR) have been reported from Ontario and Illinois, ranging from 3.6 to 5.3 [27,30]. Finally, Anthonysamy et al., (2018) found no evidence of inbreeding in E. blandingii in northeast Illinois and even found potential evidence of outbreeding (FIS ranging from -0.088-0.042). Microsatellites or short tandem repeats (STR’s) of base pairs in non-coding DNA are present in high frequencies in the eukaryotic genome [3,31]. Microsatellites have relatively high mutation rates caused by proof reading or polymerase slippage errors during DNA replication. As a result, they are prone to accumulate polymorphisms faster than other regions of the genome [32]. Microsatellite markers that are conserved across species but polymorphic between individuals can be particularly useful because they can be used to characterize genetic dissimilarity for cluster analysis. Microsatellite analysis uses the comparison of the length of DNA regions enriched with microsatellites between individuals to determine differences in the number of loci present at the region. Difference in copy numbers allows researchers to determine the presence or absence of polymorphisms within and among populations [31]. Introduction Microsatellites have proven to be an effective tool for determining genetic diversity of E. blandingii at regional scales through a number of studies [27,28,30,33]. E. blandingii originated between 5 and 19 million years ago (dating to the Hemiphillian or the Miocene), and have experienced slow but drastic changes in the landscape due to glacial expansion and reduction [34-36]. With these climactic changes the geographic range has also shifted likely causing bottlenecks and founder events, creating regional isolation and population structure [7,25,37]. Prior range-wide study using five microsatellite loci identified two evolutionary significant units being separated by the Appalachian Mountains, and found additional support for 14 recognizing Nova Scotia as its own evolutionary significant unit [25]. Recent range-wide genetic analysis using mitochondrial and nuclear loci supports the previously identified evolutionary units, and indicate that the glacial dynamics experienced by E. blandingii are responsible for the presence of at least two genetically distinct lineages: a Great Lakes/Midwest USA lineage to the west of the Appalachian Mountains and a Northeast USA/ Nova Scotia lineage to the east [7]. Region-wide microsatellite analyses find that E. blandingii seem to have relatively low levels of differentiation from locality to locality, with higher degrees of differentiation detected east of the Appalachian Mountains compared to west [24-30]. Within the Midwest and Great Lakes regions, these findings all support the south and west glacial retreat followed by north and east recolonization of E. blandingii resulting in a high degree of genetic mixing and ultimately creating a low degree of differentiation [27,28,30,38]. Despite the lack of differentiation in the Great Lakes and Midwest (low FST) there is still evidence of population structure through cluster analysis [27,28,30]. Davy et al. (2014) discovered four genetic clusters utilizing 12 microsatellite loci in southern Ontario, and Anthonysamy et al. (2018) found evidence of a hierarchical assortment of three clusters nested into two large broad clusters across six sites in northeast Illinois using 14 loci. Sethuraman et al. (2014) found four to 6 hierarchical clusters across Illinois, Iowa, Minnesota and Nebraska. Although analyses of clustering are useful for identifying the distribution of populations, the connectivity of these populations is of conservation interest to identify habitat needs for connectivity and gene flow. Introduction The relatively slow rate of genetic differentiation and the long lifespan of turtles makes it difficult to differentiate the effects of contemporary and historical gene flow especially in the presence of a rapidly changing landscape [24,27,33]. Although the genetic differentiation may be limited in scope, it can still indicate historical trends in gene flow that likely 15 underlie modern population structure [7,25,27,28]. Comparing historical gene flow with modern landscape resistance can be useful in determining where gene flow likely no longer exists between localities. Understanding historic gene flow can be used to determine where corridors or translocation may be useful in promoting gene flow and maintaining genetic diversity by staving off founder’s effects or genetic bottlenecks associated with the fragmentation of populations. Little investigation into the population genetic structure and patterns of differentiation of E. blandingii have been conducted within Indiana, Ohio, and Michigan. Two prior studies from Osentoski (2001) and McGuire et al., (2013) within the E.S. George Reserve in Michigan found no evidence of genetic structure using eight microsatellite loci. My study looks to: (1) examine levels of genetic variation and population clustering in E. blandingii localities across Indiana, Michigan, and Ohio, and (2) assess the potential for landscape variables to correlate with genetic connectivity among populations. Results of this investigation can be used to provide more focus to ongoing species conservation in the Great Lakes region and further our understanding of historic colonization patterns of E. blandingii. 1.2.2 Indiana Field Sampling Field sampling in Indiana took place from March through July of 2017-2019 and a single locality in 2021. Indiana sites were chosen based on historical records [44]. Trapping was conducted using a combination of Hoop traps (~0.8 m diameter) and Promar traps (~0.5 m diameter). 1.2.1 Ohio and Michigan Field Sampling Field sampling was conducted in April to August of 2019 to 2021 in the Lake Erie Watershed in southeast Michigan and northern Ohio. For the first trapping season in Ohio and Michigan, sites were chosen based on current observed or historic presence, along with habitat suitability. For the 2020 and 2021 trapping seasons localities that fell within a circle with a 15 kilometer radius were grouped into a genetic neighborhood. These genetic neighborhoods were intended to encapsulate the home range, breeding dispersal distance, and hatchling dispersal of E. 16 blandingii at each locality [40-42]. We then focused on obtaining a minimum of 10 samples for at least one locality within an area presumed to be within the maximum movement distance of an individual Blanding’s Turtle. Additional samples from northwest Michigan were obtained through a partnership with an ongoing study in the Kingsbury Lab (Purdue Fort Wayne). Trapping was conducted following the Northeast Blanding’s Turtle Working Group trapping protocol, using a combination of Hoop traps (~0.8 m diameter) and Promar traps (~0.3 m diameter) [43]. Blood was drawn from the nuchal sinus using IACUC approved methods, preserved in 95% ethanol, and placed in a standard freezer until extraction. Statistical Analyses Statistical Analyses 1.3.1 Hardy Weinberg Equilibrium and Disequilibrium Hardy Weinberg Equilibrium (HWE) is used as a null test for genetic forces contributing to a population. Populations exhibiting Hardy Weinberg Equilibrium are likely not experiencing the genetic effects of evolutionary forces outside of random mating in large populations [51]. PopGenReport version 3.0.4 was used to test for Hardy Weinberg Equilibrium [52]. Linkage disequilibrium can bias the analysis of genetic differentiation by creating false associations between loci within or among populations. Genepop version 1.1.7 was used to examine linkage disequilibrium by locus pair within each of the sample localities [53]. Tests for linkage disequilibrium were run in Poppr version 2.9.3 [54] using the Markov chain method with dememorization set at 10000 with 5000 iterations and 100 batches. 1.2.3 Lab Protocol DNA was extracted from 95 microliters of alcohol-preserved blood using the Qiagen, DNeasy Blood and Tissue extraction kit. Before starting extractions, stored blood was centrifuged and air-dried for ~15 minutes to separate and remove excess ethanol. A Nanodrop spectrophotometer was used to determine the concentration of extracted DNA. If sufficient DNA was not extracted and blood sample remained the sample was re-extracted. Fifteen microsatellite markers and primers were chosen from prior studies to maximize genetic variation and facilitate cross-regional comparison for future study (Table 1.1). These loci were chosen for their number of alleles, ability to be multiplexed, and high degree of use across 17 17 regions. These microsatellite markers were developed for a variety of turtle species, and have been used on E. blandingii across the geographic range [26-30,33,45-49]. The 5’ ends of the forward primers were all tagged with universal florescent tails following the methods of Blacket et al., (2012) (6-Fam, NED, PET, or VIC) so that markers could be multiplexed in 5 reactions rather than 15 (Table 1.1). The concentration of the forward primers and universal tails differed slightly to optimize allele calls (Table 1.1). PCR reactions were performed using a Qiagen Multiplex PCR Kit following manufacturer protocol. Thermocycling included a denaturation step at 95° C for 15 minutes, 35 cycles of denaturation at 94° C for 30 seconds, annealing at 56° C for 90 seconds, and elongation at 72° C for 60 seconds, and final elongation at 72° C for 30 minutes. After thermocycling, completed samples were removed and stored at -80° C. PCR was performed using 2 microliters of DNA (5- 50 nanograms per microliter) in a 10 microliter reaction. Gel electrophoresis was performed for at least six samples from each round of PCR on a 2% agarose gel to ensure amplification took place at expected product lengths. PCR products were then sent to the Yale DNA Analysis Facility or the Yale Keck DNA Sequencing Lab for fragment analysis. All samples were run on an Applied Biosystems 3730xl 96-Capillary Genetic Analyzer using the GelCo. Liz 500 size standard. Electrographs were analyzed using Geneious v. 11.1.5; all loci were scored and binned based on the expected number of repeats. Each locus was rerun at least once with a replicate sample to establish confidence in allele scoring. 18 Statistical Analyses 1.3.2 Descriptive Statistics GenAlEx 6.5 was used to check raw data for missing values, and to export data into different formats [55]. PopGenReport version 3.0.4 was used to determine the relationship between allele numbers and sample size per location, screen for null alleles, identify private alleles, and determine allelic richness with rarefaction [52]. Checking for null alleles helps increase confidence in genetic distance measures, since high frequencies of null alleles can cause inaccurate estimates of FST and other measures of genetic distance [56]. Private alleles can be an effective way of determining population structure since they are unique to a locality, however the detection of null alleles can be heavily biased by the sample size [57]. Allelic richness by rarefaction accounts for differences in samples size allowing a more accurate assumption of the presence of private alleles [57]. Overall, 492 samples were collected from 49 localities. Initially, PopGenReport was run with 19 all sites regardless of sample size, to determine the allelic richness with rarefaction, which was then used to determine the minimum sample size needed to properly determine allelic richness and private alleles. Some localities had large samples sizes (>70), they were randomly sub-sampled to a maximum of thirty individuals to avoid bias in comparison to localities with smaller samples [58]. Descriptive statistics were then run for all sites with at least ten samples and a maximum of thirty samples. DiveRsity Version 1.9.90 was used to calculate observed heterozygosity (HO), Nei’s expected heterozygosity (HE), FIS, FST, and D [59]. Measures of heterozygosity, along with allelic richness, contribute to the assessment of the amount of genetic variation within sample localities. Heterozygosity measures are used to calculate FIS, the inbreeding coefficient within sample localities, and FST, the traditional measure of differentiation among localities [60,61]. D (JostD) statistic is used for determining the relative differentiation of allele frequency among sub- divisions within localities [62]. Finally, a mixed linear model was used to determine the differences in allelic richness among sites and Tukey post-hoc test was used to assess pairwise differences. 1.3.3 Structure Analysis, Genetic Clustering Population structure based off genetic clustering was assessed using three programs with slightly different approaches: STRUCTURE version 2.3.4 [63], TESS3r version 1.1.0 [64], and Adegenet version 2.1.4 [65]. Population structure analysis is used for identifying populations and management units for a species without relying on sample location a priori. By using multiple methods, concordance in inferred clustering gives higher confidence in attributing results to a biological process. Additionally, genetic clustering is often hierarchical and using multiple methods can help to determine finer scale patterns among broader clustering schemes. Areas of disagreement in clustering between methods can also highlight areas were clear population structure is difficult to discern and may require additional sampling and analysis. 20 STRUCTURE Version 2.3.4 uses a Bayesian cluster analysis method utilizing Markov Chain Monte Carlo (MCMC) to group individuals into clusters using unlinked genetic markers [63]. STRUCTURE is a model-based approach that uses the frequencies of each allele at each locus to probabilistically assign individuals to a given population/cluster (K) based on shared allelic frequency while also avoiding departure from HWE and LDE within assumed populations [63,66]. Assuming an admixture model within STRUCTURE allows individuals to be assigned to one or more populations by utilizing a Q matrix that compares the proportion of an individual’s genome associated with a given assumed population [63,66]. Structure was run with a burn-in of 50,000 proceeded by 100,000 steps and was run 10 times for K values from 1 to 10. STRUCTURE was run with LOCPRIOR. LOCPRIOR is a function that incorporates the given sample site locations as a priori populations to determine if they influence the number of population clusters. Without LOCPRIOR sample location information is not considered. STRUCTURE results were viewed using STRUCTURE Selector [67]. STRUCTURE Selector allows the visualization of the STRUCTURE results in a bar graph format using the Puechmaille method (controls for uneven sampling size) and provides graphic representations of the Delta K and MedMeaK/MedMedK selection criteria [68]. The bar graph displays individual assignment to each given cluster represented by the different colors. Although Delta K methods are commonly presented, MedMeaK/MedMedK is more robust when sampling is uneven [68] and so only those values will be presented. 1.3.3 Structure Analysis, Genetic Clustering TESS3r also implements admixture models and MCMC but incorporates spatial trends and TESS3r also implements admixture models and MCMC but incorporates spatial trends and special autocorrelation into the prior distribution of the Q-matrix by allowing admixture of each individual to change across geographic space (individual ancestry)[66]. Individual variation in admixture also decreases at a regional and local level to allow for clines in all directions [66]. In 21 addition to the Q-matrix Tess3r also uses a G-matrix that includes the ancestral genotypic frequencies to conduct a combination of matrix factorization and quadratic programing to determine the number of clusters present in the given data set [64]. Tess3r also allows results to be represented over geographical space as well as in a traditional bar graph format [64]. This allows the incorporation of raster files and presents a unique visualization of the genetic clustering presented over geographical space [64]. Tess3r was run for K = 1 through 10, and the number of clusters (ancestral populations) was determined using cross-validation criteria. Adegenet was used to perform a discriminant analysis of principal components (DAPC). Adegenet uses a multivariate analysis approach rather than a model-based approach like STRUCTURE [69]. This allows Adegenet to avoid reliance on assumptions about population structure implicit in model-based approaches. Additionally, Adegenet can handle large amounts of data very quickly. Like a traditional principal component analysis (PCA), a (DAPC) provides a useful tool for examining clustering without relying on a Bayesian framework. DAPC does not require assumptions about populations like PCA [69]. The DAPC takes the benefits of both the traditional PCA and combines them with the genetic application of a Discernment Analysis (DA) while also overcoming the limitation of the traditional DA [69]. While a traditional PCA can be appropriate for examining genetic variation of individuals as well as variation among clusters, it lacks the ability to examine difference between clusters while ignoring the variability of individuals within those clusters, which is where the DA is effective [69]. DA however cannot handle the effects of linkage disequilibrium, and is not compatible with multi-allelic data [69]. DAPC uses a traditional PCA to transform the data to be compatible with DA to allow for between cluster analyses that ignore individual variability. Adegenet performs DAPC by using sequential K-means method and model selection to determine the appropriate number of clusters detected. 22 1.3.4 Migration Tracer v1.7.2 was used to calculate 95% confidence intervals and to view trace files from BayesAss [73]. [71]. BayesAss allows for within population frequencies to deviate from HWE and uses the temporary states of disequilibrium to make inferences about recent population gene flow [71]. Input files for BayesAss were formatted using Formatomatic [72]. BayesAss was initially run with 10,000,000 iteration of the MCMC chain utilizing a burn in of 1,000,000, and a sampling frequency of 1,000. These initial parameters did not allow for proper convergence of the Markov Chain so the number of iterations was increased to 1,000,000,000. Tracer v1.7.2 was used to calculate 95% confidence intervals and to view trace files from BayesAss [73]. Population sources and sinks were identified following the methods of Ishiyama et al. (2015), where the net immigration (immigration-emigration) was calculated for each pair of clusters and then averaged. A cluster with a negative net immigration is considered a source population whereas a cluster with a positive net immigration is considered a sink. 1.3.4 Migration An important aspect of understanding observed genetic composition is determining which populations have interacted with each other, and the extent and direction in which gene flow has occurred. Understanding migration patterns can help inform historic and current source-sink dynamics, which may make some populations less stable than others. Since we were primarily interested in movement between populations/management units due to their potential application in conservation, site localities were grouped into the four clusters identified by TESS3r (Table 1.5). TESS3r was chosen, because it produced conservative population clusters, and has been indicated to be most robust for detecting effects of multidirectional clines into clustering compared to STRUCTURE or DAPC [66]. Migrate version 4.4.3 was used to examine rates of historic migration between clusters to determine the degree to which clusters have historically interacted and to examine historic source-sink dynamics between clusters [70]. Migrate uses a Brownian motion approximation stepwise mutation model as well as Bayesian inference to determine effective population size and past migration rates [70]. Migrate assumes a migration matrix model that uses asymmetric migration rates and assumes different sub-population sizes with population divergence and admixture present. Migrate was run using a Brownian motion model with priors for theta (Θ) set from 0-1000. Simulations used one long chain with sample increments of 200 and recorded 5000 steps per chain after burn in of 1000 steps. To extend the length of the run and allow for greater convergence a multiple Markov chain statistical heating scheme was used with four chains with temperatures of 1.00, 1.50, 3.00, and 1,000,000.00 respectively with the swapping interval set to 1. BayesAss edition 3 (BA3; [71]) was used to examine more recent (past few generations) levels of migration between the same four TESS3r clusters used in Migrate. BayesAss takes a Bayesian approach to estimating recent migration using MCMC to estimate posterior probabilities 23 [71]. BayesAss allows for within population frequencies to deviate from HWE and uses the temporary states of disequilibrium to make inferences about recent population gene flow [71]. Input files for BayesAss were formatted using Formatomatic [72]. BayesAss was initially run with 10,000,000 iteration of the MCMC chain utilizing a burn in of 1,000,000, and a sampling frequency of 1,000. These initial parameters did not allow for proper convergence of the Markov Chain so the number of iterations was increased to 1,000,000,000. 1.3.5 Isolation by Distance and Geographic Isolation Geographic distance and watershed have both been identified as potential drivers of population structuring in E. blandingii [26,28]. A Mantel test was run using Adegenet in R to test for isolation by distance between individuals using 9999 permutation and pairwise FST. To test for effects of watershed on clustering, sites were grouped based on shared watersheds at the HUC-8 (cataloguing unit) and HUC-6 (accounting unit) levels (Figure 1.12). HUC-6 was the largest watershed level used because the groupings did not differ at the HUC-4 or HUC-2 levels. An AMOVA was then used to assess variation within and between sites at different watershed levels. Arlequin v. 3.5.2.2 was used to run the AMOVAs following the approach of Sethuraman et al. (2014), in which 16,000 permutations were used [75]. 24 1.3.6 Bottlenecking and Effective Population Size Population bottlenecks tend to occur when populations experience a large reduction in effective population size, and results in a reduction of the number of alleles present among polymorphic loci [76]. A loss of alleles leads to a direct loss in genetic diversity which can make a population more vulnerable to environmental change and stochasticity by constraining the available genetic plasticity [77]. When bottlenecks occur the number of alleles present in a given population tend to drop more quickly than the expected heterozygosity causing the expected heterozygosity to be greater than the observed heterozygosity (heterozygosity excess) [76]. BOTTLENECK version 2.2.02 uses each population and loci to examine the expected vs observed heterozygosity relative to the number of individuals and alleles used in each population [76,78,79]. Since Davy and Murphy ([80]) had similar sample sizes and numbers of locations and loci for a similar long lived species of turtle, the same BOTTLENECK parameters were used. BOTTLENECK was run using a two-phase model replicated 1000 times to check for evidence of population bottlenecking. Variance in the model was set at 12%, and single step mutation rate was set at 95% whereas multistep mutation rate was set to 5%. Since E. blandingii can be difficult to capture and have differing reproductive output based on age, it is important to understand the number of individuals in a population that are actually contributing to the next generation (effective population size, NE) [81,82]. NeEstimator Version 2.1 was used to assess the effective population size of each site. NeEstimator uses linkage disequilibrium under a molecular co-ancestry method to determine the NE and also provides jackknifed confidence intervals [83,84]. NeEstimator was run with the Linkage Disequilibrium random mating model. To evaluate the impact of sample size on NE estimation, NeEstimator was run using three different randomly generated sub-samples from the largest site (OH08): one with 25 the 10 individuals (our N cut off), one with 30 individuals (or N max), and one with the entire 77 individuals sampled. Bottlesim v. 2.6 was used to explore the impacts of potential future bottlenecks in the absence of gene flow [24]. Bottlesim was run for our largest population OH08 with the following assumptions: initial population size of 200 for all scenarios, a 1:1 sex ratio, dioecy with random mating, and diploid multilocus individuals. Longevity was set to 65, and age of maturity was set to 14 following Anthonysamy et al. (2018). 1.3.6 Bottlenecking and Effective Population Size In the first scenario, the population declines 50% over 200 years, and the second scenario saw a 90% population decline. Both scenarios were run with 1000 replicates. 1.4.1 Hardy Weinberg Equilibrium and Disequilibrium Out of 224 tests of HWE only GmuD40 showed deviation from HWE at one Out of 224 tests of HWE only GmuD40 showed deviation from HWE at one locality (OH 17). Since only one site exhibited deviation from HWE all loci were retained. GmuD28 and GmuD107 (p= <1.02e-19) showed significant linkage disequilibrium after Bonferroni correction. GmuD28 was removed from further analysis, and GmuD107 was retained. Descriptive and Frequency Based Statistics One hundred and sixty-nine alleles were detected across 14 loci representing 16 sample localities and a total of 313 individuals (Table 1.2). Of the 14 loci used for analysis, GmuD79 was monomorphic and uninformative leading it to be ignored for analysis. The number of alleles per locality ranged from 68 to 97 and increased according to the number of individuals sampled (Table 1.2). The number of alleles by sample size at a location appears to have reached or come close to an asymptote, with sites having around 20 individuals having nearly the same or more alleles than 26 the largest samples (n = 30) (Figure 1.3). MI-7 was an exception having around 15 more alleles than any other site. Of the 315 individuals and the 14 microsatellites used 1.51% of the genotype data was missing. The number of private alleles ranged from 0 to 7 for the sites with at least 10 samples (Table 1.2). Mean allelic richness ranged from 4.01 to 4.84 but no statistical difference (P>0.05) was observed between localities (Table 1.2). Observed heterozygosity across sites ranged from 0.58 to 0.65 (Table 1.2). FIS values indicated no evidence of inbreeding among sites, however there is potential outbreeding in MI-6 and MI-10 (FIS values below negative for the bootstrapped 95% confidence interval). Overall FST was 0.05 (pairwise FST = -0.01-0.15) and overall D was 0.08 (pairwise D = 0.00-0.17). The FST and D values showed a general pattern of increased differentiation by geographical distance from site to site Table (1.3). 1.4.2 Structure Analysis and Genetic Clustering Using LOCPRIOR, K values of 6 and 7 were identified for the MedMed/MedMeaK and MeaxMed/MaxMeaK methods respectively, at the 0.5 assignment threshold (Figure 1.5). The K=6 cluster scheme maintained the IN01, IN06, and IN07 cluster, the MI05, MI06, MI07, MI10, MI15, OH01, and OH18 cluster, the OH06, OH08, and OH09 cluster, and the OH16 and OH17 clusters (Figure 1.6). However K=6 increased the amount of admixture in OH01 and OH16 but reduced the admixture in OH13 grouping primarily with the OH06, OH08, and OH09 cluster. The K=6 scheme also introduced a new cluster (pink Figure 1.6) that gradually increases in degree of admixture west to east from Indiana and Michigan and reaching the largest degree of assignment in OH01, before gradually decreasing across the rest of Ohio (Figure 1.6). The K=7 cluster maintained the same overall clusters as K=6, with the exception of IN07 which clustered on its own (Figure 1.6). To visualize sub-clusters by localities, the STRUCUTRE results for K=6 were 27 displayed over geographic space since it produced more conservative estimates than K=7 (Figure 1.7). Only the results using a 0.5 threshold level are displayed since this is the standard, however Puechmaille (2016) recommends varying different threshold levels to make more stringent clusters with less extraneous groupings. We viewed the STRUCTURE results under a 0.8 threshold level which uncovered a K=4 for the MedMedK and MaxMedK and a K=3 for the MeMeaK and MaxMeaK. The K=4 clustering scheme produced by STRUCTURE was very similar to TESS3r but clustered OH17 on its own and OH16 with OH06-OH13. The K=3 maintained OH17 as its own cluster and grouped Indian, Michigan and the Ohio localities east of OH06 together. TESS3r identified four clusters using cross validation scores (Figure 1.8). TESS3r maintained a similar clustering pattern as STRUCTURE, but created a more gradual west-east cluster pattern. TESS3r clustered IN01, IN06, IN07, MI05, MI06, MI07, MI10, MI15, OH01, and OH18 as a cluster, OH06, OH08, OH09, and OH13 as a cluster, and OH16 and OH17 as a cluster refining the east to west trend indicated by STRUCTURE (Figures 1.6, 1.7, 1.8, & 1.9). The DAPC run through Adegenet identified five clusters (using BIC vs # of Clusters) (Figure 1.10). Cluster 1 contained 2.5-12.5 individuals from each locality in Ohio and Michigan, except OH17 which had fewer than 2.5 individuals assigned to cluster 1. 1.4.3 Migration Mean historic mutation scaled migration rates ranged from 6.90 to 20.20 (or 23.86 and 102.56 individuals per 4 generations) with the highest rate of average migration being from cluster 2 to cluster 4, and the lowest average migration rate being from cluster 1 to cluster 2 (Table 1.6 and Figure 1.13). Migrate results indicate near equal amounts of migration between clusters 1 and 3, and clusters 1 and 4, (Table 1.6 and Figure 1.13). Cluster 4 historically contributed about half of the amount of mean migration to cluster 2 as cluster 2 had to cluster 4 (Table 1.6 and Figure 1.13). Cluster 2 had nearly three times the historic genetic contribution to cluster 1 as cluster 1 had to cluster 2 (Table 1.6 and Figure 1.13). Mean recent migration rates ranged from 0.08 to 0.09 however all values crossed zero at the 95% confidence interval indicating little to no recent migration (Table 1.6 and Figure 1.13). The same general trend was seen in the mean recent migration rates as was observed in the historic analysis with the exception of migration between cluster 1 and 3 (Table 1.6 and Figure 1.13). Based on mean historic net immigration rates from Migrate, cluster two saw a net negative immigration rate implicating it as a source population at least in a historic sense to the other three clusters. Clusters 1, 3, and 4 all had positive net mean immigration rates (Figure 1.14). Looking at recent net immigration clusters 2 and 3 both had negative net immigration of about three and two individuals per generation, respectively (Figure 1.14). Whereas cluster 1 and 4 still saw a net increase in immigration of about three individuals per generation (Figure 1.14). 1.4.2 Structure Analysis and Genetic Clustering Less than two individuals from IN07 were also assigned to cluster 1(Figure 1.10). Cluster 2 contained the majority of OH17 (Figure 1.10). Cluster 3 contained the majority of the individuals from Indiana localities and 7.5 a few individuals from each Michigan localities (Figure 1.10). Cluster 4 and 5 were very similar except cluster 4 contained individuals from IN07, MI05, MI06, MI15 and no individuals from OH17 (Figure 1.10). 28 1.4.4 Isolation By Distance and Watershed Isolation The observed variance for the Mantel test was 0.69, and fell on the high end of the normal distribution of similarity indicating significant IBD in the dataset (Figure 1.11, r2 = 0.31, P <0.0001). AMOVA results showed statistically significant (p<0.05) differentiation by watershed 29 grouping at both the HUC6 and HUC8 levels (Table 1.4). As expected, the highest level of variance was explained at the within population level for both the HUC6 and HUC8 watershed clustering schemes (92.62% and 94.70%) (Table 1.4). Among groups had relatively low levels of variance explained (HUC6 = 4.10% and HUC8 = 3.4%), but both explained more variance than between populations within groups (3.28% and 1.87% respectively) (Table 1.4). 1.4.5 Bottlenecking, Effective Population Size No bottlenecks were detected in most localities, however a Wilcoxon test suggested heterozygosity excess in OH09. Conversely, sign tests indicated heterozygosity deficiency in IN01, MI06, OH01, and OH16 (Table 1.7). Effective population size estimates ranged from 7.9 to ∞ (Pcrit=0.05) and 8.5 to ∞ (Pcrit=0.02) (Table 1.7). However, effective population size estimates appear to be highly variable based on the sample size used to determine the estimate (Table 1.8). Sub-sampling from 77 individuals to 30 individuals seemed to have a much more marginal impact on estimations of effective populations size with the estimates varying by 30 to 40 individuals (for the Pcrit= 0.05 and 0.02 respectively) (Table 1.8). Over a 200 year period Bottlesim models indicated a ~9% loss of alleles under a constant population size, a ~17% loss of alleles under a 50% population reduction, and a >50% reduction of alleles in a 90% population reduction (Figure 1.4). The bottleneck models indicated a ~3% loss of alleles under a constant population size, a ~5% loss of HO under a 50% population reduction and a ~14% reduction of alleles in a 90% population reduction over 200 years (Figure 1.4). 30 31 Figure 1.2 Site Localities with greater than 10 turtles. 32 Figure 1.2 Site Localities with greater than 10 turtles. 33 Table 1.1 Summary of fifteen microsatellite loci run for all samples. Universal tail sequences were bound to the 5’ tail of the forward primer following Blacket et al., (2014). Microsatellites were grouped run together in a multiplex PCR reaction. 1.4.5 Bottlenecking, Effective Population Size Locus Size range (bp) Forward primer tail/label Forward primer sequence (5’-3’) Reverse primer sequence (5’-3’) Multiplex group Number of alleles Label Volume (ul) Forward Primer Volume (ul) Reverse Primer Volume( ul) GmuD55 175-220 Universal NED GTG ATA CTC TGC AAC CCA TCC TTG CAT TCA GAA TAT CCA TCA G 1 12 1.0 9.0 10.0 GmuD90 122-134 Universal FAM ATA GCA GGA CAA TTA CCA CCA G CCT AGT TGC TGC TGA CTC CAC 1 3 0.5 9.5 10.0 GmuD87 190-255 Universal VIC AAA CCC TAA GAC ATC AGA CAG G CAA ATC CAG TAC CCA GAA AGT C 1 10 1.0 9.0 10.0 GmuD88 115-171 Universal VIC AAC AAT GCC TGA AAA TGC A C AGG CTA CCT CTG AAA ATG CTG 2 12 0.5 9.5 10.0 Cp2 187-229 Universal PET C TCT AAG GGT TGC ACT TCT CAA A GAG GTG GCA TCA AAA CAT CAT 2 9 1.0 9.0 10.0 GmuD28 180-230 Universal NED AGC TGT TTG TCA TCA TAC ACT CTC TGG CCC TCA TGT TTT ATA AGT G 2 14 2.0 8.0 10.0 BTCA9 147-188 Universal FAM TAC TCA AGA TTT GAA GCA GAT ACA GGC TTG ATT CTA CTG TCA CTT AC 2 11 1.0 9.0 10.0 Eb19 97-110 Universal NED AGG GCT CTG AAG CAC TAA AGT AA GGC ACT GAA ATA AGA GAA AGT A 3 3 1.0 9.0 10.0 GmuD93 185-389 Universal VIC AGA CTC TCT TGA CCA GAT TTT CTC TCT GCC TTC TAT CAC TCT CCT G 3 2 1.0 9.0 10.0 GmuD107 189-209 Universal FAM GAC AAA CAT GAA CAG GAG AAG AG ATT AGA GAG ACA GAT AGA TAG GAC TTG 3 10 1.0 9.0 10.0 Eb17 94-117 Universal VIC CCC ACA AAA GTA GAC ACC TAT GGC ACT GAA ATA AGA GAA AGT A 4 6 1.0 9.0 10.0 GmuD121 138-178 Universal FAM GGCAAA TAT CCA ATA GAA ATC C CAA CTT CCT CGT GGG TTC AG 4 7 1.0 9.0 10.0 GmuD79 164-192 Universal PET GCC CTG TTC CAT TCT TAT TCT G ATC CCC TTA GTC GTC TCT TTT C 4 1 1.0 9.0 10.0 GmuD16 149-210 Universal NED ATC CCT GAA ATT TTG TGT GTT C TTT ACT CTA GAA GGG GCA ATC C 5 15 0.5 9.5 10.0 GmuD40 182-285 Universal PET T TTG TCA TAT CAT CCA CTC ACC TTT GTC ACA GAT GGG AAT TAG C 5 25 2.0 8.0 10.0 Table 1.1 Summary of fifteen microsatellite loci run for all samples. 1.4.5 Bottlenecking, Effective Population Size Universal tail sequences were bound to the 5’ tail of the forward primer following Blacket et al., (2014). Microsatellites were grouped run together in a multiplex PCR reaction. Table 1.2 Summary of descriptive statistics by locality. Listed statistics include number of turtles sampled (N), total number of alleles (A), number of private alleles (PA), mean allelic richness (AR with SE), mean observed Heterozygosity (HO with SE) expected heterozygosity (HE with SE), and inbreeding coefficient (FIS includes 95% confidence interval). Table 1.2 Summary of descriptive statistics by locality. Listed statistics include number of turtles sampled (N), total number of alleles (A), number of private alleles (PA), mean allelic richness (AR with SE), mean observed Heterozygosity (HO with SE) expected heterozygosity (HE with SE), and inbreeding coefficient (FIS includes 95% confidence interval). Site State County HUC6 HUC8 N A PA AR HO HE FIS IN-1 Indiana Lake 1 1 12 70 4 4.08 0.59 0.56 -.06 IN-6 Indiana Elkhart 2 2 15 75 3 4.27 0.63 0.60 -0.05 IN-7 Indiana LaGrange 2 2 22 92 7 4.77 0.64 0.64 0.00 MI-5 Michigan Washtenaw 4 6 20 84 1 4.42 0.61 0.61 -0.01 MI-6 Michigan Livingston 4 6 16 86 3 4.60 0.65 0.63 -0.03 MI-7 Michigan Livingston 4 6 30 97 1 4.84 0.64 0.66 0.03 MI-10 Michigan Oakland 4 6 11 74 0 4.40 0.62 0.61 -0.01 MI-15 Michigan Crawford 3 3 10 71 1 4.32 0.59 0.60 0.03 OH-1 Ohio Henry 4 5 11 81 6 4.75 0.58 0.62 0.06 OH-6 Ohio Lucas 4 7 30 87 1 4.44 0.61 0.62 0.03 OH-8 Ohio Ottawa 4 7 30 81 2 4.22 0.61 0.61 -0.01 OH-9 Ohio Ottawa 4 7 14 68 0 4.06 0.64 0.62 -0.04 OH- Ohio Ottawa 4 8 21 88 0 4.58 0.62 0.63 .01 OH- Ohio Erie 4 8 30 79 1 4.12 0.63 0.61 -0.04 OH- Ohio Erie 4 8 29 76 2 4.01 0.65 0.62 -0.04 OH- Ohio Williams 4 4 12 68 2 4.07 0.58 0.58 -0.00 34 Figure 1.3 Number of alleles versus sample size by locality. IN-01 IN-06 IN-07 MI-05 MI-06 MI-07 MI-10 MI-15 OH-01 OH-06 OH-08 OH-09 OH-13 OH-16 OH-17 OH-18 0 20 40 60 80 100 120 0 5 10 15 20 25 30 35 Figure 1.3 Number of alleles versus sample size by locality. 35 Figure 1.4 Observed alleles and observed heterozygosity over 200 years for three different 0 20 40 60 80 100 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 % OA Retained Years N=200-200 N=200-100 N=200-20 0 20 40 60 80 100 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 %Ho Years N=200-200 N=200-100 N=200-20 0 20 40 60 80 100 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 % OA Retained Years N=200-200 N=200-100 N=200-20 0 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 Years 0 20 40 60 80 100 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 %Ho Years N=200-200 N=200-100 N=200-20 Figure 1.4 Observed alleles and observed heterozygosity over 200 years for three different bottleneck scenarios. N = 200-100 Bottleneck resulting in 50% population decline. N = 200-20 Bottleneck resulting in a 90% population decline. N = 200-200 Bottleneck in population with stable population size. 36 Table 1.3 Summary of pairwise FST and D (Jost D) differentiation scores. FST below and D above. Bold values do not include 0 in the 95% confidence intervals. IN01 IN01 IN06 IN07 MI05 MI06 MI07 MI10 MI15 OH01 OH06 OH08 OH09 OH13 OH16 OH17 OH18 0 0.0284 0.0441 0.08 0.0945 0.0681 0.0541 0.0695 0.0683 0.1465 0.1727 0.1739 0.1418 0.1349 0.2093 0.0758 IN06 0.0448 0 0.0283 0.0556 0.0706 0.0548 0.0491 0.0507 0.0652 0.1395 0.1314 0.1446 0.0957 0.1112 0.1188 0.0543 IN07 0.0618 0.0451 0 0.0422 0.0683 0.0332 0.036 0.0281 0.0528 0.0972 0.1133 0.1243 0.0928 0.1049 0.1494 0.0297 MI05 0.0786 0.07 0.062 0 -1.00E-04 0.0052 2.00E-04 -4.00E-04 0.0117 0.052 0.0492 0.0549 0.042 0.041 0.0914 3.00E-04 MI06 0.0848 0.0844 0.0646 0 0 1.00E-04 -0.0035 0 2.00E-04 0.0497 0.0338 0.0322 0.0195 0.0441 0.1013 5.00E-04 MI07 0.0676 0.065 0.0418 0.0084 0.0021 0 -0.0051 0 0.0031 0.0422 0.0361 0.0258 0.0147 0.0284 0.093 0.0027 MI10 0.0643 0.0708 0.0573 0.0035 -0.0123 -0.0056 0 -0.0079 0.0038 0.0499 0.0495 0.0132 0.0112 0.0267 0.0995 0 MI15 0.0812 0.0708 0.0534 0.0023 0.0068 -0.001 -0.0126 0 0.0012 0.0308 0.0304 0.0187 0.0043 0.008 0.0595 0 OH01 0.0868 0.0689 0.0498 0.0206 0.0013 0.0075 0.0052 0.0025 0 0.0048 0.015 0.0185 0.0089 0.0175 0.0597 0.0106 OH06 0.1266 0.1103 0.0714 0.0467 0.0344 0.0304 0.0367 0.0324 0.0164 0 9.00E-04 0 2.00E-04 0.0089 0.086 0.038 OH08 0.1257 0.1062 0.0804 0.0421 0.0251 0.0311 0.0368 0.0341 0.0177 0.0054 0 0.0021 0.0087 0.0114 0.0929 0.0259 OH09 0.1236 0.1121 0.0862 0.0485 0.0305 0.0304 0.0355 0.0298 0.0274 -0.0011 0.0103 0 0 0.0109 0.0638 0.0243 OH13 0.1048 0.0884 0.0643 0.0325 0.0275 0.0142 0.0226 0.0096 0.017 0.0069 0.0148 0.0076 0 0.0092 0.0583 0.0085 OH16 0.1106 0.1034 0.0834 0.0435 0.0342 0.0246 0.0268 0.0178 0.0216 0.017 0.0256 0.0191 0.0114 0 0.068 0.0262 OH17 0.1488 0.1071 0.1055 0.0907 0.0798 0.0678 0.0842 0.0626 0.0615 0.0656 0.0715 0.0582 0.0548 0.0473 0 0.0516 OH18 0.0896 0.0661 0.0509 0.0015 0.0062 0.0111 -0.0014 0.0042 0.0253 0.0449 0.0367 0.0461 0.0293 0.0373 0.0721 0 37 Table 1.3 Summary of pairwise FST and D (Jost D) differentiation scores. FST below and D above. Bold values do not include 0 in the 95% confidence intervals. Figure 1.5 MedMeaK and MedMedK values reducing inclusion of extra clusters, estimated using the methods of Puechmaille (2016). Models are based on STRUCTURE using LOCPRIOR. Figure 1.5 MedMeaK and MedMedK values reducing inclusion of extra clusters, estimated using the methods of Puechmaille (2016). Models are based on STRUCTURE using LOCPRIOR. 38 Figure 1.6 Bar graphs showing inferred clusters by individuals by site. K = 6 inferred from MedMeaK (top); K = 7 inferred from MedMedK (bottom). Both models derived from STRUCTURE using LOCPRIOR. Localities listed from west to east. Figure 1.6 Bar graphs showing inferred clusters by individuals by site. K = 6 inferred from MedMeaK (top); K = 7 inferred from MedMedK (bottom). Both models derived from STRUCTURE using LOCPRIOR. Localities listed from west to east. Figure 1.7 Map displaying STRUCTURE results for K = 6 clusters over geographic space. 40 40 .7 Map displaying STRUCTURE results for K = 6 clusters over geographic space. Figure 1.8 Cross validation score for inferring number of clusters (top). TESS3r bar graphs showing inferred clusters by individuals by site for K=5 localities listed from west to east (bottom). 41 Figure 1.8 Cross validation score for inferring number of clusters (top). TESS3r bar graphs showing inferred clusters by individuals by site for K=5 localities listed from west to east (bottom). 41 Figure 1.8 Cross validation score for inferring number of clusters (top). TESS3r bar graphs showing inferred clusters by individuals by site for K=5 localities listed from west to east (bottom). Figure 1.9 Inferred clusters displayed over geographic space for K=5 . Note that large portions of Michigan were not sampled and this geographic interpretation does not show admixture. 42 42 Figure 1.9 Inferred clusters displayed over geographic space for K=5 . Note that large portions of Michigan were not sampled and this geographic interpretation does not show admixture. 1.9 Values of BIC for inferring number of clusters (top). DAPC scatter chart of fiv d clusters (middle). Individual assignment from given populations to inferred cluste (bottom). Figure 1.9 Values of BIC for inferring number of clusters (top). DAPC scatter chart of five inferred clusters (middle). Individual assignment from given populations to inferred clusters (bottom). 43 Figure 1.10 Mantel test for isolation by distance (IBD) (top) and regression line for individual genetic distance (Dgen) vs geographic distance (GeoDis), r2 = 0.31, P <0.0001 (bottom). Figure 1.10 Mantel test for isolation by distance (IBD) (top) and regression line for individual genetic distance (Dgen) vs geographic distance (GeoDis), r2 = 0.31, P <0.0001 (bottom). 44 Figure 1.11 HUC 8 (left) and HUC 6 (right) watershed levels. 45 Figure 1.11 HUC 8 (left) and HUC 6 (right) watershed levels. Table 1.4 AMOVA results displaying variance for the HUC6 (bottom) and HUC8 (top) watershed levels. HUC Level Source of Variation d.f. Sum of Squares Variance Components P-value %of Variation Fixation Indices HUC8 Among Groups 7 127.71 0.16 Va 0.00 3.42 0.03 (FCT) Among Pop within Group 8 63.72 0.08 Vb 0.00 1.87 0.02 (FSC) Within Pop 610 2620.34 4.30 Vc 0.00 94.70 0.05 (FST) HUC6 Among Groups 3 64.54 0.19 Va 0.00 4.10 0.04 (FCT) Among Pop within Group 12 126.89 0.15 Vb 0.00 3.28 0.03 (FSC) Within Pop 610 2620.34 4.30 Vc 0.00 92.62 0.07 (FST) Table 1.4 AMOVA results displaying variance for the HUC6 (bottom) and HUC8 (top) watershed levels. 46 Table 1.5 Locality grouping based on TESS3r cluster assignment. Table 1.5 Locality grouping based on TESS3r cluster assignment. TESS3r Cluster N Sites Cluster 01 49 IN01, IN06, IN07 Cluster 02 108 MI05, MI06, MI07, MI10, MI15, OH01, OH18 Cluster 03 97 OH06, OH08, OH09, OH13 Cluster 04 59 OH16, OH17 47 Table 1.6 Mean historic migration calculated through Migrate, recent migration rate from BayesAss. Migrate indicates the mean mutation-scaled migration rate with 95% CI. BayesAss displays mean migration rate with 95% CI derived from migration rate by population size. TESS3r Cluster Mean Historic Migration Rate Mean Recent Migration Rate Cluster 01- Cluster 02 6.90 (±6.56) 0.08 (±0.12) Cluster 01- Cluster 03 16.09 (±8.25) 0.08 (±0.12) Cluster 01- Cluster 04 8.51(±6.81) 0.09 (±0.13) Cluster 02- Cluster 01 16.76 (±8.40) 0.08 (±0.12) Cluster 02- Cluster 03 16.81 (±8.75) 0.08 (±0.13) Cluster 02- Cluster 04 20.20 (±8.89) 0.09 (±0.13) Cluster 03- Cluster 01 15.73 (±8.12) 0.08 (±0.13) Cluster 03- Cluster 02 10.37 (±9.68) 0.08 (±0.12) Cluster 03- Cluster 04 17.45 (±8.54) 0.09 (±0.13) Cluster 04- Cluster 01 10.55 (±7.75) 0.08 (±0.12) Cluster 04- Cluster 02 10.06 (±7.41) 0.08 (±0.13) Cluster 04- Cluster 03 12.37 (±7.31) 0.08 (±0.13) Table 1.6 Mean historic migration calculated through Migrate, recent migration rate from BayesAss. Migrate indicates the mean mutation-scaled migration rate with 95% CI. BayesAss displays mean migration rate with 95% CI derived from migration rate by population size. 48 Figure 1.12 Mean historic migration rate (top), mean recent migration rate (bottom). Scaled arrows indicate direction and magnitude of migration. e 1.12 Mean historic migration rate (top), mean recent migration rate (bottom arrows indicate direction and magnitude of migration. Figure 1.12 Mean historic migration rate (top), mean recent migration rate (bottom). Scaled arrows indicate direction and magnitude of migration. 49 e 1.13 Mean historic and contemporary net immigration. Contemporary uses indivi per generation, while historic uses mutation-scaled migration rate. -12 -10 -8 -6 -4 -2 0 2 4 6 8 Cluster 1 Mean Historic Net Immigration -5 -4 -3 -2 -1 0 1 2 3 4 5 1 Mean Contemporary Net Immigration -12 -10 -8 -6 -4 -2 0 2 4 6 8 Cluster 1 Mean Historic Net Immigration Mean Historic Net Immigration Cluster 1 Figure 1.13 Mean historic and contemporary net immigration. Contemporary uses individuals per generation, while historic uses mutation-scaled migration rate. -5 -4 -3 -2 -1 0 1 2 3 4 5 1 Mean Contemporary Net Immigration -5 -4 -3 -2 -1 0 1 2 3 4 5 1 Mean Contemporary Net Immigration Figure 1.13 Mean historic and contemporary net immigration. Contemporary uses individuals per generation, while historic uses mutation-scaled migration rate. 50 Table 1.7 Summary of Bottleneck tests and effective population size estimates with 95% confidence intervals. Site BOTTLENECK Effective Population Size Wilcoxon test Sign test Mode shift Ne 0.05 95% CI Ne 0.02 95% CI IN-1 P = 0.892 P = 0.049 none 53.3 15.3 - ∞ 97.5 23.8 - ∞ IN-6 P = 0.812 P = 0.271 none 450.0 33.1 - ∞ ∞ 69.0 - ∞ IN-7 P = 0.729 P = 0.473 none 323.9 55.5 - ∞ 632.7 83.4 - ∞ MI-5 P = 0.945 P = 0.069 none 71.6 31.4 - ∞ 730.4 77.3 - ∞ MI-6 P = 0.996 P = 0.002 none ∞ 53.5 - ∞ ∞ 68.4 - ∞ MI-7 P = 0.596 P = 0.157 none ∞ 448.0 - ∞ ∞ 242.3 - ∞ MI-10 P = 0.607 P = 0.452 none ∞ 44.3 - ∞ ∞ 70.9 - ∞ MI-15 P = 0.793 P = 0.224 none 1770.8 27.4 - ∞ 1770.8 27.4 - ∞ OH-1 P = 0.996 P = 0.034 none 7.9 4.4 – 13.8 8.5 5.6 – 13.3 OH-6 P = 0.446 P = 0.498 none ∞ 132.9 - ∞ 350.4 84.6 - ∞ OH-8 P = 0.607 P = 0.477 none 195.5 68.1 – ∞ 262.4 80.3 – ∞ OH-9 P = 0.040 P = 0.339 none 106.2 25.0 - ∞ ∞ 41.6 - ∞ OH-13 P = 0.473 P = 0.521 none 54.2 27.9 – 270.7 202.8 59.0 – ∞ OH-16 P = 0.905 P = 0.042 none 14.6 11.1 – 19.8 22.1 16.8 – 30.5 OH-17 P = 0.729 P = 0.259 none 10.9 8.4 – 14.1 14.0 10.9 – 18.4 OH-18 P = 0.661 P = 0.156 none 42.1 14.5 – ∞ 50.1 18.2 - ∞ 51 51 Table 1.8 Comparison of effective population size estimates (Ne) for one site subsampled to different population sizes with 95% confidence intervals. Site N Ne 0.05 95% CI Ne 0.02 95% CI OH-8 10 772.0 22.7 - ∞ 772.0 22.7 - ∞ OH-8 30 195.5 68.1 – ∞ 262.4 80.3 - ∞ OH-8 77 137.1 87.5 – 271.8 189.1 121.4 – 380.9 Table 1.8 Comparison of effective population size estimates (Ne) for one site subsampled to different population sizes with 95% confidence intervals. 52 52 Table 1.9 Comparison of descriptive statistics for E. blandingii. * HO reported rather than HE. Table 1.9 Comparison of descriptive statistics for E. blandingii. * HO reported rather than HE. Species Location Pairwise FST AR HE Sites Loci N Reference E. blandingii Nova Scotia 0.04 – 0.12 - 0.45 – 0.54 3 5 110 Mockford et al. (2005) Rangewide 0.00 – 0.47 - 0.45 – 0.71 12 5 200 Mockford et al. (2007) NE, IA, MN, IL 0.01 – 0.47 - 0.49 - 0.79 12 8 202 Sethuraman et al. (2014) Ontario 0.04 – 0.10 4.8 – 5.3 0.59 – 0.66 12 4 97 Davy et al. (2014) NY and southeast Ontario 0.01 – 0.38 0.31 – 0.63 5 7 115 McCluskey et al. (2016) WI 0.00 – 0.18 0.59 – 0.70 18 14 389 Reid et al. (2017) northeast IL 0.02 – 0.10 3.6 – 3.9 0.51 – 0.64* 6 14 186 Anthonysamy et al. (2018) IN, OH, MI 0.00 – 0.15 4.01 – 4.84 0.56 – 0.66 16 14 313 This study 53 53 Discussion In order to provide further insight into E. blandingii conservation, levels of genetic variation and population clustering in localities across Indiana, Michigan, and Ohio were examined. Additionally distance and watershed were correlated with genetic connectivity among populations. Microsatellite analysis of E. blandingii from 13 loci were examined across Indiana and the Lake Erie marshes of Ohio and Michigan. Overall genetic differentiation between localities was low across the study region whereas within locality diversity was relatively high (Tables 1.2 & 1.3). Despite low differentiation between localities, population structure was observed (Figures 1.6, 1.8, & 1.9). Pairwise FST scores as well as AR and HE observed were very similar to other studies looking at E. blandingii (Table 1.9). The relatively high genetic diversity observed across Ohio, Indiana, and Michigan is comparable to range-wide diversity (Tables 1.9). An AMOVA and a Mantel test were also used to assess the influence of geographic distance and watershed boundaries on genetic differentiation (Figures 1.10 & 1.11). Significant isolation by distance and isolation between watersheds at both the HUC6 and HUC8 levels were detected through a Mantel test and an AMOVA respectively (Figure 1.11 & 1.11). Despite the lack of observable bottlenecking, and the relatively high degree of observed genetic diversity, the predicted loss of alleles in the next 200 years by Bottlesim would imply that most localities within this region are likely less secure than then may be assumed (Tables 1.2, 1.6, and 1.9 and Figure 1.4). The inability of BOTTLENECK to detect bottlenecks in a long lived species, and the lack of recent gene flow would also indicate more genetic vulnerability than would otherwise be expected [24,80]. 54 54 1.5.1 Population Structure Across localities, little differentiation among populations was found (FST= 0.05, D=0.08), though there was an observed trend of increasing differentiation by geographic distance (Table 1.3), with the greatest pairwise differentiation occurring between IN01 (western most locality) and OH17 (second most eastern site) (FST = 0.15, D= 0.21, Table 1.3). The number of genetic clusters identified through each method ranged from K=4 to K=6 (STRUCTURE, TESS3r, and DAPC). Most comparable studies examining E. blandingii structure that utilized STRUCTURE employed the delta k method for determining the number of clusters [27-29]. Only Reid et al., (2017) reported both the MedMeaK and delta K clusters. Puechmaille (2016) argues that the MedMeaK and MedMedK interpretation of determining clusters is likely more accurate for detecting genetic clusters when sampling effort is not equal across localities. Since differentiation across sites was generally low, fewer inferred clusters likely captures the overall trend of population deviation. Higher K values from STRUCTURE and DAPC are representative of hierarchical clustering or sub-structure that fall within the broader clusters identified by TESS3r. OH17 was consistently identified as its own cluster by STRUCTURE (even using K=4 with increased assignment threshold) and DAPC, suggesting that this grouping represents some ecological significance. Some populations in New York and Illinois showed greater differentiation and additional population structure than would be expected based on the geographic distance (or lack thereof) between them, which is thought to be attributed to glacial retreat and expansion as well as impacts of the watershed on the dispersal of the turtles [7,25,28]. Due to the similar geographic and glacial history, I expected to find similar degrees of differentiation and structure across Indiana, Michigan and Ohio. Although the differentiation based on FST and D values did not necessarily support this 55 hypothesis, the K values of the STRUCTURE run, TESS3r and DAPC show evidence of this degree of population differentiation. Francois and Durand (2010) have demonstrated that Bayesian approaches that incorporate geographic priors (TESS3r and STRUCTURE LOCPRIOR) are more advantageous at detecting accurate population structure. Additionally, Francois and Durand (2010) demonstrated that TESS3r does a better job at capturing the geographic driven clustering than STRUCTURE. TESS3r and STRUCTURE with LOCPRIOR have been shown to effectively predict population structure in organisms that have experience high degrees of glacial driven expansion and contraction [65]. 1.5.1 Population Structure Since Tess3r produced the most conservative estimates (with the exception of increasing assignment threshold) and seems to be the most robust method for estimates of population clustering I suggest that the four identified clusters from TESS3r be considered management units for the purpose of conservation though it is worth noting that differentiation was generally low. It should also be noted that northwest Michigan was heavily under sampled with only one locality being included and Indiana may share population structure with un-sampled localities from Illinois. That being said, the identified management units should apply to the Lake Erie Marshes of Ohio and southeast Michigan. All observed K values, regardless of the method employed, provide support to prior findings that E. blandingii has higher levels of between locality differentiation east of the Appalachians compared to west of the Appalachians, (FST, D) but are not in panmixia across the Midwest and Great Lake Regions (Table 1.9) [25-30]. Similar to other studies, isolation by distance and watershed were observed [26,28]. Large historical migration driven by glacial dynamics are thought to have increased genetic admixture across the Midwest and Great Lakes region which may also dampen detectable distance-driven isolation [28,38]. Similar to Sethuraman et al. (2014) the majority of variance was observed within 56 localities, but a significant signature of watershed was detected by AMOVA analysis. The watershed signature may be partially explained by effect of distance especially within large watershed basins. Utilizing the clusters identified by TESS3r, Migrate helped to further explain likely historic migration patterns. Average historic migration rates tended to show a general trend of movement out of cluster 2 and into the other three clusters (Table 1.6 and Figure 1.13). The movement out of cluster 2 could in part be explained by the settlement pattern and subsequent draining of wetland in northwest Ohio and southeast Michigan [85]. As the Great Black Swamp (which stretched across northwest Ohio into northeastern Indiana) was divided by roads and railroads, and eventually drained in the mid to late 1800’s it opened up northeast Ohio, southeast Michigan, and northeast Indiana to increased settlement and land modification [85]. It is possible that as this region opened up and was converted to productive agricultural land that the E. blandingii in that region (Cluster 2) would be driven to remnant wetlands to the east and west which would explain the observed pattern of movement out of cluster 2 [85]. 1.5.1 Population Structure Further investigation into migration patterns and population cluster at a range-wide scale would help to further explore the validity of this trend. Mean recent migration estimates from BayesAss showed the same general trend in migration rates between clusters as was seen in historic migration patterns, although recent migration crossed zero at the 95% confidence interval indicating little to no actual immigration. Although the observed genetic differentiation between localities does not support a finding of recent loss of gene flow, the long generation time of E. blandingii will likely make it difficult to observe the reduction of gene flow for some time (1 to 2 generations or longer Figure 1.4). The reduction to little or no migration in the past few generations (150 to 250 years) compared to historic rates may implicate 57 the well documented effects of urbanization and habitat fragmentation as the culprit [10,15,18]. However differences in migration estimation methods between the coalescent-based Migrate and the disequilibrium-based BayesAss makes it difficult to interpret the validity of such a comparison [86]. The largest cluster, cluster 2, was identified as a source by both the historic and recent migration rates, and the second largest cluster, cluster 3 was identified as a source population by the recent migration rates (Figure 1.14). Large reductions of average migration rates from clusters 2 and 3 to cluster 1 and 4 could potentially set up conditions for bottlenecking within those clusters. Since large portions of Michigan were not sampled and the clustering scheme covered large geographical areas, the mean migration estimate should be interpreted with caution. 1.5.2 Genetic Status Within Populations The lack of observed bottlenecking does not necessarily mean bottlenecking has not occurred (or is not occurring) since BOTTLENECK poorly detects population bottlenecks in long lived species [24,80]. Studies on the similarly long-lived ornate box turtle (Terrapene ornata) [24] and spotted turtle (Clemmys guttata) [80] had similar difficulty detecting population bottlenecks using traditional methods. Kuo and Janzen (2004) also found that once bottlenecks occur they may result in rapid genetic decline. Effective population sizes for E. blandingii were as high as ∞ for four populations, but these estimates are likely biased by the sample sizes of the localities (Tables 1.7 and 1.8). Most populations of E. blandingii are thought to be small and disjunct which contradicts our estimates [2]. Citizen science based population estimates for this same locality found an estimated female population size of 87 individual E. blandingii or a population size of 174 adult individuals 58 assuming a 1:1 sex ratio [87]. Comparison of different samples size effects on Ne estimates indicates that localities with less than 30 individuals likely do not allow for accurate estimations (Table 1.8). As our sample size increase our estimates and confidence interval became closer and closer to the population estimates of Cross et al., (2021). Additional replicates with other large populations would help determine the sample size necessary for more accurate estimates of effective population size. The projection of genetic variation into the future using Bottlesim suggests that large reductions in population size can result in drastic loss of genetic diversity in isolated populations of E. blandingii (Figure 1.4). It should be noted that this model does not account for differential reproductive success or survival based on the age of the individuals, environmental stochasticity, or low recruitment, features seen in E. blandingii [2,4,81,88]. Excluding life stage dynamics in Bottlesim models likely leads to under-estimation of the genetic impacts resulting from population reductions in the absence of gene flow. Population Viability Analysis (PVA) in Illinois by King et al. (2021) included environmental stochasticity and showed that inclusion of environmental catastrophes increased the population size threshold to maintain genetic diversity (50 to 110 without, and 110 to 200 with) and reduce extinction risk (20 to 50 without, and 50 to 200 with). Furthermore, the Bottlesim results indicate that populations around 200 individuals will show a steady loss of genetic diversity over 200 years even with a constant population size. 1.5.2 Genetic Status Within Populations Since most localities in our study appear to be small and isolated, and likely have E. blandingii estimates far below 200 individuals, it is possible they have begun to lose a great degree of genetic diversity which is not yet observable due to long lifespan [24]. The PVA models used by King et al. (2021) corroborate the loss of genetic diversity and a high risk of extinction in scenarios where starting population size was small (less than 50 adults). 59 In that study, fifty individuals was used as a cut off for the minimum number of adult breeding E. blandingii necessary (assuming a 1:1 sex ratio) to reduce extinction risk and maintain a high degree of genetic diversity in the presence of environmental stochasticity. Ne tends to be much lower than the population census size for wild populations (~10% across taxonomic groups) since Ne accounts for sex ratio, number of adults, genetic makeup and population size [90]. However our best estimate of Ne (137.1 for OH08) was very close to the adult census size (174 assuming a 1:1 sex ratio) from that same locality as estimated by Cross et al. (2021). Assuming a similar relationship between adult census size and Ne as was observed for OH08 only four localities of the 16 included in this study fall below this threshold for the number of adults to prevent extinction set by King et al. (2021) for estimated Ne and two were at this or near this threshold (Table 1.7). Using the most conservative estimates of Ne (the lower 95% confidence interval) 11 of the 16 sites included fall below the 50 individual cut off (Table 1.7). Additionally, the best Ne estimates for our largest locality within the study area had an effective population size below 200 individuals indicating most actual effective population sizes are likely far below this. It is also worth noting that based on our estimates from OH08, small sample size seems to inflate estimates of Ne and only five of the sample localities included had enough individuals to provide reasonable estimates (Tables 1.2, 1.7, and 1.8 ). 1.5.3 Management Implications Although within population diversity appears to be high, this does not mean populations are ecologically secure. Based on the Bottlesim result, many localities within this region have likely seen substantial population declines and are vulnerable to lose up to 50% of the observed genetic diversity in the next 200 years (Figure 1.4). Effective population size estimates are heavily 60 influenced by sample size tending to overestimate when less than thirty samples are included, for this reason Ne estimates should be viewed conservatively focusing on the lower end of the 95% confidence interval (pcrit <0.05) for populations that had less than thirty samples (Tables 1.7 & 1.8). 1.8). King et al., (2021) estimated adult population sizes necessary to minimize extinction probability and maintain 95% of the genetic diversity in E. blandingii using genetically informed population viability analysis. Based on the estimates of King et al., (2021) an adult population size of at least 20 individuals is required to minimize (<5%) extinction risk and at least 50 individuals are needed to maintain 95% of the genetic diversity of the next 100 years in the absence of stochastic events. In the presence of stochastic events at least 50 individuals are required to minimize extinction risk and 110 are needed to maintain 95% of the genetic diversity [89]. Assuming that most localities within our study have little to no gene flow due to fragmentation and urbanization and maintain a similar relationship between Ne and adult census size as was observed in OH08 (Table 1,8 and [87]) only 9 of the 16 localities included produced conservative Ne estimates > 20 threshold and only 5 meet the > 50 individual threshold (Table 1.7). Only two localities have conservative Ne estimates above the 110 threshold indicating that in the presence of stochastic events that could increase mortality, only 2 of the 16 localities produced conservative estimates minimizing loss of genetic diversity and only 5 are large enough to minimize extinction risk (Table 1.7). Population and habitat suitability modeling for E. blandingii under different climate change scenarios indicates that the amount of available suitable habitat is likely to shift north with a decline in habitat connectivity, which argues for targeting a threshold of adult individuals > 110 for each locality to prevent genetic loss and extirpation [91,92]. Since 110 61 individuals per locality may not be a realistic goal, a minimum of 50 individuals per locality could help to reduce extinction risk, particularly if gene flow is maximized through translocation [89]. Additional population viability analysis conducted by Ross et al., (2020) indicated that head- starting individuals could help to stave off extinction and prevent local extirpations. Head-starting a minimum of 50 eggs per year (under an assumed 0 to 1 age mortality rate of 92.8% [94]) can help to prevent extinction, whereas 100 eggs per year can increase population growth [93]. Head-starting can also help to increase juvenile survival and lead to increased recruitment [95,96]. 1.8). Carstairs et al., (2019) found that although head started individuals had an acclimatization period of 1 to 2 years that resulted in reduced growth, movement, and survival they had nearly three times the probability of surviving to age 10 compared to wild hatched turtles. Thompson et al. (2020), found that in the long term head-starting can increase the body size distribution of individuals within a population, increasing the number of juveniles and ultimately leading to recruitment of reproductive adults. Although head-starting would need to be maintained until populations could naturally reach sustainable recruitment rates of at least 50 individuals a year, it provides a viable strategy for minimizing extinction risk, especially in small, isolated localities [93]. The observed genetic clusters provide a basis for population management units. These management units should be used as a guideline for determining which localities should be used for translocations or head-starting at other localities. When possible, limiting translocations to localities that share a cluster under the K=7 scheme should be maintained, however since differentiation is generally low using the K=4 cluster scheme allows for greater leeway and should be maintained when there are not an ample number of individuals from localities sharing a K=7 cluster. Additionally, the presence of IBD and the isolation between watersheds implies that when possible individuals should be translocated from nearby localities within the same HUC6 or HUC8 62 (when staying within HUC8 is not feasible) watershed. Aiming to maintaining connectivity between localities within the life time home range size and maximum movement range of E. blandingii could also act to maintain genetic diversity and increase effective population size by increasing the number of breeding individuals able to freely breed [41]. Since roads have been found to be a significant source of mortality in E. blandingii, causing as many as 61 mortalities over 4 years at a single locality in Ontario, it would make sense to target high traffic roads within a 2 kilometer distance (based on length of breeding and nesting movements) from known E. blandingii localities for reducing mortality and allowing gene flow [18,41,97]. 1.8). Reducing the effect of roads and urbanization to promote gene flow could be accomplished in a number of ways, from creating buffers of natural landscapes around localities, utilizing artificial crossing structures such as well-maintained exclusion fences and culverts interspersed based on home range size, or providing supplemental artificial nesting habitat to provide an alternative to crossing roads [41,98]. Conclusions Observed levels of within locality genetic diversity and the lack of bottlenecking imply a level of genetic security within the Great Lakes Region. However, the observed diversity may be representative of remnant population structure and historic gene flow masking ongoing or developing bottlenecks and a potential forthcoming decline in genetic diversity [24]. Despite the lack of differentiation between localities within each state, as well as between localities across the study area, a minimum of four genetic clusters were identified. Although these clusters do not necessarily represent localities connected by current gene flow, they provide guidance for genetically significant management units. As many as seven genetic clusters were observed depending on method, but a hierarchical clustering scheme was observed across methods 63 (except for OH17). Increasing the number of clusters followed the same general assignment scheme when using fewer cluster and provides insight on differentiation within those larger groupings. These higher levels of clustering help to inform within unit diversification, but in light of the low levels of differentiation observed across the study (Pairwise FST between 0 and 0.15) are likely less genetically relevant. A Mantel test and AMOVA’s indicate that part of the detected genetic clustering is explained by a combination of watershed boundaries and distance between localities. Although average migration rates lack resolution without increased sampling across the region (particularly northwest Michigan) the detected reduction in mean historic vs mean recent migration rate between genetic clusters would imply urbanization has had an effect on gene flow between identified clusters. My findings support the currently reported genetic trends observed in E. blandingii across their range; although genetic differentiation is low between localities, there is genetic structure [25- 30]. Further sampling and analysis and a range wide scale using microsatellite markers would help to further understand the genetic trends and historic drivers of population structure within E. blandingii. 64 Introduction In order to further understand the complex patterns that have driven the observed genetic composition and population structure, it is important to understand how a species moves across the landscape in reference to different geographic and geomorphic features. The practice of correlating genetic differentiation with traditional landscape ecology to look for genetic discontinuities caused by environmental features has come to be known as landscape genetics [99]. Landscape genetics takes advantage of advances in molecular genetics, statistical modeling, and computing to help further the exploration of the effects of landscape features and geographic barriers on functional gene flow and population dynamics that drive genetic clustering [99,100]. In particular, landscape genetics has provided a new approach to understand the effects of ecological succession and urban modification on both flora and fauna gene flow and clustering [101,102]. Landscape genetic approaches also prove effective in identifying specific landscape features that can act as barriers for gene flow [103]. More complex modeling utilizing high quality landscape data and fine scale spatial autocorrelation allows for the identification of movement corridors, as well as optimization of features that drive landscape resistance that can be utilized for targeted habitat conservation [104-108]. There is a large body of work focusing on the spatial ecology and landscape use of E. blandingii [6,8,11,14,16,109,110]. E. blandingii are known to use a variety of wetland habitats from season to season including open marshes, ponds, lakes, ephemeral wetlands, creeks, streams, and ditches [6,8,11,14,16,111]. Habitat use also tends to vary slightly among regions, complicating precise delineation of suitable habitat [2]. In general, E. blandingii tend to utilize shallow vegetated 65 wetlands, and at a macrohabitat level show selection of wetlands over other water bodies or uplands [2,8,16]. Despite selection of wetland habitat, Joyal et al. (2001) noted that E. blandingii will use upland habitat extensively for nesting, dormancy, and dispersal movements. Focusing on habitat selection in a mostly pristine location in Ontario, Canada, Edge et al. (2010) found no selection in microhabitat use indicating that E. blandingii was likely not overly selective of habitat when there is an abundance of open resources and low levels of landscape modification. Conversely, urbanization and habitat modification has well documented impacts on E. blandingii persistence and habitat availability [10,15,18]. Introduction For example, in two wetlands located within agriculture-dominated watersheds that are heavily invaded by European common reed (Phragmites australis), Markle and Chow Fraser (2018) found selection for aquatic and mixed organic marshes and locally avoidance of patches of European common reed. Beyond movement-based landscape analysis, prior studies utilizing microsatellite markers in E. blandingii have inferred a mixture of historic landscapes and life history affecting gene flow and genetic clustering. Since E. blandingii has long lifespans (up to 83 years in the wild) accompanied with long generation times and increasing reproductive output with age, it is possible that genetic variation will not have had time to respond to contemporary landscape change which isolates populations [22,81,113]. Davy et al. (2014) indicated low levels of historic migration between clusters in Ontario indicating a pre-settlement driver of genetic units across the landscape other than the modern urban disconnect. Anthonysamy et al. (2018) found no significant relationship between E. blandingii population structure and geographic distance indicating that landscape and or habitat features likely drive gene flow. Conversely Reid et al. (2017) saw a significant relationship between roads and population differentiation in E. blandingii in Wisconsin using a transect-based landscape metric. 66 In order to account for the lag in genetic changes associated with the life history of E. blandingii, and to determine drivers of gene flow and differentiation within the Great Lakes region, it is useful to characterize landscapes using both historic and contemporary features. The comparison of historic and contemporary population dynamics has the potential to help determine where gene flow has been restricted and where populations may experience decreases in genetic diversity or bottlenecks in the coming years. Furthermore, such analyses provide opportunities for identifying corridors of habitat that connected populations in the past to identify areas that would benefit most from habitat restoration. Publicly available GIS data can be used to examine elevation and pre-settlement land class features which can be used to infer the conditions that would have been encountered by E. blandingii as they moved across the landscape prior to contemporary landscape modification [114]. Although a transect-based landscape metric is simple to do and can quickly make inferences about movement across a landscape, it lacks the complexity of the actual landscape the turtles experience traversing the habitat. Introduction Peterman (2018) instead implemented least cost paths of random walk method using CIRCUITSCAPE to rank landscape resistance faced by individuals scored by using a genetic algorithm to optimize the resistance surface [108,115]. This approach removes the need for a priori inference or expert opinion which could potentially bias landscape models of gene flow [108]. Here, contemporary and historic landscape features within three Lake Erie watershed marshes in Michigan are analyzed to: (1) optimize landscape resistance surfaces to better understand the influence of landscape feature on movement, (2) determine the potential driving effects of landscape resistance on gene flow, and (3) compare the influence of contemporary 67 landscapes versus historic landscapes that are likely to have shaped standing genetic variation among populations of E. blandingii. landscapes versus historic landscapes that are likely to have shaped standing genetic variation among populations of E. blandingii. 2.2.1 Site Description Three localities within Livingston County in Michigan (MI6, MI7, and MI17) were chosen due to their close relative distance from each other as well as available sample size, and landscape heterogeneity (each about 10 kilometers from each other). All three of these localities are dedicate state recreation areas making their use primarily for outdoor recreation. MI06 encompasses an area of 11,000 acres, MI07 an area of 4,947 acres, and MI17 an area of 20,500 acres. Currently all three localities are dominated by deciduous forest, and woody wetlands with several kettle lakes and other bodies of open water interspersed. MI06 and MI17 as well as MI07 and MI17 are separated by mix of agricultural land and low intensity developed urban spaces. MI06 and MI07 are separated by higher density and more intensely developed urban area in addition to sparse agricultural land. The pre-settlement landscape of this area was primarily deciduous forest, scrub shrubs, and wood wetlands with interspersed grasslands and open water kettle lakes. 2.2.2 Creating Resistance Surfaces Initial runs utilized the full dataset presented in Chapter 1, however this proved to be computationally prohibitive and likely minimally informative since isolation by distance was found across populations. To focus in on landscape influence and reduce the impacts of distance, 68 the three closely clustered localities in Michigan described above had a reasonable sample size (n = 59) and provided relatively high landscape heterozygosity compared to the rest of the study. All resistance surfaces were generated at or resampled to a 30 meter by 30 meter cells to allow for timely computation. Resistance surfaces were created in ArcMap version 10.7.1 using publicly available data [116]. The 2016 national land cover database map (NLCD) was used for contemporary landscape [117]. A historic land class map was developed from pre-settlement vegetation maps from Michigan Natural Features Inventory (MNFI) [118,119]. The pre-settlement vegetation map was re-categorized to follow the same land class features as the NLCD map. The re-classified historic land class shapefile was then converted into a 30 meter by 30 meter raster file. A 1 meter by 1 meter digital elevation model (DEM) was accessed through the U.S. Geological Survey (USGS) [120] an used to develop a Topographic Position Index (TPI) which is a measure of relative elevation and better represents fine scale elevational changes that an organism would experience moving across the landscape. Landscape surfaces were selected based on prior literature reporting on E. blandingii habitat use, movement, and fragmentation [2,11,14]. Pre- settlement maps were reclassified to group similar habitats into the same land class categories used by the national land cover database map to make the historic land class layer comparable to the modern land class map. Since E. blandingii is believed to utilize ephemeral wetlands, as well as ditches to aid in seasonal movement, a TPI was generated as a proxy layer for examining wetland and elevation resistance due to the species’ ability to detect small ephemeral wetlands [121]. TPI calculates the average elevation value of each cell within a raster based on the surrounding cells within a given radius providing a finer scale picture of valleys (negative values), and ridges [122]. A TPI was generated from digital elevation models (DEM) using the model builder in ArcGIS. 2.2.2 Creating Resistance Surfaces Each surface 69 layer was then exported from ArcGIS using the export to CIRCUITSCAPE plug-in to ensure that each layer was the proper dimensions and in the correct raster format to be processed in R [123] (Figure 2.1). 2.2.3 Genetic Distance Individual based genetic distances can be calculated a number of different ways, however Principal Component Analysis (PCA) based distance matrices appear to be highly robust for inferring landscape resistance relationships [124,125]. PCA based distance metrics allow the model to focus on the loci that are driving the majority of the variance between individuals [125]. A PCA genetic distance matrix was developed following [124]. A matrix was developed comparing allele usage at each locus for every individual and then used to develop a PCA using the R package Adegenet Version 2.1.4 [65]. The Euclidean distances between the 90 principal components were then used to develop pairwise genetic distance between individuals occurring within the three different sites [124-126]. 2.3.1 Genetic Distance A total of 90 PCA axis were generated for allele usage by individual. Euclidean distance between all 90 PC axes for each individual ranged from 3.63 to 8.23 with a mean of 6.04. The overall variance for the Euclidean distance between the 90 PC axes was 0.31. 2.2.4 Landscape Resistance Optimization Genetic resistance modeling was run in Resistance GA (an R package utilizing Julia and CIRCUITSCAPE; [108]) using the previously described landscape surfaces. Resistance GA utilizes a genetic algorithm developed by Scrucca (2013) to optimize landscape surface using iterative data transformation to test all possible resistance values of the landscapes [108]. Resistance GA uses pairwise genetic data and landscape distances determined by CIRCUITSCAPE to test the fit of each iterative data transformation using a mixed effect linear model [108]. In each iteration, the best model is retained and included in the proceeding iteration until the model no longer improves 70 [108]. Resistance GA tests eight data transformations for each continuous landscape layer and explores each possible resistance value for each categorical layer [108]. Once optimized, each resistance layer is assigned an AICc score and compared to null and geographic distance models to determine which model is the best fit for the true landscape resistance. Resistance GA also generates resistance layers for each landscape surface allowing one to visualize the optimized landscape resistance layer. Each surface was run independently utilizing individual based PCA axis for genetic distance. [108]. Resistance GA tests eight data transformations for each continuous landscape layer and explores each possible resistance value for each categorical layer [108]. Once optimized, each resistance layer is assigned an AICc score and compared to null and geographic distance models to determine which model is the best fit for the true landscape resistance. Resistance GA also generates resistance layers for each landscape surface allowing one to visualize the optimized landscape resistance layer. Each surface was run independently utilizing individual based PCA axis for genetic distance. Since individuals were sampled using traps during the mating season when individual E. blandingii are known to make large terrestrial movements we wanted to include all individuals regardless of proximity [6,41]. To control for the potential effects of shared locality due to trapping, and to maximize the exploration of the landscape, comparisons between individuals within the same locality were excluded. A total of 59 individuals from three localities were included (MI06=16, MI07=36, MI17= 7). 2.3.2 Landscape Resistance Optimization Optimized resistance surfaces were generated for each provided surface layer assigning values of the relative resistance an E. blandingii would face moving through each feature (Figure 71 2.3). The resistance values increase exponentially as the relative elevation increased, and neared an asymptote at the highest relative elevation observed on the landscape (Figure 2.2). For the TPI layer lower elevation was associated with low relative resistance, and higher elevation was associated with higher relative resistance (Figure 2.3). For the contemporary landscape map (LAN) woody wetlands, open water, and deciduous forests had the lowest relative resistance values were as, developed urban lands had the highest followed by agricultural lands (Figure 2.3). For the pre- settlement land class map (PRE) emergent and woody wetlands had the lowest relative resistance values followed by deciduous forests while open water had the highest relative resistance followed by scrub/shrub (Figure 2.3). 2.3.3 Model Fit The distance model was by far the best explanation for the genetic differentiation observed across the landscape at these localities (Table 2.1). The TPI model was the second best model but was only as good as the null (AICc values of 1278.139 and 1280.037, respectively) (Table 2.1). Both the TPI model and the distance model had relatively weak fits to the data (Rm2= 0.014 and 0.015 respectively) (Table 2.1). The contemporary landscape had the highest regression value, (though still rather weak) but was also the worst model based on AICc (Rm2= 0.027) (Table 2.1). The optimized resistance surface for TPI utilized a monomolecular transformation in which the lowest relative elevation values produced the least landscape resistance (Figures 2.3 & 2.4). 72 Figure 2.1 Resistance surfaces TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes). TPI layer to show position of individuals. Locality information removed. Figure 2.1 Resistance surfaces TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes). TPI layer to show position of individuals. Locality information removed. 73 Figure 2.2 Monomolecular Transformation applied to TPI. Figure 2.2 Monomolecular Transformation applied to TPI. Table 2.1 Summary of resistance model optimization. Table 2.1 Summary of resistance model optimization. Table 2.1 Summary of resistance model optimization. Surface obj.func_LL k AIC AICc R2m R2c LL Distance -635.734 2 1275.468 1275.678 0.014486 0.257794 -635.734 Null -638.035 1 1278.07 1278.139 0 0.247083 -638.035 TPI -635.655 4 1279.31 1280.037 0.015069 0.25782 -635.655 PRE -635.540 7 1285.081 1287.234 0.019872 0.252395 -635.54 LAN -633.175 16 1298.351 1311.002 0.027415 0.250808 -633.175 74 Figure 2.3 Optimized resistance surfaces, TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes). TPI layer to show position of individuals. Locality information removed. Figure 2.3 Optimized resistance surfaces, TPI (Topographic Position Index), LAN (National Land Class Map), PRE (Pre-Settlement Land Classes). TPI layer to show position of individuals. Locality information removed. Discussion The distance model as the best model (by AICc) with weak regression reinforced the observed weak IBD detected in chapter one (Figure 1.10). The optimized TPI model indicated that low elevation exerts the least landscape resistance on E. blandingii (Figures 2.2 &2.3). However, the weak relationship (R2m 0.022) between relative elevation and genetic distance implies that the null model was just as good, indicating that TPI is not a strong driver of differentiation for E. blandingii and explains little to no differentiation. 75 The weak overall relationship between TPI resistance and genetic distance between localities is not surprising based on the previous research. Joyal et al., (2001) found extensive use of uplands for movement, nesting, and dormancy. E. blandingii are known to move extensively, use a wide variety of habitats, and have large variable home ranges [6,8,11,14,16]. Grgurovic and Sievert (2005) found an estimated home range size of 22 hectares in E. blandingii and saw little overlap in home range use from year to year indicating that E. blandingii likely roams across the landscape from year to year. It has been noted that E. blandingii will use uplands extensively for nesting and terrestrial dispersal and will move long distances to breed and nest (up to 2 km) which could aid in gene flow between localities even if individuals spend most of their time in a single wetland [6,41]. Edge et al. (2010) found selection at a macro scale for wetlands over other water bodies and uplands for habitat use (although that does not necessarily implicate them as barriers for gene flow). In the historic landscape layer it is possible that when landscapes have an abundance of available habitat, E. blandingii will show little to no microhabitat selection making it difficult to detect a correlation between differentiation and resistance distance [16]. The rather pristine landscape observed by Edge et al., (2010) is more likely be representative of pre-settlement conditions faced by E. blandingii. Lack of correlation between genetic resistance and contemporary land cover parameters could be due to the long generation time of E. blandingii [22,81,113]. Despite substantial evidence for the effect of urbanization on E. blandingii, from direct mortality to habitat loss and extirpation, prior genetic assessments have observed a lack of differentiation between localities separated by urban development [6,8,10-17,27]. Discussion 76 Although attempts were made to account for the effects of the traps on the model, it is still possible that luring individuals to one location may influence the observed relationship between genetic distance and landscape resistance distance. Increasing the extent of the model to include more sites and explore a greater diversity of landscapes could potentially allow for a more informative model, however doing so would also increase the effect of geographic distance on differentiation and require a reduction in resolution of the landscape characteristics because the raster data is large and memory intensive. Additionally, a larger extent is computationally and memory intensive, especially if attempting to utilize individual based genetic distance. Using site based genetic distance could reduce the number of parameters and reduce the time of computations but would also reduce sample size and constrain representative landscapes characteristics resulting in model bias. Conclusion Overall optimization of resistance surfaces at a localized region in Michigan found little to no influence of landscape features on the observed pattern of genetic differentiation in E. blandingii (Table 2.1). Consistent with chapter one, IBD was found to be the best explanation for the observed genetic differentiation between localities in Michigan. The degree of genetic differentiation and the observed pattern across the landscape does not appear to show any meaningful relationship with the historic or contemporary landscape, at least at this geographic extent (Table 2.1). The lack of correlation between resistance distances for land class features and genetic differentiation could be due to low levels of observed genetic differentiation across the region which is likely due to long generation time, high historic migration, and habitat flexibility in E. blandingii [22,81,113]. This would also explain why no significant pattern was observed in the 77 contemporary landscape despite the substantial evidence of the effect of urbanization on E. blandingii [6,8,10-17]. Lack of correlation in the pre-settlement model could be due to low levels of landscape resistance to gene flow in E. blandingii in unmodified landscapes [6,14,33]. Finally, although a strong relationship between genetic differentiation and landscape resistance was not seen in this region using these resistance surfaces, it does not mean there are no drivers of differentiation on the landscape but rather the resistance surface optimization that was implemented here may not be appropriate for examining the relationship between long-lived slowly differentiating organisms. Further investigation into other landscape features, or utilizing different extents or regions, may determine different relationships and shed light on the ability of this framework for assessing resistance surfaces for E. blandingii. Landscape resistance may be variable between regions and localities and should be considered when examining for drivers of differentiation. 78 REFERENCES 1. 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Implementation of disease activity measurement for rheumatoid arthritis patients in an academic rheumatology clinic
BMC health services research
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Title Implementation of disease activity measurement for rheumatoid arthritis patients in an academic rheumatology clinic Title Implementation of disease activity measurement for rheumatoid arthritis patients in an academic rheumatology clinic Authors Bays, Alison Wahl, Elizabeth Daikh, David I et al. Publication Date 2016 DOI 10.1186/s12913-016-1633-x Peer reviewed * Correspondence: Gabriela.schmajuk@ucsf.edu 2Division of Rheumatology, Veterans Affairs Medical Center – San Francisco, 4150 Clement Street, Mailstop 111R, San Francisco, CA 94121, USA Full list of author information is available at the end of the article Powered by the California Digital Library University of California eScholarship.org Bays et al. BMC Health Services Research (2016) 16:384 DOI 10.1186/s12913-016-1633-x © 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. Implementation of disease activity measurement for rheumatoid arthritis patients in an academic rheumatology clinic Alison Bays1, Elizabeth Wahl2, David I. Daikh2, Jinoos Yazdany3 and Gabriela Schmajuk2* Alison Bays1, Elizabeth Wahl2, David I. Daikh2, Jinoos Yazdany3 and Gabriela Schmajuk2* Background (VA) hospital, associated with University of California, San Francisco (UCSF) provided an ideal place to imple- ment use of disease activity measures for patients with RA. Trainees working in the rheumatology clinic were familiar with the use of disease activity measures at other locations within the UCSF healthcare system. Baseline use of disease activity measurement in the clinic was infrequent prior to the start of the study, in part be- cause the electronic medical record (EMR) does not pro- vide an easy method for documenting joint scores. Modifying the SFVA’s EHR was not feasible in the short- term, so we planned an intervention using a paper scor- ing form. We assessed whether standardization of the clinic’s workflow to incorporate these forms increased the documentation of disease activity measures in the provider notes for patients with RA. (VA) hospital, associated with University of California, San Francisco (UCSF) provided an ideal place to imple- ment use of disease activity measures for patients with RA. Trainees working in the rheumatology clinic were familiar with the use of disease activity measures at other locations within the UCSF healthcare system. Baseline use of disease activity measurement in the clinic was infrequent prior to the start of the study, in part be- cause the electronic medical record (EMR) does not pro- vide an easy method for documenting joint scores. Modifying the SFVA’s EHR was not feasible in the short- term, so we planned an intervention using a paper scor- ing form. We assessed whether standardization of the clinic’s workflow to incorporate these forms increased the documentation of disease activity measures in the provider notes for patients with RA. g Current management of many chronic diseases, such as diabetes, hyperlipidemia and hypertension employ treat- ment strategies to achieve a specific quantitative clinical measure [1]. Recently, this “treat-to-target” approach has been applied to rheumatoid arthritis (RA) [2]. Instead of targeting a laboratory test or blood pressure measure- ment, the “target” in RA is disease activity, which can be measured using a variety of validated tools. Most of these combine swollen and tender joint counts, phys- ician and patient global assessments and sometimes la- boratory values [3]. Abstract Background: Treat-to-target is the recommended strategy for the management of rheumatoid arthritis (RA) and involves regular assessment of disease activity using validated measures and subsequent adjustment of medical therapy if patients are not in remission or low disease activity. Recommendations published in 2012 detailed the preferred disease activity measures but there have been few publications on implementation of disease activity measures in a real-world clinic setting. Methods: Plan-Do-Study-Act (PDSA) methodology was used over two cycles with a goal of increasing provider measurement of disease activity during all RA patient visits. In PDSA cycle 1, we implemented a paper-based form to help providers assess disease activity in RA patients. PDSA cycle 2 included the creation of separate patient and physician forms for collection of information, identification of patients prior to their clinic visit and incorporation of medical assistants into the workflow. Results: The first PDSA cycle improved the number of RA patients with documented disease activity measures from 24 % over a 4-week period, to an average of 44 % over an 8-week period. The second PDSA cycle showed a sustained and dramatic improvement, with 85 % of patients having a disease activity measure recorded over a 27- week period. Conclusions: Implementation of disease activity measurement in a typical academic rheumatology clinic can be achieved by standardizing workflow using a simple paper form. Keywords: Quality improvement, Rheumatoid arthritis, Disease activity Abbreviations: CCP, Cyclic Citrullinated Peptide Antibody; CDAI, Clinical Disease Activity Index; DAS28 ESR or CRP, Disease Activity Score with 28 Joint Counts; DMARD, Disease-Modifying Antirheumatic Drugs; EMR, Electronic Medical Record; NQF, National Quality Forum; PAS and PASII, Patient Activity Scales; PDSA, Plan Do Study Act; PQRS, Patient Quality Reporting System; RA, Rheumatoid Arthritis; RAPID-3, Routine Assessment of Patient Index; RF, Rheumatoid Factor; SDAI, Simplified Disease Activity Index; UCSF, University of California, San Francisco; VA, Veterans Affairs Hospital Bays et al. BMC Health Services Research (2016) 16:384 Bays et al. BMC Health Services Research (2016) 16:384 Page 2 of 7 Page 2 of 7 Study setting h d The study took place in an academic rheumatology clinic at the VA Hospital in San Francisco. All providers working in the clinic were included in the intervention and analysis. The practice consists of nine rheumatology fellows (two fellows were present for only the pre- intervention period) one nurse practitioner and five at- tending physicians. In 2014, the National Quality Forum (NQF) endorsed measures requiring disease activity measurements in a majority of visits (greater than 50 %) in RA patients [8]. Acceptable measures of disease activity identified by the American College of Rheumatology include the Clinical Disease Activity Index (CDAI), Disease Activity Score with 28-joint counts (DAS28 ESR or CRP), Patient Ac- tivity Scales (PAS and PAS-II), Routine Assessment of Patient Index (RAPID-3) and Simplified Disease Activity Index (SDAI) [3]. All patients with a diagnosis of rheumatoid arthritis in the medical record (reviewed by AB) were included. They study period lasted from June 2014 until April 2015. This project was considered exempt from IRB ap- proval by the San Francisco VA IRB because it qualified as a quality improvement activity. Providers were aware of the interventions used. No funding sources were uti- lized for this quality improvement project. Despite these recommendations for regular disease ac- tivity measurement in RA patients, routine use of these measurements has not been instituted in many rheuma- tology clinics. Reports from Physician Quality Reporting System (PQRS) indicate that in 2009, 630 of 83,849 phy- sicians (<1 %), the majority of whom where rheumatolo- gists, reported on one quality measure on RA patients. Among the physicians reporting one at least one meas- ure for their RA patients (n = 630), they primarily re- ported disease-modifying antirheumatic drugs (DMARD) usage and only 29 % reported information on a disease activity measure (n = 183) [9]. Background A systematic review in 2010 assessing treat to target versus usual care strategies in RA revealed consistent improvement in clinical out- comes with treat to target: Patients managed with treat- to-target approaches had greater reductions in disease activity and a higher likelihood of achieving remission over usual care and additionally, experienced a reduction in radiographic erosions, improved physical function and quality of life [1, 4–6]. Current practice guidelines rec- ommend patients with RA be treated with the goal of achieving remission or low disease activity [7]. Preliminary work to identify workflow challenges Preliminary work involved interviewing staff, fellows and faculty to understand the barriers to documentation of RA disease activity. Prior to the intervention, a clinician wishing to document a disease activity measure would have to 1) identify RA patients requiring a measure, 2) request this patient’s global assessment on a 0–10 or 0– 100 Likert or visual analog scale during the clinical en- counter 3) conduct the history and physical, including a 28-joint count, and 4) calculate the CDAI or DAS28 score and remember or look up the corresponding dis- ease activity category 5) document a disease activity measure in the clinic note. No standard method existed for identifying patients ahead of clinic and providing them with a visual analog or Likert scale for rating their patient global assessment. Additionally, a ruler was often not available to score the patient and physician global if a visual analog scale was used. Other obstacles identified prior to the initiation of the first QI cycle were a lack of Little has been published about how to best implement disease activity measurement in the clinic. Of the publi- cations that discuss implementation, they are focused on the integration of software with their electronic health record [10, 11]. However, not all rheumatology clinics have the IT support or ability to develop or purchase ad- vanced modules to modify their system. In this study, we describe methods for implementation of disease activity measurement in a tertiary care rheumatology clinic. The San Francisco Veterans Affairs Bays et al. BMC Health Services Research (2016) 16:384 Page 3 of 7 Page 3 of 7 success of PSDA cycle 2, we continued to follow the out- come for an additional 21 weeks (about 5 months). expectation on the part of the attending physicians to re- port a disease activity score, a lack of ability to modify the electronic medical record to incorporate the disease activity measures, and time constraints in clinic. Results Between week 1 and week 39, there were 107 RA pa- tients seen at the SFVA rheumatology clinic. Basic pa- tient characteristics are listed in Table 1. Of these 107 patients, the average age at their most recent appoint- ment was 67 years. In the 103 patients whose rheuma- toid factor (RF) and/or cyclic citrullinated peptide antibody (CCP) status were known, 81 (79 %) of these patients were seropositive (73 were CCP positive and 71 were RF positive), 38 patients (35 %) were on biologic agents (Table 1). The disease activity score 28 or DAS28 (ESR or CRP) incorporates the patient global score on a scale of 0– 100, a tender joint count of 28 joints, a swollen joint count of 28 joints and either the erythrocyte sedimenta- tion rate (ESR) or the C-reactive protein (CRP) and the provider then uses a formula to calculate the disease ac- tivity score and it is again characterized as remission, low disease activity, moderate disease activity or high disease activity [3]. Disease activity measures We divided the study period into three parts – pre- intervention, PDSA cycle 1 and PDSA cycle 2. We cre- ated control charts to describe the proportion of en- counters on each clinic day with a disease activity measure documented in the clinical note (p-charts). A continuous improvement of 6 or more points in the same direction is considered a trend [13]. The Clinical Disease Activity Index (CDAI) incorporates a patient global score on a 0 to 10 scale, a physician glo- bal score on a 0 to 10 scale and a 28-joint count for both tenderness and swelling. The score is tabulated with up to 28 points for tenderness, 28 points for swelling, 10 points for the physician global and 10 points for the pa- tient global. These scores are then translated into four categories: remission, low disease activity, moderate dis- ease activity or high disease activity [3]. Outcome The outcome of interest was the proportion of RA pa- tients seen on a given day in clinic who had a docu- mented disease activity measure in the encounter note for that day. Eligible RA patients were identified prior to their clinic visit through medical chart review by one au- thor (AB) based on the assessment sections on the most recent note. Presence or absence of the disease activity measure was determined by review of the entire note. Upon reviewing the barriers to completing disease ac- tivity measures, the modifiable obstacles included at- tending physician expectations and availability of a form on which patients could indicate a global assessment and ruler with which to measure a visual analog scale line. The obstacles that were not immediately modifiable were changing the medical record (CPRS) and the time available to see a patient. aRheumatoid factor or anti-cyclic citrullinated peptide antibody positive at any point, among patients tested Interventions A Plan-Do-Study-Act (PDSA) methodology provides a structure of iterative change that adapts to feedback to result in the desired outcome. The first stage, ‘plan’, is a planning stage in which a change is identified with the goal of improvement. The second stage, ‘do’, is when this change is tested. The third stage, ‘study’, examines the success of the change and the ‘act’ stage identifies the next steps needed for beginning the next PDSA cycle [12]. We undertook two PDSA cycles in an attempt to improve use and documentation of disease activity mea- sures at the San Francisco VA rheumatology clinic. There was a 4-week pre-intervention period where we assessed use of disease activity measures prior to any specific intervention. A first PDSA cycle was planned and assessment of its effect on disease activity measure- ment documentation was planned for 8 weeks later. A second PDSA cycle was planned and assessment of its effect on disease activity measurement documentation was again planned for 8 weeks later. Because of the During the 4-week pre-intervention period, there were 29 RA patient encounters. Twenty-four percent of pre- intervention visits had a documented disease activity measure in the clinical note. A single clinician was Table 1 Characteristics of rheumatoid arthritis patients seen in the San Francisco VA rheumatology clinic during study period Table 1 Characteristics of rheumatoid arthritis patients seen in the San Francisco VA rheumatology clinic during study period Table 1 Characteristics of rheumatoid arthritis patients seen in the San Francisco VA rheumatology clinic during study period Characteristics Rheumatoid arthritis patients N = 107 Age, mean (SD) 67 (10) Male, N (%) 93 (87 %) Seropositive,a N (%) [N = 103] 81 (79 %) Medications at end of study period, N (%) Methotrexate 60 (56 %) Prednisone 42 (39 %) Biologic 38 (35 %) aRheumatoid factor or anti-cyclic citrullinated peptide antibody positive at any point, among patients tested Bays et al. BMC Health Services Research (2016) 16:384 Page 4 of 7 Page 4 of 7 responsible for nearly all of this disease activity score documentation. clinic that included the patient global visual analog scale, physician global visual analog scale, a 28-joint count with homunculus and instructions on how to calculate the CDAI and DAS-28 ESR and CRP. The form included a fold-over ruler, obviating the need for finding a ruler, in addition to instructions for calculating the CDAI. PDSA cycle 1 The cycle 1 intervention consisted of 1) developing a paper form that would be readily available in clinic for collecting patient and physician global assessments and tabulating joint counts using the homunculus (Add- itional file 1) and 2) Making the form available in clinic 3) Brief one-on-one educational discussions with incom- ing fellows on the use of this form, the calculation of CDAI and DAS 28, and the purpose and goal of disease activity measurement. The providers were encouraged to download a CDAI and DAS-28 calculator onto their smartphones [14]. PDSA cycle 1 lasted 8 weeks. During this period, pro- viders had 59 visits with RA patients, and 26 (44 %) of those encounters had disease activity measures recorded in the note (see Fig. 2). Follow-up interviews with clinicians identified several is- sues during cycle 1: 1) the patient and physician global were both completed on one form, so if the patient filled out the global score first, the physician would see the patient global score prior to the recording the physician global score, thus potentially biasing her rating; 2) the global assessment form had to be printed carefully so that the ruler lined up with the patient and physician global lines; 3) since RA patients were not pre-identified prior to their visits, providers would often forget to administer the patient global form. In the workflow (Fig. 1) for cycle 1, providers were to identify RA patients and retrieve a form located in the Patient checks in Physician identifies patient as a rheumatoid arthritis patient Physician conducts history and physical with 28 joint count assessment Physician fills out form Patient fills out patient global Physician scores and interprets results Physician locates prior results and compares trend Physican discusses treatment changes with patient Physician records disease activity in note Fig. 1 Cycle 1 workflow PDSA cycle 2 The pre-intervention, PDSA Cycle 1, and PDSA Cycle 2 phases are separated by red bars. The dark blue line show sthe proportion of patient encounters with a documented CDAI by week. The upper control limits are not seen (>1). The lower control limits vary as the denominator of patient encounters changed each week. The p-bar shows the average CDAI documentation rate. More than 6 values are seen above the p-bar after Cycle 2 was implemented, indicating a positive improvement we observed a sustained increase in the proportion of patients with of disease activity measures noted in the charts. taking their vital signs. The patients filled out the form while sitting in the waiting room. The patients would then either hand the form back to the medical assistant, who would attach it to the encounter form given to pro- viders, or the patient could give the form directly to the clinician during the appointment. The physician would then conduct the history and physical, and enter the swol- len and tender joint counts and the physician global into the table calculator on Form 2. The physician would then calculate the CDAI and/or DAS28 using simple addition or their IPhone app. When typing the note, the physician was instructed to include the score within the text of the note. This project is generalizable to other clinics that may not have the capability to easily or immediately modify the electronic health system to incorporate disease activ- ity measures. With minor changes to the workflow, we were able to incorporate the help of medical assistants, identify RA patients prior to their clinic appointment, and provide two forms for completion of global assess- ments, resulting in sustained improvement in reporting of disease activity measures. As disease activity measure- ment becomes a requirement of high quality care, we have shown that this “paper-and-pencil” intervention can result in successful documentation of disease activity measures without relying on changes to the electronic health record. This may be especially important for clinics with limited resources, or where changes to the health IT infrastructure may be difficult. PDSA cycle 2 lasted 27 weeks. During this period, pro- viders had 182 clinic visits with RA patients, and 155 (85 %) of those encounters had disease activity measures recorded in the note (see Fig. 2). PDSA cycle 2 Starting during PDSA cycle 2, there were six occurrences over the p-bar, which continued throughout the PDSA cycle, with three excep- tions. All providers showed improvement in disease ac- tivity measure documentation. There were no outliers. y Our study has several limitations. First, it is difficult to disentangle which specific aspect of our intervention was the key improving disease activity measure docu- mentation. Separating the effects of provider education or changes in culture from the effects of easy availability of patient global score for relevant patients is not pos- sible given our study design. However, given the anemic improvement in the PDSA cycle 1, we can say that pre- clinic identification of patients and score collection in the waiting room seemed to be key attributes of a suc- cessful intervention. Second, our follow-up time is not long enough and our sample size not large enough to be PDSA cycle 2 The cycle 2 intervention involved: 1) the creation of two separate forms so that the patients would complete the patient global in the waiting room, prior to the clinic visit, and the providers would not see the score until after completing their own global assessment; 2) add- itional education for providers; 3) identification and flag- ging of RA patients prior to the clinic visit so that patients could fill out global assessments in the waiting room prior to the start of their visit. The one form used previously was split into two – the first form was designed for patients and included a glo- bal assessment scale (see Additional file 2). The second form was for the providers and included a 28-joint count homunculus to record the swollen and tender joints, a physician global score (see Additional file 3). It also in- cluded an explanation of how to calculate the CDAI and DAS-28. On both forms, the global scores were changed from a visual analog scale to a numerical Likert scale, noted to be interchangeable in American College of Rheumatology’s working group recommendations [3]. This eliminated the need for a ruler to calculate patient and provider global assessments. Additional education was directed to providers. This included a post-clinic conference discussion of the his- tory and utilization of disease activity measures and a division-wide Quality Improvement conference in which there was a discussion of the changes at the VA. RA patients were identified via chart review and flagged by a single author (AB) prior to clinic (see Fig. 3). Appro- priate forms were provided to medical assistants prior to clinic. On the day of clinic, the medical assistants were instructed to give the form to flagged patients while Bays et al. BMC Health Services Research (2016) 16:384 Page 5 of 7 Fig. 2 Percent completion of CDAI by week of intervention. The pre-intervention, PDSA Cycle 1, and PDSA Cycle 2 phases are separated by red bars. The dark blue line show sthe proportion of patient encounters with a documented CDAI by week. The upper control limits are not seen (>1). The lower control limits vary as the denominator of patient encounters changed each week. The p-bar shows the average CDAI documentation rate. More than 6 values are seen above the p-bar after Cycle 2 was implemented, indicating a positive improvement Fig. 2 Percent completion of CDAI by week of intervention. Ethics approval and consent to participate This project was considered exempt from IRB approval by the San Francisco VA IRB because it qualified as a quality improvement activity. Therefore, the need to obtain informed consent was deemed unnecessary and not obtained from patients. Future projects include exploring the possibility of modifying the electronic medical record to include the CDAI or DAS-28 as structured fields. This would allow for easy identification of patients with and without dis- ease activity measures and allow clinicians to see trends Discussion In this project, we describe the implementation of a reli- able process for disease activity measurement for RA pa- tients as recommended by the American College of Rheumatology in a single academic rheumatology clinic. Prior to the intervention, only 24 % of RA patients seen in clinic had documented disease activity measures and the majority of these patients had seen one third year fellow. By the end of the quality improvement initiative, Page 6 of 7 Bays et al. BMC Health Services Research (2016) 16:384 Page 6 of 7 in their performance over time. It would also make it easy to trend a single patient’s disease activity over time to evaluate their response to therapy. Modifying the electronic medical record so that it stores disease activity over time and allows providers to see trends over time is an ideal system that would assist providers in being able to assess trends over time. This has been implemented and has shown improvement in quality of care, efficiency of care and productivity [11]. However, this is not pos- sible with all electronic medical records. Fellow identifies RA patients and prepares forms Patient checks in Medical assistants administer form Patient fills out form in waiting room Patient hands form to provider during visit Physician conducts history and physical Physician fills out form Physician scores and interprets results Physician locates prior results and compares trend Physican discusses treatment changes with patient Physician records disease activity in note Fig. 3 Cycle 2 workflow Consent for publication Not applicable. able to witness changes in mean CDAI or DAS scores over time as a result of the implementation of this “treat to target” approach, although such improvements have been documented in trial settings previously [1, 4–6]. Availability of data and materials All data supporting our findings is included in this manuscript and appendix files. Funding Funding GS received salary support from the National Institutes of Health, through K23 AR063770 (GS). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. Additional files Additional file 1: Cycle 1 form (PDF 533 kb) Additional file 2: Cycle 2 patient form (PDF 137 kb) Additional file 3: Cycle 2 provider form (PDF 447 kb) Acknowledgements None. Authors’ contributions AB contributed to the study design, acquisition of data, analysis and interpretation of data, drafting the article, final approval of the article. EW contributed to and interpretation of data, critical revision of the article, final approval of the article. DD participated study concept and design, acquisition of data, analysis and interpretation of data, critical revision the article, final approval of the article. JY participated in study design, interpretation of data, critical revision the article, final approval of the article. GS contributed to the study concept and design, acquisition of data, analysis and interpretation of data, drafting the article, final approval of the article. All authors read and approved the final version of the manuscript. Conclusions Through utilization of a simple paper form and changes to workflow, rheumatology clinics can implement the use of standardized disease activity measures to offer patients high quality care consistent with the recommendations of the American College of Rheumatology [3, 15]. Competing interests p g The authors declare that they have no competing interests. References 2007;66:1443–9. 6. Allaart CF, Geokoop-Ruiterman YPM, de Vries-Bouwstra JK, Breedveld FC, Dijkmans BAC. Aiming at low disease activity in rheumatoid arthritis with initial combination therapy or initial monotherapy strategies: The BeSt study. Clin Exp Rheumatol. 2006;24(6 SUPPL 43):2–7. 6. Allaart CF, Geokoop-Ruiterman YPM, de Vries-Bouwstra JK, Breedveld FC, Dijkmans BAC. Aiming at low disease activity in rheumatoid arthritis with initial combination therapy or initial monotherapy strategies: The BeSt study. Clin Exp Rheumatol. 2006;24(6 SUPPL 43):2–7. 7. Smolen JS, Aletaha D, Bijlsma JWJ, Breedveld FC, Boumpas D, Burmester G, Combe B, Cutolo M, De Wit M, Dou-gados M, Emery P, Gibofsky A, Gomez-Reino JJ, Haraoui B, Kalden J, Keystone EC, Kvien TK, McInnes I, Martin-Mola E, Montecucco C, Schoels M, Van Der Heijde D. Treating rheumatoid arthritis to target: Recommendations of an international task force. Revmatol. 2012;20:5–16. g 8. Rheumatoid Arthritis: Assessment of Disease Activity [http://www. qualityforum.org/]. Accessed 1 Feb 2016. 8. Rheumatoid Arthritis: Assessment of Disease qualityforum.org/]. Accessed 1 Feb 2016. 9. Curtis JR, Sharma P, Arora T, Bharat A, Barnes I, Morrisey MA, Kilgore M, Saag KG, Wright NC, Yun HG, Delzell E. Physicians’ explanations for apparent gaps in the quality of rheumatology care: Results from the US Medicare Physician Quality Reporting System. Arthritis Care Res. 2013;65:235–43. 9. Curtis JR, Sharma P, Arora T, Bharat A, Barnes I, Morrisey MA, Kilgore M, Saag KG, Wright NC, Yun HG, Delzell E. Physicians’ explanations for apparent gaps in the quality of rheumatology care: Results from the US Medicare Physician Quality Reporting System. Arthritis Care Res. 2013;65:235–43. 10. Newman ED, Lerch V, Jones JB, Stewart W. Touchscreen questionnaire patient data collection in rheumatology practice: Development of a highly successful system using process redesign. Arthritis Care Res. 2012;64:589–96. 10. Newman ED, Lerch V, Jones JB, Stewart W. Touchscreen questionnaire patient data collection in rheumatology practice: Development of a highly successful system using process redesign. Arthritis Care Res. 2012;64:589–96. 11. Newman ED, Lerch V, Billet J, Berger A, Kirchner HL. Improving the quality of care of patients with rheumatic disease using patient-centric electronic redesign software. Arthritis Care Res (Hoboken). 2015;67(4):546–53. 12. Taylor MJ, McNicholas C, Nicolay C, Darzi A, Bell D, Reed JE. Systematic review of the application of the plan-do-study-act method to improve quality in healthcare. BMJ Qual Saf. 2014;23:290–8. Bays et al. BMC Health Services Research (2016) 16:384 Bays et al. BMC Health Services Research (2016) 16:384 Bays et al. BMC Health Services Research (2016) 16:384 Veterans Affairs Medical Center – San Francisco, 4150 Clement Street, Mailstop 111R, San Francisco, CA 94121, USA. 3Division of Rheumatology, 1001 Potrero Ave, SFGH 30, San Francisco, CA 94110, USA. Veterans Affairs Medical Center – San Francisco, 4150 Clement Street, Mailstop 111R, San Francisco, CA 94121, USA. 3Division of Rheumatology, 1001 Potrero Ave, SFGH 30, San Francisco, CA 94110, USA. Received: 23 July 2015 Accepted: 18 June 2016 References 1. Schoels M, Knevel R, Aletaha D, Bijlsma JWJ, Breedveld FC, Boumpas DT, Burmester G, Combe B, Cutolo M, Dougados M, Emery P, van der Heijde D, Huizinga TWJ, Kalden J, Keystone EC, Kvien TK, Martin-Mola E, Montecucco C, de Wit M, Smolen JS. Evidence for treating rheumatoid arthritis to target: results of a systematic literature search. Ann Rheum Dis. 2010;69:638–43. 1. Schoels M, Knevel R, Aletaha D, Bijlsma JWJ, Breedveld FC, Boumpas DT, Burmester G, Combe B, Cutolo M, Dougados M, Emery P, van der Heijde D, Huizinga TWJ, Kalden J, Keystone EC, Kvien TK, Martin-Mola E, Montecucco C, de Wit M, Smolen JS. Evidence for treating rheumatoid arthritis to target: results of a systematic literature search. Ann Rheum Dis. 2010;69:638–43. 2. Saag KG, Gim GT, Patkar NM, Anuntiyo J, Finney C, Curtis JR, Paulus HE, Mudano A, Pisu M, Elkins-Melton M, Outman R, Allison JJ, Almazor MS, Bridges SL, Chatham WW, Hochberg M, Maclean C, Mikuls T, Moreland LW, O’Dell J, Turkiewicz AM, Furst DE. American College of Rheumatology 2008 recommendations for the use of nonbiologic and biologic disease- modifying antirheumatic drugs in rheumatoid arthritis. Arthritis Care Res. 2008;59:762–84. 3. Anderson J, Caplan L, Yazdany J, Robbins ML, Neogi T, Michaud K, Saag KG, O’Dell JR, Kazi S. Rheumatoid arthritis disease activity measures: American College of Rheumatology recommendations for use in clinical practice. Arthritis Care Res (Hoboken). 2012;64:640–7. 3. Anderson J, Caplan L, Yazdany J, Robbins ML, Neogi T, Michaud K, Saag KG, O’Dell JR, Kazi S. Rheumatoid arthritis disease activity measures: American College of Rheumatology recommendations for use in clinical practice. Arthritis Care Res (Hoboken). 2012;64:640–7. 4. Grigor C, Capell H, Stirling A, McMahon AD, Lock P, Vallance R, Kincaid W, Porter D. Effect of a treatment strategy of tight control for rheumatoid arthritis (the TICORA study): A single-blind randomised controlled trial. Lancet. 2004;364:263–9. 5. Verstappen SMM, Jacobs JWG, van der Veen MJ, Heurkens AHM, Schenk Y, ter Borg EJ, Blaauw AAM, Bijlsma JWJ. Intensive treatment with methotrexate in early rheumatoid arthritis: aiming for remission. Computer Assisted Management in Early Rheumatoid Arthritis (CAMERA, an open-label strategy trial). Ann Rheum Dis. 2007;66:1443–9. 5. Verstappen SMM, Jacobs JWG, van der Veen MJ, Heurkens AHM, Schenk Y, ter Borg EJ, Blaauw AAM, Bijlsma JWJ. Intensive treatment with methotrexate in early rheumatoid arthritis: aiming for remission. Computer Assisted Management in Early Rheumatoid Arthritis (CAMERA, an open-label strategy trial). Ann Rheum Dis. Author details 1 1Division of Rheumatology, University of Washington, Harborview, 1959 NE Pacific Street, Box 356428, Seattle, WA, USA. 2Division of Rheumatology, Page 7 of 7 Bays et al. BMC Health Services Research (2016) 16:384 15. Saag KG, Yazdany J, Alexander C, Caplan L, Coblyn J, Parekh Desai S, Harrington T, Liu J, McNiff K, Newman E, Olson R. Defining quality of care in rheumatology: The American College of rheumatology white paper on quality measurement. Arthritis Care Res. 2011;63:2–9. Quality Reporting System. Arthritis Care Res. 2013;65:235–43. 10. Newman ED, Lerch V, Jones JB, Stewart W. Touchscreen questionnaire patient data collection in rheumatology practice: Development of a highly successful system using process redesign. Arthritis Care Res. 2012;64:589–96. 11. Newman ED, Lerch V, Billet J, Berger A, Kirchner HL. Improving the quality of care of patients with rheumatic disease using patient-centric electronic redesign software. Arthritis Care Res (Hoboken). 2015;67(4):546–53. 12. Taylor MJ, McNicholas C, Nicolay C, Darzi A, Bell D, Reed JE. Systematic review of the application of the plan-do-study-act method to improve quality in healthcare. BMJ Qual Saf. 2014;23:290–8. 13. Carey R. Improving Healthcare with Control Charts: Basic and Advanced SPC Methos and Case Studies. Milwaukee: ASQ Quality Press; 2003. 14. DAS28/ACR-EULAR criteria on the App Store on iTunes [https://itunes.apple. com/us/app/das28-acr-eular-criteria/id443707029?mt=8]. Accessed 1 Feb 2016. 15. Saag KG, Yazdany J, Alexander C, Caplan L, Coblyn J, Parekh Desai S, Harrington T, Liu J, McNiff K, Newman E, Olson R. Defining quality of care in rheumatology: The American College of rheumatology white paper on quality measurement. Arthritis Care Res. 2011;63:2–9. 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: 13. Carey R. Improving Healthcare with Control Charts: Basic and Advanced SPC Methos and Case Studies. Milwaukee: ASQ Quality Press; 2003. • 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 • 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 14. DAS28/ACR-EULAR criteria on the App Store on iTunes [https://itunes.apple. com/us/app/das28-acr-eular-criteria/id443707029?mt=8]. Accessed 1 Feb 2016. 15. Saag KG, Yazdany J, Alexander C, Caplan L, Coblyn J, Parekh Desai S, Harrington T, Liu J, McNiff K, Newman E, Olson R. Defining quality of care in rheumatology: The American College of rheumatology white paper on quality measurement. Arthritis Care Res. 2011;63:2–9.
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Pengalaman Kesepian dan Strategi Koping pada Santri Lanjut Usia
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Pengalaman Kesepian dan Strategi Koping pada Santri Lanjut Usia Lonely Experiences and Coping Strategies for Elderly Students Alif Muhammad Zakaria Mahasiswa Pasca Sarjana Program Studi Interdisciplinary Islamic Studies Konsentrasi Ps Pendidikan Islam Universitas Islam Negeri Sunan Kalijaga Yogyakarta Mahasiswa Pasca Sarjana Program Studi Interdisciplinary Islamic Studies Konsentrasi Psikologi Pendidikan Islam Universitas Islam Negeri Sunan Kalijaga Yogyakarta alifmuzas1307@gmail.com Abstrac. Unresolved loneliness triggers negative things such as depression, anxiety, socialphobia, and other mental disorders. Loneliness in the elderly is an interesting study because at this stage a person experiences an evolutionary setback in social interactions due to physical disability. Initial studies of research found that there was a desire for elderly students to die in a state of husnul khotimah which was implemented with nyantri activities at Islamic boarding schools, but on the other hand they still wanted to be close to their families, this encouraged researchers to know and describe the experience of loneliness, types of loneliness, causal factors, and coping strategies used by elderly students. This research is a qualitative-phenomenological type with data collection techniques: interviews, observation, and documentation. This study resulted in the findings of elderly students wanting to deepen their religious knowledge, but on the other hand they also wanted to be close to loved ones because even though elderly students had structured daily and weekly schedules, they still experienced loneliness in the form of emotional isolation and social isolation, the cause of the loneliness of the elderly students. are situational factors. To overcome this feeling of loneliness, elderly students use emotional focused coping, problem focused coping, and positive religious coping strategies. Keywords: Coping Strategies Elderly Lonely Abstrak. Kesepian yang tidak teratasi memicu hal negatif seperti depresi, kecemasan, socialphobia, dan gangguan mental lainya. Kesepian pada lanjut usia menjadi kajian yang menarik karena dalam tahap ini seseorang mengalami kemunduran secara evolusional dalam interaksi sosial yang disebabkan ketidakmampuan secara fisik. Studi awal penelitian menemukan adanya keinginan santri lansia untuk meninggal dalam keadaan husnul khotimah yang diimplementasikan dengan kegiatan nyantri di Pondok Pesantren, namun di sisi lain tetap berkeinginan dekat dengan keluarga, hal tersebut mendorong peneliti untuk mengetahui dan medeskirpsikan pengalaman kesepian, jenis kesepian, faktor penyebab, dan strategi koping yang digunakan para santri lansia. Penelitian ini berjenis kualitatif-fenomenologis dengan teknik pengumpulan data berupa wawancara, observasi, dan dokumentasi. Pengalaman Kesepian dan Strategi Koping pada Santri Lanjut Usia Lonely Experiences and Coping Strategies for Elderly Students Penelitian ini menghasilkan temuan santri lansia ingin memperdalam ilmu agama, namun di sisi lain mereka juga ingin dekat dengan orang terkasih karena walaupun santri lansia memiliki jadwal harian dan mingguan yang terstruktur, mereka tetap mengalami kesepian berjenis emotional isolation dan sosial isolation, penyebab kesepian santri lansia tersebut adalah situational factor. Untuk mengatasi perasaan kesepian tersebut, santri lansia menggunakan emotional focused coping, problem focused coping, dan strategi koping religius positif. Kata Kunci: Kesepian, Lansia, Strategi Koping Kata Kunci: Kesepian, Lansia, Strategi Koping Wacana Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 E-ISSN 2716-1625 (Online) hidupnya. Penelitian yang dilakukan oleh Tegawati dkk (2009) dan Sunaryanto dkk (2015) menyebutkan hal serupa bahwa pada masa lanjut usia, seseorang akan mengalami hambatan- hambatan karena penurunan aspek fisik, mental, dan sosial yang terjadi secara bertahap (evolusional). Perkembangan ini tidak bisa ditarik mundur ke belakang, yang artinya harus ada keselarasan antara perilaku dan proses mental sebagai acuan bagi perkembangan lanjut usia yang diharapkan mampu memberikan jalan keluar dari permasalahan yang ada dalam masa lanjut usia agar kehidupan yang dijalani lebih bermakna. Seseorang dikatakan masuk dalam kategori lanjut usia dapat dilakukan dengan dua (2) pendekatan menurut Suardiman (2016) yakni: secara biologis dan kronologis. Pendekatan secara biologis meninjau seseorang dikatakan tua berdasarkan pada kapasitas fisik, sedangkan dalam pendekatan kronologis meninjau hitungan umur melalui kalender atau umur dari ulang tahun terakhir. Adapun definisi lanjut usia menurut Peraturan Pemerintah Republik Indonesia Nomor 43 Tahun 2004 Tentang Pelaksanaan Upaya Peningkatan Kesejahteraan Sosial Lanjut Usia dan Undang-undang Nomor 13 Tahun 1998 Tentang Kesejahteraan Lansia disebutkan bahwa lansia merupakan suatu masa di mana seseorang telah berusia lebih dari enam puluh (60) tahun. Dalam kacamata psikologi perkembangan, masa lanjut usia merupakan fase akhir dalam dinamika perkembangan kehidupan seorang manusia (Novitasari & Aulia, 2019). Jumlah penduduk berusia lanjut di Indonesia menurut Pusat Data dan Informasi Kementerian Kesehatan Republik Indonesia tahun 2017 berjumlah 23,66 juta jiwa atau apabila dipersentasekan jumlah lanjut usia adalah 9,03%. Dalam studi yang dilakukan oleh Munandar (2017) pada tahun 2020 jumlah populasi penduduk berusia lanjut dapat mencapai 30-40 juta jiwa sehingga menempatkan Indonesia pada posisi ke-3 dunia, studi ini diperkuat oleh data dari Badan Pusat Statistik Provinsi Jawa Tengah yang menyebut bahwa Indonesia kini memasuki aging population era (Pusdatin Kemenkes, 2017). Meningkatnya jumlah populasi penduduk berusia lanjut ini harus mendapatkan perhatian khusus, mengingat pada masa ini, lanjut usia rentan mengalami permasalahan, salah satunya ialah masalah psikologis berupa perasaan tidak berguna, perasaan kehilangan yang cenderung bermutasi menjadi perasaan kesepian karena minimnya interaksi. Minimnya intensitas interaksi ini disebabkan karena pensiun, teman dekat yang sudah meninggal dunia, anak yang sibuk bekerja atau sekolah, ataupun ketidakmampuanya secara fisik untuk melakukan interaksi. Munandar (2017) menyebutkan bahwa 50% lanjut usia di Indonesia mengalami perasaan kesepian. Kesepian menurut Perlman & Peplau didefinisikan sebagai kesenjangan antara ekspektasi dan realita yang dialami seseorang dalam hubungan sosial yang dimiliki (Dahlberg etc, 2018). Kesepian lansia merupakan hasil dari ketidakpuasan seseorang dalam hubungan sosialnya. Pendahuluan Dinamika perkembangan manusia baik maju ataupun mundur secara fisik dan mental merupakan kajian yang sangat menarik, mengingat bahwa setiap individu memiliki pengetahuan dan pengalaman yang berbeda. Masa lanjut usia merupakan tahapan akhir atau tahap kemunduran yang dialami oleh indivdu yang dianugerahi umur panjang dalam rentang 71 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Vol.14, No.1, Januari 2022, pp. 71-88 psikologis kondisi ini dinilai berpotensi negatif terhadap jiwa seseorang (Winningham & Pike, 2007). Pendapat ini diperkuat oleh Hawkey & Cacioppo (dalam Gunarsa, 2006) bahwa perasaan kesepian ini juga berpotensi negatif menurunkan kemampuan lansia dalam menghadapi masalah sosial di sekitarnya. Suardiman (2016) menyebutkan terdapat tiga (3) teori terkait lanjut usia, pertama, teori pengunduran diri yang diungkapkan oleh Cumming & Henry, teori ini menitikberatkan pada semakin tinggi usia seseorang maka semakin rendah interaksi sosial, fisik, dan emosi pada kehidupan dunia. Kedua, teori aktivitas (theory activity) yang menyebutkan bahwa agar seorang lanjut usia berhasil maka seseorang tersebut harus seaktif mungkin mengikuti kegiatan yang berhubungan dengan sosial, fisik, dan emosionalnya atau dapat dikatakan bahwa seorang lanjut usia yang masih terlibat dalam berbagai kegiatan akan memperoleh kepuasan. Ketiga, teori kontinuitas, teori ini dicetuskan oleh Atchley yang menyebut bahwa seorang lanjut usia harus bisa mengkorelasikan antara masa lalu dan masa kini (here and now) aktivitas dalam teori ini dinilai penting guna representasi yang berkesinambungan dari suatu gaya hidup. Tak hanya memaparkan mengenai teori mengenai lanjut usia, Suardiman (2016) juga memaparkan karakteristik kesepian pada individu lansia, menurutnya, lansia bisa dikatakan mengalami kesepian apabila mereka memiliki atau mengalami karakteristik sebagai berikut: Pertama, menjadi kaum minoritas, lansia termasuk golongan kecil dalam masyarakat, dan seringkali dipandang sebagai yang berbeda. Situasi ini kemudian mempengaruhi pola interaksi sosial para lansia dan berdampak pada munculnya kesepian. Kedua, tidak adanya perhatian, lansia cenderung mengalami kesepian apabila mereka tidak mendapatkan perhatian dari lingkungan sekitar. Oleh sebab itu, lansia sering lebih memilih tempat yang membuat mereka merasa diperhatikan dan sesuai dengan keinginannya. Ketiga, terisolasi dari lingkungan sosial, terisolasi dari lingkungan sosial ini lebih pada situasi yang diperparah melalui streotipe masyarakat yang menganggap lansia itu kolot, konservatif, serta tidak mau menerima masukan atas pendapat yang mereka katakan. Situasi ini membuat lansia terisolasi dari lingkungan sekitarnya. Keempat, tidak adanya tempat untuk berbagi perasaan dan pengalaman. Manusia adalah makhluk sosial maka apabila mereka tidak memiliki hubungan dengan individu lainya untuk berbagi cerita dan pengalaman maka mereka akan merasakan kesepian. Kelima, harus hidup sendiri, tanpa adanya pilihan lain, karakteristik kesepian pada lansia yang terakhir adalah keadaan yang memaksa mereka untuk hidup sendiri. Situasi ini disebabkan oleh beberapa faktor seperti kesibukan anak karena bekerja, menjadi janda atau duda akibat pasangan yang telah meninggal dan lain sebagainya. Wacana Di satu sisi mereka masih mengharapkan interaksi sosial dengan baik dan intens, namun di sisi lain ironisnya mereka mengalami berbagai keterbatasan. Berdasarkan kriteria kesehatan 72 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Vol.14, No.1, Januari 2022, pp. 71-88 Kemudian untuk mengidentifikasi cara yang digunakan oleh lanjut usia dalam mengatasi perasaan kesepian yang memiliki potensi negatif tersebut, salah satu ahli, yakni Lazarus dan Folkman (dalam Maryam, 2017) membagi jenis strategi koping menjadi 2, yaitu emotional focused coping dan problem focused coping. Emotional focused coping difokuskan pada pengaturan respon emosional yang bertujuan untuk mengelola fungsi emosi di mana individu merasa sudah tidak dapat mengubah situasi yang menekan dan hal yang bisa dilakukan hanyalah menerima keadaan tersebut. Lebih dalam lagi Lazarus dan Folkman menjelaskan 5 hal yang termasuk dalam emotional focused coping yaitu: memberi penilaian positif, penekanan pada tanggung jawab, kontrol diri, memberi jarak, dan menghindarkan diri. Adapun dalam problem focused coping atau yang disebut dengan strategi koping berfokus pada masalah dan direspon melalui tindakan untuk memecahkan masalah. Seseorang akan memilih fokus ini apabila problematika tersebut masih dapat dikontrol, dalam hal ini Lazarus dan Folkman membagi 3 strategi yang masuk dalam fokus masalah yakni: plainful problem solving, confrontative coping, dan seeking social support. Selain strategi koping secara umum, terdapat strategi koping religius. Koenig (dalam Aflakseir & Peter, 2009) mengungkapkan bahwa koping religius adalah strategi kognitif ataupun perilaku yang didasarkan pada keyakinan dan praktik ritual keagamaan untuk memberikan fasilitas pemecahan masalah dalam mencegah atau meringankan dampak negatif dari situasi atau keadaan yang menekan. Lebih dalam lagi Pargament Dkk (dalam Aflakseir & Peter, 2009) membedakan koping religius menjadi 2 jenis, yaitu: koping religius positif dan negative. Pargament mendefinisikan koping religius positif sebagai suatu ekspresi spiritualitas, hubungan yang memberikan rasa aman dengan Tuhan, adanya makna yang dapat ditemukan dalam setiap kehidupan, serta adanya hubungan spiritualitas dengan orang lain. Berikut 8 aspek koping religius positif yang memiliki manfaat bagi kesehatan mental: spiritual support, collaborative religious coping, benevolent religious rerramming, religious purificatino, connection spiritual, seeking support form clergy or members, religiois helping, dan religious forgiving. Strategi koping religius negatif menurut Pargament (dalam Utami, 2012) didefinisikan sebagai ekspresi dari hubungan yang lemah, kurang mempercayai kekuatan Tuhan, kesenangan berlebih terhadap dunia, serta tidak adanya perjuangan dalam pencarian makna. Koping religius negatif ini memiliki hubungan dengan distress, tingkat depresi, fungsi kognitif, dan kualitas hidup yang buruk. Terdapat enam (6) aspek yang terkandung, yaitu: punishing god reappraisal, demonic reappraisal, reapraisal god’s power, self-direct religious coping, spiritual discontent, dan interpersonal religious discontent. Wacana Dari pengertian mengenai teori terkait lanjut usia dan karakteristik kesepian tersebut terdapat korelasi karena manusia merupakan makhluk sosial sehingga kehidupan manusia tidak bisa terlepas dari interaksi sosial, fisik, dan emosional. 73 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Vol.14, No.1, Januari 2022, pp. 71-88 ( ) pemerintah juga telah memperhatikan kesejahteraan lansia terlantar atau lansia dalam lingkaran ekonomi lemah melalui program penampungan melalui pendirian lembaga atau instansi yang disebut dengan Panti Werdha atau yang kita kenal dengan Panti Jompo. Akan tetapi, jauh sebelum itu pada Bulan Maret tahun 1953 menariknya telah berdiri lembaga non- formal yang mewadahi lansia di wilayah Jawa Tengah dan sekitarnya untuk menjembatani lansia memperoleh kesejahteraan batiniah dan jasmaniah, yaitu Pondok Pesantren Sepuh Masjid Agung Payaman. Pondok Pesantren Sepuh Masjid Agung Payaman ini menurut peneliti merupakan pondok pesantren yang unik karena diisi oleh santri lansia, sebagaimana kita ketahui pada umumnya pondok pesantren diisi oleh santri dengan rentang usia remaja awal hingga dewasa awal (13-40 tahun). Berdasarkan studi awal yang dilakukan oleh peneliti, ditemukan bahwa keseharian santri lansia di Pondok Pesantren Sepuh Masjid Agung Payaman antara lain melakukan interaksi dengan teman seusia (sesama lansia), mengaji dengan jadwal yang telah ditetapkan oleh pengurus pondok pesantren, dan shalat berjamaah lima waktu di Masjid Agung Payaman yang bersebelahan dengan asrama. Studi awal penelitian melalui wawancara terstruktur dengan salah satu lansia di Pondok Pesantren Sepuh Masjid Agung Payaman menemukan bahwa individu lansia tersebut mengalami kesepian yang diperlihatkan melalui perilaku yakni tingginya intensitas menghubungi keluarga di rumah melalui video call. Dalam wawancara dengan salah satu pengurus Pondok Pesantren Sepuh Masjid Agung Payaman, Bapak Nuruzzaman diketahui bahwa lokasi Pondok Pesantren Sepuh Masjid Agung Payaman ini dibagi menjadi dua, yakni asrama laki-laki dan perempuan. Meskipun demikian, pondok ini mayoritas diisi oleh santri lansia perempuan (santriwati) dan memiliki latar belakang yang beragam terkait alasan keputusannya untuk tinggal di asrama (nyantri) seperti: keinginan untuk memperdalam ilmu agama, sudah tidak ada keluarga yang bersedia mengurus, tinggal sendirian di rumah, tidak mempunyai kesibukan, merasa senang dan nyaman tinggal bersama rekan seusia, tidak mau merepotkan keluarga, serta keinginan pribadi untuk meninggal dalam keadaan husnul khotimah. Atas dasar studi awal dan fenomena yang ada di Pondok Pesantren Sepuh Masjid Agung Payaman, serta paparan latar belakang yang telah dijelaskan di atas. Maka peneliti merasa terdorong untuk mengetahui lebih dalam bagaimana sesungguhnya gambaran pengalaman kesepian, jenis kesepian, dan faktor pencetus kesepian seorang lansia yang tinggal di Pondok Pesantren Sepuh Masjid Agung Payaman, serta strategi koping apa yang dilakukan untuk mengatasi permasalahan tersebut. Wacana Untuk mengatasi masalah sosial dan juga psikologis lansia yang telah dipaparkan di atas, pemerintah telah mengesahkan UU No. 13 Tahun 1998 tentang Kesejahteraan Lanjut Usia guna mensejahterakan lansia baik secara batiniah maupun jasmaniah. Selain itu, dengan konsisten 74 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Vol.14, No.1, Januari 2022, pp. 71-88 Penelitian ini berjenis kualitatif dengan pendekatan fenomenologis, jenis dan pendekatan ini dinilai cocok dan mampu mengungkapkan secara mendalam serta natural (apa adanya) sesuai realita yang ada (Moleong, 2011). Sampling penelitian ini adalah purposive sampling, secara singkat teknik ini diartikan sebagai teknik pemilihan narasumber berdasarkan tujuan penelitian agar nantinya data yang didapat sesuai dengan topik dan permasalahan yang diangkat. Moleong (2011) menyebut bahwa dalam penelitian kualitatif tidak ada penarikan sampel acak seperti halnya penelitian berjenis kuantitatif. Oleh sebab itu, berdasarkan fokus kajian pada penelitian ini peneliti memilih dua (2) narasumber primer santri lansia (laki-laki dan perempuan) yang memiliki kriteria atau karakteristik yang sesuai tujuan penelitian yakni: pertama, kondisi fisik lansia, kondisi fisik lansia menjadi karakteristik utama dalam penentuan narasumber, sebab kondisi fisik dinilai akan berpengaruh pada tahapan pengumpulan data utama penelitian. Kedua, lansia yang kurang bersosialisasi dengan lingkungan, karakteristik ini dapat dijumpai melalui observasi pra penelitian yang dilakukan secara intensif dan komprehensif yang didasarkan pada landasan teori karakteristik kesepian yang diungkapkan oleh Suardiman (2016) yakni: menjadi kaum minoritas, tidak adanya perhatian dari orang lain, terisolasi dari lingkungan sosial, tidak adanya tempat untuk berbagi perasaan dan pengalaman, dan harus hidup sendiri tanpa adanya pilihan lain. Ketiga, sikap terhadap perubahan yang mereka alami, sikap ini lebih kepada aspek penerimaan dirinya sebagai lansia, sebab ditemui beberapa lansia yang tidak bersedia untuk diwawancarai terlebih mengenai kehidupan pribadinya. Peneliti juga menggunakan narasumber sekunder yakni pengasuh pondok pesantren guna memperkuat analisis dan data. Untuk mengetahui dan mendeskripsikan pengalaman kesepian santri lansia, maka teknik pengambilan data pada penelitian ini adalah wawancara mendalam (tidak mengikat) yang didasarkan pada aspek karakteristik kesepian (Suardiman, 2016) yakni: menjadi kaum minoritas, tidak adanya perhatian dari orang lain, terisolasi dari lingkungan sosial, tidak adanya tempat untuk berbagi perasaan dan pengalaman, dan harus hidup sendiri tanpa adanya pilihan lain, untuk mengidentifikasi jenis kesepian lansia, peneliti menggunakan 2 jenis kesepian yang diungkapkan oleh Weiss (dalam Natale, 1986) yakni: emotional isolation dan social isolation. Adapun untuk mengidentifikasi strategi koping lansia, peneliti menggunakan jenis strategi koping yang diungkapkan oleh Lazarus dan Folkman (dalam Maryam, 2017) yakni: emotional focused coping dan problem focused coping. Sedangkan untuk mengidentidikasi faktor pencetus kesepian, peneliti menggunakan 2 jenis faktor pencetus kesepian yang diungkapkan oleh Cherry & Parello (2008) yakni: situational factor dan characterological factor. Selain itu peneliti juga menggunakan teknik observasi non-partisipan, dan dokumentasi. Metode 75 Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Proses analisis data terbagi menjadi tiga (3) yakni reduksi, penyajian data, dan penarikan kesimpulan. Adapun untuk menguji keabsahan data, peneliti menggunakan teknik triangulasi metode dan sumber. 76 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Hasil Pondok Pesantren Sepuh Masjid Agung Payaman didirikan oleh K.H. Muhammad Siradj Anwari bin Abdurrosyad pada masa penjajahan Belanda. Dalam penelitian skripsi yang dilakukan oleh Marzuqoh (2020) dikatakan bahwa Pondok Pesantren Sepuh Masjid Agung Payaman didirikan pada tahun 1953. Akan tetapi, hasil dari penelusuran yang dilakukan oleh peneliti secara lebih dalam terkait dengan sejarah berdirinya Pondok Pesantren Sepuh Masjid Agung Payaman ditemukan bahwa pondok pesantren tersebut telah ada dan berdiri sejak tahun 1937 bersamaan dengan pembangunan Masjid Agung Payaman. Menurut Bapak Nuruzzaman, pemberian nama Pondok Pesantren Sepuh Masjid Agung Payaman dikarenakan lokasinya yang berdampingan dengan Masjid Agung Payaman dan mayoritas diisi oleh santri yang berusia lanjut (60 tahun lebih). Saat ini pondok pesantren tersebut dihuni oleh 28 orang santri lansia yang terdiri dari 22 santriwati dan 6 santri. Berdasarkan wawancara dengan Bapak K.H. Muhammad Tibyan dan Bapak Nuruzzaman daya tampung dari Pondok Pesantren Sepuh Masjid Agung Payaman adalah 44 orang santri lansia. Para santri dan santriwati yang nyantri di Pondok Pesantren Sepuh Masjid Agung Payaman ini memiliki jadwal harian dan mingguan yang terstruktur setiap hari dan minggunya, berikut tabel jadwal harian dan mingguannya: Tabel 1. Jadwal Harian Santri Pondok Pesantren Sepuh Masjid Agung Payaman Kegiatan Tempat Waktu Sholat Tahajud Masjid Agung Payaman 02.00-03.00 WIB Membaca Al-Qur’an Masjid Agung Payaman 03.00-04.30 WIB Sholat Subuh Berjamaah Masjid Agung Payaman 04.30-05.00 WIB Sholat Isra’ dan Sholat Dhuha Masjid Agung Payaman 05.00-07.30 WIB Jam Kosong atau Diisi dengan Kegiatan Pribadi (Mencuci, Masak, Mandi) Pondok Pesantren Sepuh Masjid Agung Payaman 07.30-10.00 WIB Pengajian Masjid Agung Payaman 10.00-12.00 WIB Sholat Dzuhur Berjamaah Masjid Agung Payaman 12.00-13.00 WIB Pengajian Al-Qur’an Rumah Ibu Tibyan 13.00-14.00 WIB Istirahat - 14.00-15.00 WIB Salat Asar Berjamaah Masjid Agung Payaman 15.00-15.30 WIB Pengajian Nguping (Kajian Al-Ibriz) Masjid Agung Payaman 15.30-16.30 WIB Kegiatan Pribadi dan Shalat Maghrib Berjamaah Pondok Pesantren, Masjid Agung Payaman 16.30-18.00 Kegiatan Pribadi Masjid Agung Payaman 18.00-18.45 WIB Shalat Isya’ Berjamaah Masjid Agung Payaman 18.45-19.15 WIB Istrirahat Pondok Pesantren Sepuh Masjid Agung Payaman 19.15-02.00 WIB Tabel 2. Jadwal Mingguan Santri Pondok Pesantren Sepuh Masjid Agung Payaman Kegiatan Tempat Waktu Jadwal Harian Santri Pondok Pesantren Sepuh Masjid Agung Payaman Kegiatan Tempat Waktu Sholat Tahajud Masjid Agung Payaman 02.00-03.00 WIB Membaca Al-Qur’an Masjid Agung Payaman 03.00-04.30 WIB Sholat Subuh Berjamaah Masjid Agung Payaman 04.30-05.00 WIB Sholat Isra’ dan Sholat Dhuha Masjid Agung Payaman 05.00-07.30 WIB Jam Kosong atau Diisi dengan Kegiatan Pribadi (Mencuci, Masak, Mandi) Pondok Pesantren Sepuh Masjid Agung Payaman 07.30-10.00 WIB Pengajian Masjid Agung Payaman 10.00-12.00 WIB Sholat Dzuhur Berjamaah Masjid Agung Payaman 12.00-13.00 WIB Pengajian Al-Qur’an Rumah Ibu Tibyan 13.00-14.00 WIB Istirahat - 14.00-15.00 WIB Salat Asar Berjamaah Masjid Agung Payaman 15.00-15.30 WIB Pengajian Nguping (Kajian Al-Ibriz) Masjid Agung Payaman 15.30-16.30 WIB Kegiatan Pribadi dan Shalat Maghrib Berjamaah Pondok Pesantren, Masjid Agung Payaman 16.30-18.00 Kegiatan Pribadi Masjid Agung Payaman 18.00-18.45 WIB Shalat Isya’ Berjamaah Masjid Agung Payaman 18.45-19.15 WIB Istrirahat Pondok Pesantren Sepuh Masjid Agung Payaman 19.15-02.00 WIB Tabel 2. Jadwal Mingguan Santri Pondok Pesantren Sepuh Masjid Agung Payaman Kegiatan Tempat Waktu wal Harian Santri Pondok Pesantren Sepuh Masjid Agung Payaman Jadwal Harian Santri Pondok Pesantren Sepuh Masjid Agung Payaman 77 Wacana Vol.14, No.1, Januari 2022, pp. Tabel 1. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Berjanjen (Pembacaan Kitab Al-Barjanji Masjid Agung Payaman Selasa Malam (19.15 WIB-selesai) Pembacaan Surah Yasiin dan Dzikir Fida’ Masjid Agung Payaman Kamis Malam Jum’at (19.15 WIB -selesai) Kuliah Subuh Masjid Agung Payaman Minggu Pagi (04.45 WIB – selesai) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Hasil analisis data dan interpretasi pada narasumber primer santri lansia Ibu SS (I) dan Bapak TH (II) pada penelitian ini menunjukkan bahwa keduanya mengalami kesepian dengan jenis emotional isolation dan social isolation, adapun faktor pencetus kesepian dari kedua narasumber yakni faktor situasi (situational factor), berikut deskripsi pengalaman kesepian, jenis, faktor pencetus, dan strategi koping kedua santri lansia yang menjadi narasumber primer penelitian: Ibu SS (I) merupakan santriwati lansia di Pondok Pesantren Sepuh Masjid Agung Payaman sejak 2018. Sebelum memutuskan untuk nyantri, beliau adalah Ibu Rumah Tangga yang juga memiliki kesibukan sebagai penjahit di Yayasan, pendidikan terakhir Ibu SS adalah Sekolah Menengah Pertama (SMP) saat ini usia Ibu SS adalah 62 Tahun, suami beliau telah meninggal dunia pada tahun 2012 lalu, ia memiliki 3 orang anak dan 4 cucu. Saat ini ia tinggal bersama anaknya di Wonosobo, Jawa Tengah. Adapun motivasi Ibu SS masuk ke Pondok Pesantren Sepuh Masjid Agung Payaman menurut hasil wawancara: “Pribadi mas, kalau dari anak nanti tertekan mas, ingin sekali malah untuk bekal akhirat.” Keinginan pribadi untuk tinggal jauh dari rumah telah Ibu SS pertimbangkan sebab ia ingin meninggal dengan keadaan hunsul khotimah dan fokus dengan akhirat. Dalam observasi yang dilakukan peneliti ditemukan bahwa Ibu SS termasuk dalam kaum minoritas sebab Ibu SS hanya melakukan interaksi dengan rekan sebaya saja. Interaksi ini berbentuk kegiatan memasak bersama, mencuci baju bersama, dan juga berbelanja ke pasar bersama. Dalam observasi ditemukan bahwa Ibu SS jarang melakukan interaksi dengan warga sekitar, terkhusus pada orang yang lebih muda walaupun sudah 3 tahun berada di Pondok Pesantren tersebut, interpretasi ini pun didasarkan pada pernyataan Ibu SS yang mengatakan bahwa: “Saya tidak pernah ikut kegiatan sosial.” “Ya, ingat masa lalu, kalau ekonomi sudah biasa, kasih sayang, masa lalu.” “Mau curhat sama siapa saya bingung mas, ya seperti itulah.” “Saya tidak pernah ikut kegiatan sosial.” Selanjutnya dalam wawancara yang dilakukan dengan narasumber sekunder ditemukan bahwa: “Selama 3 tahun Ibu SS tidak pernah pindah kamar, dan selalu bersama dengan rekan- rekanya dari awal masuk hingga sekarang.” 78 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Vol.14, No.1, Januari 2022, pp. 71-88 “Kalau di sini tidak pernah diajak atau ikut kegiatan masyarakat.” “Kalau di sini tidak pernah diajak atau ikut kegiatan masyarakat.” Ibu SS dinilai kurang bisa melakukan adaptasi dengan lingkungan baru. Adapun jenis kesepian yang dialami oleh Ibu SS adalah emotional isolation dan social isolation. Dalam emotional isolation ditunjukkan dengan kurangnya kasih sayang dari orang terkasih (suami) yang telah meninggal dunia. Pada saat wawancara berlangsung telihat jelas ketika peneliti menyinggung suami, air mata dari Ibu SS menetes, Ibu SS mengatakan bahwa: “Ya, ingat masa lalu, kalau ekonomi sudah biasa, kasih sayang, masa lalu.” “Ya, ingat masa lalu, kalau ekonomi sudah biasa, kasih sayang, masa lalu.” Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Dari pernyataan tersebut peneliti menginterpretasikan bahwa Ibu SS cenderung memilih tempat di mana ia diterima, diperhatikan, dan sesuai dengan keinginan Ibu SS yang mana termasuk dalam karakteristik kesepian terkait dengan tidak adanya perhatian dari orang lain. Dalam wawancara dengan Ibu SS pun ditemukan bahwa Ibu SS juga terisolasi dari lingkungan sosial, hal ini dibuktikan dengan pernyataanya, yakni: “Kalau di sini tidak pernah diajak atau ikut kegiatan masyarakat.” “Mau curhat sama siapa saya bingung mas, ya seperti itulah.” Dari pernyataan tersebut jelas bahwa suami yang menjadi tempatnya bersandar, sebagai teman hidup telah tiada. Artinya Ibu SS kehilangan sosok yang sangat berarti untuk menjalani dinamika kehidupan. Selanjutnya kesepian berjenis social isolation ditunjukkan dengan tidak pernahnya Ibu SS mengikuti kegiatan sosial yang ada di area Pondok Pesantren Sepuh Masjid Agung Payaman dan juga tidak pernah berpindahnya kamar selama masuk hingga saat ini. Adapun faktor pencetus kesepian Ibu SS adalah faktor situasi (situational factor). Kepribadian Ibu SS yang terbuka membuat faktor karakter bukan menjadi pencetus kesepian yang ia rasakan, faktor situasi ini lebih tepat sebab Ibu SS jauh dari rumah, keluarga, anak, dan cucu. Interpretasi ini pun diperkuat dengan hasil wawancara dengan narasumber sekunder yakni: “Ya, pada awal mondok itu mas, Bu SS sering ijin pulang seminggu bisa 2 sampai 3 kali karena kangen dengan anak dan cucunya di rumah.” Selain wawancara dengan narasumber sekunder, interpretasi terkait dengan faktor pencetus kesepian ini juga dijumpai dalam wawancara dengan Ibu SS yang menyatakan bahwa: 79 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Awal-awal itu kangen dengan cucu mas, tapi lama kelamaan biasa karena pikiran saya cucu sudah ada bapak ibunya, saya tinggal fokus mengaji.” Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Daripada minta bantuan saya atasi sendiri.” Selanjutnya dalam emotional focused coping, Ibu SS juga menekankan aspek menghindarkan diri hal ini ditunjukkan pada hasil wawancara yang menyebutkan bahwa: “Ya ada sih yang tidak menerima, saya serahkan saja kepada yang lebih tua, memang ada.” “Ya ada sih yang tidak menerima, saya serahkan saja kepada yang lebih tua, memang ada.” Dari hasil wawancara yang dilakukan dengan Ibu SS dapat diinterpretasikan bahwa Ibu SS lebih memilih untuk menghindar dari permasalahan yang tengah dialami. Dalam strategi problem focused coping, Ibu SS menerapkan confrontative coping, berikut pernyataan Ibu SS terkait dengan strategi koping tersebut: “Biasanya saya keluar sebentar dan langsung minta maaf.” Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Awal-awal itu kangen dengan cucu mas, tapi lama kelamaan biasa karena pikiran saya cucu sudah ada bapak ibunya, saya tinggal fokus mengaji.” Atas dasar hasil analisis dan interpretasi tersebut maka kesepian Ibu SS termasuk dalam jenis emotional isolation dan social isolation dengan faktor pencetus situasi (situational factor). Strategi koping yang digunakan oleh Ibu SS terkait dengan kesepian adalah emotional focused coping dan problem focused coping. Saat Ibu SS tidak dipedulikan oleh orang lain, hal yang dilakukan oleh Ibu SS adalah dengan memberikan penilaian positif. Pemberian nilai ini diinterpretasikan peneliti termasuk dalam strategi emotional focused coping. Lebih detail, manifestasi dari hal tersebut adalah dengan bentuk mendoakan, hal ini diungkapkan Ibu SS saat wawancara: “Biar ingat mas, biar sadar, saya doakan, malah tidak saya benci.” “Biar ingat mas, biar sadar, saya doakan, malah tidak saya benci.” Dalam jenis emotional focused coping, Ibu SS juga menggunakan aspek penekanan pada tanggung jawab dengan menekankan pada peran dirinya serta mendudukan segala sesuatu menyesuaikan dirinya (lebih ke perasaan atau non-fisik). Hal ini ditunjukkan dengan hasil wawancara dengan Ibu SS yang menyatakan bahwa: “Daripada minta bantuan saya atasi sendiri.” “Daripada minta bantuan saya atasi sendiri.” “Biar ingat mas, biar sadar, saya doakan malah tidak saya benci.” Kemudian analisis dan interpretasi yang dilakukan peneliti pada narasumber primer Bapak TH (II) ditemukan bahwa Bapak TH merupakan seorang pensiunan Pekerja Negeri Sipil (PNS) sejak tahun 2016, lalu sebagai sopir di Mabes, yang berasal dari Jakarta Timur. Dari latar belakang inilah peneliti menyimpulkan bahwa Bapak TH memiliki kegiatan atau aktivitas rutin dengan mobilitas yang cukup tinggi, terjadwal, dan terorganisir setiap harinya. Saat ini beliau telah menginjak usia kepala 6, yakni 64 tahun, di Cipayung, Jakarta Timur, Bapak TH tinggal bersama Istri, memiliki empat (4) anak yang sudah menikah dan bekerja. Adapun motivasi Bapak TH masuk ke Pondok Pesantren Sepuh ini adalah: “Setelah saya pergi dan ke sini saya merasa mengurangi dosa yang saya perbuat.” “Biasanya saya keluar sebentar dan langsung minta maaf.” Interpretasi ini lebih menekankan pada reaksi nyata untuk mengubah keadaan yang dapat mengubah tingkat resiko. Penelitian ini menghasilkan temuan terkait dengan strategi koping religius yang dilakukan oleh Ibu SS yakni strategi koping religius positif dengan 80 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Vol.14, No.1, Januari 2022, pp. 71-88 Vol.14, No.1, Januari 2022, pp. 71-88 menekankan pada metode collaborative dan spiritual support. Berikut hasil interpretasi hasil wawancara terkait dengan strategi koping religius positif yang diterapkan oleh Ibu SS: “Saya curhat dengan Allah, alhamdulillah bisa diatasi, curhatnya sama Allah.” “Saya curhat dengan Allah, alhamdulillah bisa diatasi, curhatnya sama Allah.” Wacana Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Selama ini saya tinggal di sini belum pernah mas, belum ada yang mengajak bersosial di lingkungan sini, jadi di sini cuma mengaji saja.” “Selama ini saya tinggal di sini belum pernah mas, belum ada yang mengajak bersosial di lingkungan sini, jadi di sini cuma mengaji saja.” Lingkungan sosial dirasa kurang memberikan ruang untuk Bapak TH melakukan interaksi yang lebih luas dan membangun hubungan individu dengan sosial. Oleh sebab itu, Bapak TH lebih memilih tinggal di tempat di mana ia diterima, diperhatikan, serta sesuai dengan keinginanya. Pada wawancara yang dilakukan dengan narasumber sekunder, ditemukan bahwa Bapak TH sering menelepon rumah untuk sekadar menanyakan kabar: sedang apa, masak apa, sudah sarapan, atau ada cerita apa hari ini. Hal ini selaras dengan temuan dalam observasi yang dilakukan, peneliti menemukan bahwa selama sehari Bapak TH secara intens menelepon (video call) sebanyak 3 sampai 5 kali dengan istri, anak, atau cucunya. Dari observasi ini peneliti menginterpretasikan bahwa sejatinya Bapak TH ini kurang memiliki tempat yang nyaman untuk bercerita serta mengalami kejenuhan berada di Pondok Pesantren, interpretasi peneliti ini diperkuat dengan hasil wawancara dengan Bapak TH yang mengatakan: “Ketika saya jenuh saya pulang Jakarta terus ke sini lagi mas.” “Setelah saya pergi dan ke sini saya merasa mengurangi dosa yang saya perbuat.” “Memang saya muslim tapi kalau belajar agama itu masa bodoh, tapi setelah tua saya merasa nanti kalau saya tua itu saya sendiri yang bisa menolong.” Pernyataan tersebut menandakan bahwa keinginan untuk tinggal jauh dari rumah dan keluarga di Pondok Pesantren Sepuh Masjid Agung Payaman ini didasarkan pada dorongan pribadi untuk lebih dekat dengan Sang Pencipta karena Bapak TH merasa pada saat muda tidak pernah belajar agama dan sering berbuat dosa. Deskripsi pengalaman kesepian berdasarkan hasil wawancara dengan Bapak TH. Bapak TH masuk dalam karakteristik kesepian sebagai kaum minoritas sebab Bapak TH jarang melakukan interaksi dengan lingkungan sekitar terkecuali dengan rekan sebaya di Pondok Pesantren Sepuh, hal ini diperjelas dengan hasil wawancara: “Di sini itu sosialnya cuma dengan teman sebaya, kalau ada waktu luang kita jalan-jalan, sekitar 5 kilometer balik lagi.” Selanjutnya Bapak TH mengalami kesepian karena kurangnya perhatian dari lingkungan sosial, Bapak TH mengatakan bahwa: 81 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Selama ini saya tinggal di sini belum pernah mas, belum ada yang mengajak bersosial di lingkungan sini, jadi di sini cuma mengaji saja.” Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) “Ketika saya jenuh saya pulang Jakarta terus ke sini lagi mas.” Dalam wawancara pun peneliti menemukan bahwa selama 1 tahun tinggal di Pondok Pesantren Sepuh Bapak TH sudah pulang (Jakarta-Magelang) sebanyak 25 kali: “Setahun di sini saya pulang 25 kali mas.” “Setahun di sini saya pulang 25 kali mas.” Jenis kesepian yang dirasakan oleh Bapak TH adalah kesepian emotional isolation dan social isolation, jenis emotional isolation ditunjukkan dengan intensitas komunikasi, jauh dari keluarga sehingga merasa kurang diperhatikan atau disayangi. Hal ini menjadi pencetus kesepian emotional isolation Bapak TH, interpretasi ini didasarkan pada hasil wawancara yang mana Bapak TH mengatakan: “Kita sering video call dengan anak cucu sehari bisa lima kali, mendoakan agar saya tetap sehat.” “Kadang-kadang ke sini baru sebulan kangen jenuh di sini, setelah itu pulang sebulan kesini lagi.” Intensitas memberi kabar, lamanya melakukan video call, dan keinginan untuk terus pulang mengindikasikan bahwa sejatinya Bapak TH ingin dekat dengan keluarga, namun di sisi 82 Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ana 4, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Vol.14, No.1, Januari 2022, pp. 71-88 Vol.14, No.1, Januari 2022, pp. 71-88 lain ingin belajar agama dengan sungguh-sungguh. Selain data wawancara dengan Bapak TH peneliti juga menemukan hasil wawancara dengan narasumber sekunder dan observasi yang memperkuat interpretasi tersebut. Dalam hal ini ditemukan bahwa Bapak TH sering melamun dan menceritakan cucu dan anaknya pada narasumber sekunder yang notabenenya merupakan pengurus Pondok Pesantren Sepuh Masjid Agung Payaman. Selanjutnya dalam kesepian berjenis social isolation ditunjukkan dengan kurangnya interaksi sosial, interaksi yang dilakukan oleh Bapak TH terbatas hanya dengan rekan-rekan sebaya di Pondok Pesantren. Hal ini pun menjadi pencetus kesepian social isolation. Interpretasi ini didasarkan pada hasil wawancara dengan Bapak TH yang mengatakan bahwa: Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Dari dua pernyataan dari Bapak TH tersebut dapat diinterpretasikan bahwa strategi koping yang dilakukan oleh Bapak TH adalah confrontative coping dan seeking social support. Confrontative coping ditunjukkan dengan reaksi untuk mengubah keadaan yang dapat merubah tingkat risiko, sedangkan pada seeking social support Bapak TH adalah keterbukaan dengan cara mencari teman sebaya yang dirasa nyaman untuk dijadikan tempat berkeluh kesah. Kedua hal tersebut termasuk dalam problem focused coping. Adapun dalam penelitian ini Bapak TH juga menggunakan strategi koping religius yakni dengan collaborative religious coping, atau penekanan pada kerjasama antara Sang Pencipta dengan individu baik secara aktif atau pasif, interpretasi ini didasarkan pada pernyataan Bapak TH saat wawancara: “Kalau tidak ada kegiatan apa-apa saya ambil wudhu salat dua rekaat atau empat, setelah itu mungkin kembali lagi.” “Selama ini ya wudhu mas, shalat, mandi udah begitu saja mas.” “Selama ini ya wudhu mas, shalat, mandi udah begitu saja mas.” Strategi koping religius yang digunakan oleh Bapak TH ini masuk dalam aspek strategi koping religius positif. Koping religius positif dianggap sebagai suatu ekspresi spiritualitas, hubungan yang memberikan rasa aman dengan Tuhan, adanya makna yang dapat ditemukan dalam setiap kehidupan, serta adanya hubungan spiritualitas dengan orang lain. “Belum pernah diajak, ayo bapak-bapak ikut membersihkan masjid atau apa.” “Belum pernah diajak, ayo bapak-bapak ikut membersihkan masjid atau apa.” “Selama ini saya tinggal di sini belum pernah mas, belum ada yang mengajak bersosial di lingkungan sini, jadi di sini cuma mengaji saja.” Berdasarkan hasil analisis data observasi dan wawancara tersebut maka Bapak TH menunjukkan bahwasanya Bapak TH mengalami dua jenis kesepian, yakni kesepian berjenis isolasi emosional dan sosial yang tercetus atas faktor situasi (situational factor). Adapun strategi koping atau upaya yang dilakukan Bapak TH untuk mengatasi kesepian tersebut adalah dengan menekankan pada tanggung jawab dirinya, berikut beberapa hal yang dilakukan Bapak TH untuk mengatasi kesepian yang ia alami: “Saya merasa mampu mengatasi masalah saya mas.” “Saya itu emosinya tinggi, saya sering pergi, saat belum pensiun saya sering badminton.” Jawaban Bapak TH saat wawancara dapat diinterpretasikan sebagai strategi koping berupa penekanan pada tanggung jawab dan menghindarkan diri yang masuk dalam kategori emotional focused coping. Selanjutnya Bapak TH mengatakan: “Saya itu merasa senang mas, orangnya gampang bicara, terbuka selama saya pensiun itu tidak ada persoalan serius.” “Saya itu merasa senang mas, orangnya gampang bicara, terbuka selama saya pensiun itu tidak ada persoalan serius.” “Ya namanya juga manusia mas, ketika sepi di sini tidak ada kegiatan, merasa sepi kadang berfikir apa besok pulang saja ya, kalau lagi senang tidak ada pikiran mau pulang mas. Saya itu tidak memiliki prinsip mas, saya begini besok pagi ingin pulang saya pulang.” 83 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Pembahasan Atas dasar hasil penelitian maka berikut ini ringkasan jawaban atas rumusan masalah penelitian yang disajikan melalui tabel kemudian akan dideskripsikan dan dibahas berdasarkan landasan teori dan penelitian sebelumnya yang sesuai (relevan) pada penelitian ini sebagai bahan diskusi atau pembahasan: Tabel 3 Tabel 3 Hasil Penelitian No Nama Jenis Kelamin Usia Status Jenis Kesepian Faktor Pencetus Strategi Koping Pekerjaan Perkawinan 1 Ibu SS P 62 IRT Janda Emotional Isolation, dan Social Isolation Situational Religious Coping, Emotional Focused Coping, Problem Focused Coping 2 Bapak TH L 64 Pensiunan PNS Suami Emotional Isolation, dan Social Situational Religious Coping, Emotional Focused Coping, 84 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Isolation Problem Focused Coping Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Isolation Problem Focused Coping Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Problem Focused Coping Dengan jadwal kegiatan harian dan mingguan yang telah ditetapkan oleh pengurus Pondok Pesantren Sepuh Masjid Agung Payaman serta menempatkan lansia dalam satu wadah yang sama dengan mereka (lingkungan seusia) sebagai bentuk support atau memberikan pengertian dan memberikan keterikatan emosional: bahwa tidak hanya ‘dirinya’ saja yang mulai menua melainkan ada orang lain yang sama dengan dirinya. Dalam penelitian yang telah dilakukan ini ditemukan bahwa kedua narasumber primer, yakni santri lansia tetap mangalami kesepian dengan gambaran pengalaman kesepian yang didasarkan pada empat (4) dari lima (5) karakteristik kesepian yang diungkapkan oleh Suardiman (2016) yakni: menjadi kaum minoritas, tidak adanya perhatian dari orang lain, terisolasi dari lingkungan sosial, dan tidak adanya tempat untuk berbagi perasaan dan pengalaman. Selain itu, temuan pada penelitian ini menjadi pembanding atas teori yang diungkapkan oleh Neugarten (dalam Suardiman, 2016) tentang theory activity yang menyebutkan bahwa dengan adanya kegiatan sehari-hari (daily act) yang jelas dan aktif maka lansia akan memiliki kesehatan yang baik dalam aspek fisik, sosial, dan mental. Pada kenyataanya lansia di Pondok Sepuh Masjid Agung Payaman ini tetap mengalami kesepian dengan gambaran pengalaman seperti yang telah peneliti paparkan sebelumya. Hasil wawancara tersebut memberikan pengertian bahwa kedua narasumber primer mengalami kesepian secara emosional dan sosial, sejalan dengan apa yang diungkapkan oleh Landau Jacob (dalam Natale, 1986) yang mengatakan bahwa kesepian adalah rasa lapar yang kuat akan keintiman dan komunitas, tanda alamiah bahwa kita kurang memiliki kompansi, kedekatan, dan tempat yang ramah di lingkunganya, sehingga temuan ini pun selaras dengan apa yang diungkapkan oleh Suardiman (2016) yang menyatakan bahwa seorang lansia cenderung memilih tempat di mana ia merasa diperhatikan, diterima, dan sesuai dengan keinginanya. Simpulan Kegiatan sehari-hari yang jelas dan terstruktur tetap memberikan celah pada perasaan kesepian seeorang, temuan ini mejadi pembanding theory activity karena kedua santri lansia di pondok pesantren mengalami kesepian dengan jenis campuran (emotional isolation dan social isolation) yang ditunjukkan melalui tingginya intensitas video call dengan anggota keluarga dan ijin kepulangannye ke rumah, keinginan untuk ikut bersosial namun tidak adanya ajakan, serta memilih tempat dimana mereka diterima dan nyaman. Kesepian tersebut tercetus karena faktor situasi (situational factor) dimana santri lansia ingin memperdalam ilmu agama namun sekaligus ingin selalu dekat dengan orang yang mereka kasihi. Untuk mengatasi hal tersebut kedua santri lansia menggunakan strategi koping (emotional focused coping dan problem focused coping). Penelitian inipun menemukan bahwa kedua santri lansia juga menggunakan strategi koping religius yang memiliki perbedaan dengan lansia yang tinggal di panti werdha. Lebih dalam lagi penelitian ini menemukan bahwa gender perempuan lebih bisa mengungkapkan perasaanya secara ekspresif, serta memiliki rentang hidup yang lebih panjang daripada laki-laki. Implikasi Terdapat beberapa kekurangan dalam penelitian ini yang harus diperbaiki, oleh karena itu saran yang relevan bagi peneliti lanjutan yang memiliki minat serupa dengan fokus kajian penelitian ini yakni pertanyaan atas bagaimana karakteristik lansia yang religius itu?, apa sejatinya kebutuhan sosial bagi seorang lansia? (interaksi yang sering atau sedikit interaksi namun berkualitas?), dan apakah benar lansia di pondok pesantren memiliki strategi koping yang berbeda dengan lansia yang tinggal di panti werdha, disarankan pula peneliti lanjutan menggunakan jenis dan pendekatan yang berbeda agar data yang dihasilkan lebih bervarian dan komprehensif. Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Vol.14, No.1, Januari 2022, pp. 71 88 pondok pesantren memberikan lansia sebuah jembatan untuk mengatasi permasalahan terkait dengan kesepian melalui strategi koping religius positif dalam bentuk collaborative dan spiritual support. Namun di sisi lain temuan dari penelitian inipun mendukung penelitain yang telah dilakukan Setiawan (2013) dan Sessiani (2018) yang menyebutkan bahwa lansia dengan jenis kelamin perempuan lebih bisa mengutarakan perasaanya secara ekspresif dan langsung daripada lansia berjenis kelamin laki-laki, serta gender perempuan memiliki rentang hidup yang lebih panjang daripada laki-laki. Tabel 3 Lebih dalam lagi, peminatan lansia dalam memperdalam bidang keagamaan juga selaras dengan apa yang diungkapkan oleh Hurlock (2002) yang menyatakan bahwa lansia mengalami perubahan-perubahan baik secara fisik, mental, dan social. Salah satu perubahan tersebut adalah perubahan pada aspek spiritual dimana lansia semakin terasah dan konsisten terhadap agama yang mereka anut. Namun di satu sisi terdapat perbedaan antara lansia yang berada di Panti Werdha dengan lansia yang tinggal di pondok pesantren, sebab dalam wawancara dan observasi ditemukan strategi koping religius positif yang diterapkan oleh kedua lansia yang tinggal di pondok pesantren, hal ini berbeda dengan hasil dari penelitian yang dilakukan oleh Setiawan (2013) yang menyebut bahwa strategi koping kesepian lansia yang tinggal di Panti Werdha Sultan Fatah Demak yakni menjemur nasi dan melakukan kegiatan senam bersama, hal tersebut memberikan pengertian bahwa suasana atau atmosfer religius di 85 Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) pondok pesantren memberikan lansia sebuah jembatan untuk mengatasi permasalahan terkait Wacana Vol.14, No.1, Januari 2022, pp. 71-88 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) pondok pesantren memberikan lansia sebuah jembatan untuk mengatasi permasalahan terkait dengan kesepian melalui strategi koping religius positif dalam bentuk collaborative dan spiritual support. Namun di sisi lain temuan dari penelitian inipun mendukung penelitain yang telah dilakukan Setiawan (2013) dan Sessiani (2018) yang menyebutkan bahwa lansia dengan jenis kelamin perempuan lebih bisa mengutarakan perasaanya secara ekspresif dan langsung daripada lansia berjenis kelamin laki-laki, serta gender perempuan memiliki rentang hidup yang lebih panjang daripada laki-laki. ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Ucapan Terima Kasih Pertama peneliti ingin mengucapkan terima kasih atas rahmat yang diberikan oleh Tuhan Yang Maha Esa sehingga peneliti memiliki kesempatan untuk sedikit berkontribusi dalam 86 ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Vol.14, No.1, Januari 2022, pp. 71-88 kedua orang tuaku, serta semua pihak yang tak bisa peneliti sebutkan satu per satu. Terima kasih. DAFTAR PUSTAKA DAFTAR PUSTAKA A, Cherly & K, Parello. (2008). Loneliness in the School Setting. 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Aceh: Universitas Malikussaleh. https://pdfs.semanticscholar.org/df2f/9c2657b608da5a3162e6c44a2b1a69ef368e. pdf Diakses Pada 12 Januari 2022 Pada Pukul 02.45 WIB. p Marzuqoh, Umi Afi. (2020). Pembinaan Keagamaan bagi Santri Lansia di Pondok Pesantren Sepuh Masjid Agung Payaman Kabupaten Magelang Tahun 2020. Skripsi, Salatiga: Program Studi Pendidikan Agama Islam, Fakultas Tarbiyah dan Ilmu Keguruan, Institut Agama Islam Negeri Salatiga. http://e- repository.perpus.iainsalatiga.ac.id/9417/ Diakses Pada 12 Januari 2022 Pada Pukul 02.30 WIB. Moleong, Lexy, J. (2011). Metodologi Penelitian Kualitatif Edisi Revisi. Bandung: PT. Remaja Rosdakarya. Munandar, I., Hadi, S., & Ardiyani, V. M. (2017). Hubungan Dukungan Keluarga Dengan Tingkat Kesepian Pada Lansia yang Ditinggal Pasangan di Desa Mensere. Jurnal Nursing News, Vol. 2, No. 2. 447-457. Malang: Universitas Tribhuwana Tungga Dewi. https://doi.org/10.33366/nn.v2i2.491 Natale, Samuel M. (1986). Loneliness and Spiritual Growth. Brimigham: Religious Education Press Inc. Novitasari, R.D & Aulia, D. (2019). Kebersyukuran dan Kesepian pada Lansia yang Menjadi Janda/Duda. Jurnal Ilmiah Psikologi Terapan, 7(2), 146-157. https://doi.org/10.22219/jipt.v7i2.8951. Pusat Data & Informasi, Kementerian Kesehatan Republik Indonesia. (2017). Analisis Lansia di Indonesia. https://pusdatin.kemkes.go.id/download.php?file=download/pusdatin/lai n-lain/Analisis%20Lansia%20Indonesia%202017.pdf. Diakses Pada 12 Januari 2020 Pada Pukul 22.22 WIB. Sessiani, L. (2018). Studi Fenomenologis tentang Pengalaman Kesepian dan Kesejahteraan Subjektif pada Janda Lanjut Usia. Sawwa: Jurnal Studi Gender, 13(2), 203-236. doi:http://dx.doi.org/10.21580/sa.v13i2.2836. Setiawan, Bintang M. (2013). Kesepian pada Lansia di Panti Werdha Sultan Fatah Demak. Skripsi, Jurusan Psikologi, Fakultas Ilmu Pendidikan. Semarang: Universitas Negeri Semarang. http://lib.unnes.ac.id/18572/1/1550408086.pdf Diakses Pada 12 Januari 2022 Pada Pukul 01.30 WIB. 87 Wacana ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) ISSN 2985-0514 (Print) E-ISSN 2716-1625 (Online) Wacana Vol.14, No.1, Januari 2022, pp. 71-88 Suardiman, S.P. (2016). Psikologi: Usia Lanjut. Yogyakarta: Gadjah Mada University Press. g j g j Sunaryanto, dkk. (2015). Asuhan Keperawatan Gerontik. Yogyakarta: Andi Offset. Tegawati, L. M., Karini, S. M., & Agustin, R. W. (2009). Pengaruh Senam Lansia Terhadap Penurunan Tingkat Depresi pada Orang Lanjut Usia. Wacana, 1(2). https://doi.org/10.13057/wacana.v1i2.62 Utami & Amawidyati. (2012). Religiusitas dan Psychological Well‐Being Pada Korban Gempa. Jurnal Psikologi, Vol 34, NO. 2, 164 – 176. Yogyakarta: Universitas Gadjah Mada. doi: 10.22146/jpsi.7095. Winningham, R.G., & Pike, N.L. (2007). 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RUTI Vaccination Enhances Inhibition of Mycobacterial Growth ex vivo and Induces a Shift of Monocyte Phenotype in Mice
Frontiers in immunology
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RUTI Vaccination Enhances Inhibition of Mycobacterial Growth ex vivo and Induces a Shift of Monocyte Phenotype in Mice Satria A. Prabowo 1,2*, Hannah Painter 1,2, Andrea Zelmer 1,2, Steven G. Smith 1,2, Karin Seifert 1†, Merce Amat 3, Pere-Joan Cardona 4,5 and Helen A. Fletcher 1,2 Satria A. Prabowo 1,2*, Hannah Painter 1,2, Andrea Zelmer 1,2, Steven G. Smith 1,2, Karin Seifert 1†, Merce Amat 3, Pere-Joan Cardona 4,5 and Helen A. Fletcher 1,2 1 Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom, 2 Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom, 3 Archivel Farma S.L., Badalona, Spain, 4 Experimental Tuberculosis Unit (UTE), Fundació Institut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona (UAB), Badalona, Spain, 5 Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias, Madrid, Spain Tuberculosis (TB) is a major global health problem and there is a dire need for an improved treatment. A strategy to combine vaccination with drug treatment, termed therapeutic vaccination, is expected to provide benefit in shortening treatment duration and augmenting treatment success rate. RUTI candidate vaccine has been specifically developed as a therapeutic vaccine for TB. The vaccine is shown to reduce bacillary load when administered after chemotherapy in murine and guinea pig models, and is also immunogenic when given to healthy adults and individuals with latent TB. In the absence of a validated correlate of vaccine-induced protection for TB vaccine testing, mycobacterial growth inhibition assay (MGIA) has been developed as a comprehensive tool to evaluate vaccine potency ex vivo. In this study, we investigated the potential of RUTI vaccine to control mycobacterial growth ex vivo and demonstrated the capacity of MGIA to aid the identification of essential immune mechanism. We found an association between the peak response of vaccine-induced growth inhibition and a shift in monocyte phenotype following RUTI vaccination in healthy mice. The vaccination significantly increased the frequency of non-classical Ly6C−monocytes in the spleen after two doses of RUTI. Furthermore, mRNA expressions of Ly6C−-related transcripts (Nr4a1, Itgax, Pparg, Bcl2) were upregulated at the peak vaccine response. This is the first time the impact of RUTI has been assessed on monocyte phenotype. Given that non-classical Ly6C−monocytes are considered to play an anti-inflammatory role, our findings in conjunction with previous studies have demonstrated that RUTI could induce a balanced immune response, promoting an effective cell-mediated response whilst at the same time limiting excessive inflammation. ORIGINAL RESEARCH published: 30 April 2019 doi: 10.3389/fimmu.2019.00894 RUTI Vaccination Enhances Inhibition of Mycobacterial Growth ex vivo and Induces a Shift of Monocyte Phenotype in Mice On the other hand, the impact of RUTI on non-classical monocytes could also reflect its impact on trained innate immunity which warrants further investigation. In summary, we have demonstrated a novel mechanism of action of the RUTI vaccine, which suggests the importance of a balanced M1/M2 monocyte function in controlling mycobacterial infection. The MGIA could be used as a screening tool for therapeutic TB vaccine candidates and may aid the development of therapeutic vaccination regimens for TB in the near future. †Present Address: Karin Seifert, †Present Address: Karin Seifert, Federal Institute for Drugs and Medical Devices, Bonn, Germany Specialty section: This article was submitted to Vaccines and Molecular Therapeutics, a section of the journal Frontiers in Immunology Received: 03 December 2018 Accepted: 08 April 2019 Published: 30 April 2019 Keywords: RUTI, vaccine, tuberculosis, monocytes, mycobacteria, growth inhibition assay Edited by: Fabio Bagnoli, GlaxoSmithKline, Italy Reviewed by: Angelo Izzo, Colorado State University, United States Bingdong Zhu, Lanzhou University, China *Correspondence: Satria A. Prabowo satria.prabowo@lshtm.ac.uk INTRODUCTION cellular frequencies, phenotypes and cytokines that associate with enhanced growth inhibition (16–18). Several variations of human and murine MGIAs have been described in the literature [reviewed in (12)]. Here, we implemented the assay using direct co-culture of mouse splenocytes with mycobacteria, based on a recent optimization work (15), to investigate the potential of the RUTI vaccine to control mycobacterial growth ex vivo. Tuberculosis (TB) remains a leading cause of death from infectious disease and is responsible for an estimated annual 1.6 million deaths globally (1). With the emergence of drug- resistant TB, there is a dire need for new therapy and for shorter, more effective, safer, and better tolerated treatment regimens. Therapeutic vaccination, which is a strategy to combine vaccination with drug treatment, could help to achieve these objectives and improve current treatments (2). TB vaccines are regarded to be equally effective against drug-sensitive and drug- resistant strains, due to the nature of drug-resistant mutations which are not considered to change the immunological profile of the organism (3). Therapeutic vaccination was first introduced by Robert Koch in his initial attempts to administer tuberculin to TB patients (4), and currently several therapeutic TB vaccine candidates are available in the vaccine pipeline. Monocytes are highly plastic and heterogeneous circulating cells, which are known to change their functional phenotype in response to environmental stimulation (19, 20). Two distinct subpopulations of mouse monocytes have been identified, commonly referred to as Ly6C+ and Ly6C−monocytes (21). Ly6C+ monocytes represent classical pro-inflammatory and phagocytic monocytes which could subsequently differentiate into M1 macrophages, while Ly6C−monocytes are regarded as non-classical anti-inflammatory monocytes which could differentiate into M2 macrophages (19). In addition to the induction of an antigen-specific Th1 response, evidence suggests the potential importance of a balanced M1/M2 monocyte function in controlling mycobacterial infection (20, 22). In a previous murine study, the RUTI vaccine was shown to reduce intragranulomatous infiltration and decrease Tumor Necrosis Factor (TNF)-α expression in Mtb infected mice (6). We hypothesize that immunization with RUTI would lead to improved control of mycobacterial growth ex vivo and such observation could be used to gain insight into the mechanism of immune protection. p p The RUTI vaccine is among the few candidates currently on the clinical pipeline which is specifically developed as a therapeutic TB vaccine. Citation: Prabowo SA, Painter H, Zelmer A, Smith SG, Seifert K, Amat M, Cardona P-J and Fletcher HA (2019) RUTI Vaccination Enhances Inhibition of Mycobacterial Growth ex vivo and Induces a Shift of Monocyte Phenotype in Mice. Front. Immunol. 10:894. doi: 10.3389/fimmu.2019.00894 Keywords: RUTI, vaccine, tuberculosis, monocytes, mycobacteria, growth inhibition assay April 2019 | Volume 10 | Article 894 Frontiers in Immunology | www.frontiersin.org 1 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. Animals Six to seven week-old female C57Bl/6 mice (Charles River, UK) acclimatized for at least 5 days were housed and handled in the Biological Services Facility (BSF) at London School of Hygiene and Tropical Medicine (LSHTM), UK. Mice were provided standard sterilized food and water ad libitum. Animals were housed in specific pathogen-free individually vented cages with environmental enrichment, with equal day and light cycle, at temperature between 19◦-23◦C and relative humidity of 45– 65%. Mice were allocated to cages as groups of six. All animal work was carried out in accordance with the Animals (Scientific Procedures) Act 1986 under a license granted by the UK Home Office (PPL 70/8043), and approved locally by the LSHTM Animal Welfare and Ethics Review Body. Mycobacterial growth inhibition assay (MGIA) has been developed as a simple and comprehensive tool to evaluate vaccine immunogenicity ex vivo (11, 12). As an assay that measures the summative vaccine-mediated host capacity to control mycobacterial growth, the MGIA is proposed as a screening tool for TB vaccine candidates (13–15). The nature of the ex vivo assay does not require that the vaccine-mediated immune mechanism which underlies growth control to be known in advance, while in turn the MGIA could help to determine immune mechanisms of protection through investigation of the Frontiers in Immunology | www.frontiersin.org INTRODUCTION The vaccine is composed of purified and liposomal cellular fragments of Mycobacterium tuberculosis (Mtb) bacilli cultured under stress (to mimic intra- granulomatous conditions) to induce latency antigens which would typically be hidden from the immune system (5). The immune response to RUTI has been studied in animal models and clinical studies and is characterized by a poly-antigenic response. Its main immunotherapeutic effect is thought to be through induction of a T helper-1 (Th1) response, not only against growth-related antigens but also structural antigens as shown in the murine model (2, 6). The prophylactic capacity of RUTI vaccine has also been evaluated in a murine model and the vaccination significantly reduced bacterial counts in both lungs and spleens following challenge with virulent bacilli (7). RUTI vaccination generated a poly-antigenic response in healthy human volunteers (phase I study), as well as in HIV-positive and HIV-negative patients with latent TB after isoniazid treatment for 1 month in a phase II clinical trial (8, 9). In this study, we investigated the impact of RUTI vaccination in mice using the ex vivo MGIA assay and found an association between peak response of vaccine-induced growth inhibition and a shift in monocyte phenotype. Our study demonstrates the benefit of the ex vivo MGIA to aid the identification of immune mechanisms of action for therapeutic TB vaccine candidates. The MGIA could be used as a tool for screening such vaccine candidates and might aid the development of therapeutic vaccine regimens for TB patients. The lack of an immune correlate of protection has been hampering the development of novel TB vaccines, as lengthy and expensive clinical trials with protracted follow-up periods are needed to demonstrate efficacy and proceed to licensure (10). For a single vaccine candidate, it generally takes at least a decade to reach efficacy trials from discovery (3, 10). If we are going to achieve the WHO target to eliminate TB by 2050, major progress is required to overcome the painstakingly slow progress. Such an immune correlate could also be used to help identify vaccine candidates with the greatest potential efficacy. Immunization Seven experimental groups were established, with six mice per group (Figure 1). Mice in the treatment groups were vaccinated April 2019 | Volume 10 | Article 894 2 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. FIGURE 1 | Experimental design and vaccination schedule. As indicated in the figure, orange arrows mean RUTI vaccination (dotted if boosting). The purple X represents endpoint (mice sacrifice). Enzyme-linked immunospot assay and mycobacterial growth inhibition assay were performed at each endpoint. In total, 42 mice were sacrificed at all time points (6 mice per group). FIGURE 1 | Experimental design and vaccination schedule. As indicated in the figure, orange arrows mean RUTI vaccination (dotted if boosting). The purple X represents endpoint (mice sacrifice). Enzyme-linked immunospot assay and mycobacterial growth inhibition assay were performed at each endpoint. In total, 42 mice were sacrificed at all time points (6 mice per group). After 4 days, splenocytes-mycobacteria mixtures were collected from the 48-well plates by pipetting up and down three times before transferring to 2 ml screw cap tubes. The tubes were centrifuged at 12,000 rpm in a bench top micro centrifuge and the supernatants were removed (500 µl) while ensuring the pellets remain intact. Five hundred microliters sterile tissue culture grade water was added to the 48-well plates which were incubated at room temperature for 5 min, followed by pipetting up and down for five times before transferring to the 2 ml screw cap tubes with pellets. The pellets were dissolved by pipetting and lysates containing mycobacteria were transferred to Bactec MGIT tubes supplemented with PANTA antibiotic and oleic acid-albumin-dextrose-catalase (OADC) enrichment broth [all from Becton Dickinson (BD), Oxford, UK]. The MGIT tubes were incubated in a Bactec MGIT liquid culture system (BD) until registered positive. The resulting time to positivity (TTP) was converted to bacterial numbers (log10 CFU) using a standard curve. The standard curve was obtained by a linear regression analysis of TTP values from inoculated BCG in 10-fold dilutions against CFUs obtained from plating aliquots of BCG onto 7H11 agar plates containing 10% OADC supplement (Yorlab, York, UK) and 0.5% glycerol. Direct-to-MGIT controls were included at each time point, defined as 90 CFU BCG directly placed into Bactec MGIT system without any pre-incubation (at day 0). Mycobacteria and Culture Conditions Bacillus Calmette-Guérin (BCG) Pasteur strain was obtained from Aeras (Rockville, MD, USA) as frozen aliquots. These were stored at −80◦C until needed. Mycobacterial suspensions for infection inoculum and BACTEC MGIT standards were prepared in antibiotic-free media (described below). All work with cells pre-BCG infection and involving BCG infected samples were performed in Biosafety Level (BSL) 2 laboratory. Immunization To compare the growth inhibition between time points, log10 CFU values were normalized using the direct-to-MGIT controls by subtracting or adding the values based on the average TTP of direct-to-MGIT controls. with RUTI, which is based on purified fragments of Mtb cultured under stress conditions and liposomed, manufactured by Archivel Farma (Badalona, Catalonia, Spain). Vaccination with RUTI (batch A14, 204 µg) was performed subcutaneously once or twice (3 weeks apart), as has been performed previously (6, 7). Five groups of mice were vaccinated with RUTI at week 0, among which three groups were boosted at week 3. Mice were sacrificed at week 1, 3, 4, 6, and 9 as the designated time points of this experiment. Two groups of mice sacrificed at week 1 and 6 served as naïve controls. Ex vivo Mycobacterial Growth Inhibition Assay (MGIA) y ( ) At the determined time points, spleens were removed aseptically from mice and single splenocyte suspensions were prepared by homogenization through 100 µm cell strainers followed by lysis of red blood cells and washing. Cells were adjusted to 5 × 106 splenocytes per 300 µl in antibiotic-free media [RPMI- 1640 (Sigma-Aldrich, Dorset, UK) + 10% heat-inactivated FBS (Labtech International Ltd, Uckfield, UK) + 2 mM L-Glutamine (Fisher Scientific, Loughborough, UK)]. Mycobacteria were diluted in sufficient volume for all samples in the same media to a concentration of 90 CFU per 300 µl. Three hundred microliters aliquots of bacteria were added to the splenocytes, and the splenocytes-mycobacteria co-culture (600 µl) was then incubated in 48-well plates (Sigma-Aldrich, UK) at 37◦C for 4 days. Frontiers in Immunology | www.frontiersin.org Interferon (IFN)-γ ELISpot To measure antigen-specific response toward mycobacterial antigen following RUTI vaccination over the time course, IFN- γ ELISpot assay was performed. Single cell suspensions of mouse splenocytes were resuspended in RPMI-1640 media containing 10% heat-inactivated FBS and 2 mM L-Glutamine. 96-well April 2019 | Volume 10 | Article 894 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 3 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. 105 splenocytes were stimulated overnight with PPD (final concentration 10 µg/ml). Cells were pelleted, lysed in 200 µl RLT buffer containing 10 µl/ml β-mercaptoethanol and stored in −40 ◦C freezer from each time point. Cells were thawed and RNA was extracted using the RNAeasy mini kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions. After a DNAse treatment with RNase-free DNAse set (Qiagen, UK), total RNA concentration was determined by spectrophotometry with a Nanodrop (Labtech International, Heathfield, UK). One microgram of each sample of total RNA was reverse-transcribed into complementary DNA (cDNA) using Omniscript R⃝Reverse Transcription kit (Qiagen, UK) according to the manufacturer’s recommendation, using oligo(dT) (Invitrogen, UK) to obtain cDNA. Each PCR was carried out in a 20 µl volume in the presence of 10 µl of 2x QuantiTect SYBR Green PCR Master Mix (Qiagen, UK), 1 µl of cDNA (or water as a negative control), MgCl2 to a final concentration of 2.5 mM and primers to a final concentration of 0.5 µM. PCR was carried out for 10 min at 95◦C denaturation, followed by 40 cycles at 95◦C for 15 s, and 60◦C for 1 min in Applied Biosystems 7500 (Applied Biosystems, CA, USA). microtiter ELISpot plates (MAIPS4510, Millipore, Watford, UK) were coated with 10 µg/ml rat anti-mouse IFN-γ (clone AN18, Mabtech, Nacka Strand, Sweden). Free binding sites were blocked with the above mentioned media. 2.5 × 105 of total splenocytes were added and incubated in duplicate with 10 µg/ml Purified protein derivative (PPD) (Oxford Biosystem, Oxfordshire, UK), RPMI media as a negative control, or phytohemaglutinin (PHA) (1 µg/ml, Sigma-Aldrich) and phorbol myristate acetate (PMA) (0.1 µg/ml, Sigma-Aldrich) as a positive control. Cells were incubated overnight at 37◦C with 5% CO2. IFN-γ was detected with 1 µg/ml biotin labeled rat anti-mouse antibody (clone R4-6A2, Mabtech) and 1 µg/ml alkaline phosphatase- conjugated streptavidin (Mabtech). Flow Cytometry Single splenocyte suspensions were fixed and red blood cells were lysed using PhosFlow lyse-fix solution (Becton Dickinson, Oxford, UK) for 30 min at 4◦C prior to freezing. Fixed cells were then re-suspended in freezing media (FBS containing 10% DMSO) at the concentration of 106 cells per ml and stored in a −40 ◦C freezer from each time point. Frozen cells were thawed by adding FACS buffer (PBS containing 5% FBS) and pipetting up and down to encourage thawing. Cells were added to 10 ml of FACS buffer and centrifuged for 10 min at 1,800 rpm. Cells were re-suspended in FACS buffer (concentration 107 cells/ml) and were left for 15 min on ice for rehydration. Interferon (IFN)-γ ELISpot The enzyme reaction was developed with BCIP/NBT substrate (5-Bromo-4-chloro-3- indolyl phosphate/Nitro blue tetrazolium) (MP Biochemicals, UK) and stopped by washing the plates with tap water when individual spots could be visually detected (up to 3 min). Upon completion of the color development stage, spots were quantified using an automated plate reader with ELISpot 5.0 software. IFN- γ-specific cells are expressed as number of spot forming cells (SFC) per million splenocytes after non-specific background was subtracted using negative control wells. Analyses were performed for gene expressions of Nr4a1, Cebpb, Itgax, Pparg, Bcl2 (markers of Ly6C−), Ccr2, Sell, Ly6C2 (markers of Ly6C+), and β-actin (housekeeping gene). Primers used were listed in Table S1. mRNA expression of β-actin was quantified for every target sample to normalize for efficiency in cDNA synthesis and RNA loading. A ratio based on the β-actin mRNA expression was obtained for each sample. RUTI Vaccination Did Not Induce Antigen-Specific IFN-γ but Did Improve Mycobacterial Growth Inhibition in Murine Splenocytes To assess the immune response to mycobacterial antigens from mice vaccinated with RUTI, splenocytes were stimulated with PPD and the number of IFN-γ-producing cells was measured using the ELISpot assay (Figure 2, red line). We found a weak, non-significant response at 1 week following the second vaccination with RUTI (week 4, p = 0.08). This response appeared to have decreased by week 6. Significant control of mycobacterial growth was observed 1 week after the first vaccination and 3 weeks after the second RUTI vaccination (week 6) when compared to the baseline control (p = 0.0214, Figure 2, blue line). A trend of reduction was still observed 6 weeks after the second vaccination (week 9), although it did not reach significance (p = 0.064). Cells were incubated for 30 min at RT in the dark and washed prior to analysis. Fluorescence minus one (FMO) controls were set using cells for each antibody and used to guide gating. OneComp beads (eBioscience, Loughborough, UK) were used to calculate compensation by staining with single antibodies as per manufacturer’s instruction. Cells were acquired on a BD LSR II flow cytometer. Data was analyzed with FlowJo software version 10.4 (Treestar Inc., USA). Statistical Analysis Statistical analysis was carried out using GraphPad Prism version 7 (GraphPad, La Jolla, CA, USA). A p-value of < 0.05 was considered statistically significant. The specific tests used for each analysis are described in the figure legends. Fc block (anti-mouse CD16/32, eBioscience, Loughborough, UK) was added to cells and left for further 10 min on ice prior to surface staining. Cells were aliquoted in FACS tubes (100 µl each, 106 cells) and stained with the following titrated antibody: 1.25 µl CD3-APC/Cy7 (clone 17A2), 2.5 µl CD45R/B220-BV510 (clone RA3-6B2), 1.25 µl CD11b-PerCP/Cy5.5 (clone M1/70), 2.5 µl Ly6G-BV711 (clone 1A8), and 5 µl Ly6C-BV421 (clone HK1.4). All antibodies were purchased from Biolegend (via Fisher Scientific). Shift of Monocyte Phenotype Following RUTI Vaccination in Healthy Mouse Splenocytes In a separate experiment performed in rotating tubes instead of 48-well plates (Figure S1A in Supplementary Material), RUTI- induced control of mycobacterial growth was superior to BCG- induced control when both vaccines were given 6 weeks prior to sacrifice (p < 0.005, Figure S1B). Therefore, week 6 appeared to be the peak response of RUTI in the ex vivo MGIA system. Growth control was also significant when compared to an age-matched control group (p < 0.05, Figure S2A in Supplementary Material). In this experiment, we investigated the impact of RUTI vaccination on the population of immune cells in the spleen using flow cytometry (Figure 3 and Figure S3 in Supplementary Material). RUTI did not appear to alter the percentages of monocytes/macrophages, T-cells, and B-cells in the spleen of healthy mice (p > 0.05, Figures S3A,C,D). We also measured monocyte to lymphocyte (ML) ratio as a factor influencing mycobacterial growth inhibition (28, 29), defined as the percentage of monocytes/macrophages divided by the percentage of T-cells and B-cells. We did not find a significant change of ML ratio following RUTI vaccination across time (Figure S3B). pp y RUTI vaccination led to control of mycobacterial growth as measured by the MGIA, despite a weak, non-significant antigen-specific IFN-γ response. This was consistent with results of a separate experiment with RUTI and BCG, in which BCG induced IFN-γ-secreting cells whereas RUTI did not and yet cells from RUTI immunized mice were better able to control mycobacterial growth than cells from BCG vaccinated mice (Figures S1C,D in Supplementary Material). The lack of robust IFN-γ response following two doses of RUTI in healthy mice has been observed previously during potency testing for batch release (Archivel Farma, personal communication). Then, four doses of RUTI were required for induction of a detectable IFN-γ response. Although IFN-γ is associated with control of TB infection in mice and reduces the risk of TB disease in humans (23–25), some studies suggested IFN- γ alone was not sufficient (26, 27). As the MGIA measures the summative effect of immune responses from all cellular components, our data implied an alternative mechanism by which growth inhibition could be enhanced ex vivo following RUTI vaccination. We then further characterized monocyte phenotype based on the Ly6C marker, and observed a significant increase of Ly6C−monocytes/macrophages (non-classical) at weeks 3, 6, and 9 following RUTI vaccination (p < 0.05, Figure 3B). Real-Time Quantitative PCR Time point 0 represents unvaccinated naïve-control mice sacrificed at week 1. One-way ANOVA was used to test for significance, followed by t-test. *p < 0.05; **p < 0.01. Real-Time Quantitative PCR To quantitatively analyse the mRNA expressions in splenocytes following RUTI vaccination, real-time quantitative reverse transcriptase PCR (qRT-PCR) assays were performed. 5 × April 2019 | Volume 10 | Article 894 Frontiers in Immunology | www.frontiersin.org 4 Prabowo et al. RUTI Vaccination Shifts Monocyte Phenotype FIGURE 2 | ELISpot (Red Line). IFN-γ response in mice receiving vaccination with RUTI was measured. Modest PPD antigen-specific responses were detected in splenocytes of healthy C57BL/6 mice across time points. The splenocytes were stimulated overnight with PPD, and the responses were detected using the IFN-γ ELISpot assay. SFC, spot-forming cells. Dark red line indicates mean response, and shading indicates range. Statistical significance was tested using Mann-Whitney test. MGIA (Blue Line). RUTI vaccination induced mycobacterial growth inhibition in murine splenocytes, performed ex vivo in a 48-well plate. Dark blue line indicates mean mycobacterial growth, and shading indicates range. Time point 0 represents unvaccinated naïve-control mice sacrificed at week 1. One-way ANOVA was used to test for significance, followed by t-test. *p < 0.05; **p < 0.01. FIGURE 2 | ELISpot (Red Line). IFN-γ response in mice receiving vaccination with RUTI was measured. Modest PPD antigen-specific responses were detected in splenocytes of healthy C57BL/6 mice across time points. The splenocytes were stimulated overnight with PPD, and the responses were detected using the IFN-γ ELISpot assay. SFC, spot-forming cells. Dark red line indicates mean response, and shading indicates range. Statistical significance was tested using Mann-Whitney test. MGIA (Blue Line). RUTI vaccination induced mycobacterial growth inhibition in murine splenocytes, performed ex vivo in a 48-well plate. Dark blue line indicates mean mycobacterial growth, and shading indicates range. Time point 0 represents unvaccinated naïve-control mice sacrificed at week 1. One-way ANOVA was used to test for significance, followed by t-test. *p < 0.05; **p < 0.01. FIGURE 2 | ELISpot (Red Line). IFN-γ response in mice receiving vaccination with RUTI was measured. Modest PPD antigen-specific responses were detected in splenocytes of healthy C57BL/6 mice across time points. The splenocytes were stimulated overnight with PPD, and the responses were detected using the IFN-γ ELISpot assay. SFC, spot-forming cells. Dark red line indicates mean response, and shading indicates range. Statistical significance was tested using Mann-Whitney test. MGIA (Blue Line). RUTI vaccination induced mycobacterial growth inhibition in murine splenocytes, performed ex vivo in a 48-well plate. Dark blue line indicates mean mycobacterial growth, and shading indicates range. Shift of Monocyte Phenotype Following RUTI Vaccination in Healthy Mouse Splenocytes Dark brown and dark purple lines represent mean percentages of Ly6C+ and Ly6C−monocytes/macrophages, respectively and shading indicates range. Time point 0 represents unvaccinated naïve-control mice sacrificed at week 1. Statistical significance was tested using unpaired t-test, *p < 0.05; **p < 0.01; ***p < 0.005. following two doses of RUTI vaccination. We found a non- significant correlation between higher frequency of Ly6C− monocytes/macrophages and lower growth of mycobacteria across time points (p = 0.247, Spearman r = −0.20, data not shown). on a recent publication by Mildner et al. (21) regarding genomic characterization of murine monocytes. We chose differentially expressed transcripts between the two monocyte subsets from several gene clusters of monocyte development. Three transcripts, namely Nr4a1, Itgax, and Pparg, were selected from a cluster which was strongly upregulated in Ly6C−compared to Ly6C+ monocytes. Cebpb was selected from a cluster that showed a gradual increase of expression from Ly6C+ to Ly6C− monocytes. Bcl2 belongs to a cluster characterized by transcripts associated with a progenitor phenotype of MDP (monocyte- macrophage DC progenitor), which was highly expressed in Ly6C−monocytes. In addition, transcripts associated with Ly6C+ monocytes were selected from clusters involved in Shift of Monocyte Phenotype Following RUTI Vaccination in Healthy Mouse Splenocytes The peak increase of Ly6C−cells was observed at week 6, with the shift being evident compared to both baseline and age-matched naïve control at week 6 (Figure S2B in Supplementary Material). The Ly6C+ monocytes/macrophages (classical) population appeared to be decreasing following vaccination, although there was an initial significant increase observed at week 1 (p < 0.05, Figure 3). The shift of Ly6C+/Ly6C−phenotype at week 6 was notably consistent with the peak response of the ex vivo mycobacterial growth inhibition assay, in which enhanced inhibition was observed April 2019 | Volume 10 | Article 894 Frontiers in Immunology | www.frontiersin.org 5 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. FIGURE 3 | The shift of Ly6C+ and Ly6C−monocytes/macrophages populations following RUTI vaccination in healthy mice. (A) Gating strategy for flow cytometric analysis. Splenocytes from C57BL/6 mice were fixed, stained and data acquired as described in Materials and Methods. Cell debris was gated out by use of FSC-SSC gate, followed by gating on single cells (FSC-A and FSC-H). A sequential gating strategy was then applied to determine the frequency of T-cells (CD3+), B cells (B220+), monocytes/macrophages (CD11b+ Ly6G−ssclow), and the phenotypes of the monocytes/macrophages (Ly6C+ or Ly6C−) as a percentage of live cells. Plots shown are from a sample of a C57BL/6 spleen. (B) The frequencies of Ly6C+ and Ly6C−monocytes/macrophages were compared at each time point following RUTI vaccination. Dark brown and dark purple lines represent mean percentages of Ly6C+ and Ly6C−monocytes/macrophages, respectively and shading indicates range. Time point 0 represents unvaccinated naïve-control mice sacrificed at week 1. Statistical significance was tested using unpaired t-test, *p < 0.05; **p < 0.01; ***p < 0.005. FIGURE 3 | The shift of Ly6C+ and Ly6C−monocytes/macrophages populations following RUTI vaccination in healthy mice. (A) Gating strategy for flow cytometric analysis. Splenocytes from C57BL/6 mice were fixed, stained and data acquired as described in Materials and Methods. Cell debris was gated out by use of FSC-SSC gate, followed by gating on single cells (FSC-A and FSC-H). A sequential gating strategy was then applied to determine the frequency of T-cells (CD3+), B cells (B220+), monocytes/macrophages (CD11b+ Ly6G−ssclow), and the phenotypes of the monocytes/macrophages (Ly6C+ or Ly6C−) as a percentage of live cells. Plots shown are from a sample of a C57BL/6 spleen. (B) The frequencies of Ly6C+ and Ly6C−monocytes/macrophages were compared at each time point following RUTI vaccination. DISCUSSION Vaccination with RUTI resulted in enhanced control of mycobacterial growth, notably at 3 weeks following the second vaccination (week 6), which was considered as the peak response of the vaccine observed in the ex vivo assay system. In addition, there was also a significant reduction of mycobacterial growth at 1 week after the first vaccination. There was no significant induction of antigen-specific IFN-γ as measured by ELISpot or ELISA. These observations were replicated in a separate experiment and support the notion that the MGIA measures different aspects of immunity following vaccination as compared to the IFN-γ-based assay, with the MGIA being reflective of the summative effect of host immune responses at the point of tissue harvest, compared to the IFN-γ-based assay which is an assessment of a T-cell mediated recall response following vaccination. We confirmed the flow cytometry finding by demonstrating the upregulation of transcripts associated with Ly6C−cells at the peak time point (week 6), while one of the Ly6C+ gene transcript (Ccr2) remained unchanged. Among the significantly upregulated transcripts in our study was Nr4a1, which is obligatory for Ly6C−monocytes development (33). Expression of Nr4a1 as a monocyte survival factor is regulated by Cebpb (21, 34), which was also elevated following RUTI vaccination. In addition, the expressions of all other Ly6C−-associated transcripts (Itgax, Pparg, Bcl2) were significantly upregulated following vaccination in our study. As Ly6C−monocytes are known to mature from Ly6C+ (35, 36), the increased expression of some Ly6C+ transcripts (Sell and Ly6C2) at the peak time point was regarded as a vestige of the transition from Ly6C+ to Ly6C−. Ly6C−monocytes do not represent a distinct lineage and instead arise from the conversion of Ly6C+ cells (37) and approximately 92% of expressed transcripts are shared between the two monocyte subsets (38). Our results suggest that RUTI could enhance Ly6C+ cell frequency and induce maturation of Ly6C+ to Ly6C−monocytes. This was evidenced by our results in which an initial increase of Ly6C+ monocytes was observed at week 1 following the first RUTI vaccination, followed by the shift toward Ly6C−and the decrease of Ly6C+ monocytes at the subsequent time points. In this context, we argue that the ex vivo assay is more capable of measuring the direct, short-term effect of vaccination, while the IFN-γ response is more representative of the medium- to long-term protection conferred by vaccination. This was supported by a recent finding of Fletcher et al. Gene Expression of Ly6C+- and Ly6C−- Related Markers Induced by RUTI Vaccination To confirm findings from the flow cytometry analysis described in the previous section, we performed real-time qRT-PCR looking at transcripts associated with Ly6C+ and Ly6C− monocytes/macrophages. The selection of transcripts was based April 2019 | Volume 10 | Article 894 Frontiers in Immunology | www.frontiersin.org 6 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. cell cycle (Sell and Ly6C2) as well as maturation of Ly6C+ monocytes (Ccr2). characterize immune cells associated with enhanced growth inhibition across time. RNA was also isolated to investigate gene expression by RT-qPCR. The important finding in our present study was the impact of RUTI vaccination in shifting the phenotype of Ly6C+/Ly6C−monocytes/macrophages in the spleen of healthy mice. This was the first time the impact of RUTI on monocyte phenotype has been assessed. In addition, while others have shown a lack of correlation between antigen- specific IFN-γ and mycobacterial growth inhibition, this is the first demonstration of vaccine induced mycobacterial growth inhibition in the absence of antigen-specific IFN-γ. Our results suggest that the enhanced control of mycobacterial growth ex vivo was associated with the increase of Ly6C−monocytes (non- classical, anti-inflammatory), which were both observed 3 weeks after the second vaccination with RUTI (week 6). The mRNA expressions of Ly6C−-related transcripts, including Nr4a1, Itgax, Pparg, Bcl2, were significantly upregulated following the second RUTI vaccination at week 6 (p < 0.05, Figures 4A,C–E), with a trend of upregulation for Cebpb (p = 0.136, Figure 4B). While we did not observe a difference in expression of Ccr2, a Ly6C+ -related gene, following RUTI vaccination at the peak time point, we saw significant upregulations of Sell and Ly6C2 at week 6 (p < 0.05, Figures 4G–H). Frontiers in Immunology | www.frontiersin.org DISCUSSION in which antigen- specific IFN-γ response was associated with reduced risk of developing TB disease in BCG-vaccinated South African infants (25). In testing therapeutic vaccine candidates, it might be more relevant to measure the direct effect of vaccination, as it would represent the immediate and potentially synergistic impact of a vaccine during TB chemotherapy. This was depicted in the ex vivo assay, in which significant mycobacterial growth inhibition was observed at 1 week following the first RUTI vaccination, when there was no apparent increase of IFN-γ response at this time point. Ly6C−monocytes secrete anti-inflammatory cytokine upon bacterial infection in vivo and when recruited to tissue, are more likely to differentiate into M2 macrophages (35). This is in contrast to Ly6C+ monocytes, which are more likely to mature into pro-inflammatory M1 macrophages (36). In relation to our findings, the study by Guirado et al. (6) demonstrated a decrease of intragranulomatous infiltration in the lungs upon administration of RUTI in infected mice after treatment. One of the notable findings in that study was a significant decrease of TNF-α at the earliest time point after RUTI administration, measured by mRNA expression in the lung. Among the producers of TNF-α during bacterial infection are Ly6C+ monocytes which will subsequently differentiate into M1 macrophages (19, 39). Although our experiment differs with the one previously performed by Guirado and colleagues in several aspects (including the investigated target organ), the decrease of TNF-α observed in the previous study could be associated with the impact of The ex vivo MGIA was shown to be able to capture the impact of distinct aspects of protective immunity as a part of a summative measurement of cellular immune responses. In this study, we used BGC as the immune target of the growth inhibition assay, as previous studies have shown a good concordance of growth between BCG and Mtb in the MGIA assay when both mycobacteria were used to assess responses following vaccination and treatment (30–32). In addition, studies by Marsay et al. and Zelmer et al. also showed that the ex vivo growth inhibition using BCG as immune target was correlated with in vivo growth in mouse challenge experiment using Mtb Erdman (15, 16). In our experiment, we performed flow cytometry to April 2019 | Volume 10 | Article 894 7 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. DISCUSSION FIGURE 4 | mRNA expressions of Ly6C−-related (A–E) and Ly6C+ -related genes (F–H) in mice following vaccination with RUTI at week 6 compared to the age-matched naïve control group. Data are expressed as ratio obtained after dividing every value by the expression of β-actin in each sample and multiplying it by a factor (ranging from 101 to 103). The box plots show the minimum and maximum values (ends of the whiskers), the median (band near the middle of the box) and interquartile ranges. Statistical significance was tested using unpaired t-test, *p < 0.05; **p < 0.01; ***p < 0.005. FIGURE 4 | mRNA expressions of Ly6C−-related (A–E) and Ly6C+ -related genes (F–H) in mice following vaccination with RUTI at week 6 compared to the age-matched naïve control group. Data are expressed as ratio obtained after dividing every value by the expression of β-actin in each sample and multiplying it by a factor (ranging from 101 to 103). The box plots show the minimum and maximum values (ends of the whiskers), the median (band near the middle of the box) and interquartile ranges. Statistical significance was tested using unpaired t-test, *p < 0.05; **p < 0.01; ***p < 0.005. addition, the vaccine was also shown to induce a Th3 response as a subset population of regulatory T-cells (42). In another mouse study, RUTI administration following drug therapy in infected mice stimulated stronger IFN-γ secretion by CD4+ and CD8+ T-cells compared to BCG against early secretory antigen target (ESAT)-6, Ag85B, and PPD and also induced an immune response against structural antigens Ag16 kDa and Ag38 kDa (6). While immune responses in infected and drug-treated mice could be reasonably different in comparison to healthy mice as was done in our ex vivo study, the fact that RUTI did not induce an exacerbated immune response in various animal studies could be linked to its impact on Ly6C−monocytes which was discovered in our investigation. In the experimental animals immunized with RUTI, no elevated IgE levels were observed (43). In this study, histology also revealed no eosinophilia, necrosis or granulomatous infiltration, as well as allergic or hypersensitivity reactions. Taken together, these findings and observations suggest that RUTI could induce a balanced immune response, promoting an effective cell-mediated response whilst at the same time limiting an excessive inflammation, which could be beneficial for its implementation as a therapeutic vaccine for active TB patients undergoing treatment. Frontiers in Immunology | www.frontiersin.org ACKNOWLEDGMENTS We are very grateful to Archivel Farma S.L. for provision of RUTI vaccine vials used in this study. We would like to thank Ayad Eddaoudi and Stephanie Canning for expert technical assistance with flow cytometry. We are grateful to all staffat the Biological Service Facility at London School of Hygiene and Tropical Medicine for their assistance with animal work. We also thank Erni Marlina for technical advices with the qPCR assay. HF has received support for this project from EC HORIZON2020 TBVAC2020 (grant no. 643381). Satria Arief Prabowo (SP) received a PhD scholarship from the Indonesian Endowment Fund for Education (LPDP). KS was supported by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement (grant reference MR/J008702/1). In summary, we have demonstrated the benefit of the ex vivo MGIA assay to help streamlining and identifying immune mechanisms of a therapeutic TB vaccine candidate. Our results could be complemented by further experiments, such as by using cells from infected mice. Depleting Ly6C−monocytes and using genetically deficient mice could also provide more insight into the mechanism of protection by Ly6C−monocytes in the ex vivo assay system. Future investigation of the novel immune mechanism of RUTI observed in our study is also warranted in upcoming clinical trials of the vaccine and could potentially accelerate the development of a therapeutic vaccine regimen for TB patients in the near horizon. REFERENCES placebo-controlled phase II clinical trial in patients with latent tuberculosis infection. PLoS ONE. (2014) 9:e89612. doi: 10.1371/journal.pone.0089612 placebo-controlled phase II clinical trial in patients with latent tuberculosis infection. PLoS ONE. (2014) 9:e89612. doi: 10.1371/journal.pone.0089612 1. Tiberi S, du Plessis N, Walzl G, Vjecha MJ, Rao M, Ntoumi F, et al. Tuberculosis: progress and advances in development of new drugs, treatment regimens, and host-directed therapies. Lancet Infect Dis. (2018) 18:e183–98. doi: 10.1016/s1473-3099(18)30110-5 1. Tiberi S, du Plessis N, Walzl G, Vjecha MJ, Rao M, Ntoumi F, et al. Tuberculosis: progress and advances in development of new drugs, treatment regimens, and host-directed therapies. Lancet Infect Dis. (2018) 18:e183–98. doi: 10.1016/s1473-3099(18)30110-5 10. Dockrell HM. Towards new TB vaccines: what are the challenges? Pathog Dis. (2016) 74:ftw016. doi: 10.1093/femspd/ftw016 11. Zelmer AA, Tanner R, Stylianou E, Morris S, Izzo A, Williams A, et al. Ex vivo mycobacterial growth inhibition assay (MGIA) for tuberculosis vaccine testing - a protocol for mouse splenocytes. bioRxiv. (2015):020560. doi: 10.1101/020560 2. Cardona PJ. The progress of therapeutic vaccination with regard to tuberculosis. Front Microbiol. (2016) 7:1536. doi: 10.3389/fmicb.2016.01536 2. Cardona PJ. The progress of therapeutic vaccination with regard to tuberculosis. Front Microbiol. (2016) 7:1536. doi: 10.3389/fmicb.2016.01536 12. Tanner R, O’Shea MK, Fletcher HA, McShane H. In vitro mycobacterial growth inhibition assays: A tool for the assessment of protective immunity and evaluation of tuberculosis vaccine efficacy. Vaccine. (2016) 34:4656–65. doi: 10.1016/j.vaccine.2016.07.058 3. Fletcher HA, Schrager L. TB vaccine development and the End TB Strategy: importance and current status. Trans R Soc Trop Med Hyg. (2016) 110:212–8. doi: 10.1093/trstmh/trw016 4. Vilaplana C, Cardona PJ. Tuberculin immunotherapy: its history and lessons to be learned. Microbes Infect. (2010) 12:99–105. doi: 10.1016/j.micinf.2009.10.006 13. Parra M, Yang AL, Lim J, Kolibab K, Derrick S, Cadieux N, et al. Development of a murine mycobacterial growth inhibition assay for evaluating vaccines against Mycobacterium tuberculosis. Clin Vaccine Immunol. (2009) 16:1025– 32. doi: 10.1128/CVI.00067-09 5. Cardona PJ. RUTI: a new chance to shorten the treatment of latent tuberculosis infection. Tuberculosis. (2006) 86:273–89. doi: 10.1016/j.tube.2006.01.024 14. Fletcher HA, Tanner R, Wallis RS, Meyer J, Manjaly ZR, Harris S, et al. Inhibition of mycobacterial growth in vitro following primary but not secondary vaccination with Mycobacterium bovis BCG. Clin Vaccine Immunol. (2013) 20:1683–9. doi: 10.1128/CVI.00427-13 6. Guirado E, Gil O, Caceres N, Singh M, Vilaplana C, Cardona PJ. DISCUSSION A synthetic mycobacterial structure—muramyl tripeptide (MTP)—is also considered to induce trained immunity (47), and interestingly, both MTP and RUTI are delivered in liposome. Further studies are required to elucidate downstream and upstream pathways related to the potential effect of RUTI on trained innate immunity. took the lead in writing the manuscript. All authors reviewed, provided critical feedback and approved the final version of the manuscript. SUPPLEMENTARY MATERIAL SP and HF conceived and planned the experiments. SP performed the experiments, with HP and AZ participating in some of the qPCR and MGIA experiments. SP, HF, SS, KS, MA, and P-JC contributed to the interpretation of the results. SP The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2019.00894/full#supplementary-material DISCUSSION RUTI on monocyte populations which has been discovered in our investigation. RUTI is a poly-antigenic vaccine made from fragmented Mtb bacilli designed to induce host immune response against latency epitopes, which is grown in stress, purified and liposomed. The part of RUTI formulation that could potentially influence monocyte phenotype remains to be further explored. Nevertheless, our study has revealed an interesting mechanism of action of RUTI as a therapeutic vaccine for TB. As reviewed by Prabowo et al. (40), it is essential to prevent the occurrence of exacerbated immune response for a successful therapeutic vaccination strategy in TB. This was exemplified in a recent study, in which an excessive inflammation from the T-cell compartment could also be deleterious in TB (41). The fact that RUTI vaccination could induce a shift toward an anti-inflammatory monocyte phenotype might be considered as an advantage in this context and such approach should be further investigated in future studies. While this could imply that less inflammation might be beneficial for the ex vivo control of mycobacterial growth following RUTI vaccination in healthy mice, our results should be interpreted with prudence in relation to previous results of RUTI testing in in vivo animal models. The observed trend of correlation between the frequency of Ly6C− monocytes/macrophages and growth of mycobacteria across time points hinted that this was only one aspect contributing to the enhanced ex vivo growth control and other factors might be playing roles. In a murine model infected with Mtb, RUTI has been shown to trigger a balanced Th1/Th2 response as well as Immunoglobulin (Ig)G1, IgG2a and IgG3 antibodies against 13 Mtb antigens, reflecting its broad immunogenicity (42). In Intriguingly, a recent study by Joosten et al. demonstrated the protective effect of human non-classical CD14dim monocytes in inhibiting mycobacterial growth following recent Mtb exposure and BCG vaccination through the trained innate immunity mechanism (44). As Ly6C−monocyte is the equivalent of CD14dim monocyte in mouse (19), our results could also suggest an impact of RUTI on trained innate immunity which has not been characterized before. BCG is known to induce trained immunity on human monocytes and such ability has been April 2019 | Volume 10 | Article 894 8 RUTI Vaccination Shifts Monocyte Phenotype Prabowo et al. attributed to the non-specific protective effect conferred by the vaccine (45, 46). 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The remaining 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. 32. O’Shea MK, Tanner R, Muller J, Harris SA, Wright D, Stockdale L, et al. Immunological correlates of mycobacterial growth inhibition describe a spectrum of tuberculosis infection. Sci Rep. (2018) 8:14480. doi: 10.1038/s41598-018-32755-x Copyright © 2019 Prabowo, Painter, Zelmer, Smith, Seifert, Amat, Cardona and Fletcher. 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. 33. 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МЕДИАНИНГ ЖАМОАТЧИЛИК ФИКРИНИ ШАКЛЛАНТИРИШ ВА ИНФОРМАЦИОН СТРЕССДАН ҲИМОЯЛОВЧИ ФУНКЦИЯСИ
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МЕДИАНИНГ ЖАМОАТЧИЛИК ФИКРИНИ ШАКЛЛАНТИРИШ ВА ИНФОРМАЦИОН СТРЕССДАН ҲИМОЯЛОВЧИ ФУНКЦИЯСИ Жақсимуратова Гулжаҳан Қорақалпоқ давлат университети талабаси, Нукус АННОТАЦИЯ: Мазкур мақолада медианинг жамоатчилик фикрини шакллантириш ва информацион стрессдан ҳимояловчи функцияси ҳақида сўз боради. Шунингдек, оммавий ахборот воситалари ва маънавий-ғоявий таҳдидлар ҳақида тўқталган. Калт сўзлар: масс-медиа, жамоатчилик фикри, информацион стресс, глобаллашув, ахборот истеъмоли. Медианинг таъсир кучи унинг материаллари муайян аудиторияга мўлжаллангани билан ҳам белгиланади. Масалан, ички аудиторияга мўлжалланган материалларни ёши, жинси, ижтимоий мақоми (касб-кори), миллий, диний мансублик каби белгиларга кўра фарқлаш мумкин. Масс-медиа ижтимоий ҳаётдаги муайян воқеа, ҳодиса ёки муаммо юзасидан ахборотни етказиб бериш орқали, унинг жамият учун аҳамияти, кенг аҳоли қатламлари учун долзарблигини таъкидлайди. Ахборот оқими ҳажман кенг, мазмунан ранг-баранг, узатилишга кўра тезкор бўлган бугунги кунда бу жараён янада чуқурлашиб бормоқда. ОАВ муайян хабарни узатиш ёки бирор бир ғоянинг моҳиятини очиб бериш орқали унинг ўзлаштирилишига, кишилар онгида барқарор тасаввурлар, образлар, қадриятларнинг шаклланишига ҳам кўмаклашади. Содда қилиб айтганда, у ижтимоий фикрга доимий ва изчил таъсир ўтказиш, уни шакллантира олиш имкониятига эгадир. Медианинг бугунги кундаги ривожи ғоявий таъсир ўтказишнинг миқёси ва кўламининг кескин даражада ўсишига олиб келди. Шунинг учун ҳам медиалойиҳалар орқали амалга ошириладиган ва катта маблағ талаб қилмайдиган ғоявий таъсир ва тазйиқнинг ўзига хослиги шундаки у ўқувчи, тингловчи ёки томошабинга сездирилмасдан амалга оширилади ва бевосита қурбонларни келтириб чиқармайди. Ахборот душманни йўқ қилмаган, катта ҳаражатни талаб қилмаган ҳолда юқори самара беради. Бунда ғоявий таъсир йўналтирилган мамлакатлар аҳолисининг хоҳиш-истаклари, менталитети, мавжуд муаммолари жиддий ўрганилган ҳолда асосий диққат кишилар онги ва дунёқарашига таъсир кўрсатишга, шаклланган қадриятларни ўзгартиришга, уларнинг регуляторлик 43 ролини камайтиришга ёки бутунлай йўққа чиқаришга қаратилади. Бундай таъсир ўтказишда даврий нашрлар тадрижийлик, радио ва телевидение фрагментли узатиш усулларидан усталик билан фойдаланишмоқда. Оммавий ахборот воситалари ва маънавий-ғоявий таҳдидлар ҳақида гап кетар экан, энг аввало ғараз мақсадларда амалга оширилаётган ташқи ғоявий таъсирлар, мамлакатимиз ҳаётида содир бўлаётган ўзгаришларга холис ёндашув байроғи остида берилаётган бир ёқлама ахборотлар ва баҳоларнинг олдини олиш, уларга қарши объектив маълумотларни кишиларга тезкор, тизимли ва тадрижий етказиб бериш масаласи долзарб бўлиб турганини алоҳида қайд этиш зарур. Шундай вазиятда ҳар хил шаклу шамойилда чиқаѐтган бундай уринишларга қарши халқимиз ҳаѐтида содир бўлаѐтган ижобий ўзгаришлар ҳақида ҳикоя қилувчи чуқур таҳлилий маълумотларни мунтазам бериб бориш, фуқароларимизнинг ижтимоий фаоллигини кучайтириш, турли ижтимоий тоифа ва гуруҳларнинг қизиқиш ва интилишлари, ҳаётий манфаатларини ёритиш, фикрга қарши фикр, ғояга қарши ғоя, жаҳолатга қарши маърифат билан курашиш ҳар қачонгидан ҳам ҳаётий-амалий аҳамият касб этади. Шу билан бирга, оммавий ахборот воситалари олдида Ўзбекистондаги вазият, турли соҳаларда эришилган ютуқлар бўйича объектив ахборотларни жаҳон жамоатчилигига вақтида етказиб бериш ҳамда мамлакатдаги реал воқеликнинг ундан ташқарида ҳам тўғри ва ўринли қабул қилишларига эришишдек муҳим вазифа борлигини ҳам таъкидлаш зарур. Аҳолининг холис ва ҳаққоний ахборотга эга бўлишини таъминлаш, юртдошларимизнинг маданий савияси, билим ва дунёқарашини ошириш, қадимий анъаналаримиз, тарихий меросимизни асраб-авайлаш ва ривожлантириш, шу билан бирга, фуқароларимиз онгида демократик қадриятлар, гражданлик позициясини шакллантириш, ѐш авлодни ватанпарварлик ва умуминсоний қадриятларга ҳурмат руҳида тарбиялашни оммавий ахборот воситалари олдида турган яна бир муҳим вазифа сифатида қайд этиш мумкин. Инсон кундалик ҳаётида турли нарсалардан фойдаланади. Инсон уларни истеъмол қилар экан ҳар гал муайян тартиб-қоидалар, содда қилиб айтганда, маданиятга риоя қилади. Айтайлик, кийим-бош кийиш ёки озиқ-овқат истеъмол қилишнинг ўзига хос маданияти бор. Бугунги кунда ахборот ҳам истеъмол қилинадиган товарга айланган экан, ҳар бир инсон ёки алоҳида олинган жамият ўзида уни истеъмол қилиш маданиятини тарбиялаши лозим. Хўш, ахборот истеъмоли маданияти деганда нимани тушуниш керак? 44 Ахборот истеъмоли маданияти, энг умумий маънода, ахборот оқимидан инсон манфаатлари, камолоти ҳамда жамият тараққиётига хизмат қилувчи маълумотларни қабул қилиш, саралаш, тушуниш ва талқин этиш хизмат қиладиган билимлар, қобилият ва малака тизимини англатади. Глобаллашув, модернизация ҳаётимизга ҳар куни янги тушунчаларни олиб кираётир. Машина, ускуна, жиҳозлар, технологик жараёнлар янгиланиб, замонавийлашаётир. Чунки эскирган билим, кўникма, малака булар – иқтисодий жиҳатдан эски товар. 2020 йил чиққан планшетга 2023 йилдаги дастурни қўйиб бозорга чиқарган компания ўзини ўзи синдиради. Шунинг учун кучли, бой компаниялар “Янгисидан борми?”, дейди. Янги билим, ноу-хау, технологияларни ярата оладиган мутахассисларни дунёнинг қаерида бўлмасин, топиб олади. Фойдаланилган адабиётлар 1. Ахборот ва ахборотлаштиришга оид норматив-ҳуқуқий ҳужжатлар тўплами. — Т.: Адолат, 2008. — 41–48 б. 2. Дўстмуҳаммад Х. “Оммавий ахборот воситаларини ривожлантиришнинг демократик андозалари” Т., “Ўзбекистон”- 2005, 56 бет, Б. 3. 3. Отамуродов С. Глобаллашув ва миллий – маънавий хавфсизлик. Т.,”Ўзбекистон”, 2015, -Б.266. 45
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The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis
Frontiers in neuroscience
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To cite this version: Bruno Bonaz, Thomas Bazin, Sonia Pellissier. The Vagus Nerve at the Interface of the Microbiota-Gut- Brain Axis. Frontiers in Neuroscience, 2018, 12, pp.49. ￿10.3389/fnins.2018.00049￿. ￿hal-01987060￿ Distributed under a Creative Commons Attribution 4.0 International License Edited by: Jasenka Zubcevic, University of Florida, United States Edited by: Jasenka Zubcevic, University of Florida, United States Reviewed by: Pieter Vanden Berghe, KU Leuven, Belgium Helio Cesar Salgado, University of São Paulo, Brazil *Correspondence: Bruno Bonaz BBonaz@chu-grenoble.fr Reviewed by: Pieter Vanden Berghe, KU Leuven, Belgium Helio Cesar Salgado, University of São Paulo, Brazil Keywords: microbiota-gut-brain axis, vagus nerve, vagus nerve stimulation, cholinergic anti-inflammatory pathway, stress *Correspondence: Bruno Bonaz BBonaz@chu-grenoble.fr The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis Bruno Bonaz 1,2*, Thomas Bazin 3,4 and Sonia Pellissier 5 1 Division of Hepato-Gastroenterology, University Hospital, Grenoble Alpes, France, 2 Grenoble Institute of Neurosciences, University Grenoble Alpes, Inserm U1216, Grenoble, France, 3 Institut National de la Recherche Agronomique, Mycoplasmal and Chlamydial Infections in Humans, Univ. Bordeaux, Bordeaux, France, 4 Department of Hepato-Gastroenterology, Bordeaux Hospital University Center, Pessac, France, 5 LIP/PC2S, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France The microbiota, the gut, and the brain communicate through the microbiota-gut-brain axis in a bidirectional way that involves the autonomic nervous system. The vagus nerve (VN), the principal component of the parasympathetic nervous system, is a mixed nerve composed of 80% afferent and 20% efferent fibers. The VN, because of its role in interoceptive awareness, is able to sense the microbiota metabolites through its afferents, to transfer this gut information to the central nervous system where it is integrated in the central autonomic network, and then to generate an adapted or inappropriate response. A cholinergic anti-inflammatory pathway has been described through VN’s fibers, which is able to dampen peripheral inflammation and to decrease intestinal permeability, thus very probably modulating microbiota composition. Stress inhibits the VN and has deleterious effects on the gastrointestinal tract and on the microbiota, and is involved in the pathophysiology of gastrointestinal disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) which are both characterized by a dysbiosis. A low vagal tone has been described in IBD and IBS patients thus favoring peripheral inflammation. Targeting the VN, for example through VN stimulation which has anti-inflammatory properties, would be of interest to restore homeostasis in the microbiota-gut-brain axis. INTRODUCTION Specialty section: This article was submitted to Autonomic Neuroscience, a section of the journal Frontiers in Neuroscience A huge amount of data has highlighted a potential role of microbial dysbiosis in various chronic disorders (Lynch and Pedersen, 2016). The microbiota, the gut, and the brain communicate through the microbiota-gut-brain axis and a perturbation of this axis is involved in the pathophysiology of neurodegenerative disorders (Cenit et al., 2017; Kobayashi et al., 2017; Quigley, 2017). The brain and the gut communicate in a bidirectional way, through the autonomic nervous system (ANS) and the circumventricular organs (Bonaz and Bernstein, 2013). A perturbation of this axis is involved in the pathophysiology of gastrointestinal (GI) disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) which are biopsychosocial diseases (Mulak and Bonaz, 2004; Porcelli, 2004; Bonaz and Bernstein, 2013; O´swiecimska et al., 2017). The vagus nerve (VN), the principal component of the parasympathetic nervous system, is considered as the sixth sense (Zagon, 2001) because of its role in interoceptive awareness (Strigo and Craig, 2016; Smith et al., 2017). The VN is able to sense the microbiota, to transfer this gut information to the Received: 30 November 2017 Accepted: 22 January 2018 Published: 07 February 2018 Keywords: microbiota-gut-brain axis, vagus nerve, vagus nerve stimulation, cholinergic anti-inflammatory pathway, stress HAL Id: hal-01987060 https://hal.science/hal-01987060v1 Submitted on 27 May 2020 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 MINI REVIEW published: 07 February 2018 doi: 10.3389/fnins.2018.00049 MINI REVIEW published: 07 February 2018 doi: 10.3389/fnins.2018.00049 HOW THE MICROBIOTA COMMUNICATES WITH THE BRAIN? The human gut contains 1013–1014 microorganisms, much more than the cells of our organism, and 100 times more genes than our genome. The weight of the microbiota is about 1 kg in the adult. The vast majority of bacteria resides in the colon. In healthy adults, two bacterial phyla, Bacteroidetes and Firmicutes, dominate bacterial composition, with smaller amounts of Actinobacteria, Proteobacteria, and Verrucomicrobia. Gut microbiota also contains methanogenic archae, eucaryotes (mainly yeasts), and numerous phages (Eckburg et al., 2005; Reyes et al., 2010). The communication between the brain and the microbiota is bidirectional, through multiple pathways: neural through the VN and/or spinal cord, endocrine (through the hypothalamic pituitary adrenal, HPA, axis), immune (cytokines), and metabolic [short chain fatty acids, (SCFAs), tryptophan...] (Cryan and Dinan, 2012; Brookes et al., 2013; Perez-Burgos et al., 2015; Forsythe et al., 2016; Sarkar et al., 2016). Neuroactive compounds are released by bacteria such as γ- aminobutyric acid (GABA), serotonin, dopamine, acetylcholine (ACh), and essentially act locally on the enteric nervous system i.e., the gut brain (Lyte, 2011; Sarkar et al., 2016). Some of these compounds reach the big brain via blood and circumventricular organs or through the VN. In this minireview, we will focus on the involvement of the VN at the interface of the microbiota-gut- brain axis (Figure 1). In addition with cell-mediated sensing, VN can sense microbiota signals through direct mechanisms. For instance, SCFAs produced by the microbiota activate vagal afferent fibers by different mechanisms depending on the compound: while oleate, a long fatty acid, acts on vagal afferents through a CCK- mediated mechanism, butyrate, a short fatty acid, has a direct effect on afferent terminals (Lal et al., 2001). In addition, TLR4 are expressed on vagal afferent fibers (Goehler et al., 1999) and these fibers could sense bacterial products such as LPS to activate the brain. LPS also activate directly vagal afferent fibers at the level of the nodose ganglia (Hosoi et al., 2005) thus explaining that subdiaphragmatic vagotomy does not completely block brain mediated behavioral and neural effects of peripheral LPS or interleukin-1beta (Schwartz et al., 1997). Gut to Brain Interactions Vagal afferent fibers are distributed to all the layers of the digestive wall but do not cross the epithelial layer (Wang and Powley, 2007) so that they are not in direct contact with the gut luminal microbiota. Consequently, these fibers can sense only indirectly microbiota signals, through the diffusion of bacterial compounds or metabolites, or thanks to other cells located in the epithelium that relay luminal signals. Interactions between gut endocrine cells and vagal afferents are at the interface of gut chemosensing (Raybould, 2010). Enteroendocrine cells (EECs), 1% of intestinal epithelial cells, release their content in presence of luminal carbohydrate, triglycerides, and protein and modulate GI functions such as motility, secretion, and food intake (Näslund and Hellström, 2007; Gunawardene et al., 2011; Wu et al., 2013). EECs interact with vagal afferents either directly through the release of serotonin (5-hydroxytryptamine, 5-HT) activating 5-HT3 receptors located on vagal afferent fibers (Li et al., 2000) or gut hormones such as cholecystokinin (CCK), glucagon-like peptide-1, peptide YY targeting the brain through vagal afferents which express receptors for these anorexigenic or orexigenic (ghrelin, orexin) hormones (Strader and Woods, 2005). Brain pathways activated by these hormones have been mapped using c-fos expression as a marker of neuronal activation (Bonaz et al., 1993a,b). EECs detect signals from microbiota through toll-like receptors (TLR) which recognize bacterial products such as lipopolysaccharides (LPS) and others (Abreu et al., 2005), and are expressed by EECs (Bogunovic et al., 2007), or receptors for microbiota metabolites such as SCFAs (Samuel et al., 2008). Thus, EECs are key players in the detection of luminal bacterial content and bacterial products that can regulate GI motility, secretion, food intake, through their indirect effect on vagal afferent fibers. Citation: Bonaz B, Bazin T and Pellissier S (2018) The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. Front. Neurosci. 12:49. doi: 10.3389/fnins.2018.00049 February 2018 | Volume 12 | Article 49 Frontiers in Neuroscience | www.frontiersin.org 1 The Vagus Nerve and the Microbiota-Gut-Brain Axis Bonaz et al. central nervous system where it is integrated, and then to generate an adapted or inappropriate response; the latter could perpetuate a pathological condition of the digestive tract or favor neurodegenerative disorders (Eisenstein, 2016; Tse, 2017). A dysbiosis is observed in IBS and IBD. However, in the context of this axis, the question is whether it is a cause or a consequence of an abnormal gut-brain processing. Stress, either interoceptive or exteroceptive, is involved in the pathophysiology of IBS and IBD and can modify the gut microbiota (O’Mahony et al., 2009; Konturek et al., 2011; Bonaz, 2013; Barbara et al., 2014). Stress stimulates the sympathetic nervous system while inhibiting the VN (Porges, 1995; Sahar et al., 2001). The VN, a mixed nerve with anti-inflammatory properties both through its afferent and efferent fibers, is at the interface of the brain-gut axis (Bonaz et al., 2016a,b). An abnormal vagal tone is described in IBS and IBD (Pellissier et al., 2010, 2014). Targeting the VN could restore homeostasis in such diseases. In particular, VN stimulation (VNS), approved for the treatment of depression and epilepsy (Ben-Menachem, 2001; Bonaz et al., 2013) and for its anti- inflammatory properties (Borovikova et al., 2000a,b; Pavlov et al., 2003), should be of interest. left colonic flexure for others (Netter, 1989). In both cases, an interaction between VN fibers and microbiota-rich colonic mucosa is possible. February 2018 | Volume 12 | Article 49 THE VAGUS NERVE IN THE MICROBIOTA-GUT-BRAIN AXIS Powley et al. (2011) have shown that vagal afferent endings are divided into three subtypes: villus afferent endings are distributed at the apical tips of intestinal villi, immediately below the epithelial wall while other types of afferent endings are independently distributed either around the intestinal glands or The VN contains 80 and 20% of afferent and efferent fibers respectively (Agostoni et al., 1957) and innervates all the digestive tract for some authors (Delmas and Laux, 1933) or until the February 2018 | Volume 12 | Article 49 Frontiers in Neuroscience | www.frontiersin.org 2 Bonaz et al. The Vagus Nerve and the Microbiota-Gut-Brain Axis FIGURE 1 | Communication between the central nervous system and the microbiota through the vagus nerve (VN). VN afferent fibers can be stimulated by microbiota components either directly or indirectly via gut endocrine cells (GEC). VN afferent fibers exert stimuli on the central nervous system via the central autonomic network (CAN). VN afferent fibers are able to stimulate efferent fibers through the inflammatory reflex. VN efferent fibers can reduce digestive inflammation and reduce intestinal permeability by tight junction reinforcement. These actions of vagal efferent fibers can indirectly modulate microbiota composition. Alongside with brain-VN-microbiota axis exists bi-directional communication by various ways. FIGURE 1 | Communication between the central nervous system and the microbiota through the vagus nerve (VN). VN afferent fibers can be stimulated by microbiota components either directly or indirectly via gut endocrine cells (GEC). VN afferent fibers exert stimuli on the central nervous system via the central autonomic network (CAN). VN afferent fibers are able to stimulate efferent fibers through the inflammatory reflex. VN efferent fibers can reduce digestive inflammation and reduce intestinal permeability by tight junction reinforcement. These actions of vagal efferent fibers can indirectly modulate microbiota composition. Alongside with brain-VN-microbiota axis exists bi-directional communication by various ways. crypts (crypt afferent endings), immediately below the crypt- villus junction, or along the gastric antral glands (antral gland afferent endings) and forms terminal concentrations immediately below the luminal epithelial wall (Figure 2). These endings are both chemo- and mechanosensitive. Blackshaw et al. (Blackshaw and Grundy, 1993a,b) have recorded single afferent fibers with receptive fields in the mucosa of the upper GI tract from the cervical VN of urethane anesthetized ferrets. Single chemosensitive vagal afferent units supplying the gut respond to most luminal molecules by increasing their firing rate. Frontiers in Neuroscience | www.frontiersin.org THE VAGUS NERVE IN THE MICROBIOTA-GUT-BRAIN AXIS They observed a broad sensitivity of mucosal afferent fibers to luminal chemical and mechanical stimuli. Mucosal endings were stimulated by 5-HT acting directly on afferent endings via 5-HT3 receptors. the vagally-mediated microbiota effect on mood (Bravo et al., 2011). Using an ex vivo intestinal jejunal segment mesenteric nerve recording preparation, Perez-Burgos et al. (2013) have shown that administration of L. johnsonii in the lumen of this segment induced an increase in the firing rate of vagal afferents prevented by prior subdiaphragmatic vagotomy. As electrical stimulation of vagal afferent fibers modifies brain concentration of serotonin, GABA, and glutamate (Ressler and Mayberg, 2007) and is used in the treatment of drug resistant epilepsy and depression (Bonaz et al., 2013), this study suggests that probiotic-mediated VN activation could have beneficial effects in these diseases. However, as no in vivo experiment has been yet conducted, VN afferent fiber direct stimulation by digestive microbiota is still hypothetical. Vagal chemoreceptors are most likely involved in the communication between the microbiota and the brain by sensing SCFAs and/or gut hormones (Raybould, 2010). Indeed, intraduodenal injection of Lactobacillus johnsonii enhanced gastric VN activity (Tanida et al., 2005). Healthy mice chronically treated with Lactobacillus rhamnosus (JB- 1) presented GABA brain expression modifications which increased in the cingulate cortex and decreased in the hippocampus, amygdala, and locus coeruleus. These animals had also reduced stress-induced corticosterone and anxiety- and depression-related behavior. These effects were not observed after vagotomy. Hence, L. rhamnosus have potential therapeutic indications in stress-related disorders pointing out The activation of vagal afferent fibers by microorganisms was highlighted indirectly by the group of Mark Lyte (Gaykema et al., 2004) using c-fos as a marker of neuronal activation to map brain pathways activated by oral administration of Campylobacter jejuni at subclinical doses in mice influencing behavior and brain functions. Brain activation was observed in the nucleus tractus solitarius (NTS), the first entrance of vagal afferents in the brain, as well as in the widespread projections of the NTS such as the parabrachial nucleus, PVH, amygdala which are part of the central autonomic network (CAN) (Gaykema et al., 2004; Goehler et al., 2005, 2008). The CAN is involved in the autonomic, endocrine, cognitive, and behavioral response February 2018 | Volume 12 | Article 49 3 The Vagus Nerve and the Microbiota-Gut-Brain Axis Bonaz et al. FIGURE 2 | Vagal terminal afferent endings. THE VAGUS NERVE IN THE MICROBIOTA-GUT-BRAIN AXIS Antral gland afferent endings begin to divide at the level of the muscularis mucosae, and surrond gastric antral glands creating arbors. Villus afferent endings divide at the basal pole of the crypts, and ramify repeatedly at the apical half of the villus. Crypt afferent endings divide at the basal pole of the crypts, and collaterals encircle multiple time the crypts or the intestinal glands. FIGURE 2 | Vagal terminal afferent endings. Antral gland afferent endings begin to divide at the level of the muscularis mucosae, and surrond gastric antral glands creating arbors. Villus afferent endings divide at the basal pole of the crypts, and ramify repeatedly at the apical half of the villus. Crypt afferent endings divide at the basal pole of the crypts, and collaterals encircle multiple time the crypts or the intestinal glands. receptor potential cation channel A1, an irritant receptor for allylisothiocyanate, the olfactory receptor 558 which serves as a microbial metabolite sensor activated by isovalerate, and an α2A adrenoreceptor-TRPC4 channel signaling cascade that detects stress response-related catecholamines. Using imaging of intestinal preparations, they showed that many 5-HT3R- expressing fibers, colocalized with synaptic markers thus of neural origin, innervate gut epithelium and make close contacts with EECs. By recording mechanosensory nerve fibers from an ex vivo colonic preparation, they showed that noradrenaline or isovalerate applicated to the epithelium induced responses in the sensory neurons dependent on EEC-mediated transduction through 5-HT3 receptors. They concluded that EECs are polymodal chemosensors that integrate extrinsic and intrinsic signals within the gut and convey this information to the nervous system. These data have potential therapeutic implications in the domain of IBS and IBD. In this study, they did not characterize nerve fibers in close contact with EECs but sympathetic and vagal sensory fibers communicate with EECs (Williams et al., 2016). Serotonin released by EECs may also act on enteric neurons (Veiga-Fernandes and Mucida, 2016). Together, communication between bacterial products and the VN seems possible, but does not necessarily happen permanently during physiological conditions. to interoceptive and exteroceptive stimuli (Benarroch, 1993) and appears as the relay of vagal afferents, in particular of visceral origin, in the central nervous system (Bonaz and Bernstein, 2013). In addition, Bercik et al. (2011) have shown that Bifidobacterium longum has anxiolytic effects during non- infectious, chronic, low-grade gut inflammation induced by dextran sodium sulfate administration. Frontiers in Neuroscience | www.frontiersin.org Brain to Gut Interactions Endotoxemia following intraperitoneal LPS induces intestinal barrier dysfunction with a decreased expression of occludin and zonula occludens 1 with a disruption of tight junction and increase of intestinal permeability. These effects were prevented by VNS and dampened by pretreatment of the animals with an α7nAChR antagonist before VNS (Zhou et al., 2013). VNS also prevents burn-induced intestinal permeability by improving tight junction protein expression of occludin (Costantini et al., 2010; Krzyzaniak et al., 2011). The α7nAChR protects against burn-induced gut barrier injury by preventing the decreased expression and altered localization of occludin and zonula occludens-1 (ZO-1) (Costantini et al., 2012). The mechanism through which vagal efferents protect barrier epithelium is not well-known. One of the mechanisms could be the connection of the VN with the enteric nervous system which communicates with enteric glia cells through nicotinic cholinergic signaling (Cheadle et al., 2014). These glia cells preserve epithelial barrier against intestinal bacteria insult by increasing the expression of tight junction proteins such as occludin and ZO-1 through the secretion of S-nitrosoglutathione (Yu and Li, 2014). However, a recent study has shown that enteric glia is not required for maintenance of the intestinal epithelium (Rao et al., 2017). Consequently, vagal activity provides a protective function to the intestinal epithelial barrier and a low vagal activity makes intestinal epithelium more permeable thus promoting systemic inflammation and chronic disease. Central vagal stimulation with a thyrotropin-releasing hormone analog, known to activate preganglionic neurons of the dorsal motor nucleus of the VN, activates M2 macrophages which are in close connection with gastric cholinergic myenteric neurons and have anti-inflammatory properties, and deactivates pro-inflammatory M1 macrophages in the stomach which are involved in abdominal surgery-induced gastric inflammation and gastric ileus (Yuan and Taché, 2017). However, few objective data are available on the pro- or anti-inflammatory role of M1 and M2 macrophages on intestinal permeability. M2 macrophages did not play a role in the increase of intestinal permeability observed in a model of enteric nematode infection (Notari et al., 2014). The VN is able to inhibit M1 proinflammatory macrophages (Yuan and Taché, 2017) and this anti-inflammatory effect could modify intestinal permeability and/or the gut microbiota. p y g Vagal afferents activate vagal efferents in an inflammatory reflex described in 2000 by the group of Tracey in a model of septic shock and called the cholinergic anti-inflammatory pathway (CAP) (Borovikova et al., 2000a,b; Martelli et al., 2016). THE VAGUS NERVE IN THE MICROBIOTA-GUT-BRAIN AXIS This effect required vagal integrity, and was probably mediated by vagal pathways originating at the level of the enteric nervous system. Bellono et al. (2017) have recently detailed the mechanisms involved in the communication between gut epithelial cells, particularly EECs, and the neural system by generating murine intestinal organoids where EECs were genetically tagged with green fluorescence protein to characterize their physiologic, pharmacologic, and molecular functions through electrophysiological analysis. They showed that EECs are excitable and express voltage-gated sodium and calcium channels. They screened 30 compounds present in the gut such as microbial products, irritants and inflammatory agents, and neurotransmitters. They showed that only allyl isothiocyanate, a mustard plant component that induces visceral inflammatory pain, isovalertate, a volatile fatty acid fermentation product produced by gut microbiota associated with GI disorders, and the catecholamines (dopamine, epinephrine, and norepinephrine), involved in GI stress, specifically activate EECs. Isobutyrate and butyrate elicited small but consistent responses. They showed that EECs express sensory receptors, which detect and transduce specific signals, such as transient Non-vagal pathways are also involved in the microbiota-gut- brain axis (Mayer et al., 2015). For instance, van der Kleij et al. (2008) showed the protective effects of Lactobacillus reuteri and Bifidobacterium infantis in a model of dextran sulfate sodium colitis in mice after subdiaphragmatic vagotomy. Both strains February 2018 | Volume 12 | Article 49 4 The Vagus Nerve and the Microbiota-Gut-Brain Axis Bonaz et al. did not require the presence of an intact VN for their protective effects. receptors; this effect was prevented by vagotomy and CCK or nicotinic receptor antagonists (Luyer et al., 2005; de Haan et al., 2010). Brain to Gut Interactions Indeed, ACh released at the distal end of vagal efferents inhibits the release of TNFα by macrophages through their α7nicotinicACh receptors (α7nAChR) (Wang et al., 2003). In the same way, a vago-sympathetic pathway to the spleen inhibiting TNFα release by splenic macrophages has been described (Olofsson et al., 2012) and for some authors the splanchnic pathway is the efferent arm of the inflammatory reflex (Martelli et al., 2016). In addition, vagal afferents, through the widespread projections of the NTS, target the CAN which in return modulates the ANS, through descending pathways from the PVN, A5, and C1 noradrenergic and adrenergic group respectively (Bonaz et al., 2017). When targeting vagal afferents to the brain, the gut microbiota could modulate this inflammatory reflex either activating or inhibiting the VN thus being anti- or pro- inflammatory. There are presently no published data regarding the effect of vagal stimulation either chemically or through VNS on the gut microbiota but based on its effect on intestinal permeability and local immunity (Meregnani et al., 2011), we can hypothesize that the VN could modulate gut microbiota composition that depends on these two factors (Karl et al., 2017). Frontiers in Neuroscience | www.frontiersin.org REFERENCES Bonaz, B. (2013). Inflammatory bowel diseases: a dysfunction of brain-gut interactions? Minerva Gastroenterol. Dietol. 59, 241–259. Abreu, M. T., Fukata, M., and Arditi, M. (2005). TLR signaling in the gut in health and disease. J. Immunol. 174, 4453–4460. doi: 10.4049/jimmunol.174.8.4453 Bonaz, B. L., and Bernstein, C. N. (2013). Brain-gut interactions in inflammatory bowel disease. Gastroenterology 144, 36–49. doi: 10.1053/j.gastro.2012.10.003 Bonaz, B., De Giorgio, R., and Taché, Y. (1993a). Peripheral bombesin induces c-fos protein in the rat brain. Brain Res. 600, 353–357. doi: 10.1016/0006-8993(93)91397-B Agostoni, E., Chinnock, J. E., De Daly, M. B., and Murray, J. G. (1957). Functional and histological studies of the vagus nerve and its branches to the heart, lungs and abdominal viscera in the cat. J. Physiol. 135, 182–205. doi: 10.1113/jphysiol.1957.sp005703 Bonaz, B., Picq, C., Sinniger, V., Mayol, J. F., and Clarençon, D. (2013). Vagus nerve stimulation: from epilepsy to the cholinergic anti-inflammatory pathway. Neurogastroenterol. Motil. 25, 208–221. doi: 10.1111/nmo.12076 Barbara, G., Cremon, C., and Stanghellini, V. (2014). Inflammatory bowel disease and irritable bowel syndrome: similarities and differences. Curr. Opin. Gastroenterol. 30, 352–358. doi: 10.1097/MOG.0000000000000070 Neurogastroenterol. Motil. 25, 208–221. doi: 10.1111/nmo.1207 Bonaz, B., Sinniger, V., and Pellissier, S. (2016a). Anti-inflammatory properties of the vagus nerve: potential therapeutic implications of vagus nerve stimulation. J. Physiol. 594, 5781–5790. doi: 10.1113/JP271539 Bellono, N. W., Bayrer, J. R., Leitch, D. B., Castro, J., Zhang, C., O’Donnell, T. A., et al. (2017). Enterochromaffin cells are gut chemosensors that couple to sensory neural pathways. Cell 170, 185–198.e16. doi: 10.1016/j.cell.2017. 05.034 Bonaz, B., Sinniger, V., and Pellissier, S. (2016b). Vagal tone: effects on sensitivity, motility, and inflammation. Neurogastroenterol. Motil. 28, 455–462. doi: 10.1111/nmo.12817 Benarroch, E. E. (1993). The central autonomic network: functional organization, dysfunction, and perspective. Mayo Clin. Proc. 68, 988–1001. doi: 10.1016/S0025-6196(12)62272-1 Bonaz, B., Sinniger, V., and Pellissier, S. (2017). Vagus nerve stimulation: a new promising therapeutic tool in inflammatory bowel disease. J. Intern. Med. 282, 46–63. doi: 10.1111/joim.12611 Ben-Menachem, E. (2001). Vagus nerve stimulation, side effects, and long-term safety. J. Clin. Neurophysiol. 18, 415–418. doi: 10.1097/00004691-200109000-00005 Bonaz, B., Taylor, I., and Taché, Y. (1993b). Peripheral peptide YY induces c-fos-like immunoreactivity in the rat brain. Neurosci. Lett. 163, 77–80. doi: 10.1016/0304-3940(93)90233-B Bercik, P., Park, A. J., Sinclair, D., Khoshdel, A., Lu, J., Huang, X., et al. (2011). The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut-brain communication. Neurogastroenterol. Motil. 23, 1132–1139. doi: 10.1111/j.1365-2982.2011.01796.x Borovikova, L. STRESS, VAGUS NERVE, AND THE MICROBIOTA The intestinal epithelium is a barrier to prevent translocation of bacteria and other agents. Severe burn injuries in a rat scald model injuring 35% of the total body surface area result in intestinal barrier dysfunction due to gut ischemia and electroacupuncture has a protective role through the VN by decreasing intestinal permeability (Hu et al., 2013; Wang et al., 2015). VNS increases the expression and proper localization of tight junction proteins and decreases intestinal epithelial permeability (Zhou et al., 2013; Van Houten et al., 2015). In the same way, electroacupuncture prevents intestinal barrier dysfunction following prolonged hemorrhagic shock by decreasing intestinal permeability through a vagal anti- inflammatory mechanism (Du et al., 2013). In the same model, VNS had a protective effect, independent of the spleen but involving a cholinergic nicotinic receptor since this effect was reproduced with nicotine (Levy et al., 2013). Lipid-rich enteral nutrition prevented intestinal barrier dysfunction in a model of septic shock by activating the CAP through CCK The effect of stress on the GI tract is well-known (Taché and Bonaz, 2007). Stress, through its neuromediators, corticotrophin- releasing factor (CRF) and its related peptide urocortin(s), acting on their G protein coupled CRF (1 and 2) receptors located in the brain and the GI tract, increases intestinal permeability and modifies the gut microbiota (Taché et al., 2018); these two factors are involved in the pathophysiology of IBS and IBD. CRF2 receptors are involved in the perturbation of intestinal permeability (Ducarouge et al., 2017). CRF and urocortin are released by mastocytes of the lamina propria which have CRF1- 2 receptors, activation of which releases cytokines and other pro-inflammatory mediators by mastocytes (Theoharides and Cochrane, 2004; Theoharides et al., 2004). CRF also increases intestinal permeability via mast cell release of tumor necrosis factor (TNF)-α and proteases (Overman et al., 2012). Targeting February 2018 | Volume 12 | Article 49 5 The Vagus Nerve and the Microbiota-Gut-Brain Axis Bonaz et al. AUTHOR CONTRIBUTIONS BB wrote the first draft of the manuscript; TB and SP provided critical feedback to improve it; TB drew the figures. CONCLUSION CRF receptors by selective antagonists to inhibit mast cell activation is a therapeutic option for chronic inflammatory disorders exacerbated by stress. Chronic early life stress induces dysbiosis in rats via modifications of intestinal permeability, which may later sensitize adult rats to visceral hypersensitivity (Moussaoui et al., 2017). Classically, stress inhibits the VN and stimulates the sympathetic nervous system through autonomic- related projection neurons of the PVH to the dorsal motor nucleus of the VN and sympathetic pre-ganglionic neurons of the spinal cord (Taché and Bonaz, 2007; Wood and Woods, 2007). Since the VN has anti-inflammatory properties through its afferent and efferent fibers (Bonaz et al., 2016a), stress has thus pro-inflammatory properties. A single acute stress induces a prolonged increase of pro-inflammatory cytokines after the end of stress exposition (Marsland et al., 2017), at the moment of the recovery period which is a critical period since it corresponds to the parasympathetic rebound. Exposition to multiple repeated stressors counteracts the parasympathetic tone recovery, favoring an allostatic load (McEwen, 2008) thus blunting the anti-inflammatory regulatory action of the VN. Stress could counterbalance the overall protective effect of the VN on epithelial barrier and thus favor dysbiosis by disrupting epithelial homeostasis. The role of the VN in microbiota-brain communication is now well-established. A reduction in vagal tone reflecting dysautonomia has been shown in IBS and IBD (Pellissier et al., 2010, 2014) characterized by a leaky gut and dysbiosis (Bonaz et al., 2016b). Consequently, monitoring vagal tone would be an interesting marker of the microbiota-gut-brain axis. Relevant electrophysiological data could be then considered as a part of the—omes, and should be integrated in a converging combined approach to decipher complex IBD and IBS pathophysiology (de Souza et al., 2017). Moreover, monitoring and targeting vagal tone through VNS, microbiota modulation (using prebiotics, probiotics, fecal microbiota transplantation, diet...), drugs targeting the cholinergic system and/or complementary medicine (hypnosis, meditation), cognitive behavioral therapies, deep breathing, and moderate and sustainable physical activity would be of interest to restore a homeostatic microbiota-gut-brain axis. REFERENCES V., Ivanova, S., Nardi, D., Zhang, M., Yang, H., Ombrellino, M., et al. (2000a). Role of vagus nerve signaling in CNI-1493-mediated suppression of acute inflammation. Auton. Neurosci. 85, 141–147. doi: 10.1016/S1566-0702(00)00233-2 Blackshaw, L. A., and Grundy, D. (1993a). 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Vagus nerve stimulation attenuates intestinal epithelial tight junctions disruption in endotoxemic mice through alpha7 nicotinic acetylcholine receptors. Shock 40, 144–151. doi: 10.1097/SHK.0b013e3182 99e9c0 REFERENCES Enteric glial cells and their role in the intestinal epithelial barrier. World J. Gastroenterol. 20, 11273–11280. doi: 10.3748/wjg.v20.i32.11273 Sarkar, A., Lehto, S. M., Harty, S., Dinan, T. G., Cryan, J. F., and Burnet, P. W. (2016). Psychobiotics and the manipulation of bacteria-gut-brain signals. Trends Neurosci. 39, 763–781. doi: 10.1016/j.tins.2016.09.002 February 2018 | Volume 12 | Article 49 Frontiers in Neuroscience | www.frontiersin.org 8 The Vagus Nerve and the Microbiota-Gut-Brain Axis The Vagus Nerve and the Microbiota-Gut-Brain Axis Bonaz et al. 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. Copyright © 2018 Bonaz, Bazin and Pellissier. 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. Zhou, H., Liang, H., Li, Z. F., Xiang, H., Liu, W., and Li, J. G. (2013). Vagus nerve stimulation attenuates intestinal epithelial tight junctions disruption in endotoxemic mice through alpha7 nicotinic acetylcholine receptors. Shock 40, 144–151. doi: 10.1097/SHK.0b013e3182 99e9c0 February 2018 | Volume 12 | Article 49 Frontiers in Neuroscience | www.frontiersin.org 9
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Exponential approach to the hydrodynamic attractor in Yang-Mills kinetic theory
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I. INTRODUCTION nuclei has repeatedly been questioned [4], and different proposals have been put forward to extend the applicability of hydrodynamics to earlier times and more anisotropic systems [5]. One proposal to potentially extend the validity of hydrodynamics goes by the name of hydrodynamic attractors [6], which represent emergent constitutive rela- tions away from equilibrium. Over the course of the last few years, the emergence of such hydrodynamics attractors has been firmly established in a variety of effectively (0 þ 1)-dimensional microscopic models which feature a rather high degree of symmetry [7–14], and different theoretical [15–23] and phenomenological aspects of the emergence of hydrodynamic attractors [24–27] have been explored. See [28] for a recent review. Ultrarelativistic heavy-ion collisions at RHIC and LHC produce a collective state of matter comprised of the fundamental quark and gluon constituents of strong inter- actions. Describing ab initio formation and evolution of this quark-gluon plasma (QGP) presents an important theoretical problem. Since a first principles description directly using the theory of strong force, quantum chromo- dynamics (QCD), remains an outstanding challenge, the standard model of the space-time evolution of heavy-ion collisions is based on effective descriptions of QCD [1]. The initial nonequilibrium dynamics after the collision has been addressed in a variety of different microscopic models [2,3]. Eventually, on a time scale of ∼1 fm=c, the QGP can be well described by relativistic hydrodynamics. This is to some extent surprising, as the system can feature large spatial and temporal gradients and remains significantly out of equilibrium for a much longer period of time, as indicated e.g., by large values of the pressure anisotropy. Despite efforts in this direction [15,29], the generaliza- tion of the concept of hydrodynamic attractors to higher- dimensional systems represents an outstanding challenge. With this as a motivation, it was recently pointed out that the hydrodynamic attractor can be viewed as a dimension- ality reduction in a space of natural observables associated with nuclear collision problems [13]. From this perspective, the number of relevant degrees of freedom required to describe the evolution of a system is effectively lowered due to a rapid memory loss of initial conditions. Viewing thermalization in this way enables to approach the study of thermalization in a data-driven way and borrow methods from data science. PHYSICAL REVIEW D 106, 014016 (2022) PHYSICAL REVIEW D 106, 014016 (2022) Exponential approach to the hydrodynamic attractor in Yang-Mills kinetic theory Xiaojian Du ,1,* Michal P. Heller ,2,† Sören Schlichting,1,‡ and Viktor Svensson3,§ 1Fakultät für Physik, Universität Bielefeld, D-33615 Bielefeld, Germany 2Department of Physics and Astronomy, Ghent University, 9000 Ghent, Belgium 3Division of Solid State Physics and NanoLund, Lund University, S-221 00 Lund, Sweden Xiaojian Du ,1,* Michal P. Heller ,2,† Sören Schlichting,1,‡ and Viktor Svensson3,§ 1Fakultät für Physik, Universität Bielefeld, D-33615 Bielefeld, Germany 2Department of Physics and Astronomy, Ghent University, 9000 Ghent, Belgium 3Division of Solid State Physics and NanoLund, Lund University, S-221 00 Lund, Sweden We use principal component analysis to study the hydrodynamic attractor in Yang-Mills kinetic theory undergoing the Bjorken expansion with color glass condensate initial conditions. The late-time hydro- dynamic attractor is characterized by a single principal component determining the overall energy scale. How it is reached is governed by the disappearance of single subleading principal component character- izing deviations of the pressure anisotropy, the screening mass and the scattering rate. We find that for wide range of couplings the approach to the hydrodynamic attractor at late times is well described by an exponential. Its decay rate dependence on the coupling turns out to translate into a simple dependence on the shear viscosity to entropy density ratio. DOI: 10.1103/PhysRevD.106.014016 Published by the American Physical Society Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI. Funded by SCOAP3. *xjdu@physik.uni-bielefeld.de †michal.p.heller@ugent.be ‡sschlichting@physik.uni-bielefeld.de §viktor.svensson@ftf.lth.se I. INTRODUCTION Due to these concerns the applicability of relativistic hydrodynamics in high-energy collisions of heavy and light *xjdu@physik.uni-bielefeld.de †michal.p.heller@ugent.be ‡sschlichting@physik.uni-bielefeld.de §viktor.svensson@ftf.lth.se In the present work, we adopt the approach of [13] to study the evolution of a 0 þ 1D Bjorken flow in an effective kinetic theory (EKT) [30] of pure glue QCD [24,25] with highly anisotropic color glass condensate [31,32] initial conditions. Building on the methodology developed Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI. Funded by SCOAP3. 014016-1 2470-0010=2022=106(1)=014016(11) Published by the American Physical Society DU, HELLER, SCHLICHTING, and SVENSSON PHYS. REV. D 106, 014016 (2022) of the nuclear gluon distributions, due to Golec-Biernat and Wusthoff (GBW) [38], for which in [13], we use principal component analysis (PCA) to study the dimensionality reduction for a set of observables that describe the thermalization process at weak coupling. The mechanism behind the information loss can come from the expansion at early time or interactions at late times [19,33]. We also look more closely at the late-time behavior to gain information on transient nonhydrody- namic contributions to the pressure anisotropy, and com- pare our results in pure glue QCD kinetic theory to previous studies in conformal relaxation time approxima- tion (RTA) [34,35]. ΦA;Bðb; kÞ ¼ 4π2 ðN2c −1Þ g2Nc k2 Q2 A;BðbÞ exp  −k2 Q2 A;BðbÞ  ; ð2Þ ð2Þ where Q2 A;B ¼ Q2sðbÞ denotes the (adjoint) saturation scale [39] for nucleus. Based on Eqs. (1) and (2), the initial gluon spectrum in the GBW model can then be expressed analytically as The paper is organized in the following way. In Sec. II, we introduce our model of the initial state, along with the effective kinetic theory of pure glue QCD describing the nonequilibrium dynamics of the QGP. Subsequently, in Sec. III, we perform a PCA of the evolution for different initial conditions to study information loss and dimension- ality reduction over the course of the thermalization process of the preequilibrium QGP. Section IV is devoted to a more detailed study of the evolution towards equilibrium, focus- ing on the exponential decay of variance of the pressure anisotropy in the QGP. We conclude this paper in Sec. II. SETUP We use the color glass condensate (CGC) effective theory of high-energy QCD [31,32], to evaluate the phase-space distributions of gluons produced in the colli- sion. Due to physical differences and uncertainties in modeling the initial state, this gives rise to a multidimen- sional parameter space of early time phase-space distribu- tions of gluons. They serve as initial conditions for EKT, which we subsequently utilize to evolve expanding nuclear matter into the hydrodynamic phase. g Since the transverse spectrum in Eq. (3) features a ∝ 1=P2 infrared behavior, soft observables, such as screening mass mD and scattering rate g2T in Eq. (14), are infrared divergent. However, this divergence can be regulated by nonlinear effects, going beyond the factorization formula, see e.g., the discussion in [36]. Within our study, we will simply model this by introducing an additional infrared regulator, by virtue of the replacement 1 P2 → P2 ðP2þm2Þ2 in the first factor of Eq. (3), which ensures that mD and g2T in Eq. (14) remain finite, while the initial energy density is not affected by the regulator as long as maxðQ2 A; Q2 BÞ ≫m2. Since corrections to the factorization formula become important for P ≲minðQA; QBÞ, in the following we choose the infrared regulator as μ ≡m Q ¼ minðQA;QBÞ 2Q . We further note that due to the particular simplicity of the GBW model, the initial spectrum in Eq. (3) exhibits and expo- nential decay at high momentum P ≳Q, whereas a more realistic parametrization should give rise to a Q4=P4 power- law tail [40]. However, since the energy density of the system is dominated by momenta P ∼Q, we believe that the model is adequate to study the thermalization of the bulk QGP, while neglecting the impact of high-energy degrees of freedom. Since the transverse spectrum in Eq. (3) features a ∝ 1=P2 infrared behavior, soft observables, such as screening mass mD and scattering rate g2T in Eq. (14), are infrared divergent. However, this divergence can be regulated by nonlinear effects, going beyond the factorization formula, see e.g., the discussion in [36]. Within our study, we will simply model this by introducing an additional infrared regulator, by virtue of the replacement 1 P2 → P2 ðP2þm2Þ2 in the I. INTRODUCTION V with a short summary of our most important findings and an outlook on potential future works. dNg d2bd2Pdy¼ ðN2c −1Þ g2Ncπ2P2 ×x2e−P2=Q2 Q2 P4x2 þP2ð1−x2Þ2Q2 þ2x2Q4 ð1þx2Þ4  ; ð3Þ dNg d2bd2Pdy¼ ðN2c −1Þ g2Ncπ2P2 ×x2e−P2=Q2 Q2 P4x2 þP2ð1−x2Þ2Q2 þ2x2Q4 ð1þx2Þ4  ; ð3Þ ð3Þ where Q ≡ ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi Q2 A þ Q2 B p and x ≡max ðQB QA ; QA QBÞ denote the root mean square average and the ratio of the saturation scales. Since the saturation scales Q2 A=B are generically proportional to local density of nuclear matter, we can anticipate that for different collision geometries the ratio x ¼ QA=QB will vary, and we will consider variations 1 ≤x ≤6 in the following. B. Effective kinetic theory of pure glue QCD Starting from the phase-space distribution, the energy- momentum tensor Tμν is defined as We model the evolution of excited nuclear matter using kinetic description. We follow previous works [12,42,43] and treat the system as longitudinally boost invariant and locally homogeneous in the transverse plane. The dynamics reduces to a (0 þ 1)-dimensional problem and is governed by an effective kinetic for pure glue QCD [30] Tμν ¼ νg Z d3p ð2πÞ3 pμpν p fgðτ; b; P; y −ηÞ; ð6Þ ð6Þ where νg ¼ 2ðN2c −1Þ denotes the degeneracy factor for gluons. Specifically, one may evaluate the energy density ϵ, the transverse and the longitudinal pressure PT=L in Milne coordinates as  ∂ ∂τ −pk τ ∂ ∂pk  fgðτ; P; pkÞ ¼ −C2↔2 g ½fgðτ; P; pkÞ −C1↔2 g ½fgðτ; P; pkÞ; ð8Þ  ∂ ∂τ −pk τ ∂ ∂pk  fgðτ; P; pkÞ ϵ ¼ Tττ ¼ Z d2P ð2πÞ2 dpk ð2πÞ pνgfgðτ; b; P; pkÞ; ð7aÞ PT ¼ Tii=2 ¼ Z d2P ð2πÞ2 dpk ð2πÞ jPj2 2p νgfgðτ; b; P; pkÞ; ð7bÞ ϵ ¼ Tττ ¼ Z d2P ð2πÞ2 dpk ð2πÞ pνgfgðτ; b; P; pkÞ; ð7aÞ ð7aÞ where C2↔2 g ½f denotes the leading order elastic collision integral for gluons and C1↔2 g ½f is the inelastic collision integral that describes emission/absorption of gluon radiation PT ¼ Tii=2 ¼ Z d2P ð2πÞ2 dpk ð2πÞ jPj2 2p νgfgðτ; b; P; pkÞ; ð7bÞ C2↔2 g ½fðpÞ ¼ 1 2νg2Ep Z d3p2 ð2πÞ32Ep2 d3p3 ð2πÞ32Ep3 d3p4 ð2πÞ32Ep4 ð2πÞ4δð4Þðp þ p2 −p3 −p4ÞjMgg→ggðp; p2jp3; p4Þj2 × ðfðpÞfðp2Þð1 þ fðp3ÞÞfð1 þ fðp4ÞÞ −fðp3Þfðk4Þð1 þ fðpÞÞfð1 þ fðp2ÞÞÞ; ð9aÞ C1↔2 g ½fðpÞ ¼ 1 2 Z 1 0 dz dΓg gg dz ðp; zÞ½fðpÞð1 þ fðzpÞÞð1 þ fð¯zpÞÞÞ −fðzpÞfð¯zpÞð1 þ fðpÞÞ −1 z3 dΓg gg dz p z ; z  f p z  ð1 þ fðpÞÞ  1 þ f ¯z z p  −fðpÞf ¯z z p  1 þ f p z  : ð9bÞ ð9aÞ ð9bÞ [30]. Details of the algorithms and numerical implementa- tions can be found in [49]. A. Color glass condensate initial conditions We will compute the initial spectrum of gluons based on the kT-factorization formula [36,37] dNg d2bd2Pdy¼ g2Nc 4π5P2ðN2c −1Þ × Z d2k ð2πÞ2ΦA  bþb0 2 ;k  ΦB  b−b0 2 ;P−k  ; ð1Þ ð1Þ where dNg d2bd2Pdy describes the transverse momentum ðPÞ spectrum of gluons produced per unit rapidity (y) and transverse area ðbÞ. By Nc ¼ 3, we denote the number of colors, g is the Yang-Mills coupling, b0 denotes the impact parameter of the nucleus-nucleus collision and ϕA=Bðb; kÞ is the unintegrated gluon distribution from each nucleus (A or B). We employ a particularly simple parametrization Based on the transverse momentum spectrum, the initial phase-space distribution fðx; pÞ can then be obtained as [41] 014016-2 PHYS. REV. D 106, 014016 (2022) EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … fgðτ0; b; P; y −ηÞ ¼ ð2πÞ3 2ðN2c −1Þ δðy −ηÞ jPjτ0 dNg d2bd2Pdy ; ð4Þ ð4Þ PL ¼ τ2Tζζ ¼ Z d2P ð2πÞ2 dpk ð2πÞ p2 k p νgfgðτ; b; P; pkÞ; ð7cÞ ð7cÞ where η denotes the space-time rapidity and we employ these as initial conditions for the subsequent kinetic description at an initial proper time τ0 ¼ 1=Q, where a quasiparticle description first becomes applicable [2,3]. While in the high-energy boost-invariant limit, the initial distribution is proportional to δðy −ηÞ, any interactions will immediately broaden the longitudinal momentum distribution and we therefore consider a smearing form of the delta function where we have reexpressed the phase-space distribution fg in terms of the momentum variables p ¼ pτ ¼ ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi P2 þ p2 k q and pk ¼ τpη ¼ jPj sinhðy −ηÞ. They denote the total and the longitudinal momentum in the comoving frame. When considering variations of the parameters x and σ, we adjust the value of the average saturation scale Q, to keep the initial transverse pressure per unit rapidity g2τ0PT (which is independent of the coupling g) constant in physical units. Hence the parameter space of the initial conditions is two dimensional and spanned by the ratio of the nuclear saturation scales x and the longitudinal smear- ing width σ. δðy −ηÞ → 1ffiffiffiffiffiffi 2π p σ exp  −ðy −ηÞ2 2σ2  : ð5Þ ð5Þ in the initial conditions. We treat the width of longitudinal rapidity distribution σ as the second free parameter in the initial conditions and consider variations in the range 0.05 < σ < 0.50 in the following. B. Effective kinetic theory of pure glue QCD Early initialization requires a fine discretization of the momentum space variables for the EKT simulations, and if not stated otherwise we employ Np ¼ 1024 and NcosðθÞ ¼ 512 to discretize p and We note that the matrixelement jMgg→ggðp; p2jp3; p4Þj2 for elastic scattering is self-consistently screened [30,44] fol- lowing theprescription of [45], andthat the effective inelastic rates dΓg gg dz ðp; zÞ account for the Landau-Pomeranchuk- Migdal effect [46–48] via an effective vertex resummation 014016-3 PHYS. REV. D 106, 014016 (2022) DU, HELLER, SCHLICHTING, and SVENSSON 0.05 0.10 0.50 1 5 10 0.0 0.2 0.4 0.6 0.8 1.0 FIG. 1. Evolution of the ratio of the longitudinal pressure to what would the equilibrium pressure PL=ðϵ=3Þ as a function of the conformal scaling variable ˜w in Eq. (11). Different curves show results from pure glue QCD kinetic theory simulations for different initial conditions ðσ; xÞ at three different coupling strength λ ¼ 5, 10, and 20. cos θ ¼ pk p in the range between pmin=ðg2τ0PTÞ1=3 ¼ 0.01 and pmax=ðg2τ0PTÞ1=3 ¼ 20. cos θ ¼ pk p in the range between pmin=ðg2τ0PTÞ1=3 ¼ 0.01 and pmax=ðg2τ0PTÞ1=3 ¼ 20. ð Þ Finally, note that in pure glue QCD kinetic theory the interaction strength g and the number of colors Nc enter the Boltzmann together as the ’t Hooft coupling λ [50] 0.05 0.10 0.50 1 5 10 0.0 0.2 0.4 0.6 0.8 1.0 λ ≡g2Nc: ð10Þ ð10Þ Therefore, in the following we will express the interaction strength in terms of λ. Therefore, in the following we will express the interaction strength in terms of λ. III. EARLY-TIME DYNAMICS, ATTRACTORS, AND DIMENSIONALITY REDUCTION A. Hydrodynamization and emergence of attractors A. Hydrodynamization and emergence of attractors FIG. 1. Evolution of the ratio of the longitudinal pressure to what would the equilibrium pressure PL=ðϵ=3Þ as a function of the conformal scaling variable ˜w in Eq. (11). Different curves show results from pure glue QCD kinetic theory simulations for different initial conditions ðσ; xÞ at three different coupling strength λ ¼ 5, 10, and 20. One prominent indicator of transition to hydrodynamics is the longitudinal pressure over what would be the equilibrium pressure ratio PL=ðϵ=3Þ or any of its closely related variants. We present it in Fig. 1 as a function of the universal time scale [14,51–53] ˜w ¼ τðϵ þ PÞ 4πη ; ð11Þ and at intermediate times approaches a small value irre- spective of the initial conditions. Eventually, on a time scale ˜w ≃1, all the different curves merge towards the hydro- dynamic limit, which to first order in gradients can be universally expressed as [53] ð11Þ where η is the shear viscosity and P ¼ ϵ=3 is the thermo- dynamic pressure for a conformal system. It can be thought of as measuring the physical proper time in units of an effective equilibrium relaxation time PL ϵ=3  hydro ¼ 1 −16 3 η ðϵ þ PÞτ ¼ 1 − 4 3π ˜w : ð13Þ ð13Þ τR ¼ 4πη ϵ þ P ≡1 T η s = 1 4π ; ð12Þ ð12Þ While the emergence of a pressure attractor at 0.1 < ˜w < 1 clearly indicates an early reduction of the variance due to the initial free-streaming expansion dynamics, it is equally important to point out that the full convergence to a common attractor only occurs at later times ˜w > 1, when the system relaxes towards hydrodynamics. where T is an effective temperature of nonequilibrium system determined by ϵ ¼ νg π2T4 30 and s is the entropy density. While the overall scaling with T follows on dimensional grounds for a conformal system, the normali- zation factor of 1=4π is conventional and inspired by the strong coupling result η=s ¼ 1=4π of [54,55]. Different colored curves in Fig. 1 show results obtained for different ratios of the saturation scales x and different longitudinal smearing width σ. Different dash styles cor- respond to the evolution for three different coupling strengths λ ¼ 5, 10, 20, for which the relevant viscosities η=s ∼Oð1Þ as summarized in Table I in the Appendix. EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … Each solution is represented as a vector ¯m2 D ≡ m2 D ð90PT=π2νgÞ1=2g2Nc=3 ; ð15bÞ ¯T ≡ T ð90PT=π2νgÞ1=4 : ð15cÞ ð15bÞ ð15cÞ Xð ˜wÞ ¼ ð ¯Tð ˜wÞ ¯PLð ˜wÞ ¯m2 Dð ˜wÞ ¯PTð ˜wÞ Þ; ð16Þ ð16Þ All of them by construction approach unity in thermal equilibrium. While initially, the transverse pressure PT is kept constant for different initial conditions, differences in the kinetic evolution gives rise to variations of the overall energy scale, which we monitor in terms of the dimension- less quantity All of them by construction approach unity in thermal equilibrium. While initially, the transverse pressure PT is kept constant for different initial conditions, differences in the kinetic evolution gives rise to variations of the overall energy scale, which we monitor in terms of the dimension- less quantity evolving in time. Evidently, to perform a meaningful comparison of the different directions in Xð ˜wÞ space, the units and overall scales of the different components of Xð ˜wÞ must be comparable, which is precisely the reason that the observables have been normalized as in Eq. (15). From this point of view, thermalization is achieved through dimensionality reduction. With sufficient variation of the initial phase-space distribution function, the set of initial conditions fX0g collectively spans some volume in the four-dimensional space. However, since the initial conditions used here only depend on two parameters, we only expect to span (at most) a two-dimensional subspace. Over the course of the thermalization process, the dimen- sionless variables ¯PL; ¯m2 D; ¯T all approach unity, and only ¯PT which is sensitive to the overall energy scale should have a significant variation at late times, implying that ultimately the solutions will span a one dimensional evolving in time. Evidently, to perform a meaningful comparison of the different directions in Xð ˜wÞ space, the units and overall scales of the different components of Xð ˜wÞ must be comparable, which is precisely the reason that the observables have been normalized as in Eq. (15). ¯PT ≡ τ4=3PT 1=3ð2PT0τ0Þ8=9ðπ2 30 νgÞ1=9ð4π η sÞ4=9C∞ : ð15dÞ From this point of view, thermalization is achieved through dimensionality reduction. With sufficient variation of the initial phase-space distribution function, the set of initial conditions fX0g collectively spans some volume in the four-dimensional space. However, since the initial conditions used here only depend on two parameters, we only expect to span (at most) a two-dimensional subspace. EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … PHYS. REV. D 106, 014016 (2022) EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … 0.05 0.10 0.50 1 0.0 0.2 0.4 0.6 0.8 1.0 1.2 FIG. 2. Evolution of the observables ¯PT; ¯PL; ¯m2 D; ¯T as a function of the universal time scale ˜w for a variety of different initial conditions at three different coupling strengths λ ¼ 5, 10, and 20. The observable ¯PT has been chosen to contain the information on the overall energy scale and features the only sizable variation at late times. Conversely, all other observables are insensitive to the overall energy scale and show an attractor behavior. 0.05 0.10 0.50 1 0.0 0.2 0.4 0.6 0.8 1.0 1.2 m2 D ¼ 4g2 dA Z d3p ð2πÞ3 νgCAfgð⃗pÞ 2p ¼ ðeqÞ g2NcT2eq 3 T ¼ g2 dAm2 D Z d3p ð2πÞ3 fνgCAfgð⃗pÞð1 þ fgð⃗pÞÞg ¼ ðeqÞ Teq: ð14Þ ð14Þ Since m2 D and g2T govern the strength of elastic and inelastic interactions in pure glue QCD kinetic theory, they present the most natural quantities to include in a weak coupling analysis. 2 Since all of the above quantities PL; PT; m2 D; T are dimensionful, it is natural to consider dimensionless ratios along with one single quantity that is sensitive to the overall energy scale. Specifically, for our analysis, we choose to consider PL=ðϵ=3Þ and normalize m2 D; T by the transverse pressure PT. This gives us the following dimensionless quantities FIG. 2. Evolution of the observables ¯PT; ¯PL; ¯m2 D; ¯T as a function of the universal time scale ˜w for a variety of different initial conditions at three different coupling strengths λ ¼ 5, 10, and 20. The observable ¯PT has been chosen to contain the information on the overall energy scale and features the only sizable variation at late times. Conversely, all other observables are insensitive to the overall energy scale and show an attractor behavior. ¯PL ≡PL ϵ=3 ; ð15aÞ ¯m2 D ≡ m2 D ð90PT=π2νgÞ1=2g2Nc=3 ; ð15bÞ ¯T ≡ T ð90PT=π2νgÞ1=4 : ð15cÞ ¯PL ≡PL ϵ=3 ; ð15aÞ ð15aÞ in the emergence of the attractor phenomenon, namely the principal components of the attractor. For this purpose, rather than studying these quantities separately, we can also consider these quantities as parametrizing a four- dimensional space. B. Principal component analysis Next, in order to better understand the emergence and properties of the attractor in pure glue QCD kinetic theory, we will scrutinize the evolution further by including addi- tional observables, which go beyond probing the bulk anisotropy of the system. Beyond the anisotropic pressure PL and PT in Eqs. (15), we will study the screening mass m2 D and the collision rate g2T Starting from the initial conditions, one observes a significant variation of PL=ðϵ=3Þ, where small smearing parameters σ feature a highly anisotropic initial distribu- tion, with almost vanishing longitudinal pressure. Since in all cases the initial time τ0 ¼ 1=Q is kept fixed, the curves for different simulation parameters x, σ, λ start at different values of ˜w; in this way larger saturation scale ratios x also tends to provide relevantly more anisotropic initial distri- bution. During the initial stages the evolution is dominated by the longitudinal expansion of the system [19,33], such that the ratio of PL=ðϵ=3Þ undergoes a quick memory loss TABLE I. Numerically extracted viscosity, averaged over different solutions. These values were used in the subsequent analysis. λ 0.1 0.2 0.5 1 2 5 10 20 η=s 1361 394.9 79.69 24.55 7.845 1.848 0.6472 0.2313 λ 0.1 0.2 0.5 1 2 5 10 20 η=s 1361 394.9 79.69 24.55 7.845 1.848 0.6472 0.2313 λ 0.1 0.2 0.5 1 2 5 10 20 η=s 1361 394.9 79.69 24.55 7.845 1.848 0.6472 0.2313 014016-4 Cmn ¼ CovðXm; XnÞ: ð17Þ EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … Snapshots of the evolution of an ensemble of different initial conditions in the ¯PL, ¯PT plane at three different times ˜w ¼ 0.2, 0.9, and 1.3 for λ ¼ 10. Each point corresponds to the evolution for a particular initial condition; blue and orange arrows indicate the first and second principle components. While initially the points are scattered in the two-dimensional plane, they collapse onto a one dimensional subspace at late times. The length of the vectors is set to three times the square root the of the explained variance for better visibility. to produce a set of orthonormal vectors such that the first vector points along the direction of the largest variance of the data set, and the subleading vectors are similarly optimized in the space orthogonal to the leading vector. Each vector is associated with an explained variance, quantified by the variance of the set of points in its direction. The number of non-negligible explained varian- ces gives a measure of the dimensionality of the region occupied by the states of interest at a given value of time variable. PL direction, the effective reduction of the dimensionality of the distribution is clearly visible, as at late times ˜w ¼ 1.3 all points converge towards a one-dimensional manifold oriented along the ¯PT direction. By applying PCA to the set of solutions at each point in the universal time ˜w, we can study the dimensionality of the dataset through the explained variances, and identify which directions in the space of observables that show the greatest variance. Our results are compactly summarized in Figs. 4 and 5, where we show the evolution of the explained We illustrate this behavior in Fig. 3, where we show the distribution of values in the ¯PL, ¯PT plane at three different times ˜w ¼ 0.2, 0.9, 1.3 of the evolution. Each point in Fig. 3 corresponds to the evolution for a particular initial condition, while the blue and orange arrows indicate the first and second principle components. While at early times ð ˜w ¼ 0.2Þ the different initial conditions cover a two- dimensional subspace, with the largest variations in the 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.0 0.5 0.0 0.5 1.0 1.0 0.5 0.0 0.5 1.0 FIG. 5. Decomposition of the leading (top) and first subleading (bottom) principal component vectors. EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … Over the course of the thermalization process, the dimen- sionless variables ¯PL; ¯m2 D; ¯T all approach unity, and only ¯PT which is sensitive to the overall energy scale should have a significant variation at late times, implying that ultimately the solutions will span a one dimensional subspace. ð15dÞ where we employ C∞¼ 0.98 [25]. By following the arguments of [14,25], the denominator in Eq. (15d) pro- vides an estimate for the late-time asymptotic value of τ4=3PT, such that for typical initial conditions this quantity can again be expected to be close to unity at late times. We can directly verify these expectations in Fig. 2, where we present the evolution of the observables ¯PT; ¯PL; ¯m2 D; ¯T as a function of the universal time scale ˜w for a variety of different initial conditions at three different coupling strengths λ ¼ 5, 10, 20. While the self-normalized quan- tities ¯PL; ¯m2 D; ¯T all converge to a common attractor behavior at late times, the overall energy scale ¯PT develops a ∼15% variation over the course of the nonequilibirum evolution of the system. PCA is a simple method to study this process of dimensionality reduction. Given a set of points fXg, the PCA calculates the eigenvectors and eigenvalues of the covariance matrix With the set of observables in Eq. (15), we can further perform a PCA to extract the most significant contributions ð17Þ 014016-5 DU, HELLER, SCHLICHTING, and SVENSSON PHYS. REV. D 106, 014016 (2022) –0.10 –0.05 0.00 0.05 0.1 –0.10 –0.05 0.00 0.05 0.10 0.15 .10 –0.05 0.00 0.05 0.1.10 –0.05 0.00 0.05 0.10 FIG. 3. Snapshots of the evolution of an ensemble of different initial conditions in the ¯PL, ¯PT plane at three different times ˜w ¼ 0.2, 0.9, and 1.3 for λ ¼ 10. Each point corresponds to the evolution for a particular initial condition; blue and orange arrows indicate the first and second principle components. While initially the points are scattered in the two-dimensional plane, they collapse onto a one dimensional subspace at late times. The length of the vectors is set to three times the square root the of the explained variance for better visibility. –0.10 –0.05 0.00 0.05 0.1 –0.10 –0.05 0.00 0.05 0.10 0.15 .10 –0.05 0.00 0.05 0.1.10 –0.05 0.00 0.05 0.10 FIG. 3. IV. EVOLUTION TOWARDS EQUILIBRIUM So far we have statistically analyzed the emergence of hydrodynamics attractors starting from CGC initial con- ditions at very early times ˜w ≪1. While in this case the dynamics is initially dominated by the longitudinal expan- sion, we performed additional simulations that focus on the late-time approach to hydrodynamic behavior to further analyze the memory loss and convergence towards hydro- dynamic behavior in pure glue QCD kinetic theory. By initializing the system according to a Romatschke- Strickland type distribution [56], In order to further characterize the approach towards an attractor, we compute the variances of PL=ðϵ=3Þ for the different initial conditions ξ0 at each value of the initial- ization time ˜w0 and coupling strength λ. Before we discuss our results in pure glue QCD kinetic theory, shown in the middle panel of Fig. 6, it proves insightful to recall the behavior previously observed in different microscopic models of early-time dynamics of the QGP. fgðτ0; P; pkÞ ¼ cðξ0Þ e ffiffiffiffiffiffiffiffiffiffiffi P2þξ2 0p2 k p T0 −1 ð18Þ ð18Þ Starting with [6] (see also [57,58] for a more complete discussion), it was understood that in a class of models employing the Müller-Israel-Stewart (MIS) approach to embed hydrodynamics in a framework compatible with relativistic causality [59–61], the late-time behavior of PL=ðϵ=3Þ can be elevated into a transseries [62] of the form for different initial anisotropies ξ0 ¼ 1.25, 2.5, 5, 10 at initial time ˜w0 ¼ 0.1, 0.3 and ξ0 ¼ 1.1, 1.2, 1.3 at initial time ˜w0 ¼ 1, 3, 10, we are then able to analyze the effective memory loss at late times for a large range of couplings λ ¼ 0.1–20. We note that in all cases, the normalization factor cðξ0Þ ¼ 2 1=ξ2 0 þ arctanð ffiffiffiffiffiffiffiffiffiffiffiffi ξ2 0 −1 p Þ= ffiffiffiffiffiffiffiffiffiffiffiffi ξ2 0 −1 p ð19Þ PL ϵ=3 ¼ X ∞ n¼0 bn ˜wn þ X j e−Ωj ˜w ˜wβ j X ∞ n¼0 bj;n ˜wn : ð20Þ ð19Þ ð20Þ is chosen such that the initial energy density ϵð ˜w0Þ ¼ π2 30 νgT4 0 remains the same irrespective of the initial anisotropy ξ0; while in order to initialize the simulations at the same ˜w0, the initial proper time is adjusted as The key aspect of this expression is the exponentially suppressed effects with decay rates Ωj. EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … 4, that at late times, there is indeed only a single dominant component, which is associated with an approximately constant explained variance. Beyond the leading principal component, the explained variance of the second most relevant component decays approximately exponentially at times ˜w ≳0.5. variances along with the evolution of the composition of two dominant principle component vectors. One clearly observes from Fig. 4, that at late times, there is indeed only a single dominant component, which is associated with an approximately constant explained variance. Beyond the leading principal component, the explained variance of the second most relevant component decays approximately exponentially at times ˜w ≳0.5. A. Exponential approach to hydrodynamics at late times In order to investigate direct approach to viscous hydro- dynamics at late times, we will focus on the evolution of PL=ðϵ=3Þ in ˜w. As we discussed in Sec. III B, this quantity has a significant contribution to the leading principal component characterizing deviations from the attractor, and exhibits a universal late-time hydrodynamic behavior determined by Eq. (13). The decomposition of the first and second principal components are shown in Fig. 5. The abrupt shift in behavior at ˜w ≈0.5 is correlated with the crossing of explained variances in Fig. 4, and should be thought of as the two vectors switching identity. At late times the first component is dominated by ¯PT, which was chosen to be sensitive to the energy scale of the state. The second component is dominated by ¯PL and ¯m2 D. The evolution of the PL=ðϵ=3Þ for the initial conditions (18) is depicted in Fig. 6. Different colored curves correspond to the results for different coupling strength λ ¼ 0.1–20, while curves of the same color correspond to different initial conditions ξ0 at different initialization times ˜w0. Irrespective of the coupling strength, one observes that very quickly after the initialization, different initial con- ditions appear to converge towards a common attractor curve. By careful inspection, one notes that for varying coupling strength slight differences in the attractors persist at intermediate times ˜w ≲3, before all curves eventually converge towards the same (by construction) hydrody- namic late-time behavior (13). Note that contributions from the terms second and higher order in derivatives are expected to exhibit residual coupling dependence, which might at least partially explain the slight differences between attractors at earlier times. While Fig. 2 already shows that the observables ¯m2 D; ¯T also features a similar attractor behavior as the well-known ¯PL, it does not tell us whether these attractors are actually the same. In contrast, the principal component analysis in Figs. 4 and 5 reveals that the evolution of the different observables is highly correlated and can be captured with a single principal component. EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … By design, the leading vector is dominated by ¯PT, which carries information about the overall energy scale. The second principal component corre- sponds to an exponentially decaying transient, and characterizes the variation in the other observables. Since no other principal component is sizable, we learn that the observables ¯m2 D; ¯T; ¯PL are highly correlated and governed by the same attractor. 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.0 0.5 0.0 0.5 1.0 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 10–6 10–5 10–4 0.001 0.010 0.100 FIG. 4. Explained variances for the observables in Fig. 2. The colors distinguish between different principal components, ordered by the explained variance. Starting from a complicated behavior at early times, the only relevant contributions at late times are associated with a single dominant component that remains approximately constant and a second component which is approximately exponentially decaying. Separate contributions of the different observables to the these two principal components are shown in Fig. 5. 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 10–6 10–5 10–4 0.001 0.010 0.100 FIG. 4. Explained variances for the observables in Fig. 2. The colors distinguish between different principal components, ordered by the explained variance. Starting from a complicated behavior at early times, the only relevant contributions at late times are associated with a single dominant component that remains approximately constant and a second component which is approximately exponentially decaying. Separate contributions of the different observables to the these two principal components are shown in Fig. 5. FIG. 5. Decomposition of the leading (top) and first subleading (bottom) principal component vectors. By design, the leading vector is dominated by ¯PT, which carries information about the overall energy scale. The second principal component corre- sponds to an exponentially decaying transient, and characterizes the variation in the other observables. Since no other principal component is sizable, we learn that the observables ¯m2 D; ¯T; ¯PL are highly correlated and governed by the same attractor. 014016-6 PHYS. REV. D 106, 014016 (2022) EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … τ0 ¼ 4πη=s T0 ˜w0 in Eq. (18) for the respective coupling strength. For completeness, our numerical implementation employs the following discretization; Np ¼ 64 and NcosðθÞ ¼ 64 with pmin=T0 ¼ 0.01 and pmax=T0 ¼ 8. variances along with the evolution of the composition of two dominant principle component vectors. One clearly observes from Fig. IV. EVOLUTION TOWARDS EQUILIBRIUM To this end, inspection of the evolution of the variances in the middle plot in Fig. 6 shows a clear exponential decay of the variance for most values of λ and ˜w0. Clear deviations from an exponential decay are only seen for data initialized at very early times, particularly for small coupling, where instead of a direct relaxation towards equilibrium the dynamics is initially dominated by free streaming and subsequently undergoes the bottom-up thermalization process [42,71]. 0.1 0.5 1 5 10 –9 –8 –7 –6 –5 –4 We extract the effective decay rate Ωeff of the variance for each choice of λ and ˜w0 by a linear fit in a variety of windows. Extracted values of the decay rate are presented in the bottom plot of Fig. 6, along with the mean value of those fits and for comparison, we also show the decay rate 12 5 π in conformal RTA kinetic theory. FIG. 6. (top) Evolution of the pressure to what would be the equilibrium pressure ratio pL=ðϵ=3Þ. (middle) Evolution of variance of PL=ðϵ=3Þ. The exponential decay is associated to decay of nonhydrodynamic contributions to PL=ðϵ=3Þ. (bottom) Exponential decay rates of the variance extracted from the middle figure. Different points are obtained by varying the extraction range and the curve is formed from the mean result. While not perfectly exponential, the data initialized at early times have a smaller effective decay rate at smaller couplings. For the data initialized at late times, which show a clear exponential decay, the decay rate is approximately independent of the coupling strength λ (with variations within 5% as the coupling varies by over two orders of magnitude) and turns out to be rather close to the value in RTA. The same structure was verified to appear in RTA kinetic theory [34,35,63] and in holography [63–66]. While our finding suggests that, just like in RTA, the decay rate in QCD kinetic theory appears to be closely connected to the value of viscosity, we certainly do not have a good explanation of this behavior. We note however, that similar observations were made also at the level of second- order transport coefficients [72]. In particular, this implies that the contribution at ˜w−2 in Eq. (13) exhibits very weak residual dependence on the coupling λ. IV. EVOLUTION TOWARDS EQUILIBRIUM In MIS different Ωj are just integer multiples (due to nonlinear effects) of a single relaxation scale present in this class of theories. 014016-7 DU, HELLER, SCHLICHTING, and SVENSSON PHYS. REV. D 106, 014016 (2022) 0.1 0.5 1 5 10 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.5 1.0 1.5 2.0 101 10- 1 10–3 10–5 10–7 10–9 0.1 0.5 1 5 10 –9 –8 –7 –6 –5 –4 FIG. 6. (top) Evolution of the pressure to what would be the equilibrium pressure ratio pL=ðϵ=3Þ. (middle) Evolution of variance of PL=ðϵ=3Þ. The exponential decay is associated to decay of nonhydrodynamic contributions to PL=ðϵ=3Þ. (bottom) Exponential decay rates of the variance extracted from the middle figure. Different points are obtained by varying the extraction range and the curve is formed from the mean result. DU, HELLER, SCHLICHTING, and SVENSSON Following [68], the relaxation time determines the decay rate of nonhydrodynamic contributions in the boost-invariant background as − Z dτ τrðτÞ ¼ − Z TðτÞdτ 5η=s ≈−3 2 TðτÞτ 5η=s ¼ −6 5 π ˜w; ð22Þ ð22Þ where we have used the fact that TðτÞ scales as τ−1=3 at sufficiently late times in Bjorken flow and dropped sub- leading contributions at late time. While Eq. (22) provides the rate of decay of nonhydrodynamic contributions in each individual realization, the variance measures the square of these contributions and thus decays twice as fast. While the structure of nonhydrodynamic excitations in QCD kinetic theory is generally expected to be rather complicated [69,70], it is nevertheless interesting to inves- tigate to what extent a simple parametrization of the type in Eq. (20) can describe the convergence towards an attractor. To this end, inspection of the evolution of the variances in the middle plot in Fig. 6 shows a clear exponential decay of the variance for most values of λ and ˜w0. Clear deviations from an exponential decay are only seen for data initialized at very early times, particularly for small coupling, where instead of a direct relaxation towards equilibrium the dynamics is initially dominated by free streaming and subsequently undergoes the bottom-up thermalization process [42,71]. While the structure of nonhydrodynamic excitations in QCD kinetic theory is generally expected to be rather complicated [69,70], it is nevertheless interesting to inves- tigate to what extent a simple parametrization of the type in Eq. (20) can describe the convergence towards an attractor. IV. EVOLUTION TOWARDS EQUILIBRIUM Most importantly, the contributions Ωi describe the decay of transient nonhydrodynamic contributions to the pressure anisotropy, which in the aforementioned examples can be related to the analytic structure of retarded correlation functions of the energy-momentum tensor in equilibrium [5,67]. In the conformal RTA kinetic theory the shear viscosity and the relaxation time are related by APPENDIX: EXTRACTION OF η=s Below we explain our procedure for the extraction of the shear viscosity to entropy density ratio η=s from the kinetic theory simulations. Starting point of the extraction, is the universal hydrodynamic late-time behavior, where the ratio of longitudinal pressure to energy density behaves as PL ϵ ¼ 1 3 −16 9 η=s τT þ …: ðA1Þ ðA1Þ By inverting Eq. (A1) for η=s, we can use the ratio 9=16ð1=3 −PL=ϵÞTτ to extract the ratio of shear viscosity to entropy density η=s from the asymptotic behavior of each numerical solution, and in subsequent analysis we use the mean value for each λ. We illustrate this extraction in the left panel of Fig. 7, while the right panel of Fig. 7 shows the extracted values in comparison to Next Leading Log (NLL) parametrization of η=s in [78]. We note that for small couplings λ, the extracted values of η=s are in excellent agreement with the NLL parametrization, while for larger values of λ the NLL parametrization breaks down, and as discussed in [45] the transport coefficients also become more sensitive to the precise implementation of the screening of the elastic matrix elements. We also provide the extracted values in Table I. By inverting Eq. (A1) for η=s, we can use the ratio 9=16ð1=3 −PL=ϵÞTτ to extract the ratio of shear viscosity to entropy density η=s from the asymptotic behavior of each numerical solution, and in subsequent analysis we use the mean value for each λ. We illustrate this extraction in the left panel of Fig. 7, while the right panel of Fig. 7 shows the extracted values in comparison to Next Leading Log (NLL) parametrization of η=s in [78]. We note that for small couplings λ, the extracted values of η=s are in excellent agreement with the NLL parametrization, while for larger values of λ the NLL parametrization breaks down, and as discussed in [45] the transport coefficients also become more sensitive to the precise implementation of the screening of the elastic matrix elements. We also provide the extracted values in Table I. y g p Beyond further explorations of the surprising similarity in the highly-symmetric Bjorken flow, it would also be interesting to compare the evolution of the energy- momentum tensor in a variety of other settings. ACKNOWLEDGMENTS We thank V. Ambrus, A. Kurkela, A. Mazeliauskas, A. Serantes, M. Spaliński and B. Withers for insightful discussions and collaboration on related topics. X. D. and S. S. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the CRC-TR 211 ‘Strong- interaction matter under extreme conditions’—Project No. 315477589—TRR 211. V. S. acknowledges support from the National Centre for Nuclear Research, Poland. The authors also acknowledge computing time provided by the Paderborn Center for Parallel Computing (PC2) and the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The second principal component represents a transient contribution, which we studied in more detail by consid- ering ¯PL using other initial conditions initialized at differ- ent times. A clear exponential decay can be seen at late times by comparing different profiles of ¯PL, signaling the presence of an exponential approach to the hydrodynamic attractor at late times. Quite surprisingly, for the whole range of the couplings considered, i.e., for λ between 0.1 and 20, the decay rate is close to the value predicted by the conformal RTA kinetic theory. What this means in practical terms is that the effective decay rate is simply expressible in terms of the shear viscosity-to-entropy density ratio, see Eq. (21). It is an interesting question to ask if the similarities between the EKT and conformal RTA go beyond this crude characteristic. To this end, an in-depth analysis of the RTA kinetic theory in [35] reveals that the exponentially decaying contribution there is not a single excitation, but actually a sum of infinitely many contributions whose occupation numbers are initial condition dependent. While they all are characterized by the same exponential decay rate, their subleading behavior is distinct yet impossible to disentangle over the short time scales probed in the present project. This indicates that in reality the exponential decay, we are reporting here is likely to be understood as an effective description (appropriate for the conformal Bjorken flow with no transverse dynamics) of an under- lying more complicated structure. V. SUMMARY AND OUTLOOK We have studied the transition to hydrodynamics of Yang-Mills kinetic theory undergoing Bjorken expansion. For initial conditions inspired by the CGC effective theory, τrðτÞ ¼ 5η sTðτÞ : ð21Þ ð21Þ 014016-8 PHYS. REV. D 106, 014016 (2022) EXPONENTIAL APPROACH TO THE HYDRODYNAMIC … we analyzed the subsequent evolution of a natural set of four observables given by Eq. (15) using PCA. Such an analysis may be sensitive to the precise initial conditions used, which is why we studied realistic initial conditions from the CGC effective theory. energy-momentum tensor were calculated analytically in [76], a dedicated study in QCD kinetic theory would certainly shed further light on the structure and importance of nonhydrodynamic excitations. One can view the results of [69] obtained in RTA kinetic theory with momentum- dependent relaxation time (see, however, [77] for a subtlety in this model that emerged after [69] was completed) as a first step in this direction. Our studies showed that at late times there is a single dominant principal component that describes the variation of the overall energy scale ¯PT. Furthermore, the late-time evolution of ¯PL, ¯m2 D, and ¯T is highly correlated and can be captured by a second subleading principal component. While at this point it remains a logical possibility that this correlation is an artifact of the considered initial conditions, this could be further explored within a higher-dimensional parameter space. APPENDIX: EXTRACTION OF η=s While first steps in this direction have been reported in [43,73] for linearized perturbations around Bjorken flow and in [29,74,75] for systems undergoing both longitudinal and transverse expansion, a particularly clean probe concerns the evolution of energy-momentum (or metric) perturba- tions in equilibrium. While for conformal RTA kinetic theory the corresponding retarded correlators of the 014016-9 DU, HELLER, SCHLICHTING, and SVENSSON PHYS. REV. D 106, 014016 (2022) 0.5 1 5 10 0.1 1 10 100 1000 0.1 0.5 1 5 10 FIG. 7. (left) Extraction of the shear viscosity to entropy density ratio η=s from the late-time hydrodynamic behavior of Yang-Mills kinetic theory simulations. (right) Extracted values of η=s as a function of λ ¼ g2Nc. 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https://openalex.org/W2979583772
https://www.biorxiv.org/content/biorxiv/early/2019/03/20/582296.full.pdf
English
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Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1
eLife
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. 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 1 1 2 Dynamic ubiquitination determines transcriptional 3 activity of the plant immune coactivator NPR1 4 5 Michael J. Skelly1, James J. Furniss1, Heather L. Grey1, Ka-Wing Wong1 and Steven 6 H. Spoel1,* 7 8 1Institute of Molecular Plant Sciences, School of Biological Sciences, University of 9 Edinburgh, Edinburgh, EH9 3BF, UK 10 *Correspondence: steven.spoel@ed.ac.uk 11 12 13 14 15 16 17 18 19 20 21 Dr. Steven H. Spoel (ORCID: 0000-0003-4340-7591) 22 Institute of Molecular Plant Sciences 23 School of Biological Sciences 24 University of Edinburgh 25 King's Buildings 26 Max Born Crescent 27 Edinburgh, EH9 3BF 28 United Kingdom 29 30 Email: steven.spoel@ed.ac.uk 31 Phone: +44 (0)131 650 7065 32 2 Dynamic ubiquitination determines transcriptional 3 activity of the plant immune coactivator NPR1 4 5 Michael J. Skelly1, James J. Furniss1, Heather L. Grey1, Ka-Wing Wong1 and Steven 6 H. Spoel1,* 7 8 1Institute of Molecular Plant Sciences, School of Biological Sciences, University of 9 Edinburgh, Edinburgh, EH9 3BF, UK 10 *Correspondence: steven.spoel@ed.ac.uk 11 12 13 14 15 16 17 18 19 20 21 Dr. Steven H. Spoel (ORCID: 0000-0003-4340-7591) 22 Institute of Molecular Plant Sciences 23 School of Biological Sciences 24 University of Edinburgh 25 King's Buildings 26 Max Born Crescent 27 Edinburgh, EH9 3BF 28 United Kingdom 29 30 Email: steven.spoel@ed.ac.uk 31 Phone: +44 (0)131 650 7065 32 Dynamic ubiquitination determines transcriptional 3 activity of the plant immune coactivator NPR1 4 1 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Keywords: NPR1, salicylic acid, systemic acquired resistance, plant immunity, 49 ubiquitin. 50 ABSTRACT 33 Activation of systemic acquired resistance in plants is associated with transcriptome 34 reprogramming induced by the unstable coactivator NPR1. Immune-induced 35 ubiquitination and proteasomal degradation of NPR1 are thought to facilitate 36 continuous delivery of active NPR1 to target promoters, thereby maximising gene 37 expression. Because of this potentially costly sacrificial process, we investigated if 38 ubiquitination of NPR1 plays transcriptional roles prior to its proteasomal turnover. 39 Here we show ubiquitination of NPR1 is a processive event in which initial modification 40 by a Cullin-RING E3 ligase promotes its chromatin association and expression of target 41 genes. Only when polyubiquitination of NPR1 is enhanced by the E4 ligase, UBE4, it 42 is targeted for proteasomal degradation. Conversely, ubiquitin ligase activities are 43 opposed by UBP6/7, two proteasome-associated deubiquitinases that enhance NPR1 44 longevity. Thus, immune-induced transcriptome reprogramming requires sequential 45 actions of E3 and E4 ligases balanced by opposing deubiquitinases that fine-tune 46 activity of NPR1 without strict requirement for its sacrificial turnover. 47 Keywords: NPR1, salicylic acid, systemic acquired resistance, plant immunity, 49 ubiquitin. 50 2 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint INTRODUCTION 51 ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Upon activation of SAR, NPR1 is subject to an array of post-translational 76 modifications. A combination of alterations in redox-based modifications, 77 phosphorylation and SUMOylation of NPR1 result in the formation of a transactivation 78 complex that induces the transcription of immune-responsive target genes (Skelly et 79 al., 2016; Withers and Dong, 2016). Subsequent to these post-translational control 80 points, NPR1 becomes phosphorylated at Ser11 and Ser15, which surprisingly results 81 in recruitment of CRL3 followed by its degradation (Spoel et al., 2009). 82 Pharmacological inhibition of the proteasome, genetic mutation of CRL3, and mutation 83 of Ser11/15 all stabilised NPR1 protein, yet impaired the expression of SA-induced 84 NPR1 target genes (Spoel et al., 2009). These findings indicate that paradoxically, 85 ubiquitination and degradation of NPR1 are required for the full expression of its target 86 genes. We previously proposed a proteolysis-coupled transcription model in which 87 activation of target gene transcription results in NPR1 being marked as ‘spent’ by 88 Ser11/15 phosphorylation (Spoel et al., 2009). SUMOylation of NPR1 was required for 89 Ser11/15 phosphorylation and facilitates its interaction with other transcriptional 90 activators (Saleh et al., 2015), suggesting that NPR1 becomes inactivated only after it 91 has initiated gene transcription. Removal of inactive NPR1 from target promoters may 92 be necessary to allow binding of new active NPR1 protein that can reinitiate 93 transcription, thereby correlating the rate of NPR1 turnover to the level of target gene 94 expression (Spoel et al., 2009). This type of transcriptional control by unstable 95 (co)activators has also been reported in other eukaryotes, including for key 96 transcriptional regulators such as the nutrient sensor GCN4 in yeast and the estrogen 97 receptor ERα as well as oncogenic cMyc and SRC-3 activators in humans (Kim et al., 98 2003; Lipford et al., 2005; Métivier et al., 2003; Reid et al., 2003; von der Lehr et al., 99 2003; Wu et al., 2007). This suggests that the use of unstable transcriptional 100 Upon activation of SAR, NPR1 is subject to an array of post-translational 76 modifications. A combination of alterations in redox-based modifications, 77 phosphorylation and SUMOylation of NPR1 result in the formation of a transactivation 78 complex that induces the transcription of immune-responsive target genes (Skelly et 79 al., 2016; Withers and Dong, 2016). INTRODUCTION 51 Immune responses must be tightly controlled to provide appropriate, efficient 52 and timely resistance to pathogenic threats. A major hallmark of eukaryotic immune 53 responses is dramatic reprogramming of the transcriptome to prioritise defences over 54 other cellular functions. In plants transcriptional reprogramming is largely orchestrated 55 by the immune hormone salicylic acid (SA) that accumulates upon recognition of 56 biotrophic pathogens. SA not only induces resistance in infected local tissues, it is also 57 required for establishment of systemic acquired resistance (SAR), a form of induced 58 resistance with broad-spectrum effectiveness that is long-lasting and protects the 59 entire plant from future pathogen attack (Spoel and Dong, 2012). Establishment of 60 SAR and associated transcriptome reprogramming are mediated by the transcriptional 61 coactivator NPR1 (nonexpressor of pathogenesis-related (PR) genes 1). The majority 62 of SA-induced genes are NPR1 dependent, indicating NPR1 is a master regulator of 63 plant immunity (Wang et al., 2006). Consequently, loss of NPR1 function results in 64 severely immune-compromised plants unable to activate SAR. 65 Since NPR1 exerts its activity in the nucleus (Kinkema et al., 2000), controlling 66 its nuclear entry provides a means to prevent spurious activation of immune 67 responses. Indeed, in resting cells NPR1 is sequestered in the cytoplasm as a large 68 redox-sensitive oligomer that is formed by intermolecular disulphide linkages between 69 conserved cysteine residues (Mou et al., 2003). NPR1 monomers that escape 70 oligomerization and enter the nucleus are ubiquitinated by a Cullin-RING Ligase 3 71 (CRL3), a modular E3 ubiquitin ligase, resulting in their degradation by the 26S 72 proteasome (Spoel et al., 2009). Importantly, constitutive clearance of NPR1 from 73 nuclei of resting cells by concerted action of CRL3 and the proteasome is necessary 74 to prevent untimely activation of its target genes and associated autoimmunity. 75 3 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. INTRODUCTION 51 Subsequent to these post-translational control 80 points, NPR1 becomes phosphorylated at Ser11 and Ser15, which surprisingly results 81 in recruitment of CRL3 followed by its degradation (Spoel et al., 2009). 82 Pharmacological inhibition of the proteasome, genetic mutation of CRL3, and mutation 83 of Ser11/15 all stabilised NPR1 protein, yet impaired the expression of SA-induced 84 NPR1 target genes (Spoel et al., 2009). These findings indicate that paradoxically, 85 ubiquitination and degradation of NPR1 are required for the full expression of its target 86 genes. We previously proposed a proteolysis-coupled transcription model in which 87 activation of target gene transcription results in NPR1 being marked as ‘spent’ by 88 Ser11/15 phosphorylation (Spoel et al., 2009). SUMOylation of NPR1 was required for 89 Ser11/15 phosphorylation and facilitates its interaction with other transcriptional 90 activators (Saleh et al., 2015), suggesting that NPR1 becomes inactivated only after it 91 has initiated gene transcription. Removal of inactive NPR1 from target promoters may 92 be necessary to allow binding of new active NPR1 protein that can reinitiate 93 transcription, thereby correlating the rate of NPR1 turnover to the level of target gene 94 expression (Spoel et al., 2009). This type of transcriptional control by unstable 95 (co)activators has also been reported in other eukaryotes, including for key 96 transcriptional regulators such as the nutrient sensor GCN4 in yeast and the estrogen 97 receptor ERα as well as oncogenic cMyc and SRC-3 activators in humans (Kim et al., 98 2003; Lipford et al., 2005; Métivier et al., 2003; Reid et al., 2003; von der Lehr et al., 99 4 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint (co)activators may be an evolutionary conserved mechanism for fine-tuning gene 101 expression (Geng et al., 2012; Kodadek et al., 2006). The E4 ligase UBE4 regulates SA- and NPR1-mediated plant immunity 119 The E4 ligase UBE4 regulates SA and NPR1 mediated plant immunity 119 To examine if processive ubiquitination of NPR1 plays a role in plant immune 120 responses we examined a potential role for E4 ligases. Unlike E3 ligases, the E4 class 121 do not contribute towards initial ubiquitination of substrates but rather extend pre- 122 existing ubiquitin chains (Hoppe, 2005; Koegl et al., 1999). In Arabidopsis the E4 ligase 123 UBE4/MUSE3 has been implicated in immune signalling (Huang et al., 2014). We 124 investigated if UBE4 is involved in NPR1-dependent immune signalling by acquiring a 125 loss-of-function T-DNA insertion mutant (Figure S1A). Like mutants in CRL3 ligase that 126 fails to degrade NPR1 (Spoel et al., 2009), adult ube4 plants displayed enhanced 127 expression of immune genes in absence of pathogen challenge (Figure 1A). In 128 agreement, adult ube4 mutants showed autoimmunity against a high inoculum of Psm 129 ES4326 (Figure 1B). To establish if these phenotypes were dependent on SA 130 signalling, ube4 mutant plants were crossed with SA-deficient ics1 mutants 131 (Wildermuth et al., 2001). The constitutive immune gene expression observed in ube4 132 was abolished in ube4 ics1 double mutant plants (Figure 1C). Furthermore, while wild- 133 type (WT) and mutant ube4 plants were completely immune to a low inoculum dosage 134 of Psm ES4326, mutant ics1 plants sustained bacterial proliferation. In agreement with 135 the gene expression data, enhanced susceptibility was maintained in ube4 ics1 double 136 mutants (Figure 1D), indicating the autoimmune phenotype of adult ube4 plants is 137 completely dependent on SA. Because SA-dependent immunity is largely regulated by 138 the transcription coactivator NPR1 (Cao et al., 1997), we crossed ube4 with npr1-1 139 mutant plants. Constitutive immune gene expression in ube4 plants was completely 140 abolished in ube4 npr1 plants (Figure 1E) and this double mutant was equally 141 susceptible to a low Psm ES4326 inoculum as npr1 single mutants (Figure 1F). 142 g g p y To examine if processive ubiquitination of NPR1 plays a role in plant immune 120 responses we examined a potential role for E4 ligases. Unlike E3 ligases, the E4 class 121 do not contribute towards initial ubiquitination of substrates but rather extend pre- 122 existing ubiquitin chains (Hoppe, 2005; Koegl et al., 1999). In Arabidopsis the E4 ligase 123 UBE4/MUSE3 has been implicated in immune signalling (Huang et al., 2014). INTRODUCTION 51 102 (co)activators may be an evolutionary conserved mechanism for fine-tuning gene 101 expression (Geng et al., 2012; Kodadek et al., 2006). 102 expression (Geng et al., 2012; Kodadek et al., 2006). 102 While transcription-coupled degradation of unstable (co)activators is an 103 attractive model for controlling transcriptional outputs in eukaryotes, it is potentially 104 also a costly sacrificial process. Therefore we explored the alternative possibility that 105 prior to degradation, ubiquitination itself might act as a transcriptional signal. As chains 106 of four or more ubiquitin molecules are thought to be necessary for recruitment of most 107 substrates to the proteasome (Thrower et al., 2000), it is plausible that processive 108 ubiquitination could provide a window of opportunity for NPR1 to activate its target 109 genes. In this study we demonstrate that the transcriptional activity of NPR1 is 110 controlled by several ubiquitin chain modifying enzymes. Both processive ubiquitin 111 chain extension and trimming activities contribute to the regulation of NPR1 target 112 genes and establishment of plant immunity. Our findings imply that in eukaryotes 113 transcriptional outputs of unstable (co)activators may not be fine-tuned by their 114 proteasomal turnover per se but rather by conjugated ubiquitin chains of dynamic 115 variable length. 116 117 5 5 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint The E4 ligase UBE4 regulates SA- and NPR1-mediated plant immunity 119 We 124 investigated if UBE4 is involved in NPR1-dependent immune signalling by acquiring a 125 loss-of-function T-DNA insertion mutant (Figure S1A). Like mutants in CRL3 ligase that 126 fails to degrade NPR1 (Spoel et al., 2009), adult ube4 plants displayed enhanced 127 expression of immune genes in absence of pathogen challenge (Figure 1A). In 128 agreement, adult ube4 mutants showed autoimmunity against a high inoculum of Psm 129 ES4326 (Figure 1B). To establish if these phenotypes were dependent on SA 130 signalling, ube4 mutant plants were crossed with SA-deficient ics1 mutants 131 (Wildermuth et al., 2001). The constitutive immune gene expression observed in ube4 132 was abolished in ube4 ics1 double mutant plants (Figure 1C). Furthermore, while wild- 133 type (WT) and mutant ube4 plants were completely immune to a low inoculum dosage 134 of Psm ES4326, mutant ics1 plants sustained bacterial proliferation. In agreement with 135 the gene expression data, enhanced susceptibility was maintained in ube4 ics1 double 136 mutants (Figure 1D), indicating the autoimmune phenotype of adult ube4 plants is 137 completely dependent on SA. Because SA-dependent immunity is largely regulated by 138 the transcription coactivator NPR1 (Cao et al., 1997), we crossed ube4 with npr1-1 139 mutant plants. Constitutive immune gene expression in ube4 plants was completely 140 abolished in ube4 npr1 plants (Figure 1E) and this double mutant was equally 141 susceptible to a low Psm ES4326 inoculum as npr1 single mutants (Figure 1F). 142 6 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Collectively, these data indicate that in unchallenged plants UBE4 suppresses the 143 expression of SA-mediated NPR1 target genes and prevents autoimmunity. 144 145 Collectively, these data indicate that in unchallenged plants UBE4 suppresses the 143 expression of SA-mediated NPR1 target genes and prevents autoimmunity. 144 UBE4 polyubiquitinates NPR1 coactivator and targets it for degradation 146 Because ube4 mutant phenotypes resemble those of mutants in CRL3 ligase (Spoel 147 et al., 2009), we investigated if UBE4 also controls NPR1 stability in the nucleus. 148 Expression of an YFP-UBE4 fusion protein in Arabidopsis protoplasts confirmed it is 149 indeed partly localised to the nucleus (Figure S1B). We used the protein synthesis 150 inhibitor cycloheximide to examine if UBE4 controls the stability of SA-induced NPR1. 151 Both SA-induced constitutively expressed NPR1-GFP (in npr1-1) (Kinkema et al., 152 2000) and endogenous NPR1 from WT plants were degraded within a few hours after 153 exposure to cycloheximide (Figure 2A and 2B). By contrast, both proteins were 154 considerably more stable in the ube4 mutant genetic background, indicating UBE4 155 promotes NPR1 degradation. Recruitment of NPR1 to CRL3 for ubiquitination and 156 subsequent degradation requires phosphorylation at residues Ser11 and Ser15 (Spoel 157 et al., 2009). Therefore we examined if ube4 mutants were impaired in NPR1 Ser11/15 158 phosphorylation. However, Ser11/15 phosphorylation of NPR1-GFP was unaffected 159 by the ube4 mutation (Figure 2C), indicating UBE4 mediates NPR1 turnover 160 downstream of CRL3-mediated ubiquitination. 161 We then investigated if UBE4 is involved in polyubiquitination of NPR1. 162 Pulldown of polyubiquitinated proteins using tandem-repeated ubiquitin-binding 163 entities (TUBE) (Hjerpe et al., 2009) followed by detection of NPR1-GFP, revealed that 164 SA stimulated polyubiquitination of NPR1-GFP (Figure 2D). By contrast, SA-induced 165 polyubiquitination of NPR1-GFP was compromised in ube4 mutants (Figure 2D), but 166 ubiquitinated NPR1 was still detected at high-molecular weight. Therefore we sought 167 7 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint to distinguish if in ube4 mutants, NPR1 was modified by long ubiquitin chains or 168 multiple shorter chains, both of which yield high-molecular weights on SDS-PAGE. UBE4 polyubiquitinates NPR1 coactivator and targets it for degradation 146 169 Thus, we performed pull down experiments with recombinant S5a ubiquitin interacting 170 motifs (S5aUIM) that preferentially bind chains of four or more ubiquitin molecules 171 (Deveraux et al., 1994; Young et al., 1998). Compared to plants carrying wild-type 172 UBE4 alleles, the amount of SA-induced polyubiquitinated NPR1-GFP pulled down 173 with recombinant S5aUIM was strikingly lower in ube4 mutants (Figure 2E), indicating 174 that UBE4 promotes formation of long ubiquitin chains on NPR1 leading to its 175 proteasomal degradation. 176 Processive ubiquitination controls transcriptional activity of NPR1 178 Because UBE4 enhanced polyubiquitination of NPR1 and controlled its stability (Figure 179 2), we investigated if similar to CRL3 (Spoel et al., 2009), it also promotes 180 transcriptional activity of NPR1. In stark contrast to cul3a cul3b mutants that were 181 compromised in SA-induced expression of NPR1 target genes, ube4 mutants exhibited 182 elevated expression levels that were much higher than in WT (Figure 3A, 3B). To 183 explore the effect of UBE4 on the NPR1-dependent transcriptome, we performed RNA 184 Seq on SA-treated WT, ube4 and npr1 plants. Among 2612 genes whose expression 185 changed by ≥ 2-fold in response to SA in WT or ube4 mutants, 75% were stringently 186 dependent on NPR1 (i.e. ≥ 1.5-fold difference compared to npr1) (Table S1). We 187 separated these genes into two categories: (1) genes that were regulated by SA in 188 both WT and mutant ube4 plants, and (2) genes that did not make the ≥ 2-fold change 189 cut-off in WT but were highly regulated by SA in ube4 mutants. The majority of SA- 190 induced genes in category 1, including PR1 and WRKY marker genes, received a 191 boost in expression when UBE4 was knocked out (Figure 3C). This positive effect was 192 8 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint even clearer for category 2 genes (Figure 3C, 3D). Similarly, genes suppressed by SA 193 treatment displayed further downregulation in ube4 mutants compared to WT (Figure 194 3C). By contrast, SA-regulated genes that were not dependent on NPR1 behaved 195 similarly in WT and mutant ube4 plants (Figure S2A), suggesting UBE4 exerts its 196 effects predominantly through NPR1. Together these data suggest that in absence of 197 UBE4-mediated long-chain polyubiquitination, NPR1 remains in a highly active 198 transcriptional state. Processive ubiquitination controls transcriptional activity of NPR1 178 199 To understand the opposing effects of CRL3 and UBE4 on transcriptional 200 activity of NPR1, we examined endogenous NPR1 protein levels. Compared to WT 201 plants, SA-induced NPR1 accumulated to elevated levels in both cul3a/b and ube4 202 mutants (Figure 3E). Thus, NPR1 protein levels cannot explain differences in 203 transcriptional output of NPR1. We then examined if changes in polyubiquitin chain 204 length regulate NPR1 association with its target promoters. To that end we performed 205 chromatin immunoprecipitation experiments on plants that constitutively expressed 206 NPR1-GFP, thereby eliminating genotype-dependent differences in NPR1 protein 207 level. Coinciding with elevated PR1 gene expression, at 8h after SA treatment more 208 NPR1-GFP was bound to the PR1 promoter in ube4 mutants compared to plants 209 carrying wild-type UBE4 alleles (Figure 3F). This indicates that in absence of long 210 polyubiquitin chains, early occupancy by transcriptionally competent NPR1 is 211 increased at target promoters. We also examined a later time point after SA treatment 212 (24h) and found that NPR1-GFP was still associated with the PR1 promoter in plants 213 expressing wild-type UBE4, but not in ube4 mutants (Figure 3G). Nonetheless, PR1 214 gene expression remained at elevated levels in these mutants (Figure 3G), implying 215 that in absence of long-chain polyubiquitination NPR1 strongly switches on target 216 genes without the need for long-term residency at their promoters. 217 9 9 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint To investigate if CRL3 and UBE4 act independently or in tandem, we crossed 218 ube4 single with cul3a cul3b double mutants and analysed the expression of NPR1 219 target genes in the resulting triple mutant. Strikingly, cul3a cul3b ube4 mutants showed 220 severe developmental defects, including stunted growth and complete sterility (Figure 221 S2B, S2C). Processive ubiquitination controls transcriptional activity of NPR1 178 Very few viable homozygous plants were recovered, perhaps suggesting 222 these two ligases work together and share substrates. Nonetheless we were able to 223 select just enough plants to examine the behaviour of NPR1 target genes. In cul3a 224 cul3b ube4 mutants the SA-induced expression of several genes, including PR genes, 225 was impaired to a similar extend as in cul3a cul3b double mutants, indicating that 226 elevated gene expression observed in ube4 plants is dependent on CRL3 (Figure 3H, 227 3I). However, a subset of NPR1 target genes (i.e. WRKY18, WRKY38, WRKY62) were 228 dramatically upregulated in cul3a cul3b ube4 mutants to a level higher than in any of 229 the other genotypes. This suggests that in absence of CRL3 and UBE4, these genes 230 were activated through another pathway or were highly responsive to elevated 231 homeostatic levels of NPR1 protein and may therefore not be suitable readouts for this 232 particular epistatic analysis (Figure 3I). Regardless of this specific, our broader findings 233 suggest that CRL3 and UBE4 function sequentially in the processive addition or 234 extension of ubiquitin chains on NPR1 but with opposing effects on its transcriptional 235 activity. 236 218 We then examined if in ube4 mutants NPR1 was trapped in a highly 237 transcriptional active state that does not require proteasome-mediated turnover. To 238 negate any feedback effects of loss of UBE4 activity on endogenous NPR1 expression, 239 seedlings constitutively expressing NPR1-GFP were treated with SA plus a range of 240 MG132 concentrations. SA-induced PR1 and WRKY gene expression was inhibited 241 by increasing concentrations of MG132 in NPR1-GFP (in npr1) plants (Figure 3J and 242 10 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint S2D). By contrast, the SA-induced expression of these NPR1 target genes was largely 243 unresponsive to MG132 in ube4 mutants, especially at lower concentrations. Processive ubiquitination controls transcriptional activity of NPR1 178 Thus, 244 loss of UBE4 largely uncoupled NPR1 target gene expression from proteasome 245 activity, demonstrating the importance of processive ubiquitination for NPR1 activity. 246 In summary, our findings indicate that initial CRL3-mediated ubiquitination is required 247 for NPR1 to attain its full transcriptional activity, while processive long ubiquitin chain 248 formation mediated by UBE4 inactivates NPR1 and promotes its degradation by the 249 proteasome. 250 S2D). By contrast, the SA-induced expression of these NPR1 target genes was 243 unresponsive to MG132 in ube4 mutants, especially at lower concentration 244 loss of UBE4 largely uncoupled NPR1 target gene expression from prot 245 activity, demonstrating the importance of processive ubiquitination for NPR1 246 In summary, our findings indicate that initial CRL3-mediated ubiquitination is 247 for NPR1 to attain its full transcriptional activity, while processive long ubiquit 248 formation mediated by UBE4 inactivates NPR1 and promotes its degradatio 249 proteasome. 250 251 Deubiquitinases regulate NPR1-dependent transcription 252 Trimming or removal of ubiquitin chains is performed by deubiquitinases (DU 253 may provide another layer of regulation of NPR1 activity. The Arabidopsis ge 254 predicted to encode for at least 65 DUBs (Vierstra, 2009; Yang et al., 2007) w 255 likelihood of redundancy among gene families. Therefore identifying candidat 256 that potentially regulate NPR1 by genetically screening mutant collections 257 feasible. Instead, we used a range of pharmacological broad-spectrum and s 258 DUB inhibitors and assessed their effect on SA-induced gene expression. The 259 spectrum inhibitors PR-619 (Altun et al., 2011) and NSC632839 (Aleo et al 260 strongly impaired SA-induced gene expression across all NPR1 target gene 261 (Figure 4A), suggesting that DUB activity is required for their optimal exp 262 Furthermore, while treatment with PR-619 or NSC632839 did not affect SA- 263 transcription of the NPR1 gene, it depleted NPR1 protein levels (Figure 4B 264 DUB activity may not only be required for NPR1-dependent gene expression 265 for increasing NPR1 stability. 266 Deubiquitinases regulate NPR1-dependent transcription 252 Trimming or removal of ubiquitin chains is performed by deubiquitinases (DUBs) and 253 may provide another layer of regulation of NPR1 activity. The Arabidopsis genome is 254 predicted to encode for at least 65 DUBs (Vierstra, 2009; Yang et al., 2007) with high 255 likelihood of redundancy among gene families. Therefore identifying candidate genes 256 that potentially regulate NPR1 by genetically screening mutant collections was not 257 feasible. Instead, we used a range of pharmacological broad-spectrum and selective 258 DUB inhibitors and assessed their effect on SA-induced gene expression. The broad- 259 spectrum inhibitors PR-619 (Altun et al., 2011) and NSC632839 (Aleo et al., 2006) 260 strongly impaired SA-induced gene expression across all NPR1 target genes tested 261 (Figure 4A), suggesting that DUB activity is required for their optimal expression. 262 Furthermore, while treatment with PR-619 or NSC632839 did not affect SA-induced 263 transcription of the NPR1 gene, it depleted NPR1 protein levels (Figure 4B). Thus, 264 DUB activity may not only be required for NPR1-dependent gene expression but also 265 for increasing NPR1 stability. 266 11 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Next we tested more selective inhibitors that more specifically target one or a 267 few DUBs. First we treated WT seedlings with various DUB inhibitors and compared 268 the cellular levels of global ubiquitin conjugates with control-, and MG132-treated 269 seedlings. While NSC632839 and MG132 treatments dramatically enhanced 270 accumulation of ubiquitin conjugates, especially in combination with SA treatment, all 271 other inhibitors had little effect on cellular ubiquitination levels (Figure 4C). We then 272 examined the effect of these DUB inhibitors on SA-induced gene expression. All 273 inhibitors strongly suppressed SA-induced expression of NPR1 target genes (Figure 274 4D). Furthermore, most inhibitors were effective at low micromolar concentrations and 275 suppressed NPR1 target genes in a dose-dependent manner (Figure S3). Deubiquitinases regulate NPR1-dependent transcription 252 Collectively 276 these data provide a first indication that DUB activity may be crucial for NPR1 stability 277 and efficient activation of SA-induced NPR1 target genes. 278 267 Identification of DUBs that regulate NPR1-dependent transcription 280 The more selective inhibitors used in experiments described above have been shown 281 to target DUBs in mammalian cells (Figure S4A) (Altun et al., 2011; Kapuria et al., 282 2010; Liu et al., 2003). To find potential homologues we used the sequences of these 283 mammalian DUBs to search the Arabidopsis genome using BLASTp. The identified 284 Arabidopsis DUBs included members of the ubiquitin-specific protease (UBP) and 285 ubiquitin C-terminal hydrolase (UCH) multi-gene families (Figure S4A). We then 286 searched mutant collections to identify T-DNA knockouts for each of these DUBs. 287 UBP14 knockouts are lethal in Arabidopsis (Doelling et al., 2001), while no T-DNA 288 insertions were identified for either UCH1 or UCH2 in mutant collections of the Col-0 289 genetic background. Therefore we did not pursue these DUBs further. The DUB 290 inhibitor TCID is thought to target mammalian UCH-L3 for which we identified a single 291 12 12 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Arabidopsis homologue, UCH3. We acquired a T-DNA insertion line that displayed 292 complete knockout of UCH3 expression (Figure S4B) and analysed SA-induced NPR1 293 target gene expression. Figure 5A shows that SA-induced PR1 and WRKY gene 294 expression was comparable between uch3 and WT plants, indicating UCH3 is unlikely 295 to play a major role. Next we identified UBP12 and UBP13 as potential plant targets of 296 both WP1130 and P22077 inhibitors (Figure S4A). Previous research has suggested 297 a role for these two proteins in plant immunity, as ubp12 ubp13 double knockdown 298 RNAi plants exhibited elevated expression of PR1 and increased resistance to the 299 virulent pathogen P. syringae pv. tomato (Ewan et al., 2011). Single knockout mutants 300 of UBP12 and UBP13 have no observable phenotype and double knockouts are 301 seedling lethal (Cui et al., 2013; Ewan et al., 2011). Identification of DUBs that regulate NPR1-dependent transcription 280 However we acquired the ubp12- 302 2w allele, previously described as a weak ubp12 ubp13 double mutant (Cui et al., 303 2013), and analysed this mutant for SA-induced gene expression. Similar to a previous 304 report (Ewan et al., 2011), we observed elevated PR1 expression in ubp12-2w plants 305 but other NPR1 target genes were activated to a similar extent as in WT (Figure 5B). 306 This phenotype does not explain the suppressive effects we observed with 307 pharmacological DUB inhibitors. Finally, we acquired T-DNA knockout lines for the 308 mammalian USP14 homologues, UBP6 and UPB7 that are potentially targeted by the 309 WP1130 inhibitor (Figure S4A, S4C). SA-induced expression of PR1 was slightly lower 310 in these mutants but WRKY gene expression was largely comparable to WT plants 311 (Figure 5C). Since UBP6 and UBP7 are close homologues (Figure S5A, S5B), we 312 generated ubp6 ubp7 double knockout mutants (Figure S4C) that were viable and 313 showed no observable developmental phenotypes. However, ubp6 ubp7 mutants were 314 impaired in activation of SA-induced gene expression (Figure 5D). This indicates that 315 Arabidopsis homologue, UCH3. We acquired a T-DNA insertion line that displayed 292 complete knockout of UCH3 expression (Figure S4B) and analysed SA-induced NPR1 293 target gene expression. Figure 5A shows that SA-induced PR1 and WRKY gene 294 expression was comparable between uch3 and WT plants, indicating UCH3 is unlikely 295 to play a major role. Next we identified UBP12 and UBP13 as potential plant targets of 296 both WP1130 and P22077 inhibitors (Figure S4A). Previous research has suggested 297 a role for these two proteins in plant immunity, as ubp12 ubp13 double knockdown 298 RNAi plants exhibited elevated expression of PR1 and increased resistance to the 299 virulent pathogen P. syringae pv. tomato (Ewan et al., 2011). Single knockout mutants 300 of UBP12 and UBP13 have no observable phenotype and double knockouts are 301 seedling lethal (Cui et al., 2013; Ewan et al., 2011). However we acquired the ubp12- 302 2w allele, previously described as a weak ubp12 ubp13 double mutant (Cui et al., 303 2013), and analysed this mutant for SA-induced gene expression. Similar to a previous 304 report (Ewan et al., 2011), we observed elevated PR1 expression in ubp12-2w plants 305 but other NPR1 target genes were activated to a similar extent as in WT (Figure 5B). UBP6 and UBP7 are functionally redundant and required for NPR1 target gene 316 expression. 317 UBP6 and UBP7 are functionally redundant and required for NPR1 target gene 316 expression. 317 318 UBP6 is a proteasome-associated DUB that deubiquitinates NPR1 319 Human USP14 and its yeast homologue Ubp6 have both been shown to associate with 320 the 26S proteasome, which is necessary for their activity (Borodovsky et al., 2001; 321 Leggett et al., 2002). We tested if this is also the case for Arabidopsis UBP6 by 322 constitutively expressing FLAG-tagged UBP6 in the ubp6 ubp7 double mutant 323 background followed by co-immunoprecipitation experiments. The proteasomal 324 subunits S5a and RPN6 both co-immunoprecipitated with FLAG-tagged UBP6 (Figure 325 6A), indicating UBP6 is also a proteasome-associated DUB in plants. 326 Identification of DUBs that regulate NPR1-dependent transcription 280 306 This phenotype does not explain the suppressive effects we observed with 307 pharmacological DUB inhibitors. Finally, we acquired T-DNA knockout lines for the 308 mammalian USP14 homologues, UBP6 and UPB7 that are potentially targeted by the 309 WP1130 inhibitor (Figure S4A, S4C). SA-induced expression of PR1 was slightly lower 310 in these mutants but WRKY gene expression was largely comparable to WT plants 311 (Figure 5C). Since UBP6 and UBP7 are close homologues (Figure S5A, S5B), we 312 generated ubp6 ubp7 double knockout mutants (Figure S4C) that were viable and 313 showed no observable developmental phenotypes. However, ubp6 ubp7 mutants were 314 13 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint UBP6 is a proteasome-associated DUB that deubiquitinates NPR1 319 Human USP14 and its yeast homologue Ubp6 have both been shown to associate with 320 the 26S proteasome, which is necessary for their activity (Borodovsky et al., 2001; 321 Leggett et al., 2002). We tested if this is also the case for Arabidopsis UBP6 by 322 constitutively expressing FLAG-tagged UBP6 in the ubp6 ubp7 double mutant 323 background followed by co-immunoprecipitation experiments. The proteasomal 324 subunits S5a and RPN6 both co-immunoprecipitated with FLAG-tagged UBP6 (Figure 325 6A), indicating UBP6 is also a proteasome-associated DUB in plants. 326 Next we examined if UBP6 exhibits typical DUB activity. We produced 327 recombinant T7-tagged UBP6 and incubated it with HA-tagged ubiquitin vinyl sulfone 328 (HA-UbVS), an ubiquitin mimic that cannot be hydrolysed upon irreversible binding to 329 DUB active sites (Borodovsky et al., 2001). HA-UbVS readily labelled T7-UBP6 but 330 only upon addition of 26S proteasomes (Figure 6B), indicating UBP6 has proteasome- 331 activated DUB activity. Moreover, addition of WP1130 inhibitor completely blocked HA- 332 UbVS labelling (Figure 6B), illustrating the effectiveness of this inhibitor on Arabidopsis 333 UBP6. 334 To examine if UBP6 can cleave ubiquitin chains we incubated recombinant 335 UBP6 with free ubiquitin chains or with di-ubiquitin of different linkage types and 336 compared it to activity of recombinant human USP14. Similar to human USP14, 337 Arabidopsis UBP6 displayed very little deubiquitination activity on free ubiquitin chains 338 or di-ubiquitin of K48 and K63 linkage types (Figures S5C-S5E). Only wild-type UBP6 339 but not UBP6(C113S) in which the catalytic cysteine residue was mutated, was weakly 340 14 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint capable of trimming K63-linked chains in presence of 26S proteasomes, although this 341 activity required very long incubation times (Figure S5D). These findings mirror the 342 poor in vitro activity of human USP14 on free ubiquitin chains (Lee et al., 2016). UBP6 is a proteasome-associated DUB that deubiquitinates NPR1 319 343 Instead, human USP14 deubiquitinates anchored ubiquitin chains of various linkage 344 types, including K48 linkages that target proteins for proteasome-mediated 345 degradation (Lee et al., 2016). Therefore we proceeded to investigate if UBP6 activity 346 cleaves ubiquitin chains anchored to NPR1. Indeed, incubation of purified 347 polyubiquitinated NPR1-GFP with recombinant UBP6 and 26S proteasomes led to the 348 release of ubiquitin conjugates of approximately hexa-ubiquitin chain length (Figure 349 6C). These results demonstrate that UBP6 is an active DUB capable of removing 350 ubiquitin chains en bloc from NPR1. 351 352 Deubiquitination by UBP6 and UBP7 regulates NPR1 stability and transcriptional 353 activity 354 So what is the effect of UBP6- and UBP7-mediated deubiquitination on NPR1 function? 355 We found that treatment of NPR1-GFP (in npr1) seedlings with WP1130 inhibitor 356 increased the levels of SA-induced polyubiquitinated NPR1-GFP while reducing the 357 total amount of this protein (Figure 6D). This suggests that UBP6 and UBP7 activities 358 are required for deubiquitination of SA-induced NPR1-GFP, thereby rescuing it from 359 degradation. To further examine this possibility, we analysed the stability of 360 endogenous NPR1 protein in SA-treated ubp6 ubp7 double mutants. CHX chase 361 experiments revealed that compared to WT plants, NPR1 was destabilised in ubp6 362 ubp7 mutants (Figure 6E). These results demonstrate that UBP6 and UBP7 serve to 363 stabilise NPR1 by removing ubiquitin chains that signal for its proteasome-mediated 364 degradation. 365 capable of trimming K63-linked chains in presence of 26S proteasomes, although this 341 activity required very long incubation times (Figure S5D). These findings mirror the 342 poor in vitro activity of human USP14 on free ubiquitin chains (Lee et al., 2016). 343 Instead, human USP14 deubiquitinates anchored ubiquitin chains of various linkage 344 types, including K48 linkages that target proteins for proteasome-mediated 345 degradation (Lee et al., 2016). Therefore we proceeded to investigate if UBP6 activity 346 cleaves ubiquitin chains anchored to NPR1. Indeed, incubation of purified 347 polyubiquitinated NPR1-GFP with recombinant UBP6 and 26S proteasomes led to the 348 release of ubiquitin conjugates of approximately hexa-ubiquitin chain length (Figure 349 6C). These results demonstrate that UBP6 is an active DUB capable of removing 350 ubiquitin chains en bloc from NPR1. 351 Deubiquitination by UBP6 and UBP7 regulates NPR1 stability and transcriptional 353 So what is the effect of UBP6- and UBP7-mediated deubiquitination on NPR1 function? 355 We found that treatment of NPR1-GFP (in npr1) seedlings with WP1130 inhibitor 356 increased the levels of SA-induced polyubiquitinated NPR1-GFP while reducing the 357 total amount of this protein (Figure 6D). This suggests that UBP6 and UBP7 activities 358 are required for deubiquitination of SA-induced NPR1-GFP, thereby rescuing it from 359 degradation. To further examine this possibility, we analysed the stability of 360 endogenous NPR1 protein in SA-treated ubp6 ubp7 double mutants. CHX chase 361 experiments revealed that compared to WT plants, NPR1 was destabilised in ubp6 362 ubp7 mutants (Figure 6E). These results demonstrate that UBP6 and UBP7 serve to 363 stabilise NPR1 by removing ubiquitin chains that signal for its proteasome-mediated 364 degradation. 365 15 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Given the importance of processive ubiquitination for the transcriptional activity 366 of NPR1, we explored how UBP6- and UBP7-mediated deubiquitination might affect 367 NPR1 coactivator function. Because UBP6 and UBP7 were required for NPR1- 368 dependent PR1 gene expression (Figure 5D), we questioned if NPR1 was still 369 associated with the PR1 promoter in absence of UBP6 and UBP7 activities. 370 Surprisingly, ChIP experiments showed that SA-induced association of NPR1-GFP 371 with the PR1 promoter was strongly enhanced in presence of WP1130 inhibitor (Figure 372 6F). This suggests that UBP6 and UBP7 prevent the build-up of long polyubiquitin 373 chains that block the transcriptional activity of NPR1. It also implies that similar to their 374 yeast homologue, UBP6 and UBP7 exhibit proteasome inhibitory activity (Hanna et al., 375 2006). This activity is thought to delay degradation of proteasome substrates, thereby 376 creating a window of opportunity for DUBs to deubiquitinate substrates and pardon 377 them from proteolysis. Deubiquitination by UBP6 and UBP7 regulates NPR1 stability and transcriptional 353 Importantly, proteasome inhibitory activity does not require the 378 catalytic active site (Hanna et al., 2006). Thus, to investigate how deubiquitination and 379 proteasome inhibitory activities of UBP6 contribute to the regulation of NPR1 380 coactivator activity, we expressed FLAG-tagged wild-type UBP6 (FLAG-UBP6) and 381 catalytically inactive UBP6(C113S) (FLAG-UBP6m) in ubp6 ubp7 double mutants. 382 While ubp6 ubp7 mutants were compromised in SA-induced activation of all NPR1 383 target genes tested, expression of FLAG-UBP6 fully restored SA-responsiveness 384 (Figure 6G). By contrast, FLAG-UBP6m restored SA-induced expression of only a 385 subset, but not all NPR1 target genes. A distinction was observed between WRKY and 386 PR genes, with the former requiring catalytic DUB activity of UBP6 while the latter did 387 not (Figure 6G). These data indicate that catalytic and non-catalytic activities of UBP6 388 regulate distinct NPR1-dependent gene sets. 389 Given the importance of processive ubiquitination for the transcriptional activity 366 of NPR1, we explored how UBP6- and UBP7-mediated deubiquitination might affect 367 NPR1 coactivator function. Because UBP6 and UBP7 were required for NPR1- 368 dependent PR1 gene expression (Figure 5D), we questioned if NPR1 was still 369 associated with the PR1 promoter in absence of UBP6 and UBP7 activities. 370 Surprisingly, ChIP experiments showed that SA-induced association of NPR1-GFP 371 with the PR1 promoter was strongly enhanced in presence of WP1130 inhibitor (Figure 372 6F). This suggests that UBP6 and UBP7 prevent the build-up of long polyubiquitin 373 chains that block the transcriptional activity of NPR1. It also implies that similar to their 374 yeast homologue, UBP6 and UBP7 exhibit proteasome inhibitory activity (Hanna et al., 375 2006). This activity is thought to delay degradation of proteasome substrates, thereby 376 creating a window of opportunity for DUBs to deubiquitinate substrates and pardon 377 them from proteolysis. Importantly, proteasome inhibitory activity does not require the 378 catalytic active site (Hanna et al., 2006). Thus, to investigate how deubiquitination and 379 proteasome inhibitory activities of UBP6 contribute to the regulation of NPR1 380 coactivator activity, we expressed FLAG-tagged wild-type UBP6 (FLAG-UBP6) and 381 catalytically inactive UBP6(C113S) (FLAG-UBP6m) in ubp6 ubp7 double mutants. 382 While ubp6 ubp7 mutants were compromised in SA-induced activation of all NPR1 383 target genes tested, expression of FLAG-UBP6 fully restored SA-responsiveness 384 (Figure 6G). By contrast, FLAG-UBP6m restored SA-induced expression of only a 385 subset, but not all NPR1 target genes. Deubiquitination by UBP6 and UBP7 regulates NPR1 stability and transcriptional 353 A distinction was observed between WRKY and 386 PR genes, with the former requiring catalytic DUB activity of UBP6 while the latter did 387 not (Figure 6G). These data indicate that catalytic and non-catalytic activities of UBP6 388 regulate distinct NPR1 dependent gene sets 389 16 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint Finally we examined what the relevance is of UBP6- and UBP7-regulated 390 transcriptional activity of NPR1 in context of plant immunity. We first treated plants with 391 or without SA before challenge inoculation with virulent Psm ES4326. SA treatment 392 induced resistance in WT plants but did not block bacterial propagation in ubp6/7 393 plants (Figure 6H). Collectively, these data clearly demonstrate that UBP6 and UBP7 394 are required for NPR1 coactivator activity and associated development of SA- 395 dependent immunity. 396 390 17 17 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint DISCUSSION 397 The ubiquitin-mediated proteasome system plays vital roles in the regulation of 398 eukaryotic gene expression, in large part by controlling the abundance of 399 transcriptional regulators. Paradoxically, proteasome-dependent instability of selected 400 potent eukaryotic transcriptional activators is necessary for the expression of their 401 target genes. It is thought that their transcription-coupled degradation ensures the 402 target promoter is continuously supplied with fresh activators that reinitiate 403 transcription, thereby maximising gene expression (Geng et al., 2012; Kodadek et al., 404 2006). However, this sacrificial process is energy-expensive (Collins and Goldberg, 405 2017; Peth et al., 2013), raising a dilemma of why such mechanisms evolved to 406 regulate transcriptional activators. Our study on the immune coactivator NPR1, 407 however, indicates that ubiquitin chain extension and trimming activities can fine-tune 408 transcriptional outputs of unstable eukaryotic activators without strict requirement for 409 sacrificial turnover. 410 We discovered that ubiquitination of NPR1 is processive, requiring the actions 411 of CRL3 and the E4 ligase UBE4. In resting cells, CRL3-mediated turnover of NPR1 is 412 important for preventing autoimmunity in absence of pathogen threat (Spoel et al., 413 2009). The NPR1-dependent autoimmune phenotype of ube4 mutants is reminiscent 414 of that observed in cul3a cul3b mutants (Figure 1) (Spoel et al., 2009), suggesting that 415 in addition to CRL3 ligase, UBE4 is required to clear NPR1 from the nucleus and 416 prevent untimely activation of immunity. In presence of SA, however, CRL3-mediated 417 ubiquitination induced NPR1 coactivator activity, whereas formation of polyubiquitin 418 chains by UBE4 blocked its activity and ultimately led to proteasome-mediated 419 turnover (Figures 2 and 3). Rather than initiating substrate ubiquitination, E4 ligases 420 are thought to extend existing ubiquitin chains (Crosas et al., 2006; Koegl et al., 1999), 421 18 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. DISCUSSION 397 ; https://doi.org/10.1101/582296 doi: bioRxiv preprint thereby determining substrate commitment to proteasome-mediated degradation and 422 contributing to proteasome processivity (Aviram and Kornitzer, 2010; Koegl et al., 423 1999). Functionally these enzymes are emerging as important players in limiting the 424 activity of immune receptors as well as potent eukaryotic transcriptional regulators. 425 Arabidopsis UBE4/MUSE3 works in concert with a CRL1/SCFCPR1 ligase to regulate 426 stability of the intercellular immune receptors SNC1 and RPS2 that recognise 427 pathogen invasion (Cheng et al., 2011; Gou et al., 2012; Huang et al., 2014). Taken 428 together with our finding that UBE4 acts in concert with CRL3 (Figures 3 and S2), this 429 suggests a single E4 enzyme may assist in diverse ubiquitin-mediated pathways 430 controlled by different E3 ligases. 431 The role of Arabidopsis UBE4 in ubiquitination and degradation of NPR1 are 432 reminiscent of processive ubiquitination of the mammalian tumour suppressor p53, a 433 potent transcriptional activator of genes involved in apoptosis, cell cycle arrest and 434 cellular senescence. The stability of p53 is regulated by amongst others the E3 ligase 435 MDM2 (or HDM2 in humans)(Pant and Lozano, 2014). Although MDM2 limits p53 436 activity by promoting its turnover, MDM2 only catalyses multi-monoubiquitination of 437 p53, which is insufficient for recognition by the proteasome (Lai et al., 2001). 438 Progression to the polyubiquitinated form of p53 in the nucleus is carried out by the U- 439 box E4 ligase UBE4B that interacts with both MDM2 and p53 (Li et al., 2003; Wu and 440 Leng, 2011; Wu et al., 2011). Although this is similar to the proposed roles of CRL3 441 and UBE4 in controlling NPR1 stability, initial ubiquitination has different effects on p53 442 and NPR1. While MDM2-mediated monoubiquitination controls nucleocytoplasmic 443 trafficking of p53 (Li et al., 2003), it probably does not have a direct effect on intrinsic 444 p53 activator activity. Instead, initial ubiquitination boosts NPR1 transcriptional 445 coactivator activity, at least in part by enhancing target promoter occupancy in the short 446 19 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint . DISCUSSION 397 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint term and potentially also by promoting genomic mobility of NPR1 in the longer term 447 (Figure 3). Although it remains unclear if CRL3 adds only monoubiquitin or generates 448 short chains shy of tetraubiquitin, the minimal signal required for proteasome 449 recognition (Thrower et al., 2000), progression to polyubiquitin chain formation by 450 UBE4 results in transcriptional shut down as polyubiquitinated NPR1 still occupied 451 target promoters but lacked transcriptional potency (Figure 6D and 6F). This type of 452 processive ubiquitination may be a general mechanism to control unstable 453 transcriptional (co)activators in eukaryotes. For example, multi-monoubiquitination of 454 the oncogenic growth coactivator SRC-3 results in its transcriptional activation, while 455 subsequent chain extension targets it for degradation, but E4 ligases have not yet been 456 implicated. We propose here that processive ubiquitination established by the 457 sequential actions of E3 and E4 ligases may generate a transcriptional timer that 458 controls the activity and lifetime of unstable (co)activators (Figure 7). 459 The complexity of the ubiquitin-dependent transcriptional timer was further 460 revealed by the identification of UBP6 and UBP7 that deubiquitinated NPR1, thereby 461 regulating its transcriptional activity and lifetime (Figures 5 and 6). Several unstable 462 mammalian transcription activators, including p53 and the immune activator NF-κB, 463 are also regulated by diverse DUBs (Colleran et al., 2013; Pant and Lozano, 2014; 464 Schweitzer and Naumann, 2015). In these cases DUBs promote transcription by 465 stabilising p53 and NF-κB at their target promoters. For example, loss of USP7- 466 mediated deubiquitination of NF-κB resulted in increased turnover and decreased 467 promoter occupancy of NF-κB (Colleran et al., 2013). Similarly, we found that knockout 468 of UBP6 and UBP7 resulted in enhanced turnover and transcriptional output of NPR1 469 (Figure 6). However, inhibition of UBP6/7 deubiquitination activities with WP1130 470 resulted in enhanced occupancy of transcriptionally inactive NPR1 at the PR1 target 471 20 . 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. DISCUSSION 397 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint ACKNOWLEDGEMENTS 494 DISCUSSION 397 It is made The copyright holder for this preprint (which was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint promoter (Figure 6F). These data suggest that (i) like their yeast and mammalian 472 counterparts (Hanna et al., 2006; Lee et al., 2016), UBP6 and UBP7 exhibit 473 proteasome inhibitory activities that at least temporarily prolong promoter occupancy 474 by NPR1, and (ii) UBP6 and UBP7 prevent inactivation of NPR1 by opposing the 475 formation of long ubiquitin chains. 476 UBP6 showed a similar DUB activity as its mammalian homologue USP14 (Lee 477 et al., 2016), in that it appeared to deubiquitinate NPR1 by removing ubiquitin chains 478 en bloc (Figure 6C, 6D). Such activity places this DUB in direct opposition to UBE4- 479 mediated chain extension activity. In yeast Ubp6 was previously reported to oppose 480 ubiquitin chain extension activity of the E4 ligase Hul5, thereby regulating substrate 481 recruitment to the proteasome (Crosas et al., 2006). Similarly, Arabidopsis UBP6 and 482 UBP7 opposed ubiquitin ligase activities to extend the lifetime of transcriptionally active 483 NPR1. Although we cannot rule out that these DUBs function in opposition to CRL3, 484 their en bloc ubiquitin removal activity suggests they more likely remove longer 485 ubiquitin chains generated by UBE4 (Figure 7). 486 In summary, we report that disparate ubiquitin modifying enzymes play 487 important roles in establishment of plant immune responses. We demonstrate that the 488 opposing actions of an E3 and E4 ligase pair and two DUBs can fine-tune 489 transcriptional outputs of the unstable immune coactivator NPR1 without strict 490 requirement for its sacrificial turnover. Dynamicity in conjugated ubiquitin chain length 491 may be a powerful mechanism for controlling the activity of unstable eukaryotic 492 (co)activators in general. 493 21 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint . ACKNOWLEDGEMENTS 494 ACKNOWLEDGEMENTS 494 We thank Dr Xia Cui for sharing ubp12-2w seeds. This work was supported by a Royal 495 Society University Research Fellowship (UF090321), a BBSRC grant (BB/L006219/1), 496 and the European Research Council (ERC) under the European Union’s Horizon 2020 497 research and innovation programme (grant agreement No 678511). 498 499 AUTHOR CONTRIBUTIONS 500 Conceptualisation, M.J.S. and S.H.S.; Methodology, M.J.S. and S.H.S.; Formal 501 analysis, M.J.S., and S.H.S.; Investigation, M.J.S. and, J.J.F., H.L.G, K.W.W, and 502 S.H.S.; Writing, M.J.S. and S.H.S.; Visualisation, M.J.S. and S.H.S.; Supervision, 503 M.J.S. and S.H.S.; Project administration, S.H.S.; Funding acquisition, S.H.S. 504 505 DECLARATION OF INTERESTS 506 The authors declare no competing interests. 507 We thank Dr Xia Cui for sharing ubp12-2w seeds. This work was supported by a Royal 495 Society University Research Fellowship (UF090321), a BBSRC grant (BB/L006219/1), 496 and the European Research Council (ERC) under the European Union’s Horizon 2020 497 research and innovation programme (grant agreement No 678511). 498 We thank Dr Xia Cui for sharing ubp12-2w seeds. This work was supported by a Royal 495 Society University Research Fellowship (UF090321), a BBSRC grant (BB/L006219/1), 496 and the European Research Council (ERC) under the European Union’s Horizon 2020 497 research and innovation programme (grant agreement No 678511). 498 AUTHOR CONTRIBUTIONS 500 Conceptualisation, M.J.S. and S.H.S.; Methodology, M.J.S. and S.H.S.; Formal 501 analysis, M.J.S., and S.H.S.; Investigation, M.J.S. and, J.J.F., H.L.G, K.W.W, and 502 S.H.S.; Writing, M.J.S. and S.H.S.; Visualisation, M.J.S. and S.H.S.; Supervision, 503 M.J.S. and S.H.S.; Project administration, S.H.S.; Funding acquisition, S.H.S. 504 The authors declare no competing interests. 507 22 . 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. 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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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint . CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 J 678 Bi l Ch 273 5461 5467 679 Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a. J 678 Biol Chem 273, 5461-5467. 679 Biol Chem 273, 5461-5467. 679 29 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint FIGURES 680 680 FIGURES 680 681 682 683 Figure 1. The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immunity 684 (A) Expression of NPR1 target genes normalised relative to constitutively expressed 685 UBQ5 in four-week old plants of the indicated genotypes. Data points represent mean 686 ± SD (n=3). 687 (B) Adult plants were treated with or without 0.5 mM SA 24h prior to inoculation with 688 5x106 colony forming units (cfu)/ml Psm ES4326. Leaf discs were analysed for 689 bacterial growth 4 days post-infection (dpi). Error bars represent 95% confidence limits, 690 while letters denote statistically significant differences between samples (Tukey 691 Kramer ANOVA; α = 0.05, n = 8). 692 (C) Expression of NPR1 target genes was analysed as in (A). 693 (D) Adult plants were inoculated with 5x105 cfu/ml Psm ES4326 and leaf discs were 694 analysed for bacterial growth at 4 dpi. Error bars represent 95% confidence limits, while 695 letters denote statistically significant differences between samples (Tukey Kramer 696 ANOVA; α = 0.05, n = 8). 697 (E) Basal expression of NPR1 target genes were analysed as in (A). 698 (F) Adult plants of indicated genotypes were infected and analysed as in (D). 699 See also Figure S1. 700 681 2 3 Figure 1. The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immunity 4 (A) Expression of NPR1 target genes normalised relative to constitutively expressed 5 UBQ5 in four-week old plants of the indicated genotypes. Data points represent mean 6 ± SD (n=3). 7 682 683 Figure 1. CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 701 702 Figure 2. UBE4 facilitates polyubiquitination and degradation of NPR1 703 coactivator 704 (A) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 705 treated with 0.5 mM SA for 24h before addition of 100 μM CHX to inhibit protein 706 synthesis. NPR1-GFP protein levels were monitored by immunoblot analysis, while 707 S5a levels confirmed equal loading. 708 (B) Seedlings were treated with 0.5 mM SA for 24h before addition of 100 μM CHX. 709 Endogenous NPR1 protein levels were then monitored at the indicated times by 710 immunoblot analysis, while GAPDH levels confirmed equal loading. 711 (C) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 712 pre-treated with 0.5 mM SA for 2h followed by addition of vehicle (DMSO) or 100 μM 713 MG132 for an additional 4h. Phosphorylated Ser11/15 (pS11/15) and total NPR1-GFP 714 levels were then determined by immunoblotting. 715 (D) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 716 pre-treated with 0.5 mM SA for 6h followed by addition of 100 μM MG132 for an 717 additional 18h before ubiquitinated proteins were pulled down using GST-TUBEs. 718 Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were detected by immunoblotting with 719 a GFP antibody. 720 (E) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 721 pre-treated with 0.5 mM SA for 2h followed by addition of 100 μM MG132 for an 722 additional 4h before ubiquitinated proteins were pulled down (PD) using His6-V5-S5a- 723 UIMs. Total and long-chain polyubiquitinated NPR1-GFP (NPR1-Ubn>4) were detected 724 by immunoblotting with GFP antibodies. 725 See also Figure S1. 726 701 702 Figure 2. UBE4 facilitates polyubiquitination and degradation of NPR1 703 coactivator 704 (A) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 705 treated with 0.5 mM SA for 24h before addition of 100 μM CHX to inhibit protein 706 synthesis NPR1-GFP protein levels were monitored by immunoblot analysis while 707 02 Figure 2. UBE4 facilitates polyubiquitination and degradation of NPR1 03 coactivator 04 (B) Seedlings were treated with 0.5 mM SA for 24h before addition of 100 μM CHX. CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immunity 684 (A) Expression of NPR1 target genes normalised relative to constitutively expressed 685 UBQ5 in four-week old plants of the indicated genotypes. Data points represent mean 686 ± SD (n=3). 687 (B) Adult plants were treated with or without 0.5 mM SA 24h prior to inoculation with 688 5x106 colony forming units (cfu)/ml Psm ES4326. Leaf discs were analysed for 689 bacterial growth 4 days post-infection (dpi). Error bars represent 95% confidence limits, 690 while letters denote statistically significant differences between samples (Tukey 691 Kramer ANOVA; α = 0.05, n = 8). 692 (C) Expression of NPR1 target genes was analysed as in (A). 693 (D) Adult plants were inoculated with 5x105 cfu/ml Psm ES4326 and leaf discs were 694 analysed for bacterial growth at 4 dpi. Error bars represent 95% confidence limits, while 695 letters denote statistically significant differences between samples (Tukey Kramer 696 ANOVA; α = 0.05, n = 8). 697 (E) Basal expression of NPR1 target genes were analysed as in (A). 698 (F) Adult plants of indicated genotypes were infected and analysed as in (D). 699 See also Figure S1 700 683 Figure 1. The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immunity 684 (A) Expression of NPR1 target genes normalised relative to constitutively expressed 685 UBQ5 in four week old plants of the indicated genotypes Data points represent mean 686 683 Figure 1. The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immunity 684 (A) Expression of NPR1 target genes normalised relative to constitutively expressed 685 UBQ5 in four-week old plants of the indicated genotypes. Data points represent mean 686 ± SD (n=3). 687 igure 1. The E4 ubiquitin ligase UBE4 regulates SA-mediated plant immuni q g g p y pression of NPR1 target genes normalised relative to constitutively expressed n four-week old plants of the indicated genotypes. Data points represent mean =3). (D) Adult plants were inoculated with 5x105 cfu/ml Psm ES4326 and leaf discs were 694 analysed for bacterial growth at 4 dpi. Error bars represent 95% confidence limits, while 695 letters denote statistically significant differences between samples (Tukey Kramer 696 ANOVA; α = 0.05, n = 8). 697 (E) Basal expression of NPR1 target genes were analysed as in (A). (F) Adult plants of indicated genotypes were infected and analysed as in (D). 30 . CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 9 Endogenous NPR1 protein levels were then monitored at the indicated times by 0 immunoblot analysis, while GAPDH levels confirmed equal loading. 1 (C) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 2 pre-treated with 0.5 mM SA for 2h followed by addition of vehicle (DMSO) or 100 μM 3 MG132 for an additional 4h. Phosphorylated Ser11/15 (pS11/15) and total NPR1-GFP 4 levels were then determined by immunoblotting. 5 (D) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were pre-treated with 0.5 mM SA for 6h followed by addition of 100 μM MG132 for an additional 18h before ubiquitinated proteins were pulled down using GST-TUBEs. Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were detected by immunoblotting with a GFP antibody. (E) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 721 pre-treated with 0.5 mM SA for 2h followed by addition of 100 μM MG132 for an 722 additional 4h before ubiquitinated proteins were pulled down (PD) using His6-V5-S5a- 723 UIMs. Total and long-chain polyubiquitinated NPR1-GFP (NPR1-Ubn>4) were detected 724 by immunoblotting with GFP antibodies. 725 S l Fi S1 726 (E) Seedlings expressing 35S::NPR1-GFP in the indicated genetic backgrounds were 1 pre-treated with 0.5 mM SA for 2h followed by addition of 100 μM MG132 for an 2 additional 4h before ubiquitinated proteins were pulled down (PD) using His6-V5-S5a- 3 UIMs. Total and long-chain polyubiquitinated NPR1-GFP (NPR1-Ubn>4) were detected 4 by immunoblotting with GFP antibodies. 5 See also Figure S1. 31 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 27 28 Figure 3. Processive ubiquitination controls transcriptional activity of NPR1 29 (A) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with 0.5 mM SA for 30 6h before determining PR1 gene expression normalised relative to constitutively 31 expressed UBQ5. Data points represent mean ± SD (n=3). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 32 (B) Heat map of the expression of additional NPR1 target genes analysed as in (A). 33 (C) Seedlings treated with water (Ctrl) or 0.5 mM SA for 12h were analysed by RNA- 34 Seq. Only genes that were induced ≥2-fold by SA in WT and/or ube4 plants and 35 727 728 Figure 3. Processive ubiquitination controls transcriptional activity of NPR1 729 (A) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with 0.5 mM SA for 730 6h before determining PR1 gene expression normalised relative to constitutively 731 expressed UBQ5. Data points represent mean ± SD (n=3). 732 (B) Heat map of the expression of additional NPR1 target genes analysed as in (A). 733 (C) Seedlings treated with water (Ctrl) or 0.5 mM SA for 12h were analysed by RNA- 734 Seq. Only genes that were induced ≥2-fold by SA in WT and/or ube4 plants and 735 showed ≥1.5-fold difference in expression in npr1 mutants are shown (Benjamini 736 Hochberg FDR, 2-way ANOVA p ≤ 0.05). Graphs indicate genes that are up or down 737 regulated in both WT and ube4 or only in ube4. PR-1, WRKY18, WRKY38 and 738 728 Figure 3. Processive ubiquitination controls transcriptional activity of NPR1 729 (A) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with 0.5 mM SA for 730 6h before determining PR1 gene expression normalised relative to constitutively 731 expressed UBQ5. Data points represent mean ± SD (n=3). 732 (B) Heat map of the expression of additional NPR1 target genes analysed as in (A). 733 (C) Seedlings treated with water (Ctrl) or 0.5 mM SA for 12h were analysed by RNA- 734 728 Figure 3. Processive ubiquitination controls transcriptional activity of NPR1 729 (A) WT c l3a c l3b (c l3) be4 and npr1 seedlings ere treated ith 0 5 mM SA for 730 ure 3. Processive ubiquitination controls transcriptional activity of NPR1 g q p y (A) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with 0.5 mM SA for 730 6h before determining PR1 gene expression normalised relative to constitutively 731 expressed UBQ5. Data points represent mean ± SD (n=3). 732 (B) Heat map of the expression of additional NPR1 target genes analysed as in (A). 733 (C) Seedlings treated with water (Ctrl) or 0.5 mM SA for 12h were analysed by RNA- 734 Seq. CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 Only genes that were induced ≥2-fold by SA in WT and/or ube4 plants and 735 showed ≥1.5-fold difference in expression in npr1 mutants are shown (Benjamini 736 Hochberg FDR, 2-way ANOVA p ≤ 0.05). Graphs indicate genes that are up or down 737 regulated in both WT and ube4 or only in ube4. PR-1, WRKY18, WRKY38 and 738 32 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint WRKY62 marker genes are indicated by green lines, whereas mean expression 739 patterns are indicated by black lines. 740 (D) Heat map representation of genes from (C) that were upregulated by SA. 741 (E) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with water (-) or 0.5 742 mM SA (+) for 6h. Endogenous NPR1 protein levels were monitored by immunoblot 743 analysis, while GAPDH levels confirmed equal loading. 744 (F) Adult plants expressing 35S::NPR1-GFP in the indicated genetic backgrounds 745 were treated with 0.5 mM SA for 8h before analysing either PR1 gene expression (left 746 panel) or NPR1-GFP binding to the as-1 motif of the PR1 promoter (right panel). 747 Mutant npr1 plants served as a negative control. Data points represent mean ± SD 748 (n=3). 749 (G) As in (F) except plants were treated with 0.5 mM SA for 24h. 750 (H) WT, cul3a cul3b (cul3) double, ube4 single, cul3a cul3b ube4 (cul3 ube4) triple and 751 npr1 single mutant seedlings were treated with 0.5 mM SA for 6h and PR1 gene 752 expression determined by normalising against constitutively expressed UBQ5. Data 753 points represent mean ± SD (n=3). 754 (I) Heat map of the expression of additional NPR1 target genes analysed as in (F). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 755 (J) WT (closed circles) and mutant ube4 (open circles) seedlings expressing 756 35S:NPR1-GFP were treated with 0.5 mM SA for 4h followed by the addition of 757 indicated concentrations of MG132 for an additional 2 h. PR1 gene expression was 758 determined and normalised relative to constitutively expressed UBQ5. MG132 759 treatments as well as a control (Ctrl) that received 4h of water treatment followed by 760 the addition of vehicle (DMSO), were plotted relative to maximal SA-induced PR1 761 expression. Data points represent mean ± SD (n=3). 762 See also Figure S2. 763 WRKY62 marker genes are indicated by green lines, whereas mean expression patterns are indicated by black lines. (D) Heat map representation of genes from (C) that were upregulated by SA. (D) Heat map representation of genes from (C) that were upregulated by SA. 741 (E) WT, cul3a cul3b (cul3), ube4 and npr1 seedlings were treated with water (-) or 0.5 742 mM SA (+) for 6h. Endogenous NPR1 protein levels were monitored by immunoblot 743 analysis, while GAPDH levels confirmed equal loading. 744 (F) Adult plants expressing 35S::NPR1-GFP in the indicated genetic backgrounds 745 were treated with 0.5 mM SA for 8h before analysing either PR1 gene expression (left 746 panel) or NPR1-GFP binding to the as-1 motif of the PR1 promoter (right panel). 747 Mutant npr1 plants served as a negative control. Data points represent mean ± SD 748 (n=3). 749 ( ) ( ) p p (H) WT, cul3a cul3b (cul3) double, ube4 single, cul3a cul3b ube4 (cul3 ube4) triple and 751 npr1 single mutant seedlings were treated with 0.5 mM SA for 6h and PR1 gene 752 expression determined by normalising against constitutively expressed UBQ5. Data 753 points represent mean ± SD (n=3). 754 (I) Heat map of the expression of additional NPR1 target genes analysed as in (F). 755 (J) WT (closed circles) and mutant ube4 (open circles) seedlings expressing 756 35S:NPR1-GFP were treated with 0.5 mM SA for 4h followed by the addition of 757 indicated concentrations of MG132 for an additional 2 h. PR1 gene expression was 758 determined and normalised relative to constitutively expressed UBQ5. MG132 759 treatments as well as a control (Ctrl) that received 4h of water treatment followed by 760 the addition of vehicle (DMSO), were plotted relative to maximal SA-induced PR1 761 expression. Data points represent mean ± SD (n=3). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 769 (B) WT seedlings were treated as in (A) before endogenous NPR1 and GAPDH 770 (loading control) protein levels were analysed by immunoblotting (top panel). NPR1 771 gene expression was also analysed from the same samples (bottom panel). Data 772 points represent mean ± SD (n=3). 773 (C) WT seedlings were treated for 6h with vehicle (DMSO) or either the indicated DUB 774 inhibitors (50 μM) or MG132 (100 μM) in presence or absence of 0.5 mM SA before 775 immunoblotting against conjugated ubiquitin (FK2). Ponceau S staining indicated 776 equal loading. 777 (D) WT seedlings were treated as in (C) and NPR1 target gene expression analysed. 778 Data points represent mean ± SD (n=3). 779 See also Figure S3 and S4. 780 764 Figure 4. Deubiquitinases regulate NPR1-dependent transcription 765 (A) WT seedlings were treated for 6h with either vehicle control (DMSO) or the 766 indicated DUB inhibitors (50 μM) in presence or absence of 0.5 mM SA before 767 analysing the expression of NPR1 target genes. Data points represent mean ± SD 768 (n=3). 769 (B) WT seedlings were treated as in (A) before endogenous NPR1 and GAPDH 770 (loading control) protein levels were analysed by immunoblotting (top panel). NPR1 771 gene expression was also analysed from the same samples (bottom panel). Data 772 points represent mean ± SD (n=3). 773 (C) WT seedlings were treated for 6h with vehicle (DMSO) or either the indicated DUB 774 inhibitors (50 μM) or MG132 (100 μM) in presence or absence of 0.5 mM SA before 775 immunoblotting against conjugated ubiquitin (FK2). Ponceau S staining indicated 776 equal loading. 777 (D) WT seedlings were treated as in (C) and NPR1 target gene expression analysed. 778 Data points represent mean ± SD (n=3). 779 See also Figure S3 and S4. 780 764 Figure 4. Deubiquitinases regulate NPR1-dependent transcription 765 (A) WT dli t t d f 6h ith ith hi l t l (DMSO 766 Figure 4. Deubiquitinases regulate NPR1-dependent transcription (A) WT seedlings were treated for 6h with either vehicle control (DMSO) or the 766 indicated DUB inhibitors (50 μM) in presence or absence of 0.5 mM SA before 767 analysing the expression of NPR1 target genes. Data points represent mean ± SD 768 (n=3). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 762 See also Figure S2. 763 33 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 4 Figure 4. Deubiquitinases regulate NPR1-dependent transcription 5 (A) WT seedlings were treated for 6h with either vehicle control (DMSO) or the 6 indicated DUB inhibitors (50 μM) in presence or absence of 0.5 mM SA before 7 analysing the expression of NPR1 target genes. Data points represent mean ± SD 8 (n=3). 9 764 Figure 4. Deubiquitinases regulate NPR1-dependent transcription 765 (A) WT seedlings were treated for 6h with either vehicle control (DMSO) or the 766 indicated DUB inhibitors (50 μM) in presence or absence of 0.5 mM SA before 767 analysing the expression of NPR1 target genes. Data points represent mean ± SD 768 (n=3). 769 (B) WT seedlings were treated as in (A) before endogenous NPR1 and GAPDH 770 (loading control) protein levels were analysed by immunoblotting (top panel). NPR1 771 gene expression was also analysed from the same samples (bottom panel). Data 772 points represent mean ± SD (n=3). 773 (C) WT seedlings were treated for 6h with vehicle (DMSO) or either the indicated DUB 774 inhibitors (50 μM) or MG132 (100 μM) in presence or absence of 0.5 mM SA before 775 immunoblotting against conjugated ubiquitin (FK2). Ponceau S staining indicated 776 equal loading. 777 (D) WT seedlings were treated as in (C) and NPR1 target gene expression analysed. 778 Data points represent mean ± SD (n=3). 779 See also Figure S3 and S4. 780 764 Figure 4. Deubiquitinases regulate NPR1-dependent transcription 765 (A) WT seedlings were treated for 6h with either vehicle control (DMSO) or the 766 indicated DUB inhibitors (50 μM) in presence or absence of 0.5 mM SA before 767 analysing the expression of NPR1 target genes. Data points represent mean ± SD 768 (n=3). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 769 (C) WT seedlings were treated for 6h with vehicle (DMSO) or either the indicated DUB inhibitors (50 μM) or MG132 (100 μM) in presence or absence of 0.5 mM SA before immunoblotting against conjugated ubiquitin (FK2). Ponceau S staining indicated equal loading. (D) WT seedlings were treated as in (C) and NPR1 target gene expression analysed. 78 Data points represent mean ± SD (n=3). 79 34 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 81 82 Figure 5. UBP6 and UBP7 deubiquitinases are required for SA-induced 83 expression of NPR1 target genes 84 (A) WT and uch3-1 seedlings were treated for 6h with 0.5 mM SA followed by analysis 85 of NPR1 target gene expression. Data points represent mean ± SD (n=3). 86 (B) WT and ubp-12-2w seedlings were treated and analysed as in (A). 87 (C) WT, ubp6-1 and ubp7-1 plants were treated with 0.5 mM SA for 24h before analysis 88 of NPR1 target gene expression. Data points represent mean ± SD (n=3). 89 (D) WT and ubp6-1 ubp7-1 double mutant plants were treated and analysed as in (C). 90 See also Figure S4. 91 782 Figure 5. UBP6 and UBP7 deubiquitinases are required for SA-induced 783 expression of NPR1 target genes 784 (A) WT and uch3-1 seedlings were treated for 6h with 0.5 mM SA followed by analysis 785 of NPR1 target gene expression. Data points represent mean ± SD (n=3). 786 (B) WT and ubp-12-2w seedlings were treated and analysed as in (A). 787 (C) WT, ubp6-1 and ubp7-1 plants were treated with 0.5 mM SA for 24h before analysis 788 of NPR1 target gene expression. Data points represent mean ± SD (n=3). 789 (D) WT and ubp6-1 ubp7-1 double mutant plants were treated and analysed as in (C). 790 See also Figure S4. CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint (C) 35S::NPR1-GFP seedlings were treated for 6h with 0.5 mM SA followed by addition 803 of 100 μM MG132 for a further 18h. Polyubiquitinated NPR1-GFP protein was then 804 purified with GFP-Trap agarose and incubated for the indicated times with recombinant 805 UBP6 in presence or absence of 26S proteasomes. Remaining polyubiquitinated 806 NPR1-GFP and released ubiquitin species were detected by immunoblotting using an 807 antibody against ubiquitin (P4D1), while unmodified NPR1-GFP was detected with an 808 anti-GFP antibody. 809 (C) 35S::NPR1-GFP seedlings were treated for 6h with 0.5 mM SA followed by addition 803 of 100 μM MG132 for a further 18h. Polyubiquitinated NPR1-GFP protein was then 804 purified with GFP-Trap agarose and incubated for the indicated times with recombinant 805 UBP6 in presence or absence of 26S proteasomes. Remaining polyubiquitinated 806 NPR1-GFP and released ubiquitin species were detected by immunoblotting using an 807 antibody against ubiquitin (P4D1), while unmodified NPR1-GFP was detected with an 808 anti-GFP antibody. 809 (D) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 810 of 50 μM WP1130 or DMSO vehicle for a further 4h. Ubiquitinated proteins were pulled 811 down using GST-TUBEs. Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were 812 detected by immunoblotting with a GFP antibody. 813 (E) Seedlings were treated with SA for 24h to induce NPR1 before addition of 100 μM 814 CHX. Endogenous NPR1 protein levels were monitored by immunoblotting and 815 GAPDH levels confirmed equal loading. 816 (F) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 817 of 50 μM WP1130 or DMSO vehicle for a further 4h. NPR1-GFP binding to the as-1 818 motif of the PR1 promoter element was quantified by ChIP with npr1 seedlings serving 819 as a negative control. Data points represent mean ± SD (n=3). 820 (G) Plants of the stated genotypes were treated with 0.5 mM SA for 24h before the 821 expression of NPR1 target genes was analysed by qPCR. Data points represent mean 822 ± SD (n=3). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 823 (H) Plants were treated with or without 0.5 mM SA 24h prior to inoculation with 5x106 824 colony forming units (cfu)/ml Psm ES4326. Leaf discs were analysed for bacterial 825 growth at 3 dpi. Error bars represent 95% confidence limits, while letters denote 826 statistically significant differences between samples (Tukey Kramer ANOVA; α = 0.05, 827 n = 8). 828 See also Figure S5. 829 (C) 35S::NPR1-GFP seedlings were treated for 6h with 0.5 mM SA followed by addition 803 of 100 μM MG132 for a further 18h. Polyubiquitinated NPR1-GFP protein was then 804 purified with GFP-Trap agarose and incubated for the indicated times with recombinant 805 UBP6 in presence or absence of 26S proteasomes. Remaining polyubiquitinated 806 NPR1-GFP and released ubiquitin species were detected by immunoblotting using an 807 antibody against ubiquitin (P4D1), while unmodified NPR1-GFP was detected with an 808 anti-GFP antibody. 809 (D) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 810 of 50 μM WP1130 or DMSO vehicle for a further 4h. Ubiquitinated proteins were pulled 811 down using GST-TUBEs. Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were 812 detected by immunoblotting with a GFP antibody. 813 (E) Seedlings were treated with SA for 24h to induce NPR1 before addition of 100 μM 814 CHX. Endogenous NPR1 protein levels were monitored by immunoblotting and 815 GAPDH levels confirmed equal loading. 816 (F) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 817 of 50 μM WP1130 or DMSO vehicle for a further 4h. NPR1-GFP binding to the as-1 818 motif of the PR1 promoter element was quantified by ChIP with npr1 seedlings serving 819 as a negative control. Data points represent mean ± SD (n=3). 820 (G) Plants of the stated genotypes were treated with 0.5 mM SA for 24h before the 821 expression of NPR1 target genes was analysed by qPCR. Data points represent mean 822 ± SD (n=3). 823 (H) Plants were treated with or without 0.5 mM SA 24h prior to inoculation with 5x106 824 colony forming units (cfu)/ml Psm ES4326. Leaf discs were analysed for bacterial 825 growth at 3 dpi. Error bars represent 95% confidence limits, while letters denote 826 statistically significant differences between samples (Tukey Kramer ANOVA; α = 0.05, 827 n = 8). CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 791 (D) WT and ubp6-1 ubp7-1 double mutant plants were treated and analysed as in (C). 790 See also Figure S4. 791 35 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 92 93 Figure 6. Deubiquitination by UBP6/7 regulates transcriptional activity of NPR1 94 (A) FLAG-UBP6 was immunoprecipitated (IP) from ubp6 ubp7 plants transformed with 95 or without 35S::FLAG-UBP6. Co-immunoprecipitates were analysed by 96 immunoblotting against FLAG as well as the proteasome subunits S5a and RPN6. 97 Input protein levels are shown in the bottom panel. 98 (B) Purified recombinant His6-T7-UBP6 was preincubated with or without WP1130 and 99 26S proteasomes before labelling with HA-UbVS. Immunoblotting with HA antibodies 00 detected active, labelled UBP6 while immunoblotting with T7 antibodies detected total 01 . CC BY 4.0 International license available under a 792 793 Figure 6. Deubiquitination by UBP6/7 regulates transcriptional activity of NPR1 794 (A) FLAG-UBP6 was immunoprecipitated (IP) from ubp6 ubp7 plants transformed with 795 792 793 Figure 6. Deubiquitination by UBP6/7 regulates transcriptional activity of NPR1 794 (A) FLAG-UBP6 was immunoprecipitated (IP) from ubp6 ubp7 plants transformed with 795 or without 35S::FLAG-UBP6. Co-immunoprecipitates were analysed by 796 immunoblotting against FLAG as well as the proteasome subunits S5a and RPN6. 797 Input protein levels are shown in the bottom panel. 798 (B) Purified recombinant His6-T7-UBP6 was preincubated with or without WP1130 and 799 26S proteasomes before labelling with HA-UbVS. Immunoblotting with HA antibodies 800 detected active, labelled UBP6 while immunoblotting with T7 antibodies detected total 801 levels of UBP6. 802 p p p (B) Purified recombinant His6-T7-UBP6 was preincubated with or without WP1130 and 799 26S proteasomes before labelling with HA-UbVS. Immunoblotting with HA antibodies 800 detected active, labelled UBP6 while immunoblotting with T7 antibodies detected total 801 levels of UBP6. 802 36 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint . CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 828 (D) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 810 of 50 μM WP1130 or DMSO vehicle for a further 4h. Ubiquitinated proteins were pulled 811 down using GST-TUBEs. Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were 812 detected by immunoblotting with a GFP antibody. 813 (D) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 810 of 50 μM WP1130 or DMSO vehicle for a further 4h. Ubiquitinated proteins were pulled 811 down using GST-TUBEs. Input and ubiquitinated NPR1-GFP (NPR1-Ubn) were 812 detected by immunoblotting with a GFP antibody. 813 (E) Seedlings were treated with SA for 24h to induce NPR1 before addition of 100 μM 814 CHX. Endogenous NPR1 protein levels were monitored by immunoblotting and 815 GAPDH levels confirmed equal loading. 816 (E) Seedlings were treated with SA for 24h to induce NPR1 before addition of 100 μM 814 CHX. Endogenous NPR1 protein levels were monitored by immunoblotting and 815 GAPDH levels confirmed equal loading. 816 (F) 35S::NPR1-GFP seedlings were treated for 2h with 0.5 mM SA followed by addition 817 of 50 μM WP1130 or DMSO vehicle for a further 4h. NPR1-GFP binding to the as-1 818 motif of the PR1 promoter element was quantified by ChIP with npr1 seedlings serving 819 as a negative control. Data points represent mean ± SD (n=3). 820 (G) Plants of the stated genotypes were treated with 0.5 mM SA for 24h before the 821 expression of NPR1 target genes was analysed by qPCR. Data points represent mean 822 ± SD (n=3). 823 (G) Plants of the stated genotypes were treated with 0.5 mM SA for 24h before the 821 expression of NPR1 target genes was analysed by qPCR. Data points represent mean 822 ± SD (n=3). 823 (H) Plants were treated with or without 0.5 mM SA 24h prior to inoculation with 5x106 824 colony forming units (cfu)/ml Psm ES4326. Leaf discs were analysed for bacterial 825 growth at 3 dpi. Error bars represent 95% confidence limits, while letters denote 826 statistically significant differences between samples (Tukey Kramer ANOVA; α = 0.05, 827 n = 8). 828 37 . 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. CULLIN1-F-box (SCF)-mediated protein degradation. Proc Natl Acad Sci U S A 108, 532 14694-14699. 533 It is made The copyright holder for this preprint (which was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint 830 831 Figure 7. Working model for how dynamic ubiquitination regulates 832 transcriptional outputs of NPR1. 833 NPR1 occupancy at target gene promoters initiates low-level transcription (dashed 834 green arrow). Initial ubiquitin (grey circles) modifications mediated by CRL3 ligase 835 enhances target gene expression to maximum levels (solid green arrow), while 836 progression to long-chain polyubiquitination mediated by UBE4 promotes the 837 proteasome-mediated degradation of NPR1 and inactivates target gene expression. 838 UBP6/7 activity at the proteasome serves to limit the degradation of NPR1, thereby 839 promoting its active state. 840 830 831 Figure 7. Working model for how dynamic ubiquitination regulates 832 transcriptional outputs of NPR1. 833 Figure 7. Working model for how dynamic ubiquitination regulates 832 transcriptional outputs of NPR1. 833 NPR1 occupancy at target gene promoters initiates low-level transcription (dashed 834 NPR1 occupancy at target gene promoters initiates low-level transcription (dashed 834 green arrow). Initial ubiquitin (grey circles) modifications mediated by CRL3 ligase 835 enhances target gene expression to maximum levels (solid green arrow), while 836 progression to long-chain polyubiquitination mediated by UBE4 promotes the 837 proteasome-mediated degradation of NPR1 and inactivates target gene expression. 838 UBP6/7 activity at the proteasome serves to limit the degradation of NPR1, thereby 839 promoting its active state. 840 38 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint MATERIALS AND METHODS 841 Plant maintenance, transformation, chemical treatments and pathogen infection 842 All Arabidopsis plants used in this study were in the Columbia genetic 843 background, with WT referring to wild-type Col-0 throughout. Plants were grown under 844 long day conditions (16 hour photoperiod) on soil in controlled-environment growth 845 chambers at 65% humidity and 22°C unless otherwise stated. Seeds were stratified at 846 4-8°C in darkness for 2 days before moving to growth chambers. Plants were grown 847 in a soil mix composed of peat moss, vermiculite and sand at a ratio of 4:1:1 848 respectively, and illumination was provided by fluorescent tube lighting at an intensity 849 of 70-100 μmol m-2sec-1. For experiments on seedlings, seeds were sterilized by 850 washing in 100% ethanol for 2 mins before incubating in 50% household bleach for 20 851 mins. After removal of bleach, seeds were washed at least 3 times with sterile H2O 852 before use. Sterilized seeds were spotted on Murashige and Skoog agar media and 853 stratified before placing under lighting conditions as above. All T-DNA insertion 854 mutants used were genotyped by PCR using standard conditions with gene specific 855 primers in combination with left-border primers specific to each mutant collection 856 (Table S2). 857 The coding sequences of the UBE4 (At5g15400) and UBP6 (At1g51710) genes 858 were amplified using Phusion polymerase (NEB) from WT Arabidopsis cDNA with the 859 addition of CACC at the 5’ end required for TOPO cloning. The PCR products were 860 gel-purified and cloned in to the pENTR/D-TOPO vector (Invitrogen) according to 861 manufacturers’ instructions. The active site residue of UBP6 was then mutagenised to 862 serine (C113S) using QuikChange Site-Directed Mutagenesis Kit according to 863 manufacturers’ instructions. Genes were then recombined into pEarleyGate 104 and 864 202 plasmids by LR reaction (Invitrogen) as described previously (Earley et al., 2006) 865 39 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. Plant maintenance, transformation, chemical treatments and pathogen infection 842 ; https://doi.org/10.1101/582296 doi: bioRxiv preprint to generate 35S::YFP-UBE4, 35S::FLAG-UBP6 and 35S::FLAG-UBP6(C113S) 866 constructs. These plasmids were used to transform protoplasts or to transform 867 Agrobacterium tumifaciens strain GV3101 (pMP90) as described previously 868 (Kneeshaw et al., 2014). After selection of positive Agrobacterium clones carrying the 869 transgenes, approximately 6-week old flowering ubp6/7 plants were transformed as 870 previously described (Clough and Bent, 1998). Selection of transformants was 871 performed by spraying 10-day old seedlings with 120 μg/l BASTA at least three times. 872 Further confirmation of transformation was performed by immunoblotting. Segregation 873 of BASTA resistance was analysed in the T2 generation to confirm plants had single 874 transgene insertions. 875 For SA treatments, adult plants were sprayed with, while seedlings were 876 immersed in 0.5 mM SA or H2O. CHX, MG132 and DUB inhibitors were all used to 877 treat seedlings by immersion at the concentrations stated in respective figure legends. 878 Vehicle controls consisted of DMSO at the appropriate concentration for each chemical 879 used. 880 Psm ES4326 was grown in LB media supplemented with 10 mM MgCl2 and 50 881 μg/ml streptomycin. Cultures were grown overnight then centrifuged at 4,000 rpm for 882 10 mins. Cells were resuspended in 10 mM MgCl2 and absorbance was measured at 883 600nm before necessary dilutions were made to adjust concentrations to those 884 indicated in figure legends. Plants were infected by pressure infiltration with a syringe 885 through the abaxial leaf surface. For measurement of bacterial growth, a single leaf 886 disc per plant was cut from infected leaves at the stated dpi and ground in 10 mM 887 MgCl2. Serial dilutions were plated on LB supplemented with 10 mM MgCl2 and 50 888 μg/ml streptomycin and colonies were counted after 2 days incubation at 30°C. 889 890 For SA treatments, adult plants were sprayed with, while seedlings were 876 immersed in 0.5 mM SA or H2O. CHX, MG132 and DUB inhibitors were all used to 877 treat seedlings by immersion at the concentrations stated in respective figure legends. 878 Vehicle controls consisted of DMSO at the appropriate concentration for each chemical 879 used. 880 Psm ES4326 was grown in LB media supplemented with 10 mM MgCl2 and 50 881 μg/ml streptomycin. Cultures were grown overnight then centrifuged at 4,000 rpm for 882 10 mins. Plant maintenance, transformation, chemical treatments and pathogen infection 842 Cells were resuspended in 10 mM MgCl2 and absorbance was measured at 883 600nm before necessary dilutions were made to adjust concentrations to those 884 indicated in figure legends. Plants were infected by pressure infiltration with a syringe 885 through the abaxial leaf surface. For measurement of bacterial growth, a single leaf 886 disc per plant was cut from infected leaves at the stated dpi and ground in 10 mM 887 MgCl2. Serial dilutions were plated on LB supplemented with 10 mM MgCl2 and 50 888 μg/ml streptomycin and colonies were counted after 2 days incubation at 30°C. 889 890 40 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint RNA extraction, cDNA synthesis and qPCR 891 It is made The copyright holder for this preprint (which was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint instructions. qPCR was carried out to confirm appropriate induction of SA-responsive 916 marker genes. RNA was then quantified and submitted to GATC Biotech/Eurofins 917 (Constance, Germany) for RNA sequencing. The RNA-Seq reads were aligned to the 918 Arabidopsis thaliana TAIR10 genome using Bowtie. TopHat identified potential exon- 919 exon splice junctions of the initial alignment. Strand NGS software in RNA-Seq 920 workflow was used to quantify transcripts. Raw counts were normalised using DESeq 921 with baseline transformation to the median of all samples. Data were then expressed 922 as normalised signal values (i.e. log2[RPKM] where RPKM is read count per kilobase 923 of exon model per million reads) for all statistical tests and plotting. Genes were then 924 filtered by expression (20%-100%) and differentially expressed genes determined by 925 Benjamini Hochberg FDR with 2-way ANOVA (p = 0.05). Additionally, we required SA- 926 induced genes to meet a ≥ 2-fold change cut-off, whereas NPR1-dependent genes 927 required ≥ 1.5-fold change in Col-0 or ube4 plants when compared to npr1 mutants. 928 929 RNA extraction, cDNA synthesis and qPCR 891 Leaf tissue or whole seedlings were frozen and ground to a fine powder in liquid 892 nitrogen. Samples were homogenised in RNA extraction buffer (100 mM LiCl, 100 mM 893 Tris pH 8, 10 mM EDTA, 1% SDS) before addition of an equal volume of 894 phenol/chloroform/isoamylalcohol (25:24:1). The homogenate was vortexed and 895 centrifuged at 13,000 rpm for 5 min. The aqueous phase was transferred to an equal 896 volume of 24:1 chloroform/isoamylalcohol, vortexed and then centrifuged at 13,000 897 rpm for 5 min. This step was repeated once before the aqueous layer was added to a 898 1/3 volume of 8 M LiCl and incubated overnight at 4°C. The extract was then 899 centrifuged at 13,000 rpm for 5 min at 4°C. The resulting pellet was washed with ice 900 cold 70% ethanol then rehydrated and dissolved in 400 μl H2O for 30 min on ice. 901 Finally, 40 μl of NaAc (pH 5.3) and 1 ml of ice cold 96% ethanol was added before 902 incubating for 1 h at -20°C. The precipitate was then centrifuged at 13,000 rpm for 5 903 min at 4°C, the pellet was washed with ice cold 70% ethanol and resuspended in 50 904 μl of H2O. Before cDNA synthesis, RNA samples were quantified using a NanoDrop 905 spectrophotometer (Thermo Scientific) and appropriate dilutions were made to 906 ensure all samples contained equal amounts of RNA. Reverse transcription was then 907 performed using SuperScript II reverse transcriptase (Invitrogen) according to the 908 manufacturers’ instructions. qPCR was carried out on 20-fold diluted cDNA using 909 Power SYBR Green (Life Technologies) and gene-specific primers (Table S2) on a 910 StepOne Plus Real Time PCR machine (Life Technologies). 911 912 RNA was extracted from biological duplicate samples as described above and further 914 purified using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s 915 41 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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. Chromatin immunoprecipitation 930 Chromatin immunoprecipitation was performed on leaf tissue of 4 week-old soil- 931 grown adult plants essentially as described (Yamaguchi et al., 2014) but with minor 932 modifications. 500 mg tissue was crosslinked with 1% formaldehyde by vacuum 933 infiltration for 30 mins at room temperature. Glycine was added to a final concentration 934 of 100 mM to quench crosslinking and vacuum infiltrated for a further 10 mins. 935 Crosslinked tissue was washed twice with ice-cold PBS before all liquid was removed 936 and tissue was frozen in liquid nitrogen. Nuclei were isolated and lysed as described 937 (Yamaguchi et al., 2014) while sonication was performed using a BioRuptor Plus 938 (Diagenode). Sonication consisted of 15 cyles of 30s ON, 30s OFF at high power. 939 NPR1-GFP was immunoprecipitated using ChIP grade anti-GFP (Abcam) before 940 42 42 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint capture of immune complexes with Protein A agarose (Millipore). Crosslink reversal 941 and protein removal was performed as described previously (Nelson et al., 2006), by 942 boiling in the presence of Chelex 100 resin (BioRad) before incubation at 55°C with 943 Proteinase K. Finally, DNA was cleaned up using PCR purification columns (Qiagen) 944 and analysed by qPCR using primers listed in Table S2. 945 946 Protein analysis 947 For protein degradation assays and analysis of NPR1 levels, seedlings were 948 frozen and ground to a fine powder in liquid nitrogen before homogenising in protein 949 extraction buffer (PEB) (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.1% 950 Triton X-100, 0.2% Nonidet P-40, and inhibitors: 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 951 mM PMSF) (Spoel et al., 2009). For analyses of NPR1 phosphorylation PEB buffer 952 was supplemented with 1X phosphatase inhibitor cocktail 3 (Sigma). Chromatin immunoprecipitation 930 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint For analysis of long chain polyubiquitination, seedlings were ground to a fine 966 powder in liquid nitrogen and homogenised in 1X PBS, supplemented with 1% Triton 967 X-100, 10 mM NEM, 80 μM MG115, 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 mM PMSF, 968 1X phosphatase inhibitor cocktail 3 (Sigma). Homogenates were centrifuged at 13,000 969 rpm at 4°C for 20 mins to remove cellular debris and filtered through 0.22 µm filters 970 before overnight incubation with 300 μg His6-V5-S5aUIM protein immobilised on 971 agarose. Agarose beads were washed 5 times with extraction buffer before elution at 972 80°C for 15 mins in 1X SDS-PAGE sample buffer including 50 mM DTT. NPR1-GFP 973 was detected by immunoblotting with anti-GFP (Roche). 974 966 For proteasome co-immunoprecipitation with FLAG-UBP6, seedlings were 975 frozen and ground to a fine powder in liquid nitrogen before homogenising in 976 proteasome extraction buffer (50 mM Tris-HCl (pH 7.4), 25 mM NaCl, 2 mM MgCl2, 1 977 mM EDTA, 10 mM ATP, 5% glycerol, and inhibitors: 50 μg/ml TPCK, 50 μg/ml TLCK, 978 0.6 mM PMSF). Extracts were centrifuged at 13,000 rpm at 4°C for 20 mins to remove 979 cellular debris and filtered through 0.22 µm filters. Anti-FLAG M2 affinity gel was 980 washed with the above buffer before incubating with samples overnight with rotation 981 at 4°C. The resin was washed 3 times with the same buffer before immunoprecipitated 982 proteins were eluted by boiling in 1X SDS-PAGE sample buffer including 50 mM DTT. 983 FLAG-UBP6 was detected using rabbit anti-FLAG antibodies while co- 984 immunoprecipitating proteins were detected with indicated antibodies. 985 986 Chromatin immunoprecipitation 930 Samples were 953 centrifuged at 13,000 rpm for 15 min at 4°C to clarify extracts, and the resulting 954 supernatant was used for SDS-PAGE and immunoblot analysis. All antibodies used 955 are listed in the Table S3. 956 For analysis of polyubiquitination with TUBEs, seedlings were ground to a fine 957 powder in liquid nitrogen and homogenized in 1x PBS supplemented with 1% Triton X- 958 100, 10 mM NEM, 40 µM MG132, 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 mM PMSF, 959 capture of immune complexes with Protein A agarose (Millipore). Crosslink reversal 941 and protein removal was performed as described previously (Nelson et al., 2006), by 942 boiling in the presence of Chelex 100 resin (BioRad) before incubation at 55°C with 943 Proteinase K. Finally, DNA was cleaned up using PCR purification columns (Qiagen) 944 and analysed by qPCR using primers listed in Table S2. 945 For protein degradation assays and analysis of NPR1 levels, seedlings were 948 frozen and ground to a fine powder in liquid nitrogen before homogenising in protein 949 extraction buffer (PEB) (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.1% 950 Triton X-100, 0.2% Nonidet P-40, and inhibitors: 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 951 mM PMSF) (Spoel et al., 2009). For analyses of NPR1 phosphorylation PEB buffer 952 was supplemented with 1X phosphatase inhibitor cocktail 3 (Sigma). Samples were 953 centrifuged at 13,000 rpm for 15 min at 4°C to clarify extracts, and the resulting 954 supernatant was used for SDS-PAGE and immunoblot analysis. All antibodies used 955 are listed in the Table S3. 956 For analysis of polyubiquitination with TUBEs, seedlings were ground to a fine 957 powder in liquid nitrogen and homogenized in 1x PBS supplemented with 1% Triton X- 958 100, 10 mM NEM, 40 µM MG132, 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 mM PMSF, 959 and 0.2 mg/ml GST-TUBE (Hjerpe et al., 2009). Homogenates were centrifuged at 960 13,000 rpm at 4°C for 20 mins to remove cellular debris and filtered through 0.22 µm 961 filters before overnight incubation with Protino Glutathione Agarose 4B (Machery 962 Nagel), at 4°C with rotation. The agarose beads were washed 5 times with 1X PBS + 963 1% Triton X-100 before elution by boiling in 1X SDS-PAGE sample buffer including 50 964 mM DTT. NPR1-GFP was detected by immunoblotting with anti-GFP (Roche). 965 43 . Recombinant protein and NPR1 antibody production 987 N-terminal GST-tagged TUBE was generated by cloning the coding sequence 988 of hHR23A into pGEX-6P-1 using EcoRI and SalI restriction sites. Primers used are 989 listed in Table S2. GST-TUBE expression was induced in BL21(DE3) E. coli cells with 990 44 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint the addition of 1 mM IPTG and cultures were incubated for a further 4 hrs at 28°C 991 before collecting by centrifugation. Cells were then lysed in 1X PBS supplemented with 992 1 mg/ml lysozyme, 25 U/ml Benzonase nuclease, 0.1% Triton-X-100 and a protease 993 inhibitor cocktail before GST-TUBE was purified using Protino Glutathione Agarose 4B 994 according to the manufacturers’ instructions. Purified GST-TUBE was dialysed against 995 1X PBS and stored with the addition of 10% glycerol at -80°C until use. 996 Recombinant S5aUIM protein was generated by synthesising residues 196 – 997 309 from human S5a with codon optimisation for E. coli into pET151/D-TOPO. The 998 resulting His6-V5-S5aUIM protein was expressed in BL21(DE3) E. coli cells by addition 999 of 1 mM IPTG and incubation for 24 hrs at 28°C before collecting by centrifugation. 1000 Cells were then lysed in lysis buffer (50 mM KHPO4 pH 8, 100 mM NaCl, 10 mM 1001 Imidazole, 1X BugBuster (Merck), 25 U/ml Benzonase nuclease, 50 μg/ml TPCK, 50 1002 μg/ml TLCK and 0.5 mM PMSF). His6-UBP6 was then purified using HisPur cobalt 1003 resin (Thermo Fisher) according to manufacturers’ instructions. Purified His6-V5- 1004 S5aUIM was dialysed against 1X PBS and covalently coupled to NHS-activated 1005 agarose to a final concentration of approximately 10 μg/μl following the manufacturer’s 1006 instructions (Thermo Fisher). 1007 the addition of 1 mM IPTG and cultures were incubated for a further 4 hrs at 28°C 991 before collecting by centrifugation. Recombinant protein and NPR1 antibody production 987 1022 1023 HA-UbVS labelling and in vitro deubiquitination assays 1024 For HA-UbVS labelling, 10 μl reactions were prepared in 50 1025 7.4, 5 mM MgCl2, 1 mM DTT and 1 mM ATP. Before labelling, 350 n 1026 was pre-incubated with 50 μM WP1130 or DMSO control for 10 min 1027 of 10 nM Ub-VS treated 26S proteasomes (Ubiquigent). Reactions w 1028 a further 20 mins before addition of 700 nM HA-UbVS and further 1029 mins. All steps were carried out at room temperature. Labelling was 1030 the addition of SDS-PAGE sample buffer including 50 mM DTT. Sam 1031 at 70°C for 10 mins before SDS-PAGE and immunoblot analyses. 1032 All in vitro deubiquitination assays were performed in DUB bu 1033 HisPur cobalt resin (Thermo Fisher) according to manufacturers’ instructions. Purified 1016 His6-UBP6 was dialysed against 50 mM Tris-HCl pH 7.4, 5M NaCl and stored with the 1017 addition of 10% glycerol at -80°C until use. 1018 The anti-NPR1 polyclonal antibody was generated by immunising rabbits with 1019 a synthetic peptide based on a region of the NPR1 protein with the sequence N’- 1020 SALAAAKKEKDSNNTAAVKL-Cys. Rabbits were subsequently bled and antibodies 1021 were enriched by affinity purification (Proteintech, USA). 1022 Recombinant protein and NPR1 antibody production 987 Cells were then lysed in 1X PBS supplemented with 992 1 mg/ml lysozyme, 25 U/ml Benzonase nuclease, 0.1% Triton-X-100 and a protease 993 inhibitor cocktail before GST-TUBE was purified using Protino Glutathione Agarose 4B 994 according to the manufacturers’ instructions. Purified GST-TUBE was dialysed against 995 1X PBS and stored with the addition of 10% glycerol at -80°C until use. 996 Recombinant S5aUIM protein was generated by synthesising residues 196 – 997 309 from human S5a with codon optimisation for E. coli into pET151/D-TOPO. The 998 resulting His6-V5-S5aUIM protein was expressed in BL21(DE3) E. coli cells by addition 999 of 1 mM IPTG and incubation for 24 hrs at 28°C before collecting by centrifugation. 1000 Cells were then lysed in lysis buffer (50 mM KHPO4 pH 8, 100 mM NaCl, 10 mM 1001 Imidazole, 1X BugBuster (Merck), 25 U/ml Benzonase nuclease, 50 μg/ml TPCK, 50 1002 μg/ml TLCK and 0.5 mM PMSF). His6-UBP6 was then purified using HisPur cobalt 1003 resin (Thermo Fisher) according to manufacturers’ instructions. Purified His6-V5- 1004 S5aUIM was dialysed against 1X PBS and covalently coupled to NHS-activated 1005 agarose to a final concentration of approximately 10 μg/μl following the manufacturer’s 1006 instructions (Thermo Fisher). 1007 N-terminal His6-T7-tagged UBP6 was generated by cloning the coding 1008 sequence of Arabidopsis UBP6 in to the expression vector pET28a using EcoRI and 1009 SalI restriction sites. Primers used are listed in Table S2. Expression was induced in 1010 BL21(DE3) E. coli cells with the addition of 1 mM IPTG and cultures were incubated 1011 for a further 3 hrs at 28°C before collecting by centrifugation. Cells were then lysed in 1012 lysis buffer (50 mM KHPO4 pH 8, 300 mM NaCl, 10 mM Imidazole, 1 mg/ml lysozyme, 1013 25 U/ml Benzonase nuclease, 0.1% Triton-X- 100, 10 mM β-mercaptoethanol, 50 1014 μg/ml TPCK, 50 μg/ml TLCK and 0.5 mM PMSF). His6-UBP6 was then purified using 1015 45 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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. Recombinant protein and NPR1 antibody production 987 It is made The copyright holder for this preprint (which was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint HisPur cobalt resin (Thermo Fisher) according to manufacturers’ instructions. Purifie 1016 His6-UBP6 was dialysed against 50 mM Tris-HCl pH 7.4, 5M NaCl and stored with th 1017 addition of 10% glycerol at -80°C until use. 1018 The anti-NPR1 polyclonal antibody was generated by immunising rabbits w 1019 a synthetic peptide based on a region of the NPR1 protein with the sequence N 1020 SALAAAKKEKDSNNTAAVKL-Cys. Rabbits were subsequently bled and antibodie 1021 were enriched by affinity purification (Proteintech, USA). 1022 1023 HA-UbVS labelling and in vitro deubiquitination assays 1024 For HA-UbVS labelling, 10 μl reactions were prepared in 50 mM Tris-Hcl p 1025 7.4, 5 mM MgCl2, 1 mM DTT and 1 mM ATP. Before labelling, 350 nM His6-T7-UBP 1026 was pre-incubated with 50 μM WP1130 or DMSO control for 10 mins before additio 1027 of 10 nM Ub-VS treated 26S proteasomes (Ubiquigent). Reactions were incubated f 1028 a further 20 mins before addition of 700 nM HA-UbVS and further incubation for 3 1029 mins. All steps were carried out at room temperature. Labelling was terminated w 1030 the addition of SDS-PAGE sample buffer including 50 mM DTT. Samples were heate 1031 at 70°C for 10 mins before SDS-PAGE and immunoblot analyses. 1032 All in vitro deubiquitination assays were performed in DUB buffer (50 mM Tr 1033 HCl pH 7.4, 5 mM MgCl2, 1 mM DTT, 5 mM ATP). Where indicated, 1.25 nM Ub-V 1034 treated 26S proteasomes and 20 nM UBP6 were added. Di-ubiquitin and polyubiquit 1035 chain substrates were included at 400 nM. Reactions were incubated at 30°C for th 1036 times indicated in figure legends before terminating with addition of SDS-PAGE samp 1037 buffer including 50 mM DTT. Samples were heated at 70°C for 10 mins before SD 1038 PAGE and immunoblot analyses. 1039 HisPur cobalt resin (Thermo Fisher) according to manufacturers’ inst 1016 His6-UBP6 was dialysed against 50 mM Tris-HCl pH 7.4, 5M NaCl an 1017 addition of 10% glycerol at -80°C until use. 1018 The anti-NPR1 polyclonal antibody was generated by immun 1019 a synthetic peptide based on a region of the NPR1 protein with th 1020 SALAAAKKEKDSNNTAAVKL-Cys. Rabbits were subsequently bled 1021 were enriched by affinity purification (Proteintech, USA). HA-UbVS labelling and in vitro deubiquitination assays 1024 For HA-UbVS labelling, 10 μl reactions were prepared in 50 mM Tris-Hcl pH 1025 7.4, 5 mM MgCl2, 1 mM DTT and 1 mM ATP. Before labelling, 350 nM His6-T7-UBP6 1026 was pre-incubated with 50 μM WP1130 or DMSO control for 10 mins before addition 1027 of 10 nM Ub-VS treated 26S proteasomes (Ubiquigent). Reactions were incubated for 1028 a further 20 mins before addition of 700 nM HA-UbVS and further incubation for 30 1029 mins. All steps were carried out at room temperature. Labelling was terminated with 1030 the addition of SDS-PAGE sample buffer including 50 mM DTT. Samples were heated 1031 at 70°C for 10 mins before SDS-PAGE and immunoblot analyses. 1032 All in vitro deubiquitination assays were performed in DUB buffer (50 mM Tris- 1033 HCl pH 7.4, 5 mM MgCl2, 1 mM DTT, 5 mM ATP). Where indicated, 1.25 nM Ub-VS 1034 treated 26S proteasomes and 20 nM UBP6 were added. Di-ubiquitin and polyubiquitin 1035 chain substrates were included at 400 nM. Reactions were incubated at 30°C for the 1036 times indicated in figure legends before terminating with addition of SDS-PAGE sample 1037 buffer including 50 mM DTT. Samples were heated at 70°C for 10 mins before SDS- 1038 PAGE and immunoblot analyses. 1039 46 . 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 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 was this version posted March 20, 2019. ; https://doi.org/10.1101/582296 doi: bioRxiv preprint For in vitro deubiquitination of NPR1-GFP isolated from plants, seedlings were 1040 treated with SA and MG132 as described in figure legends. Seedlings were frozen and 1041 ground to a fine powder in liquid nitrogen before homogenising in protein extraction 1042 buffer (PEB) (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.1% Triton X- 1043 100, 0.2% Nonidet P-40, and inhibitors: 50 μg/ml TPCK, 50 μg/ml TLCK, 0.6 mM 1044 PMSF). HA-UbVS labelling and in vitro deubiquitination assays 1024 Extracts were centrifuged at 13,000 rpm at 4°C for 20 mins to remove cellular 1045 debris and filtered through 0.22 µm filters. GFP-Trap A agarose (Chromotek) was 1046 incubated with extracts for 2h with rotation at 4°C before washing 10 times with PEB 1047 (without inhibitors) then twice with DUB buffer. Supernatant was completely removed 1048 before DUB reactions were set up as described above but with NPR1-GFP immobilised 1049 on GFP-Trap A as the substrate. Proteins were eluted by boiling in 1X SDS-PAGE 1050 sample buffer including 50 mM DTT, before analysis by immunoblotting. 1051 1052 1040 Quantification and statistical analyses 1053 No statistical methods were used to predetermine sample sizes, nor were any methods 1054 of randomization. All experiments were repeated a minimum of two times with similar 1055 results. In all figure legends, the statistical tests applied are stated while n refers to 1056 sample size. 1057 1058 47
https://openalex.org/W2881337585
https://researchonline.lshtm.ac.uk/id/eprint/4648457/1/Haemolysis%20and%20haem%20oxygenase-1%20induction%20during%20persistent%20%E2%80%9Casymptomatic%E2%80%9D%20malaria%20infection%20in%20Burkinab%C3%A9%20children_GOLD%20VoR.pdf
English
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Haemolysis and haem oxygenase-1 induction during persistent “asymptomatic” malaria infection in Burkinabé children
Malaria journal
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cc-by
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© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/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://creat​iveco​mmons​.org/ publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Mooney et al. Malar J (2018) 17:253 https://doi.org/10.1186/s12936-018-2402-6 Mooney et al. Malar J (2018) 17:253 https://doi.org/10.1186/s12936-018-2402-6 Malaria Journal RESEARCH Haemolysis and haem oxygenase‑1 induction during persistent “asymptomatic” malaria infection in Burkinabé children Jason P. Mooney1,2*, Aissata Barry3, Bronner P. Gonçalves1, Alfred B. Tiono3, Shehu S. Awandu5, Lynn Grignard1, Chris J. Drakeley1, Christian Bottomley4, Teun Bousema5 and Eleanor M. Riley1,2 Open Access Open Access Abstract Background:  The haemolysis associated with clinical episodes of malaria results in the liberation of haem, which activates the enzyme haem oxygenase-1 (HO-1). HO-1 has been shown to reduce neutrophil function and increase susceptibility to invasive bacterial disease. However, the majority of community-associated malaria infections are subclinical, often termed “asymptomatic” and the consequences of low-grade haemolysis during subclinical malaria infection are unknown. Study design and results:  As part of an ongoing study of subclinical malaria in Burkina Faso, 23 children with sub- clinical Plasmodium falciparum infections (determined by qPCR) were compared with 21 village-matched uninfected control children. Infected children showed evidence of persistent haemolysis over 35 days, with raised plasma haem and HO-1 concentrations. Concentrations of IL-10, which can also directly activate HO-1, were also higher in infected children compared to uninfected children. Regression analysis revealed that HO-1 was associated with haemolysis, but not with parasite density, anaemia or IL-10 concentration. Conclusions:  This study reveals that subclinical P. falciparum malaria infection is associated with sustained hae- molysis and the induction of HO-1. Given the association between HO-1, neutrophil dysfunction and increased risk of Salmonella bacteraemia, prolonged HO-1 induction may explain epidemiological associations and geographic overlap between malaria and invasive bacterial disease. Further studies are needed to understand the consequences of persistent subclinical malaria infection, low-grade haemolysis and raised HO-1 on immune cell function and risk of comorbidities. Keywords:  Subclinical malaria, Anaemia, Haemolysis, IL-10, HO-1, Burkina Faso Haemolysis and haem oxygenase‑1 induction during persistent “asymptomatic” malaria infection in Burkinabé children Jason P. Mooney1,2*, Aissata Barry3, Bronner P. Gonçalves1, Alfred B. Tiono3, Shehu S. Awandu5, Lynn Grignard1, Chris J. Drakeley1, Christian Bottomley4, Teun Bousema5 and Eleanor M. Riley1,2 Ethics and sample collection f d Informed consent was provided by the parent or guard- ian of each child. The study was approved by the eth- ics committees of the London School of Hygiene and Tropical Medicine (reference number 9008) and the Ministry of Health in Burkina Faso (reference number 2015-3-033). Venous blood was collected into RNApro- tect, heparin and EDTA-containing vacutainers. Whole blood samples were collected for parasitology from the EDTA tube. The blood from the heparin tube was cen- trifuged, and the plasma layer aspirated, aliquoted and stored at − 80  °C until use. Unfortunately, no leuco- cytes were collected for functional analysis. In this preliminary study, the hypothesis was that subclinical malaria infection causes persistent hae- molysis and low grade inflammation leading to raised HO-1 and inflammatory and/or regulatory cytokines. Plasma concentrations of markers of haemolysis and inflammation were compared among 23 children from Burkina Faso with subclinical P. falciparum infections and 21 village-matched, uninfected, control children. Subclinical P. falciparum infection was associated with persistent haemolysis with elevated concentrations of IL-10 and HO-1. These findings suggest that further exploration of haemolysis, immune function and sus- ceptibility to bacterial coinfection in ‘asymptomati- cally’ infected children is warranted. Plasmodium falciparum PCR A MagNAPure LC automatic extractor (Roche Applied Science) was used to extract total nucleic acids from 100 µL venous blood samples collected in RNAprotect. Parasite density was quantified using 18  s qPCR [28] and serially diluted ring-stage NF54 parasites as the positive control [29]. Methods Study populationh immune individuals harbour frequent, persistent or recurrent infections throughout their lives [7–11]. These subclinical infections have been associated with persistent low-grade haemolysis, and fluctuations in parasite density may result in intermittent, higher density parasitaemia and further haemolysis [12, 13]. Over time, extensive destruction of both parasitized and non-parasitized red blood cells [14, 15] can lead to moderate and even severe anaemia [16]. Very low parasite densities can also lead to diagnostic confusion given the numerous comorbidities that may occur in malaria endemic regions [17]. immune individuals harbour frequent, persistent or recurrent infections throughout their lives [7–11]. These subclinical infections have been associated with persistent low-grade haemolysis, and fluctuations in parasite density may result in intermittent, higher density parasitaemia and further haemolysis [12, 13]. Over time, extensive destruction of both parasitized and non-parasitized red blood cells [14, 15] can lead to moderate and even severe anaemia [16]. Very low parasite densities can also lead to diagnostic confusion given the numerous comorbidities that may occur in malaria endemic regions [17]. Study populationh The study was conducted in Balonghin in southwest Burkina Faso, a region of intense and highly seasonal malaria transmission occurring between June and October each year [26]. Two groups of children aged 5–10  years were surveyed. The first group was sur- veyed at the end of the dry season (June–July 2015); these children were included in the current analyses if they were free of infection by microscopy (reading 100 microscopic fields) and by 18  s qPCR [27]. The second group was surveyed on a monthly basis during the peak malaria season (September–December 2016). Children from this second cohort were included in the current analyses if they had chronic subclinical malaria infections (defined as two consecutive positive qPCRs 1 month apart in the absence of measured or reported fever) and samples were taken on the day this condition was met (d0, moment at which PCR + infections were present for at least 1  month) and 35  days later. After this last sample was collected, children received a full curative course of artemether–lumefantrine to clear their infections. Associations between bacteraemia (especially due to non-Typhoidal Salmonella, NTS), malaria infection and anaemia have been noted since 1929 [18, 19], with the first large case series published from The Gambia in 1987: seventy percent of NTS bacteraemia patients were anaemic and carried malaria parasites, typically at very low densities [20]. Recently, the molecular and cellular basis for malaria and NTS coinfection has been elucidated. Experiments in mice have shown that the immunoregulatory cytokine interleukin (IL)-10 impairs control of Salmonella through reduced neu- trophil migration into infected tissues [21–23]. Fur- ther, malaria-induced haemolysis results in liberation of haem, a highly toxic pro-oxidant that is degraded by haem oxygenase-1 (HO-1). In turn, HO-1 impairs the function of circulating neutrophils in mice [24]; this impaired neutrophil function leads to increased susceptibility to invasive bacterial disease [21, 24]. Importantly, raised IL-10, HO-1 and impaired neutro- phil respiratory burst have also been observed in chil- dren recovering from an acute symptomatic malaria infection [25]. However, it is not clear to what extent these defects are also induced by low density, subclini- cal malaria infections and/or may underlie the high incidence of invasive bacterial infections observed in malaria endemic areas. Background blood of these individuals either microscopically or by highly sensitive PCR [1–3]. Asymptomatic infections may perpetuate malaria transmissions and, as individu- als rarely seek treatment, can act as a reservoir of ‘cryptic’ transmission, undermining efforts at malaria elimina- tion [4, 5]. Moreover, there is accumulating evidence that these infections may be harmful to the infected individ- ual; being associated with, for example, reduced school attendance and cognitive ability [6], strengthening the argument that they should be referred to as subclinical rather than asymptomatic and should be treated [3]. In malaria endemic areas, the vast majority of malaria infections that are detected in community surveys are ‘asymptomatic’, that is they do not present with fever or other obvious clinical signs that prompt treatment-seek- ing behaviour. Individuals carrying these infections are often referred to as being ‘clinically immune’. However, Plasmodium falciparum parasites, sometimes present at very low densities, can be detected in the peripheral *Correspondence: jason.mooney@roslin.ed.ac.uk 2 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK Full list of author information is available at the end of the article Acquired immunity to malaria develops after repeated exposure but is non-sterilizing; clinically Mooney et al. Malar J (2018) 17:253 Page 2 of 11 Plasma protein quantification Enzyme-linked immunosorbent assays (ELISA) were conducted according to the manufacturers’ instruc- tions to measure plasma concentrations of haptoglobin (HPT, GWB-8DA44B, Genway Biotech), haemopexin (HPX, GWB-4B6D1A, Genway Biotech), haem oxyge- nase-1 (HO-1, ADI-EKS-800, Enzo Life Sciences), trans- ferrin (Tf, ab108911, abcam), and ferritin (ab108837, abcam). Colorimetric determination of haem in plasma samples was conducted according to the manufactur- er’s instructions (DIHM-250, Bioassay Systems). Sam- ples were diluted prior to testing as follows: 1:50,000 (HPT); 1:1 (haem), 1:40,000 (HPX), 1:10 (Ferritin), 1:6.6 (HO-1), and 1:200 (Tf). Plasma cytokine concentra- tions were determined by magnetic bead multiplex assay (EPX01A-10228-901 (IFN-γ), EPX01A-10215-901 (IL- 10), EPX01A-12001-901 (G-CSF), EPX01A-10213-901 (IL-6), EPX01A-10223-901 (TNFα), EPX01A-10224-901 (IL-1β), EPX01A-10225-901 (IL-4), EPX01A-10204-901 (IL-8), ProcartaPlex Multiplex Immunoassay, Invitro- gen, USA) following the manufacturer’s instructions, and analysed on a Luminex 100 (LuminexCorp, Austin, Children with subclinical Plasmodium falciparum infections have persistent haemolysis HbA(C) (5′CTT​AAA​CTC​TAC​TTA​CTT​CTA​ATT​CAT​ GGT​GCA​TCT​GAC​TCC​TG3′, bead set MTAG-A056), HbA(C) (5′CTT​AAA​CTC​TAC​TTA​CTT​CTA​ATT​CAT​ GGT​GCA​TCT​GAC​TCC​TG3′, bead set MTAG-A056), At enrollment, the parasite densities of the 23 P. falcipa- rum qPCR positive children ranged from 1 to 18967 par- asites/µL (Table 1). Twenty-two of the children (95.6%) were still qPCR positive 35 days later and there was no consistent or statistically significant change in parasite density over that 5 week period (Fig. 1a, Table 1). Twenty- one children who were negative by microscopy and qPCR at enrollment were designated uninfected. Mean haemo- globin concentrations did not differ between uninfected and infected children either at enrollment or at follow up, although there was a trend for mean Hb to decline over the follow up period in infected children (Fig. 1b). None of the children were severely anaemic (defined as Hb < 8 g/dL) and the proportion of children with mild or moderate anaemia did not differ significantly between infected (50%) and uninfected (45%) children (Fig. 1c). Nevertheless, there was clear evidence of haemolysis among the infected children but not among the unin- fected children: haptoglobin (HPT) concentrations were significantly lower (Fig. 1d) and haem, haemopexin (HPX), and haem oxygenase-1 (HO-1) concentrations were significantly higher (Fig. 1e–g) among infected chil- dren. Haemolysis, as defined by raised plasma haem and HPT concentrations, was persistent between days 1 and 35 among infected children. HbC (5′AAC​TTT​CTC​TCT​CTA​TTC​TTA​TTT​CAT​ GGT​GCA​TCT​GAC​TCC​TA3′, bead set MTAG-A043), HbC (5′AAC​TTT​CTC​TCT​CTA​TTC​TTA​TTT​CAT​ GGT​GCA​TCT​GAC​TCC​TA3′, bead set MTAG-A043), GGT​GCA​TCT​GAC​TCC​TA3 , bead set MTAG A043), HbA(S) (5′CTA​AAC​ATA​CAA​ATA​CAC​ATT​TCA​CAG​ TAA​CGG​CAG​ACT​TCT​CCT3′, bead set MTAG-A062), HbS (5′AAT​CAA​CAC​ACA​ATA​ACA​TTC​ATA​CAG​ TAA​CGG​CAG​ACT​TCT​CCA3′, bead set MTAG-A048). This methodology is described in detail elsewhere (Grig- nard et al. pers.comm.). HbA(S) (5′CTA​AAC​ATA​CAA​ATA​CAC​ATT​TCA​CAG​ TAA​CGG​CAG​ACT​TCT​CCT3′, bead set MTAG-A062), HbS (5′AAT​CAA​CAC​ACA​ATA​ACA​TTC​ATA​CAG​ TAA​CGG​CAG​ACT​TCT​CCA3′, bead set MTAG-A048). This methodology is described in detail elsewhere (Grig- nard et al. pers.comm.). HbA(S) (5′CTA​AAC​ATA​CAA​ATA​CAC​ATT​TCA​CAG​ TAA​CGG​CAG​ACT​TCT​CCT3′, bead set MTAG-A062), Haemoglobin l b Haemoglobin concentrations were determined by self- calibrating Hemocue photometer (HemoCue 301 + , Angelholm, Sweden). Anaemia was defined using WHO guidelines for circulating levels of haemoglo- bin (g/dL) [30]. For children 5–11  years of age these Mooney et al. Malar J (2018) 17:253 Page 3 of 11 are: non-anaemic (> 11.5), mild (11–11.4), moderate (8–10.9), and severe (< 8) anaemia. USA) running Bioplex Manager software. Samples were diluted 1:2.5. Samples giving values below the limit of detection were arbitrarily assigned a concentration at the limit of detection for the purposes of statistical analyses (13.008 pg/mL for IFN-γ, 9.5146 pg/mL for IL-10). Haemoglobin genotypes were determined in 21 of the 23 infected patients. Extracted DNA was amplified using previously published primers (300 nM each) [32]. After amplification, primers and nucleotides from the genomic PCR were removed using ExoSAP-IT reagent (Applied Biosystems). Cleaned PCR product was added to an ASPE (allele specific primer extension) reaction mix con- taining 250 nM of each ASPE probe and 200 µM Biotin- 14-dCTP (Invitrogen). ASPE products were hybridised to 2500 beads (Luminex corp., The Netherlands) of each set, washed twice in 1 × Tm buffer (0.2 M NaCl, 0.1 M Tris, 0.8% TritonX-100, pH 8.0) and incubated for 15 min at 37 °C in 1 × Tm containing 0.1% bovine serum albumin (BSA) and 2.5 µg/mL Streptavidin, R-Phycoerythrin Con- jugate (SAPE, Invitrogen). Fifty µl of the hybridized beads were read on a Magpix (Luminex corp., The Netherlands) and genotypes were called according to fluorescent sig- nal. Probe sequences were as follows; Statistical analysis f Concentrations of cytokines and markers of haemolysis (haem, HPX, HO-1) were compared between uninfected controls and infected (PCR-positive) children at enroll- ment using the Mann–Whitney test. Correlations and partial correlations were calculated using the combined log-transformed data (day 1 and day 35). For the latter analysis, p-values were calculated using robust stand- ard errors to account for repeated measures and within- individual correlation. Analyses were conducted using GraphPad Prism 7 and Stata version 14. Haemoglobin genotypes and haemolysis parameters in children with subclinical Plasmodium falciparum infections Genetic structural variants of haemoglobin can result in haemolytic anaemia, which may in themselves lead to raised plasma heme and elevated HO-1. Therefore, Page 4 of 11 Mooney et al. Malar J (2018) 17:253 Table 1  Plasmodium falciparum densities and  haemo­ globin genotypes of subclinically infected cohort ND not determined ID Age Gender Hb Genotype Plasmodium falciparum (parasites/uL, qPCR) Day 0 Day 35 1 6 F HbAA 5445 1403 2 7 M HbAA 583 1180 3 8 F HbAA 492 1107 4 8 M HbAA 993 265 5 6 M HbAS 124 18967 6 8 F HbAA 236 307 7 9 F HbAA 2084 145 8 9 F HbAA 175 386 9 9 M HbAA 2118 2275 10 9 M HbAC 2173 1268 11 9 F HbAC 1012 815 12 6 M HbAA 3 1 13 9 F HbSC 37 16 14 8 M HbAA 396 74 15 8 M HbAA 237 340 16 5 F HbAA 81 Resolved 17 9 M HbAA 156 356 18 7 M HbAC 185 2 19 9 M HbAA 296 222 20 8 M HbAA 1600 1315 21 9 M ND 1871 1641 22 9 M HbAC 160 89 23 8 F ND 78 370 Median 8 296 363 Table 1  Plasmodium falciparum densities and  haemo­ globin genotypes of subclinically infected cohort day 35 (Table 2) suggesting that this genotype may be associated with exacerbated haemolysis. Subclinical malaria is associated with raised plasma IL‑10 concentrations and IFN‑γ is associated with haemolysisl Subclinical malaria is associated with raised plasma IL‑10 concentrations and IFN‑γ is associated with haemolysis Acute malaria infection induces a robust inflammatory response (typically marked by high concentrations of cytokines such as IFN-γ and TNFα) and is accompanied by a compensatory (homeostatic) increase in circulating interleukin (IL)-10) [35–37]. To determine whether low density, subclinical infections induced a similar inflam- matory/anti-inflammatory state, plasma IFN-γ and IL-10 concentrations were determined by multiplex bead array. Plasma IFN-γ concentrations did not differ significantly between infected and uninfected children (Fig. 3a) how- ever plasma IL-10 concentrations were modestly but significantly higher in infected children and these raised IL-10 concentrations were sustained during the 35 days of follow up (Fig. 3b). ND not determined To understand the possible causal relationships between parasite infection, haemolysis (haem), inflam- mation (IFN-γ) and immunoregulation (IL-10), asso- ciations between these different factors in infected children were calculated, combining observations from days 1 to 35 if qPCR positive (n = 45). Plasma IFN-γ and IL-10 concentrations were positively correlated (r = 0.318, p = 0.04) (Fig. 3c). IL-10 concentration was statistically significantly correlated with qPCR parasite density (r = 0.491, p = 0.0002) (Fig. 3d) while concentra- tions of IFN-γ (r = − 0.181, p = 0.34) (Fig. 3e) and haem (r = − 0.270, p = 0.09) (Fig. 3f) were not. While IFN-γ concentration was not correlated with parasite density (Fig. 3e), it was positively correlated with haem concen- tration (r = 0.359, p = 0.0003) (Fig. 3g). In addition, while IL-10 concentration was correlated with parasite density (Fig. 3d), it was not correlated with haem concentration (r = 0.026, p = 0.79) (Fig. 3h). haemoglobin A, C and S carriage within the infected cohort was determined (Table 1). Fifteen children had normal haemoglobin genotype (HbAA) and four chil- dren were haemoglobin C carriers (HbAC). While car- riage of homozygous HbC can be protective against severe falciparum infection [31, 32], HbC trait does not affect steady state haemoglobin concentration or red cell counts [33]. In agreement with this, levels of hae- moglobin, heme, and HO-1 were not statistically differ- ent between infected children with hemoglobin HbAA and HbAC genotypes (Table  2). One child carried sickle-cell trait (HbAS) but their Hb, heme and HO-1 values were within the range for the HBAA children at day 0 and day 35. Low density parasitaemia is not associated with iron deficiencyhi The findings of persistent haemolysis in infected children in the absence of anaemia suggests that infected children were able to respond to haemolysis by increasing hae- mopoesis. This suggests that the children are iron suffi- cient (defined as ferritin concentration > 30 ng/mL [34]). Indeed, plasma concentrations of both ferritin (indicating iron stores) and transferrin (a high-affinity iron-binding plasma protein which sequesters free iron preventing its uptake by pathogens) were slightly, but significantly, higher among infected children than among controls (Fig. 2). Subclinical malaria is associated with raised plasma IL‑10 concentrations and IFN‑γ is associated with haemolysisl P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05 These data indicate that parasite density is likely the major driver of IL-10 production while haemolysis is the major driver of HO-1 (proposed model, Fig. 5). After adjusting for haem and IFN-γ concentrations (potential confounders of the association between HO-1 and IL-10, Fig. 5), the correlation between HO-1 and IL-10 became stronger and was of borderline statistical significance (adjusted, r = 0.337, p = 0.05), suggesting that IL-10 may indeed contribute to HO-1 induction, independently of haem. Nevertheless, haem concentration is the strongest predictor of HO-1 concentration in children with sub- clinical P. falciparum infections (r = 0.389, p = 0.0001, Fig. 4g). HO‑1 induction is associated with haemolysis but not parasite density, haemoglobin concentration or IL‑10 concentration Plasmodium falciparum infection was associated with both haemolysis (Fig. 1) and elevated plasma IL-10 (Fig. 3). HO-1 is directly induced by both free haem (which is released during erythrocyte destruc- tion) and IL-10 [38–41]; induction of HO-1 to reduce haem-induced tissue damage is a major mechanism of IL-10-mediated tissue protection [42]. Accordingly, in infected children, HO-1 concentration was nega- tively correlated with HPT (r = − 0.339, p = 0.04) and positively correlated with haem (r = 0.389, p = 0.0001) concentrations (Fig. 4f, g). However, there was no sig- nificant correlation between parasite density and HO-1 (r = 0.048, p = 0.77) (Fig. 4a). Furthermore, HO-1 concentration was not significantly associated with IFN-γ (r = 0.086, p = 0.55), IL-10 (r = 0.291, p = 0.10), haemoglobin (r = -−  0.110, p = 0.49) or haemopexin (r = − 0.004, p = 0.98) concentrations (Fig. 4b–e). Subclinical malaria is associated with raised plasma IL‑10 concentrations and IFN‑γ is associated with haemolysisl However, the one child who was heterozygous for sickle-cell and hemoglobin C (HbSC) had an Hb concentration that was below the range for HbAA children, and an HO-1 concentration that was above the range for HbAA children, on day 0 but not on Mooney et al. Malar J (2018) 17:253 Page 5 of 11 8 12 16 Hb (g/dL) ns ns Ctrl D1 D35 Infected a 1 10 100 1000 HPT (mg/dL) p=0.0014 ns Ctrl D1 D35 Infected b c d 0.1 1 10 100 1000 Heme (uM) p<0.0001 ns Ctrl D1 D35 Infected 0 50 100 150 200 HPX (mg/dL) p<0.0001 p=0.0008 Ctrl D1 D35 Infected f 0.01 0.1 1 10 100 HO-1 (ng/mL) p=0.0015 p=0.0532 Ctrl D1 D35 Infected g e Ctrl Non-Anemic : Hb >11.5g/dL Mild/Moderate Anemia : Hb = 8-11.5g/dL 55% 45% Infected Day1 50% 50% Infected Day35 45% 55% 100 101 102 103 104 105 Pf PCR (parasites/uL) ns Ctrl D1 D35 Fig. 1  Haemolysis in children with subclinical malaria. At study enrollment (Day 1) or follow-up (Day 35), (a) Plasmodium falciparum (Pf) burden was determined by 18S qPCR for uninfected controls (Ctrl) (n = 21) or subclinically malaria-infected (n = 23) children (Table 1). b Haemoglobin (Hb) levels were determined by Hemocue analyzer. c Pie charts show proportion (%) of children with differing levels of anaemia (WHO classification: non-anaemic (> 11.5 g/dL), mild (11–11.5 g/dL), and moderate (8–10.9 g/dL)]. Plasma concentration of (d) haptoglobin (HPT), (e) haem, (f) haemopexin (HPX), or (g) haem oxygenase-1 (HO-1) determined by ELISA. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. Subclinical malaria is associated with raised plasma IL‑10 concentrations and IFN‑γ is associated with haemolysisl ‘ns’ indicates P > 0.05 8 12 16 Hb (g/dL) ns ns Ctrl D1 D35 Infected a b 100 101 102 103 104 105 Pf PCR (parasites/uL) ns Ctrl D1 D35 a 100 101 102 103 104 105 Pf PCR (parasites/uL) ns Ctrl D1 D35 a c Infected Day35 45% 55% Ctrl 55% 45% Infected Day1 50% 50% Infected Day35 45% 55% Infected Day35 0 50 100 150 200 HPX (mg/dL) p<0.0001 p=0.0008 Ctrl D1 D35 Infected f 0.1 1 10 100 1000 Heme (uM) p<0.0001 ns Ctrl D1 D35 Infected e 0.01 0.1 1 10 100 HO-1 (ng/mL) p=0.0015 p=0.0532 Ctrl D1 D35 Infected g 1 10 100 1000 HPT (mg/dL) p=0.0014 ns Ctrl D1 D35 Infected d d Fig. 1  Haemolysis in children with subclinical malaria. At study enrollment (Day 1) or follow-up (Day 35), (a) Plasmodium falciparum (Pf) burden was determined by 18S qPCR for uninfected controls (Ctrl) (n = 21) or subclinically malaria-infected (n = 23) children (Table 1). b Haemoglobin (Hb) levels were determined by Hemocue analyzer. c Pie charts show proportion (%) of children with differing levels of anaemia (WHO classification: non-anaemic (> 11.5 g/dL), mild (11–11.5 g/dL), and moderate (8–10.9 g/dL)]. Plasma concentration of (d) haptoglobin (HPT), (e) haem, (f) haemopexin (HPX), or (g) haem oxygenase-1 (HO-1) determined by ELISA. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05 Fig. 1  Haemolysis in children with subclinical malaria. At study enrollment (Day 1) or follow-up (Day 35), (a) Plasmodium falciparum (Pf) burden was determined by 18S qPCR for uninfected controls (Ctrl) (n = 21) or subclinically malaria-infected (n = 23) children (Table 1). b Haemoglobin (Hb) levels were determined by Hemocue analyzer. c Pie charts show proportion (%) of children with differing levels of anaemia (WHO classification: non-anaemic (> 11.5 g/dL), mild (11–11.5 g/dL), and moderate (8–10.9 g/dL)]. Plasma concentration of (d) haptoglobin (HPT), (e) haem, (f) haemopexin (HPX), or (g) haem oxygenase-1 (HO-1) determined by ELISA. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. Discussionh Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05 a b 10 100 1000 Ferritin (ng/mL) p=0.0017 p=0.0794 Ctrl D1 D35 Infected 0 500 1000 1500 2000 Tf (ng/mL) Ctrl D1 D35 p=0.0021 ns Infected Fig. 2  Iron indices during subclinical malaria. Plasma concentrations of (a) ferritin or (b) transferrin (Tf) determined by ELISA. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05 neutrophil defects and the potential for treatment of sub- clinical malaria infections to restore neutrophil function and thereby reduce the incidence of bacteraemia. a 10 100 1000 Ferritin (ng/mL) p=0.0017 p=0.0794 Ctrl D1 D35 Infected In support of this hypothesis, this preliminary study indicated that children with persistent, low density parasite infections show clear evidence of haemolysis (evidenced by raised plasma haem and depleted HPT) which is sustained for at least 35 days as infections per- sist. Moreover, haemolysis is accompanied by, and highly correlated with, sustained induction of HO-1. This obser- vation highlights the need for larger and more extensive studies of neutrophil function in subclinically infected children.i Fig. 2  Iron indices during subclinical malaria. Plasma concentrations of (a) ferritin or (b) transferrin (Tf) determined by ELISA. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected controls (Ctrl) and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05 Clinically, haemolytic anaemia is defined by low hae- moglobin concentration accompanied by low HPT and low haemopexin (HPX) [45]. HPT binds haemoglobin and targets it for phagocytic uptake (and degradation) via the CD163 receptor on macrophages. The low HPT concentrations in infected children suggest that hae- molysis has been ongoing for sufficient time to deplete available stores of HPT. Discussionh The purpose of this study was to begin to test the hypoth- esis that subclinical P. falciparum malaria infections are associated with persistent haemolysis and that this is sufficient to lead to sustained induction of HO-1. The rationale for the study is that-given the documented Mooney et al. Malar J (2018) 17:253 Page 6 of 11 Table 2  Analysis of  anaemia and  haemolysis in  subclinically Plasmodium falciparum infected children grouped by haemoglobin genotype ND, medians not determined for HbAS (sickle cell carrier) and HbSC (heterozygous sickle-C carrier) as only one patient carried each of these genotypes P-values for comparisons between HbAA and HbAC (haemoglobin C carriers) determined by Mann–Whitney test Genotype HbAA (n = 15) HbAC (n = 4) P-value (HbAA v. HbAC) HbAS (n = 1) HbSC (n = 1) Median (range) Median (range) Value Value Day 0  Patients (n) 15 4 1 1  Hb (g/dL) 11.9 (9.8–14.3) 11.4 (10.7–13.8) 0.90 11.2 9.3  Haem (uM) 23.1 (13–142.3) 17.5 (11.7–23.1) 0.19 11.2 21.4  HO-1 (ng/mL) 2.4 (0.3–6.8) 3.3 (1.0–4.2) 0.73 0.6 7.6 Day 35  Patients (n) 14 4 1 1  Hb (g/dL) 11.1 (9.6–14.9) 11.2 (10.3–13.7) 0.98 12.3 8.8  Haem (uM) 16.2 (8.2–38.2) 16.3 (9.3–22.8) 0.86 10.3 25.5  HO-1 (ng/mL) 0.7 (0.4–4.0) 1.2 (0.1–11.5) 0.82 1.2 2.5 All Dates  Patients (n) 29 8  Hb (g/dL) 11.7 (9.6–14.9) 11.4 (10.3–13.8) 0.93 ND ND  Haem (uM) 17.1 (8.2–142.3) 17.5 (9.3–23.1) 0.44 ND ND  HO-1 (ng/mL) 1.3 (0.3–6.8) 2.4 (0.1–11.5) 0.57 ND ND Table 2  Analysis of  anaemia and  haemolysis in  subclinically Plasmodium falciparum inf by haemoglobin genotype Table 2  Analysis of  anaemia and  haemolysis in  subclinically Plasmodium falciparum infected children grouped by haemoglobin genotype Genotype HbAA (n=15) HbAC (n=4) P-value (HbAA v. HbAS (n=1) HbSC (n=1) sis in  subclinically Plasmodium falciparum infected children grouped ed for HbAS (sickle cell carrier) and HbSC (heterozygous sickle-C carrier) as only one patient carried each of these genotypes between HbAA and HbAC (haemoglobin C carriers) determined by Mann–Whitney test ND, medians not determined for HbAS (sickle cell carrier) and HbSC (heterozygous sickle-C carrier) as only one pa P-values for comparisons between HbAA and HbAC (haemoglobin C carriers) determined by Mann–Whitney test a b 10 100 1000 Ferritin (ng/mL) p=0.0017 p=0.0794 Ctrl D1 D35 Infected 0 500 1000 1500 2000 Tf (ng/mL) Ctrl D1 D35 p=0.0021 ns Infected Fig. 2  Iron indices during subclinical malaria. Plasma concentrations of (a) ferritin or (b) transferrin (Tf) determined by ELISA. Discussionh Conversely, HPX binds cell- free haem and the haem-HPX complex binds to mac- rophage CD91, again triggering phagocytic uptake and degradation of haem, thereby protecting the body from haem-mediated tissue damage [46]. However, despite evidence of haemolysis, HPX concentrations were in fact higher in subclinically infected children than in uninfected children. This suggests that the levels of haemolysis in these children are sufficient to deplete causal association between HO-1, neutrophil dysfunction and increased susceptibility to non-typhoidal Salmonella bacteraemia [24, 25] -evidence of sustained HO-1 induc- tion in subclinically infected children might explain the epidemiological association between the prevalence of malaria and the incidence of invasive bacterial disease [19, 43, 44]. This would, in turn, justify further studies to understand the impact of subclinical infection on neu- trophil function, to describe the nature of any observed Mooney et al. Malar J (2018) 17:253 Page 7 of 11 1 10 100 1000 IFN (ng/mL) ns ns Infected 1 10 100 1000 IL-10 (ng/mL) p=0.0254 p=0.0760 Ctrl D1 D35 Ctrl D1 D35 Infected c 100 101 102 103 100 101 102 103 IL-10 (ng/mL) IFN (ng/mL) r= 0.318 p= 0.0363 a b d e f 100 101 102 103 104 105 100 101 102 103 Pf (parasites/uL) IFN (ng/mL) r= -0.181 p= 0.3439 100 101 102 103 104 105 100 101 102 103 Pf (parasites/uL) IL-10 (ng/mL) r= 0.491 p= 0.0002 100 101 102 103 104 105 100 101 102 Pf (parasites/uL) Heme (uM) r= -0.270 p= 0.0905 g 100 101 102 100 101 102 103 Heme (uM) IFN (ng/mL) r= 0.359 p= 0.0003 h 100 101 102 100 101 102 103 Heme (uM) IL-10 (ng/mL) r= 0.026 p= 0.7913 Fig. 3  Elevated plasma IL-10 during subclinical malaria. Plasma concentrations of (a) interferon gamma (γ) or (b) interleukin (IL-) 10 determined by cytokine bead array. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05. c–h For infected children, correlations were calculated using log-transformed data (combined D1 and D35). c Correlation between IFN-γ and IL-10. Further, parasite density (determined by qPCR) was correlated with (d) IL-10, (e) IFN-γ and (f) haem. Finally, correlations were determined between haem and both (g) IFN-γ, and (h) IL-10. Discussionh Log-transformed data shown with linear regression line, Pearson’s correlation coefficient and p value; n = 45 1 10 100 1000 IFN (ng/mL) ns ns Infected Ctrl D1 D35 a c 100 101 102 103 100 101 102 103 IL-10 (ng/mL) IFN (ng/mL) r= 0.318 p= 0.0363 1 10 100 1000 IL-10 (ng/mL) p=0.0254 p=0.0760 Ctrl D1 D35 Infected b f 100 101 102 103 104 105 100 101 102 Pf (parasites/uL) Heme (uM) r= -0.270 p= 0.0905 d 100 101 102 103 104 105 100 101 102 103 Pf (parasites/uL) IL-10 (ng/mL) r= 0.491 p= 0.0002 g 100 101 102 100 101 102 103 Heme (uM) IFN (ng/mL) r= 0.359 p= 0.0003 f d 100 101 102 103 104 105 Pf (parasites/uL) h 100 101 102 100 101 102 103 Heme (uM) IL-10 (ng/mL) r= 0.026 p= 0.7913 h g Fig. 3  Elevated plasma IL-10 during subclinical malaria. Plasma concentrations of (a) interferon gamma (γ) or (b) interleukin (IL-) 10 determined by cytokine bead array. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05. c–h For infected children, correlations were calculated using log-transformed data (combined D1 and D35). c Correlation between IFN-γ and IL-10. Further, parasite density (determined by qPCR) was correlated with (d) IL-10, (e) IFN-γ and (f) haem. Finally, correlations were determined between haem and both (g) IFN-γ, and (h) IL-10. Log-transformed data shown with linear regression line, Pearson’s correlation coefficient and p value; n = 45 Fig. 3  Elevated plasma IL-10 during subclinical malaria. Plasma concentrations of (a) interferon gamma (γ) or (b) interleukin (IL-) 10 determined by cytokine bead array. Dot plots show individual patient parameters. Red lines represent medians. P-values for comparisons between uninfected and infected children at enrollment were determined by Mann–Whitney test. P-values for comparisons between infected children at days 1 and 35 were determined by Wilcoxon matched-pair test. ‘ns’ indicates P > 0.05. c–h For infected children, correlations were calculated using log-transformed data (combined D1 and D35). c Correlation between IFN-γ and IL-10. Further, parasite density (determined by qPCR) was correlated with (d) IL-10, (e) IFN-γ and (f) haem. Finally, correlations were determined between haem and both (g) IFN-γ, and (h) IL-10. Discussionh Partial correlation coefficient and p-value for the association between IL-10 and HO-1 adjusted for IFN-γ and haem shown in c 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IFN (ng/mL) r= 0.086 p= 0.5526 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IL-10 (ng/mL) r= 0.291 p= 0.0986 adjusted: r= 0.337 p= 0.052 10-1 100 101 100 101 102 103 104 105 HO-1 (ng/mL) Pf (parasites/uL) r= 0.048 p= 0.7662 10-1 100 101 100 101 102 103 104 105 HO-1 (ng/mL) Hb (g/dL) r= -0.110 p= 0.4903 a b c d 10-1 100 101 100 101 102 103 104 105 HO-1 (ng/mL) Pf (parasites/uL) r= 0.048 p= 0.7662 a 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IFN (ng/mL) r= 0.086 p= 0.5526 b 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IL-10 (ng/mL) r= 0.291 p= 0.0986 adjusted r= 0.337 p= 0.052 c 10-1 100 101 100 101 102 103 HO-1 (ng/mL) HPT (mg/dL) r= -0.339 p= 0.0440 10-1 100 101 101.6 101.8 102.0 102.2 102.4 HO-1 (ng/mL) HPX (mg/dL) r= -0.004 p= 0.9836 e f 10-1 100 101 100 101 102 103 HO-1 (ng/mL) HPT (mg/dL) r= -0.339 p= 0.0440 f 10 -1 100 101 101 102 HO-1 (ng/mL) Heme (uM) r= 0.389 p= 0.0001 g g e Fig. 4  HO-1 induction correlates with markers of haemolysis, but not parasitaemia or anaemia. For infected children, correlations were calculated on log-transformed data (combined D1 and D35). Correlations between haem oxygenase-1 (HO-1) and a parasite density, b interferon gamma (IFN-γ), c interleukin(IL-) 10, d haemoglobin (Hb), e haemopexin (HPX), f haptoglobin (HPT), and g haem. Log-transformed data shown with linear regression line, Pearson’s correlation coefficient and p-value; n = 45. Partial correlation coefficient and p-value for the association between IL-10 and HO-1 adjusted for IFN-γ and haem shown in c While haemolysis and liberation of free haem induces HO-1, and these data show a clear correlation between plasma concentrations of haem and HO-1, it is impor- tant to consider the possibility that IL-10 may also play a role. Malaria-induced inflammation leads to a com- pensatory secretion of the anti-inflammatory cytokine IL-10 [35] and IL-10 can directly induce HO-1 [38]. In this study of subclinical malaria infections, plasma inflammatory cytokine concentrations did not differ between infected and uninfected children. Discussionh Log-transformed data shown with linear regression line, Pearson’s correlation coefficient and p value; n = 45 children with subclinical malaria infections and that the children are iron sufficient and able to mount a sufficient erythropoietic response to sustain red cell counts and haemoglobin concentrations. The lack of correlation between parasite density and the extent of haemolysis may be explained by the observation that much of the anaemia associated with malaria is due to lysis or phagocytosis of uninfected erythrocytes as well as parasitized cells [48]. HPT and induce HO-1 but not sufficient to deplete available stores of HPX. Indeed, these data suggest that modest levels of haemolysis may in fact stimulate the synthesis of HPX. When taken together with the obser- vation that haemoglobin concentrations were not sig- nificantly different from those in uninfected children, and that ferritin and transferrin concentrations were within the normal range for healthy children [34, 47], these data suggest that haemolysis is well tolerated in Mooney et al. Malar J (2018) 17:253 Page 8 of 11 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IFN (ng/mL) r= 0.086 p= 0.5526 10-1 100 101 100 101 102 103 HO-1 (ng/mL) IL-10 (ng/mL) r= 0.291 p= 0.0986 adjusted: r= 0.337 p= 0.052 10-1 100 101 100 101 102 103 HO-1 (ng/mL) HPT (mg/dL) r= -0.339 p= 0.0440 10-1 100 101 100 101 102 103 104 105 HO-1 (ng/mL) Pf (parasites/uL) r= 0.048 p= 0.7662 10 -1 100 101 101 102 HO-1 (ng/mL) Heme (uM) r= 0.389 p= 0.0001 10-1 100 101 100 101 102 103 104 105 HO-1 (ng/mL) Hb (g/dL) r= -0.110 p= 0.4903 10-1 100 101 101.6 101.8 102.0 102.2 102.4 HO-1 (ng/mL) HPX (mg/dL) r= -0.004 p= 0.9836 a b e f g c d Fig. 4  HO-1 induction correlates with markers of haemolysis, but not parasitaemia or anaemia. For infected children, correlations were calculated on log-transformed data (combined D1 and D35). Correlations between haem oxygenase-1 (HO-1) and a parasite density, b interferon gamma (IFN-γ), c interleukin(IL-) 10, d haemoglobin (Hb), e haemopexin (HPX), f haptoglobin (HPT), and g haem. Log-transformed data shown with linear regression line, Pearson’s correlation coefficient and p-value; n = 45. Discussionh IL-10 con- centrations were, nevertheless, raised in the infected children and correlated with parasite density, con- firming many previous studies of circulating cytokine responses to malaria infection [49, 50]. While there was no significant correlation between IL-10 and HO-1 con- centrations in univariate analyses, a multivariate model suggested that IL-10 may contribute to HO-1 induction alongside haem. Further work is needed to understand the relative contribution of these two factors to HO-1 induction during low-density infections. One limita- tion of the current study is that the duration of infec- tions prior to the first qPCR positive observation was unknown and the study was terminated on day 35; it is not known, therefore, how long these children had been infected or how long they had been experiencing hae- molysis. More detailed studies are required to ascertain the detailed natural history of subclinical P. falciparum infections. While these preliminary data suggest that subclini- cal malaria infections induce persistent haemolysis and sustained production of HO-1, the analyses and inter- pretations are limited by the relatively small sample size and the lack of data on neutrophil function. Moreover, absolute concentrations of HO-1 were lower than previ- ously reported for children recovering from acute febrile malaria [25], raising the possibility that HO-1 levels may not be sufficient to cause neutrophil defects. Further, parasite densities varied by 3 orders of magnitude even among this small, subclinically-infected group. How- ever, this is the first published report of raised plasma haemoxygenase-1 (HO-1) during persistent, subclinical malaria infections and, when taken together with raised plasma IL-10 concentrations, suggests that further stud- ies would be justified to determine the impact of HO-1 Page 9 of 11 Mooney et al. Malar J (2018) 17:253 P.f. Burden [qPCR] Hemolysis (heme) IL-10 HO-1 p=0.0986 r=0.291 adjusted: p=0.052 r=0.337 p=0.0001 r=0.389 p=0.0002 r=0.491 "Asymptomatic" Malaria p=0.0363 r=0.318 Inflammation (IFN ) p=0.0003 r=0.359 p=0.3439 r=-0.181 p=0.0905 r=-0.270 Fig. 5  Proposed model of the relation between haemolysis, IFN-γ, IL-10, HO-1 and parasitaemia in subclinically infected children. Approximately half the children with subclinical malaria infection had anaemia, but neither the Hb concentration nor the proportion of those with anaemia differed from uninfected children (Fig. 1). However, those who were PCR positive for Plasmodium falciparum had evidence of haemolysis (haem and haemopexin, HPX). Further, while the level of circulating parasites correlated with IL-10 concentration, it did not correlate with free haem, IFN-γ or haem oxygenase-1 (HO-1) induction. Funding Funding Supported by UK Medical Research Council (MR/P000959/1 awarded to E.R.), the Bill & Melinda Gates Foundation (OPP1034789, OPP1173572 awarded to C.D. and L.G.), and a fellowship from the European Research Council (ERC- 2014-StG 639776 awarded to T.B.). Funding Supported by UK Medical Research Council (MR/P000959/1 awarded to E.R.), the Bill & Melinda Gates Foundation (OPP1034789, OPP1173572 awarded to C.D. and L.G.), and a fellowship from the European Research Council (ERC- 2014-StG 639776 awarded to T.B.). Acknowledgements h h d b The authors are indebted to the participants who donated their blood for this study and to the clinical staff for sample collection. Also to Maimuna Jahateh for critical review. Ethics approval and consent to participate The study was approved by the ethics committees of the London School of Hygiene and Tropical Medicine (reference number 9008) and the Ministry of Health in Burkina Faso (Reference Number 2015-3-033). The study was approved by the ethics committees of the London School of Hygiene and Tropical Medicine (reference number 9008) and the Ministry of Health in Burkina Faso (Reference Number 2015-3-033). The study was approved by the ethics committees of the London School of Hygiene and Tropical Medicine (reference number 9008) and the Ministry of Health in Burkina Faso (Reference Number 2015-3-033). Abbreviations Hb h l bi Hb: haemoglobin; HPT: haptoglobin; HPX: haemopexin; HO-1: haem oxyge- nase-1; IL-10: interleukin-10. Authors’ contributions d d d Study concept and design: JPM, TB, and ER; data generation and analysis: JPM, AB, BG, SSA, LG, and TA; statistical review: JPM, and CB; drafting and revision of manuscript: JPM, CB, CD, TB, and ER; critical appraisal and approval for submis- sion: all authors. All authors read and approved the final manuscript. Competing interests h h d l h In this pilot study, children with subclinical malaria infec- tions showed evidence of persistent haemolysis; with raised plasma haem, IL-10 and HO-1. This study sup- ports the growing evidence that these low density malaria infections are not strictly “asymptomatic”. Further work is needed to clarify the impact of these observations on immune status and resilience to co-infection. Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Competing interests The authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests. Discussionh Rather, HO-1 levels were positively correlated with circulating free haem and, to a lesser extent, with IL-10 concentrations. Line thickness represents significance level; 6pt = p < 0.001, 3pt = p > 0.001 to p = 0.05, 1/2pt = p > 0.05 and IL-10 on neutrophil function and susceptibility to bacterial infection. Availability of data and materials h d d d/ l d d y The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Consent for publication Consent for publication was granted by study participants. Consent for publication Consent for publication was granted by study participants. Discussionh Rather, HO-1 levels were positively correlated with circulating free haem and, to a lesser extent, with IL-10 concentrations. Line thickness represents significance level; 6pt = p < 0.001, 3pt = p > 0.001 to p = 0.05, 1/2pt = p > 0.05 P.f. Burden [qPCR] "Asymptomatic" Malaria Hemolysis (heme) Fig. 5  Proposed model of the relation between haemolysis, IFN-γ, IL-10, HO-1 and parasitaemia in subclinically infected children. Approximately half the children with subclinical malaria infection had anaemia, but neither the Hb concentration nor the proportion of those with anaemia differed from uninfected children (Fig. 1). However, those who were PCR positive for Plasmodium falciparum had evidence of haemolysis (haem and haemopexin, HPX). Further, while the level of circulating parasites correlated with IL-10 concentration, it did not correlate with free haem, IFN-γ or haem oxygenase-1 (HO-1) induction. Rather, HO-1 levels were positively correlated with circulating free haem and, to a lesser extent, with IL-10 concentrations. Line thickness represents significance level; 6pt = p < 0.001, 3pt = p > 0.001 to p = 0.05, 1/2pt = p > 0.05 Fig. 5  Proposed model of the relation between haemolysis, IFN-γ, IL-10, HO-1 and parasitaemia in subclinically infected children. Approximately half the children with subclinical malaria infection had anaemia, but neither the Hb concentration nor the proportion of those with anaemia differed from uninfected children (Fig. 1). However, those who were PCR positive for Plasmodium falciparum had evidence of haemolysis (haem and haemopexin, HPX). Further, while the level of circulating parasites correlated with IL-10 concentration, it did not correlate with free haem, IFN-γ or haem oxygenase-1 (HO-1) induction. Rather, HO-1 levels were positively correlated with circulating free haem and, to a lesser extent, with IL-10 concentrations. Line thickness represents significance level; 6pt = p < 0.001, 3pt = p > 0.001 to p = 0.05, 1/2pt = p > 0.05 Fig. 5  Proposed model of the relation between haemolysis, IFN-γ, IL-10, HO-1 and parasitaemia in subclinically infected children. Approximately half the children with subclinical malaria infection had anaemia, but neither the Hb concentration nor the proportion of those with anaemia differed from uninfected children (Fig. 1). However, those who were PCR positive for Plasmodium falciparum had evidence of haemolysis (haem and haemopexin, HPX). Further, while the level of circulating parasites correlated with IL-10 concentration, it did not correlate with free haem, IFN-γ or haem oxygenase-1 (HO-1) induction. Conclusions Competing interests The authors declare that they have no competing interests. References Wipasa J, Okell L, Sakkhachornphop S, Suphavilai C, Chawansuntati K, Liewsaree W, et al. Short-lived IFN-γ effector responses, but long-lived IL-10 memory responses, to malaria in an area of low malaria endemicity. PLoS Pathog. 2011;7:e1001281. yg 14. Looareesuwan S, Merry AH, Phillips RE, Pleehachinda R, Wattanagoon Y, Ho M, et al. Reduced erythrocyte survival following clearance of malarial parasitaemia in Thai patients. Br J Haematol. 1987;67:473–8. 15. Gwamaka M, Fried M, Domingo G, Duffy PE. Early and extensive CD55 loss from red blood cells supports a causal role in malarial anaemia. Malar J. 2011;10:386. 37. Montes de Oca M, Kumar R, de Labastida Rivera F, Amante FH, Sheel M, Faleiro RJ, et al. 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Examining the human infectious reservoir for Plasmodium falci- parum malaria in areas of differing transmission intensity. Nat Commun. 2017;8:1133. 3. Chen I, Clarke S, Gosling R, Hamainza B, Killeen G, Magill A, et al. “Asymp- tomatic malaria” is a chronic, debilitating infection that should be treated. PLoS Med. 2016;13:e1001942. 4. Alves FP, Gil LH, Marrelli MT, Ribolla PE, Camargo EP, Da Silva LH. Asymp- tomatic carriers of Plasmodium spp. as infection source for malaria vector mosquitoes in the Brazilian Amazon. J Med Entomol. 2005;42:777–9. 4. Alves FP, Gil LH, Marrelli MT, Ribolla PE, Camargo EP, Da Silva LH. Asymp- tomatic carriers of Plasmodium spp. as infection source for malaria vector mosquitoes in the Brazilian Amazon. J Med Entomol. 2005;42:777–9. 27. Snounou G, Viriyakosol S, Zhu XP, Jarra W, Pinheiro L, do Rosario VE, et al. High sensitivity of detection of human malaria parasites by the use of nested polymerase chain reaction. Mol Biochem Parasitol. 1993;61:315–20. 5. Tadesse FG, Slater HC, Chali W, Teelen K, Lanke K, Belachew M, et al. The relative contribution of symptomatic and asymptomatic Plasmodium vivax and Plasmodium falciparum infections to the infectious reservoir in a low-endemic setting in Ethiopia. Clin Infect Dis. 2018;66:1883–91. 28. Hermsen CC, Telgt DS, Linders EH, van de Locht LA, Eling WM, Mensink EJ, et al. Detection of Plasmodium falciparum malaria parasites in vivo by real-time quantitative PCR. Mol Biochem Parasitol. 2001;118:247–51. 6. Author details 1 Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. 1 Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK. 2 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlo- thian EH25 9RG, UK. 3 Centre National de Recherche et de Formation sur le Paludisme, Université de Ouagadougou, Ouagadougou, Burkina Faso. 4 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK. 5 Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands. Received: 7 March 2018 Accepted: 3 July 2018 Received: 7 March 2018 Accepted: 3 July 2018 Page 10 of 11 Page 10 of 11 Mooney et al. Malar J (2018) 17:253 24. Cunnington AJ, de Souza JB, Walther M, Riley EM. Malaria impairs resist- ance to Salmonella through heme- and heme oxygenase-dependent dysfunctional granulocyte mobilization. Nat Med. 2011;18:120–7. 46. Sher EA, Hemi K, Efrati S, Weissgarten J, Shaklai M, Shaklai N. Hemopexin is protective against intravascular hemolysis–induced vascular damage. Blood. 2010;116:3207. 49. Peyron F, Burdin N, Ringwald P, Vuillez J, Rousset F, Banchereau J. High levels of circulating IL-10 in human malaria. Clin Exp Immunol. 1994;95:300–3. Mooney et al. Malar J (2018) 17:253 48. Kai OK, Roberts DJ. The pathophysiology of malarial anaemia: where have all the red cells gone? BMC Med. 2008;6:24. 47. WHO. Serum transferrin receptor levels for the assessment of iron status and iron deficiency in populations. Geneva: World Health Organization, WHO/NMH/NHD/EPG/14.6, 2014. 49. Peyron F, Burdin N, Ringwald P, Vuillez J, Rousset F, Banchereau J. High levels of circulating IL-10 in human malaria. Clin Exp Immunol. 1994;95:300–3. 50. Jagannathan P, Eccles-James I, Bowen K, Nankya F, Auma A, Wamala S, et al. IFNγ/IL-10 co-producing cells dominate the CD4 response to malaria in highly exposed children. PLoS Pathog. 2014;10:e1003864. 50. Jagannathan P, Eccles-James I, Bowen K, Nankya F, Auma A, Wamala S, et al. IFNγ/IL-10 co-producing cells dominate the CD4 response to malaria in highly exposed children. PLoS Pathog. 2014;10:e1003864. 46. Sher EA, Hemi K, Efrati S, Weissgarten J, Shaklai M, Shaklai N. Hemopexin is protective against intravascular hemolysis–induced vascular damage. Blood. 2010;116:3207. 47. WHO. Serum transferrin receptor levels for the assessment of iron status and iron deficiency in populations. Geneva: World Health Organization, WHO/NMH/NHD/EPG/14.6, 2014. 48. Kai OK, Roberts DJ. The pathophysiology of malarial anaemia: where have all the red cells gone? BMC Med. 2008;6:24. References Malaria parasite infection compromises control of concurrent sys- temic non-typhoidal Salmonella infection via IL-10-mediated alteration of myeloid cell function. PLoS Pathog. 2014;10:e1004049. 43. Park SE, Pak GD, Aaby P, Adu-Sarkodie Y, Ali M, Aseffa A, et al. The relation- ship between invasive nontyphoidal Salmonella disease, other bacterial bloodstream infections, and malaria in sub-Saharan Africa. Clin Infect Dis. 2016;62(suppl 1):S23–31. 22. Mooney JP, Butler BP, Lokken KL, Xavier MN, Chau JY, Schaltenberg N, et al. The mucosal inflammatory response to non-typhoidal Salmonella in the intestine is blunted by IL-10 during concurrent malaria parasite infection. Mucosal Immunol. 2014;7:1302–11. 44. Uche IV, MacLennan CA, Saul A. A systematic review of the incidence, risk factors and case fatality rates of invasive nontyphoidal Salmonella (iNTS) disease in Africa (1966 to 2014). PLoS Neglect Trop Dis. 2017;11:e0005118. 23. 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https://zenodo.org/records/8035825/files/WJBPHS-2023-0134.pdf
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Antioxidant activity and the estimation of total phenolic content of Citrullus colocynthis stem
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Sushila Saini * Sushila Saini * Department of Botany, Janta Vidya Mandir Ganpat Rai Rasiwasia College, Charkhi Dadri-127306, Haryana, India. World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 Publication history: Received on 03 February 2023; revised on 17 March 2023; accepted on 20 March 2023 Article DOI: https://doi org/10 30574/wjbphs 2023 13 3 0134 ublication history: Received on 03 February 2023; revised on 17 March 2023; accepted on 20 March Article DOI: https://doi.org/10.30574/wjbphs.2023.13.3.0134 Abstract To examine the antioxidant and free radical scavenging activity of Citrullus colocynthis stem, five different extracts were investigated. Various in vitro antioxidant assay including DPPH (2,2-diphenylpicrylhydrazyl) radical, superoxide radical, hydroxyl radical scavenging activity along with reducing power and metal chelating activity were done and compared with standard antioxidants such as ascorbic acid, BHT (Butylated hydroxytoluene) and EDTA (Ethylene diamine tetra acetic acid). Total phenolic content was determined as mg/g Gallic acid equivalent and was correlated with antioxidant assays. All the five extracts showed significant antioxidant activity in dose dependent manner. Methanolic extract possesses the highest scavenging ability for all the assays and total phenolic content in it was 40.12 mg/g gallic acid equivalent. In case of methanolic extract significant correlation was observed between total phenolic content and various antioxidant assays suggesting its role as a source of valuable antioxidants against free radicals associated oxidative stress. Keywords: Citrullus colocynthis; Antioxidant activity; Free radicals; Total phenolic content Antioxidant activity and the estimation of total phenolic content of Citrullus Antioxidant activity and the estimation of total phenolic content of Citrullus * Corresponding author: Saini Sushila Copyright © 2023 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Copyright © 2023 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0. Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4 2.3. Statistical analysis On way ANOVA (Analysis of Variance) followed by Duncan’s multiple range tests at p<0.05 were used. Pearson’s correlation coefficient was used to determine correlation between TPC and antioxidant assays. 1. Introduction Many human diseases are the outcome of oxidative stress caused by free radicals generated by aerobic respiration, environmental contaminants, unhealthy food and stress. Most common oxygen derived free radicals are hydrogen peroxide (H2O2) superoxide anion (O2•-) peroxyl (ROO•), reactive hydroxyl (OH•) and hypochlorous acid (HOCl) [1,2]. Free radicals generated in the cells attack biological membranes, cell organelles and DNA thereby initiating chain reactions leading to detrimental effects such as enzyme inactivation, DNA breakage and even cell death. Thus oxidative stress induced by reactive oxygen species implicated in serious health problems such as inflammatory diseases, stroke, hyperglycemia, neurodegenerative diseases, cancer and premature aging [3,4]. Plant based antioxidants could show great potential as therapeutic agents by avoiding oxidative damage thereby preventing occurrence of degenerative diseases, cancer and aging. These are secondary metabolites produced naturally in plants and can counter free radicals generation by donating their electrons thus terminating the chain reactions [5,6]. Citrullus colocynthis (L.) Schard (Cucurbitaceae) commonly called Bitter apple or tumba is a perennial viny herb widely distributed in dry regions of Africa, Asia, Arabia and Mediterranean. Its utility as a medicinal plant is well documented in indigenous system of medicine for the treatment of leprosy, diabetes, asthma, bronchitis, edema, fever, joint pain and cancer. In Indian subcontinent its fruits are used for bacterial infections, hepatic and abdominal diseases, diabetes and rheumatism [7,8]. Preliminary phytochemical analysis of different parts of C. colocynthis affirm the presence of tannins, flavonoids, phenolics, glycosides and triterpenoids [9,10,11] of which flavonoids and phenolics could play a role in scavenging of free radicals and thus inhibiting harmful effects resulting from oxidative stress [12]. This study was carried out to investigate the antioxidant potential of various solvent extracts of C. colocynthis stem. World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 2.1. Preparation of different extracts Plants of Citrullus were collected from the dry regions of Southern Haryana and identified with voucher number 10814 at FRI, Dehradun. Stem was cut into pieces, dried in shade and grounded to fine powder. For preparation of extracts 100 gram of powder was extracted separately with petroleum ether, benzene, chloroform, methanol and water using cold percolation method. Each extract was evaporated using a rotary evaporator at 400C and stored for further use. 2.2. Total phenolic content and antioxidant assays Total phenolic content was measured according to the method of Singleton and Rossi [13] with some modifications and expressed as Gallic acid equivalent (GAE). The ability of the extracts to reduce DPPH radical was assayed by decreased absorbance at 517 nm according to the method of Lee et al [14]. Nitro blue tetrazolium reduction method was employed for finding out superoxide radical scavenging activity [15]. The hydroxyl radical scavenging capability was evaluated by means of the deoxyribose method described by Kunchandy and Rao, [16]. Ability of extracts to chelate metal ions and to compete with Ferrozine for ferrous iron in solution was measured by method of Dinis et al [17]. Reducing power ability was assayed by observing Fe3+ to Fe2+ reduction by different extracts using the method of Yen and Duh [18]. Increased absorbance with increasing concentration indicates increased reducing power. All the assessments were done in triplicate and to measure percentage inhibition following formu were done in triplicate and to measure percentage inhibition following formula was used. % Inhibition = A (control)-A (sample or standard) / A (control) × 100, A (control) = absorbance of the control A (sample or standard) = absorbance of sample extract or standard 3. Results and discussion 3. Results and discussion 3.1. Total Phenolic Content (TPC) Figure 1 Total phenolic content (TPC) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE-chloroform extract, ME- methanol extract, AE- aqueous extract) Phenolic compounds are the secondary metabolites present in plants having the capacity to quench free radicals. They 3.2. DPPH Radical scavenging activity To evaluate the free radical scavenging ability of natural antioxidants DPPH assay is most widely used. DPPH radical gives a violet solution in ethanol with maximum absorption at 517 nm. As the antioxidants in the extract scavenge the DPPH radical, it resulted in discoloration of the solution which coincides with the number of electrons consumed. More bleaching of the solution from violet to yellow indicates greater efficacy of the extract to neutralize the radicals [20]. Ascorbic acid was used as a standard compound at varying concentration of 10µg-50µg/ml for determination of antioxidant activity. Table 1 exhibited the scavenging effect of different concentrations of solvents and ascorbic acid on DPPH radical. Methanolic extract has the maximum scavenging potential followed by benzene> aqueous> chloroform> petroleum extract. The IC50 values of different extracts were much greater as compared to ascorbic acid indicating that plant extract has weaker DPPH radical scavenging ability than reference compound. Table 1 DPPH free radical scavenging activity (%) of stem extracts of C. colocynthis Stem extracts Concen- tration (mg/ml) PE BE CE ME AE Concentration (µg/ml) of AS AS 0.2 8.43±0.35e 10.35±0.38e 7.12±0.20e 25.13±0.58e 9.93±0.89e 10 20.84±0.62e 0.4 12.61±0.42d 13.63±0.46d 13.34±0.56d 40.45±0.42d 12.53±0.23d 20 38.63±0.40d 0.6 18.15±0.60c 22.42±0.12c 17.91±0.28c 45.34±0.75c 19.60±0.22c 30 75.17±0.60c 0.8 21.02±0.55b 34.83±0.35b 23.34±0.32b 50.78±0.51b 23.19±0.11b 40 80.28±0.12b 1.0 25.33±0.66a 38.43±0.57a 27.72±0.66a 56.45±0.62a 30.28±0.15a 50 84.80±0.66a Values are expressed as mean±S.D., (n=3). Values with in the column not sharing common superscript letters (a-e) differ significantly at p<0.05 by Duncan’s multiple range test. (PE- petroleum ether, BE- Benzene extract, CE- Chloroform extract, ME- Methanol extract, AE- Aqueous extract, AS- Ascorbic acid) 3.3. Superoxide radical scavenging activity Figure 2 Superoxide radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, BHT- Butylated hydroxytoluene) Table 1 DPPH free radical scavenging activity (%) of stem extracts of C. colocynthis Stem extracts Concen- tration (mg/ml) PE BE CE ME AE Concentration (µg/ml) of AS AS 0.2 8.43±0.35e 10.35±0.38e 7.12±0.20e 25.13±0.58e 9.93±0.89e 10 20.84±0.62e 0.4 12.61±0.42d 13.63±0.46d 13.34±0.56d 40.45±0.42d 12.53±0.23d 20 38.63±0.40d 0.6 18.15±0.60c 22.42±0.12c 17.91±0.28c 45.34±0.75c 19.60±0.22c 30 75.17±0.60c 0.8 21.02±0.55b 34.83±0.35b 23.34±0.32b 50.78±0.51b 23.19±0.11b 40 80.28±0.12b 1.0 25.33±0.66a 38.43±0.57a 27.72±0.66a 56.45±0.62a 30.28±0.15a 50 84.80±0.66a Values are expressed as mean±S.D., (n=3). Values with in the column not sharing common superscript letters (a-e) differ significantly at p<0.05 by Duncan’s multiple range test. 3.1. Total Phenolic Content (TPC) 3.1. Total Phenolic Content (TPC) Figure 1 Total phenolic content (TPC) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE-chloroform extract, ME- methanol extract, AE- aqueous extract) Phenolic compounds are the secondary metabolites present in plants having the capacity to quench free radicals. They act as reducing agents, hydrogen donors or metal iron chelators. The antioxidant activity of plant extracts can be due to phenolic compounds because of their ability to neutralize free radicals [19]. TPC was determined using the Folin- Phenolic compounds are the secondary metabolites present in plants having the capacity to quench free radicals. They act as reducing agents, hydrogen donors or metal iron chelators. The antioxidant activity of plant extracts can be due to phenolic compounds because of their ability to neutralize free radicals [19]. TPC was determined using the Folin- 164 World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 ciocalteu reagent and expressed as Gallic acid equivalent. TPC content in different extracts is shown in Figure 1. In C. colocynthis stem highest total phenolic content was found in methanolic extract (40.12 mg/g GAE). Phenolic content in different stem extract was in the order: methanolic> aqueous> chloroform> benzene> petroleum ether extracts. ciocalteu reagent and expressed as Gallic acid equivalent. TPC content in different extracts is shown in Figure 1. In C. colocynthis stem highest total phenolic content was found in methanolic extract (40.12 mg/g GAE). Phenolic content in different stem extract was in the order: methanolic> aqueous> chloroform> benzene> petroleum ether extracts. World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 showed highest inhibition of superoxide radical (46.62%). The IC50 values of methanolic extract and standard BHT (Butylated hydroxytoluene) were 1.2 and 0.18 mg/ml respectively. showed highest inhibition of superoxide radical (46.62%). The IC50 values of methanolic extract and standard BHT (Butylated hydroxytoluene) were 1.2 and 0.18 mg/ml respectively. 3.4. Hydroxyl radical scavenging activity Hydroxyl radicals are highly reactive radicals reacting to membrane phospholipids and causing tremendous cell damage. It is capable of damaging every biomolecule leading to mutagenesis, cytotoxicity and cancer [22]. Hydroxyl radical scavenging ability of plant extracts may inhibit the lipid peroxidation and prevent associated damage. Percentage scavenging activity of different solvents was in the order: methanolic> aqueous> chloroform> benzene> petroleum ether extracts as shown in figure 3. At 1.0mg/ml concentration percentage inhibition of hydroxyl radical generation by methanolic extract and ascorbic acid was 55.32% and 72.39% respectively, with IC50 of methanolic extract (1.2 mg/ml) much higher than the standard (0.094 mg/ml). Figure 3 Hydroxyl radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, AS- Ascorbic acid) Figure 3 Hydroxyl radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, AS- Ascorbic acid) 3.2. DPPH Radical scavenging activity (PE- petroleum ether, BE- Benzene extract, CE- Chloroform extract, ME- Methanol extract, AE- Aqueous extract, AS- Ascorbic acid) Table 1 DPPH free radical scavenging activity (%) of stem extracts of C. colocynthis 3.3. Superoxide radical scavenging activity 3.3. Superoxide radical scavenging activity Figure 2 Superoxide radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, BHT- Butylated hydroxytoluene) 3.3. Superoxide radical scavenging activity Figure 2 Superoxide radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, BHT- Butylated hydroxytoluene) Figure 2 Superoxide radical scavenging activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, BHT- Butylated hydroxytoluene) Superoxide radical itself is a weak oxidant but is a precursor of H2O2, OH radical, singlet oxygen species which are more potent reactive oxygen species contributing to oxidative stress [21]. Superoxide anion causes lipid peroxidation, damage to biomolecules and tissues leading to the onset of various diseases. The percentage inhibition of superoxide anion generated in the PMS-NADH system was evaluated by comparing the absorbance values of control and solvents at 560 nm. In the present study all the extracts showed superoxide radical scavenging activity in a concentration dependent manner (Figure 2). In comparison with other solvents methanolic extract at the 1.0mg/ml concentration 165 World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 3.6. Reducing power assay Reducing power assay method depends on the presence of reductants that react with Potassium Ferricyanide and reduce it to ferrocyanide which on reaction with FeCl2 form ferric-ferrous complex having maximum absorbance at 700 nm [24,25]. In this method the yellow color of the solution changes to green/blue depending on the reducing ability of extracts. Increase in absorbance with increased concentration exhibits increased reducing power of test specimens. Methanolic stem extract showed the highest reductive potential that increased with increased concentration; however it is lower than standard ascorbic acid. The reducing power ability of different solvents was in the sequence: methanolic> benzene> chloroform> aqueous> petroleum ether extracts as depicted in figure 5. Figure 5 Reducing power assay of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, AS- Ascorbic acid) Figure 5 Reducing power assay of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, AS- Ascorbic acid) 3.5. Metal chelating activity In biological systems, transition metals lead to the generation of hydroxyl radicals by Haber-Weiss and Fenton type of reactions. Plant extracts having antioxidants can form chelates with transition metal ions resulting in the suppression of generation of hydroxyl radicals thus saving the biological molecules from peroxidation [23]. In the present study plant extracts chelate iron and thus Ferrozine-Fe2+ complex formation is disrupted resulting in decreased absorption at 562 nm in concentration dependent manner. The methanolic, aqueous, chloroform, benzene and petroleum ether extracts of C. colocynthis stem were found to possess dose dependent chelation activity as shown in results depicted in figure 4. In the stem extracts metal chelating ability was maximum in methanolic extract which varied from 25.29% at 0.2 mg/ml to 56.69% at 1.0mg/ml concentration. The mean IC50 value of methanolic extract (1.2 mg/ml) was higher than standard EDTA (0.19 mg/ml). Figure 4 Metal chelating activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, EDTA- Ethylenediamine tetra acetic acid) Figure 4 Metal chelating activity (%) of stem extracts of C. colocynthis (PE- petroleum ether extract, BE- benzene extract, CE- chloroform extract, ME- methanol extract, AE- aqueous extract, EDTA- Ethylenediamine tetra acetic acid) 166 4. Conclusion On the basis of various in vitro assays used in present study it can be concluded that methanolic extract of C. colocynthis possess significant antioxidant activity. These activities may be due to phenolic compounds present in the extract thus establishing its role in preventing oxidative stress related diseases and promotion of longevity. 3.7. Correlation between total phenolic content and antioxidant activity Phenolic compounds such as phenolic acids, flavonoids, tannins and anthocyanins are secondary metabolites naturally occurring in plants having free radical scavenging ability by donating electrons or by acting as metal chelators. Several previous reports showed good correlation between antioxidant activity and total phenolic content in plant extracts [26,10]. Methanolic extract of C. colocynthis stem exhibited highest antioxidant activity and also showed good correlation between TPC and different antioxidant assays. Table 2 shows the value of correlation coefficient as 0.913168, 0.941537, 0.912252 and 0.928704 respectively for DPPH, superoxide, hydroxyl and metal chelating activity. These results indicate that phenolic content might be contributing towards antioxidant activity of C. colocynthis. From different parts of C. colocynthis various phenolic compounds have been previously reported [27,28]. Aqueous and ethanolic extract of C. colocynthis fruits, leaves and whole plant were found to contain alkaloids, flavonoids, coumarins, saponins and glycosides [29,30,31]. Different parts of C. colocynthis (roots, stem, leaves, and fruits) found to contain flavonoids such as quercetin, myricetin and kaempferol [32,33]. Ariel parts were found to possess flavonoids such as 8- C-p-hydroxybenzoylisovitexin, 6-C-p-hydroxybenzoylvitexin, 8-C-p-hydroxybenzoylisovitexin-4’-O-glycoside while the fruits showed the presence of isovitexin, isoorientin and isoorientin3’-o-methyl ether [34]. In nutshell, C. colocynthis is rich in polyphenols and flavonoids which confer to the plant antioxidant activity. Table 2 Correlation analysis between different antioxidant tests with their respective total phenolic content at 1 mg/ml concentration in C. colocynthis stem methanolic extract Assays Total phenolics in stem r R2 DPPH radical scavenging 0.913168* 0.832* Superoxide radical scavenging 0.941537* 0.886* Hydroxyl radical scavenging 0.912252* 0.833* Metal chelating assay 0.928704* 0.862* r- correlation coefficient, R2- coefficient of determination, *significance at p<0.05 Table 2 Correlation analysis between different antioxidant tests with their respective total phenolic content at 1 mg/ml concentration in C. colocynthis stem methanolic extract Table 2 Correlation analysis between different antioxidant tests with their respective total phenol concentration in C. colocynthis stem methanolic extract on analysis between different antioxidant tests with their respective total phenolic content at 1 mg/m . colocynthis stem methanolic extract 167 World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 Disclosure of conflict of interest No conflict of interest. Acknowledgments I express my gratitude to the University Grant Commission for sanctioning Minor Research project to carry out this research. Disclosure of conflict of interest References 168 World Journal of Biology Pharmacy and Health Sciences, 2023, 13(03), 163–169 [15] Liu F, Ooi VEC, Chang ST. Free radical scavenging activities of mushroom polysaccharide extracts. Life sciences. 1997; 60(10): 763-771. [16] Kunchandy E, Rao MNA. Oxygen radical scavenging activity of curcumin. International journal of pharmaceutics. 1990; 58(3): 237-240. [17] Dinis TC, Madeira VM, Almeida LM. Action of phenolic derivatives (acetaminophen, salicylate, and 5- aminosalicylate) as inhibitors of membrane lipid peroxidation and as peroxyl radical scavengers. Archives of biochemistry and biophysics. 1994; 315(1): 161-169. [18] Yen GC, Duh PD. Antioxidative properties of methanolic extracts from peanut hulls. Journal of the Aerican oil chemists' society. 1993; 70(4): 383-386. 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Claustrum projections to prefrontal cortex in the capuchin monkey (Cebus apella)
Frontiers in systems neuroscience
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INTRODUCTION Although it was first described over 200 years ago, the claus- trum remains an enigma in modern neuroscience (Crick and Koch, 2005; Smythies et al., 2014). The convoluted geometry and difficult surgical approach to the claustrum, combined with its close proximity to the insula and putamen, have contributed to the uncertainty regarding claustrum function, as has the poor understanding of its cytoarchitectonic and chemoarchitectonic organization. The dearth of information regarding the claus- trum is particularly acute among primate species. Although it has been shown that the claustrum has widespread reciprocal con- nectivity with the cerebral cortex, there is growing evidence for species differences in morphology, neurochemistry, and connec- tivity (reviewed in Baizer, 2014). In macaques, Pearson et al. (1982) and Tanne-Gariepy et al. (2002) examined claustrum afferents to lateral prefrontal areas, including areas 8, 9, 12, and 46, and to motor and premotor areas of frontal cortex. These studies showed that projections to area 46 were widespread, and extended along the majority of the rostral- caudal axis of the claustrum (this includes the injections of area 9 in Pearson et al., 1982). Projections to area 12 overlapped the distribution of area 9 connections, but extended more ventrally, especially in the more caudal portion of the claustrum. Afferent input from the claustrum to supplementary and premotor areas in both studies were segregated from prefrontal inputs along the dorsal-ventral axis of the claustrum, with less prominent separation of labeled cells along the rostral-caudal axis. Claustrum connections to prefrontal areas have been exam- ined in rodents (Vertes, 2004; Hoover and Vertes, 2007) and primates (Pearson et al., 1982; Tanne-Gariepy et al., 2002), as well as humans (Fernandez-Miranda et al., 2008; Milardi et al., 2013). In the rat, projections to the prelimbic area arise from the dor- sal or insular portion of the claustrum, while projections to the infralimbic cortex are concentrated in the ventral (endopiriform) portion of the claustrum (Vertes, 2004). Hoover and Vertes (2007) expanded the range of observed rat prefrontal areas to include the anterior cingulate and frontal agranular areas, but reported a sim- ilar distribution of afferent projections to the earlier study, along In humans, Fernandez-Miranda et al. SYSTEMS NEUROSCIENCE published: 03 July 2014 doi: 10.3389/fnsys.2014.00123 Keywords: claustrum, primate, cortical networks, neuroanatomy, prefrontal Frontiers in Systems Neuroscience Claustrum projections to prefrontal cortex in the capuchin monkey (Cebus apella) David H. Reser 1*, Karyn E. Richardson 1,2, Marina O. Montibeller 1, Sherry Zhao 1, Jonathan M. H. Chan 1, Juliana G. M. Soares 3, Tristan A. Chaplin 1, Ricardo Gattass 3 and Marcello G. P. Rosa 1,4 1 Department of Physiology, Monash University, Clayton, VIC, Australia 2 Department of Psychology and Psychiatric Medicine, Monash University, Clayton, VIC, Australia 3 Programa de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 4 Australian Research Council Centre of Excellence for Integrative Brain Function, Clayton, VIC, Australia 1 Department of Physiology, Monash University, Clayton, VIC, Australia 2 Department of Psychology and Psychiatric Medicine, Monash University, Clayton, VIC, Australia 3 Programa de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 4 Australian Research Council Centre of Excellence for Integrative Brain Function, Clayton, VIC, Australia We examined the pattern of retrograde tracer distribution in the claustrum following intracortical injections into the frontal pole (area 10), and in dorsal (area 9), and ventral lateral (area 12) regions of the rostral prefrontal cortex in the tufted capuchin monkey (Cebus apella). The resulting pattern of labeled cells was assessed in relation to the three-dimensional geometry of the claustrum, as well as recent reports of claustrum-prefrontal connections in other primates. Claustrum-prefrontal projections were extensive, and largely concentrated in the ventral half of the claustrum, especially in the rostral 2/3 of the nucleus. Our data are consistent with a topographic arrangement of claustrum-cortical connections in which prefrontal and association cortices receive connections largely from the rostral and medial claustrum. Comparative aspects of claustrum-prefrontal topography across primate species and the implications of claustrum connectivity for understanding of cortical functional networks are explored, and we hypothesize that the claustrum may play a role in controlling or switching between resting state and task-associated cortical networks. ORIGINAL RESEARCH ARTICLE published: 03 July 2014 ORIGINAL RESEARCH ARTICLE published: 03 July 2014 Reviewed by: *Correspondence: David H. Reser, Department of Physiology, Monash University Clayton, Bldg. 13F, Clayton, VIC 3800, Australia e-mail: david.reser@monash.edu with dense projections from the dorsal claustrum to anterior cingulate and frontal agranular areas. Edited by: Edited by: Brian N. Mathur, University of Maryland School of Medicine, USA Reviewed by: Brian N. Mathur, University of Maryland School of Medicine, USA Peter M. Kaskan, National Institutes of Mental Health, USA *Correspondence: David H. Reser, Department of Physiology, Monash University Clayton, Bldg. 13F, Clayton, VIC 3800, Australia e-mail: david.reser@monash.edu TRACER INJECTIONS order to make accurate comparisons. To date, there have been few studies of claustro-cortical connections in New World monkey species. All tracers were injected using a 1 µL Hamilton syringe. The animals were pre-medicated with atropine (0.15 mg/kg IM) and diazepam (0.5 mg/kg IM) and anesthetized with ketamine (30 mg/kg IM) and maintained using intramuscular ketamine and xylazine (1:5). All animals received peri-operative antibiotics (penicillin G, 300,000 IU, IM) and dexamethasone (0.3 mg/kg, IM). The present study describes the claustral projections to the prefrontal cortex of the Cebus (capuchin) monkey, a species of New World monkey. The anatomy of Cebus monkey prefrontal cortex has recently been described in detail by Cruz-Rizzolo et al. (2011), including identification of cytoarchitectonic and myeloar- chitectonic boundaries of cortical areas corresponding to those identified in macaques (Petrides and Pandya, 1999, 2002; Chaplin et al., 2013) and marmosets (another species of New World mon- key; Burman et al., 2006; Burman and Rosa, 2009; Paxinos et al., 2012). We have previously reported that the dorsal and lateral portions of the frontal pole (area 10) of the marmoset receives a rich claustrum projection (Burman et al., 2011a,b). A craniotomy was performed over the target regions of cor- tex, and the tracer was deposited in 50–100 nL increments over approximately 15 min. The micropipette tip was left in place for an additional 5–10 min following the last deposit, in order to min- imize leakage of tracer into non-target areas. The injection into area 12o was accessed from the dorsal surface of the frontal cor- tex and intervening white matter. Tracer leakage along the needle track was minimized by slow withdrawal; however, it is possible that some contamination of the adjacent white matter occurred. After the final injection, the tip was withdrawn, and the bone flap excised during the craniotomy was replaced and cemented into place. The overlying tissue was sutured and the animal was allowed to recover until it could make spontaneous and coordi- nated movements, after which it was returned to the home cage. Each animal was carefully monitored during the 14 day post- injection survival period, during which analgesics and antibiotics were provided as required. At the end of the survival period, each animal was humanely euthanized with an overdose of sodium pentobarbital (40 mg/kg) and transcardially perfused with saline followed by 4% paraformaldehyde in phosphate buffered saline. HISTOLOGICAL PROCESSING Perfused brains were cryoprotected in increasing concentrations of glycerol (5–15% in 4% PFA), then sectioned on a cryostat at 50 µm thickness. Every tenth section was mounted unstained for fluorescence microscopy. These sections were dried and coverslipped with di-n-butyl phthalate xylene (DPX) following quick dehydration (2 × 100% ethanol) and immersion in xylene. Adjacent series of sections were stained for Nissl, myelin (Gallyas, 1979), and cytochrome oxidase (Wong-Riley, 1979). Table 1 | Case information and tracer injection locations. Animal Body Sex Hemisphere Tracer Amount Location ID weight (kg) (uL) FR01 3.3 M R FB 0.4 Area 10 DY 0.4 Area 10 FE 1.0 Area 10 FR 1.0 Area 10 FR02 3.0 M R FB 0.5 Area 10 FE 1.0 Area 10 DY 0.5 Area 12 FR04 3.0 M R FB 0.5 Area 9 DY 0.5 Area 12o Summary of individual case data and injection targets. Recovery time for all animals was 2 weeks post-injection. Table 1 | Case information and tracer injection locations. MICROSCOPY AND PHOTOGRAPHY Fluorescence labeled sections were examined unstained using a Zeiss Axioplan fluorescence microscope, and labeled cell bodies were plotted with an X-Y stage digitizer (MD-3, Accustage) and associated software (MD-Plot, v. 5.3). Photographs of selected tis- sue sections and injection sites were obtained using a Zeiss ICC5 camera. The resulting images were cropped, adjusted for level, brightness, and contrast, and re-sized using Adobe Photoshop. TRACER INJECTIONS The brain was extracted and further post-fixed for 24 h in 4% paraformaldehyde. MATERIALS AND METHODS Three adult Cebus apella monkeys were injected with fluores- cent tracers, including fluororuby (FR, 10% in dH20), fluo- roemerald (FE, 10% in dH20), diamidino yellow (DY, 2% in dH20), and fast blue (FB, 2% in dH20), at multiple loca- tions in prefrontal and orbitofrontal cortex. Case details for each animal are summarized in Table 1. All surgical and exper- imental procedures were approved in advance by the Animal Ethics Committee of the Centro de Ciências da Saúde of the Universidade Federal do Rio de Janeiro (CEUA IBCCF189- 06/16), and conformed to the guidelines of the Brazilian Federal Arouca law governing laboratory animal use and care, as well as the Australian Code of Practice for Care and Use of Animals for Scientific Purposes. Tracer injections and histological pro- cessing were conducted at the Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, Brazil. Microscopic examina- tion and data analysis were performed in the Department of Physiology of Monash University. Throughout this report, the numerical designations used for the various prefrontal areas conform to those of Cruz-Rizzolo et al. (2011). Stereotaxic location estimates are based on the Eidelberg and Saldias atlas (1960). INTRODUCTION (2008) described segre- gation of the claustro-cortical white matter tracts using a combi- nation of cadaver dissection and diffusion tensor imaging, with clear separation of frontal and prefrontally projecting axons from those projecting to other cortical areas, e.g., temporal and pari- etal cortex. Despite advances in tractographic imaging methods (e.g., Milardi et al., 2013), non-human primates remain the best experimental model for detailed studies of connectivity of larger networks of cortical areas. It is therefore essential to understand the homology between identified cortical areas across species, in July 2014 | Volume 8 | Article 123 | 1 www.frontiersin.org www.frontiersin.org www.frontiersin.org Claustrum-prefrontal connections Reser et al. GENERAL FINDINGS The cytoarchitectonic and myeloarchitectonic characteristics of the Cebus monkey claustrum have not been previously described in detail. The appearance of the claustrum in frontal sections is generally consistent with that of other commonly used labora- tory primate species, including the macaque (Pearson et al., 1982; Kowianski et al., 1999), vervet monkey (Kowianski et al., 1999), and marmoset (Burman et al., 2011a; Paxinos et al., 2012). One morphological difference between the cebus monkey and the mar- moset is the dorsolateral extension of the insular claustrum into the white matter of the parietal operculum overlying the lateral sulcus, as shown in Figure 1. This is not observed in marmosets, but is present in macaques (Baizer, 2014) and humans, though the functional significance and cortical connectivity of this region remain poorly characterized. FIGURE 1 | Histological boundaries of Cebus claustrum. (A) Myelin (a,c) and nissl (b,d) stained frontal sections showing the dorsal and ventral extent of the claustrum at approximately A-P +13.0 in the atlas of Eidelberg and Saldias (1960). Dashed lines in the low magnification images (A) show the maximum dorsal extent of the claustrum, which is difficult to appreciate in most histological preparations. The rectangular outlines in (a,b) indicate areas shown at high magnification in (c,d). Panels (c,d) show the difficulty of accurate estimation of the ventromedial boundary of the claustrum in standard histological preparations. Red arrowheads show a small cluster of cells separated from the putative claustrum boundary by a portion of the external capsule white matter. Small arrows in (d) show the approximate boundary between the dorsal endopiriform nucleus and the insular claustrum as estimated from the histological characteristics of the marmoset (Paxinos et al., 2012). Detailed cytoarchitectonic information is not currently available for Cebus, so this parcellation should be considered provisional, pending identification of reliable markers of internal and external claustrum boundaries in this species. Scale bars = 1 mm in (b); 0.2 mm in (d). (B) shows frontal (left) and lateral (right) views of case FR01, modeled as described in Materials and Methods. The lateral view was used as the template for heat mapping of tracer distribution in subsequent figures. Red and yellow asterisks provide common points of reference for the rotated views. GENERAL FINDINGS Definition of claustrum borders with respect to the adja- cent white matter tracts was clearest in myelin-stained sections (Figures 1Aa,c), with the claustrum appearing as a region of lightly myelinated tissue between the external and extreme cap- sules. The dorsolateral extension of the claustrum was evident in both Nissl and myelin stains, although it was faint (Figures 1Aa,b, upper dotted lines). In addition, precise determination of the rostral and ventral boundaries of the claustrum was difficult, especially at the rostral-caudal level, where it converges with the anterior insula, consistent with findings from both rodent and other primate species (Figure 1; Mathur et al., 2009; Paxinos et al., 2012). In several sections, small clusters of cells were located away from the apparent medial boundary of the claustrum (Figures 1Ac,d; red arrows). In caudal sections, the boundary between the dorsal endopiriform nucleus and insular claustrum was best appreciated in Nissl stained sections (dark arrowheads in Figures 1Ad). The general location of this boundary is consistent with the demarcation reported for the marmoset (Paxinos et al., 2012), but the presence of detached cell clusters (green arrow- heads in Figures 1Ac,d) precluded volumetric measurement or direct comparisons between species. Cytochrome oxidase was not particularly useful for delineation of either boundaries or internal compartments of the claustrum (data not shown). FIGURE 1 | Histological boundaries of Cebus claustrum. (A) Myelin (a,c) and nissl (b,d) stained frontal sections showing the dorsal and ventral extent of the claustrum at approximately A-P +13.0 in the atlas of Eidelberg and Saldias (1960). Dashed lines in the low magnification images (A) show the maximum dorsal extent of the claustrum, which is difficult to appreciate in most histological preparations. The rectangular outlines in (a,b) indicate areas shown at high magnification in (c,d). Panels (c,d) show the difficulty of accurate estimation of the ventromedial boundary of the claustrum in standard histological preparations. Red arrowheads show a small cluster of cells separated from the putative claustrum boundary by a portion of the external capsule white matter. Small arrows in (d) show the approximate boundary between the dorsal endopiriform nucleus and the insular claustrum as estimated from the histological characteristics of the marmoset (Paxinos et al., 2012). Detailed cytoarchitectonic information is not currently available for Cebus, so this parcellation should be considered provisional, pending identification of reliable markers of internal and external claustrum boundaries in this species. DATA ANALYSIS Digital files containing cell count and position information were processed in Adobe Illustrator CS6, which was used to extract and align the claustrum outlines and surgical schemat- ics. A three-dimensional model of the claustrum from case FR01 was created using manually aligned Nissl-stained sections with mid-thickness drawings, resulting in a series of contours that were July 2014 | Volume 8 | Article 123 | 2 Frontiers in Systems Neuroscience Frontiers in Systems Neuroscience www.frontiersin.org www.frontiersin.org Claustrum-prefrontal connections Reser et al. (e.g., 20–100% yellow for the minimum-maximum range) for labeled cell density within each grid square. In practice, the cell density across all cases ranged from 1 cell to approximately 25 cells/grid, with the vast majority of grid squares containing fewer than 5 cells. Although this method yields a valuable display for comparison across injections and cases, it necessarily introduces some distortions, especially at the extreme dorsal and ventral por- tions of the map, where the Cebus claustrum varies the most in its medial-lateral extent. Moreover, the relative medial and lateral positions of labeled cells are lost in this flattened display. The dis- tortion was considered acceptable in this study, as there were no cells in the dorsal-most or dorso-lateral portions of the insular claustrum in any of the cases studied. Spatial separation of cells in the ventral regions of the insular claustrum was observed, but this information is not captured in the flattened 2-D map format. then reconstructed into a 3D triangular mesh (Figure 1B), using the program CARET (Van Essen et al., 2001). The lateral view of this 3-dimensional model was then traced and smoothed in Illustrator, and overlaid with a 200 × 200 µm square grid, which was used as a template for plotting cells from each case, in order to facilitate comparison across injections. Each case was normal- ized to the maximum dorsal-ventral distance of the claustrum sections, and the grid was subsequently applied across all sec- tions (24–26 sections per case). Cells within each grid square were counted and translated to a “heat map.” Color scales were derived by setting the low value to 20% of the respective color on the CMYK color scale, with the 100% value as the maximum FIGURE 1 | Histological boundaries of Cebus claustrum. (A) Myelin (a,c) FRONTAL POLE CONNECTIONS Six injections were placed in the frontal pole region of two monkeys. The resulting distribution of labeled neurons in the ipsilateral claustrum is shown for a representative case (FR02) in Figure 2, which received two injections within area 10. Both injections resulted in patches of retrogradely labeled cells in the claustrum, which occupied a ventral position across multiple lev- els of the rostral-caudal axis. Areas of particularly dense clustering of labeled neurons were observed in the rostral and middle lev- els of the claustrum. However, no labeled cells were observed in the dorsal part the claustrum. The medial FE injection yielded far fewer labeled cells than the central FB injection, with the cells clustered into smaller areas (Figures 2B,C); these were completely encompassed within the area containing FB label. This pattern As viewed from the lateral aspect, the Cebus claustrum is shaped like a distended rhomboid, slightly elongated on the rostral-caudal axis. Because of the undulating structure of the claustrum, this view has been used to demonstrate topography FIGURE 2 | Distribution of labeled neurons following injections in area 10. The placements of fast blue and fluoroemerald injections into the frontal pole are shown in (A). Coronal section locations are shown schematically on the left, while the positions of the main tracer deposits are shown in the digitized tracings on the right. Note that the fluid volume of the fluoro emerald (FE) injection in this case (FR02) was quite large (1 µl, Table 1), but the largest fraction of the deposit was located in the histologically stained sections between the unstained fluorescence sections plotted in this figure. Panel (B) shows the location of each of the labeled neurons from these injections in coronal sections of the claustrum. The corresponding heat maps are shown in (C), illustrating the overall distribution of labeled cells overlaid on the lateral view of the 3-D model of the Cebus claustrum. Asterisks indicate the position of approximately 2 sections lost at the interface of the rostral and caudal tissue blocks during tissue cutting. sections between the unstained fluorescence sections plotted in this figure. Panel (B) shows the location of each of the labeled neurons from these injections in coronal sections of the claustrum. The corresponding heat maps are shown in (C), illustrating the overall distribution of labeled cells overlaid on the lateral view of the 3-D model of the Cebus claustrum. GENERAL FINDINGS Scale bars = 1 mm in (b); 0.2 mm in (d). (B) shows frontal (left) and lateral (right) views of case FR01, modeled as described in Materials and Methods. The lateral view was used as the template for heat mapping of tracer distribution in subsequent figures. Red and yellow asterisks provide common points of reference for the rotated views. FIGURE 1 | Histological boundaries of Cebus claustrum. (A) Myelin (a,c) and nissl (b,d) stained frontal sections showing the dorsal and ventral Tracer injections were deemed successful if the main tracer deposit was predominantly confined to an area of cortical gray July 2014 | Volume 8 | Article 123 | 3 Frontiers in Systems Neuroscience www.frontiersin.org Claustrum-prefrontal connections Reser et al. matter which could be clearly localized by cytoarchitectonic and myeloarchitectonic characteristics, and for which long range transport of the tracer material could be definitively established by the presence of labeled cells in thalamic nuclei, cortical areas far removed from prefrontal cortex, or the homotopic contralat- eral cortical hemispheres. Nine successful tracer injections were placed in three monkeys. The majority of tracer deposits targeted the frontal pole (area 10). One deposit was placed in the rostral dorsolateral prefrontal cortex (area 9). Two injections were placed in area 12, one in the orbital subdivision (area 12o; case FR04-DY) near the border with the lateral subdivision of area 11, and one in ventrolateral prefrontal area 12 (FR02-DY). Double-labeled neu- rons were not observed, although it is still possible that these exist in small numbers. of cortical projections in previous studies (Pearson et al., 1982), and we employed it in this study to map the distribution of retro- gradely labeled neurons, as detailed in the Materials and Methods. Frontiers in Systems Neuroscience FRONTAL POLE CONNECTIONS Asterisks indicate the position of approximately 2 sections lost at the interface of the rostral and caudal tissue blocks during tissue cutting. FIGURE 2 | Distribution of labeled neurons following injections in area 10. The placements of fast blue and fluoroemerald injections into the frontal pole are shown in (A). Coronal section locations are shown schematically on the left, while the positions of the main tracer deposits are shown in the digitized tracings on the right. Note that the fluid volume of the fluoro emerald (FE) injection in this case (FR02) was quite large (1 µl, Table 1), but the largest fraction of the deposit was located in the histologically stained July 2014 | Volume 8 | Article 123 | 4 Frontiers in Systems Neuroscience www.frontiersin.org www.frontiersin.org Claustrum-prefrontal connections Reser et al. FIGURE 3 | Medial-lateral gradient of claustrum projections. Locations of 4 tracer injections in area 10 of case FR01 are shown schematically in (A). The distributions of labeled neurons for each tracer are overlaid in the heatmap format in panel (B). Scale bars = 1 cm in (A); 1 mm in (B). FB, fast blue; DY, diamidino yellow; FR, fluoro ruby; FE, fluoro emerald. in the heatmap format in panel (B). Scale bars = 1 cm in (A); 1 mm in (B). FB, fast blue; DY, diamidino yellow; FR, fluoro ruby; FE, fluoro emerald. FIGURE 3 | Medial-lateral gradient of claustrum projections. Locations of 4 tracer injections in area 10 of case FR01 are shown schematically in (A). The distributions of labeled neurons for each tracer are overlaid DORSAL PREFRONTAL CONNECTIONS of increased claustrum label density following tracer injections in more rostral and lateral portions of area 10 was also evident in the second case, in which three of the injections were well con- tained within area 10 (FR01- FB, FR, DY), and one injection was located near the boundary with area 9 (FR01-FE). The distribu- tions of tracer resulting from those injections are summarized in the heat map in Figure 3. The central and lateral injections (FB and DY, respectively) labeled a much broader area of ventral and medial claustrum than the medial injections (FE and FR), both in terms of overall tissue area and density of labeled neurons. Both medial injections yielded only isolated labeled cells in the claus- trum. Whether this trend reflects functional differences within area 10, or different transport properties of the dextran-based tracers (FR and FE) will require further study. However, both of the medial area 10 injections resulted in long-range transport of tracer, confirmed by the presence of labeled neurons in various thalamic nuclei (data not shown). The dorsal prefrontal region includes areas 8, 9, and 46 (Petrides and Pandya, 1999; Sallet et al., 2013). In this study, a large fast blue injection was deposited in area 9 of one animal (case FR04- FB), which yielded patches of retrogradely labeled neurons in a band which closely tracked the distribution of label observed following injections into the frontal pole, although in a slightly more dorsal position within the claustrum. A discrete, longitu- dinal patch centered in the rostral part of the claustrum was the dominant pattern, with isolated cells and scattered small patches extending along the ventral border to the caudal terminus (Figure 4). Consistent with the pattern observed following injec- tions in area 10, the dorsal and dorsolateral parts of the claustrum were devoid of label, and no interhemispheric projections from the contralateral claustrum were evident. A single isolated cell body was observed in the mid-dorsal region of the contralateral claustrum following this area 9 injection. July 2014 | Volume 8 | Article 123 | 5 www.frontiersin.org www.frontiersin.org Claustrum-prefrontal connections Reser et al. FIGURE 5 | Distribution of labeled neurons in claustrum following injections in area 12. Heat map projections for two injections of diamidino yellow (DY) in area 12 (cases FR02- left; FR04- right). Line drawings show injection locations in frontal sections. DORSAL PREFRONTAL CONNECTIONS Center schematic image shows location of claustrum relative to tissue sections and major sulci of the Cebus brain (gray silhouette). Red dashed lines correspond to tissue sections as marked. The dotted arrows on the right indicate the approach used for injection of area 12o, which traversed the cortical white matter overlying that area. Implications of this approach for interpretation of the data are described in the text. FIGURE 4 | Distribution of labeled neurons in claustrum following tracer injection in area 9. Line drawings show placement of fast blue injection in case FR04, along with the resulting retrogradely labeled cell bodies in the ipsilateral claustrum. Asterisk indicates the position of a single tissue section lost due to slide damage during coverslipping. Scale bar = 1 mm. FIGURE 4 | Distribution of labeled neurons in claustrum following tracer injection in area 9. Line drawings show placement of fast blue injection in case FR04, along with the resulting retrogradely labeled cell bodies in the ipsilateral claustrum. Asterisk indicates the position of a single tissue section lost due to slide damage during coverslipping. Scale bar = 1 mm. FIGURE 5 | Distribution of labeled neurons in claustrum following FIGURE 5 | Distribution of labeled neurons in claustrum following injections in area 12. Heat map projections for two injections of diamidino yellow (DY) in area 12 (cases FR02- left; FR04- right). Line drawings show injection locations in frontal sections. Center schematic image shows location of claustrum relative to tissue sections and major sulci of the Cebus brain (gray silhouette). Red dashed lines correspond to tissue sections as marked. The dotted arrows on the right indicate the approach used for injection of area 12o, which traversed the cortical white matter overlying that area. Implications of this approach for interpretation of the data are described in the text. ORGANIZATION OF CLAUSTRUM-PREFRONTAL CONNECTIONS The distribution of retrograde label in the claustrum following prefrontal injections in Cebus was largely consistent with our pre- vious findings in the marmoset (Burman et al., 2011a), and with the topography of claustrum-prefrontal projections reported in macaques (Pearson et al., 1982). In particular, labeled neurons following injections in areas 9 and 10 were concentrated in a band located along the ventral portion of the claustrum. While the injection in area 9 labeled cells primarily in the rostral part of the claustrum, those in area 10 resulted in strong label in a second, more caudal cluster (compare Figures 2, 4). Claustrum projections to area 12 originated from a similar territory. Labeled neurons were largely absent from the narrow dorsal region of the claustrum, medial to insular cortex, and were completely absent from the extreme dorsal and dorsolateral regions, which have been reported to contain the bulk of claustral neurons project- ing to somatomotor cortex in the macaque (Pearson et al., 1982; Minciacchi et al., 1991). It should be noted that the injection of area 12o (Case FR04-DY) likely involved the white matter dorsal to this area, as the injection needle passed through the overlying tissue. However, we are confident that this did not affect the valid- ity of our observations to an appreciable extent, given the lack of non-specific label in both cerebral hemispheres, which is gener- ally observed in cases of significant white matter intrusion, and the similarity of the pattern of claustrum label resulting from this injection to the other area 12 case (case FR02-DY), in which the white matter was not involved. SUMMARY OF CONNECTIONS The full extent of claustrum projections to prefrontal cortex is summarized in Figures 6A–C, which shows the relative position of the claustrum in lateral view (Figure 6A), as well as some of its proposed subdivisions (frontal- fCl, middle- mCl, and ventral- vCl; see Gattass et al.; this volume) within which prefrontal con- nections originated (Figure 6B). A smoothed representation of the extent of labeled cells originating from each case is shown in Figure 6C, which indicates the degree of homogeneity observed from injections into specific prefrontal areas. Frontiers in Systems Neuroscience VENTRAL LATERAL PREFRONTAL AND LATERAL ORBITOFRONTAL CONNECTIONS Two injections were placed in subdivisions of area 12. One DY injection was deposited in the ventral lateral prefrontal cortex (rostrolateral area 12; case FR02-DY), while the other was pre- dominantly in orbital area 12 (case FR04-DY). In the latter case, the injection site obscured the likely cytoarchitectural boundary with area 11, so we cannot definitively exclude the possibility that some of the tracer was deposited in this area. However, the distri- bution of labeled neurons from both injections was qualitatively similar, as shown in Figure 5. As observed following prefrontal injections in areas 9 and 10, the majority of labeled cells were observed in a band running along the ventral part of the claus- trum, with no cells in the dorsal or dorsolateral insular claustrum. frontal pole and dorsolateral prefrontal areas arising from insular claustrum. DISCUSSION However, the nature of these methods does not allow disambiguation between projections to or from the cortex (see also Kunzle, 1975). Our data suggest that the interhemispheric claustrum-prefrontal projections in primates are qualitatively weaker than those of the rodent. and interestingly, the lateral portion of area 10 undergoes con- siderably greater postnatal expansion in humans than does the medial portion (Hill et al., 2010). A systematic review of the area 10 literature by Gilbert et al. (2006) found evidence for a significant difference in activation of medial vs. lateral area 10, with the lateral region exhibiting greater responses to tasks involved in episodic retrieval of non-emotional content. Whether the apparent difference in claustrum connectivity with the lateral vs. medial area 10 is present in humans and potentially corre- lated with the functionality of this area is an open question, which may be addressable using high definition tractography or similar approaches. Somewhat curiously, no double labeled neurons were observed in the claustrum in FR04 or any of the other cases exam- ined, suggesting that projections from individual claustrum neu- rons to prefrontal areas in Cebus are restricted to relatively small cortical populations. The apparent absence of double labeled cells is especially surprising in case FR04, in which the tracers were placed in close proximity within a relatively small cortical area. It will be interesting to see if this pattern holds among tracer injec- tions in widely disparate cortical areas, e.g., simultaneous tracer placement in PFC and cingulate or parietal areas, for instance. In the macaque, Selemon and Goldman-Rakic (1988) reported over- lapping fields of terminal label from simultaneous parietal and prefrontal injections using anterograde tracer injections. Consistent with results in the marmoset (Burman et al., 2011a), tracer injections into medial area 10 of Cebus yielded far fewer labeled cell bodies in the claustrum than injections in the dorsal and lateral portions of area 10. Whereas that result is to be considered preliminary based on the small number of injections and potential variation in transport of different tracer types, these results are in line with the hypothesis that differ- ences in connectivity with the claustrum are related to other functional differences described between the lateral and medial subregions of area 10 (Ongur et al., 2003; Burman et al., 2011a,b). DISCUSSION The claustrum in most mammals has been broadly divided into a dorsal compartment, the “insular claustrum” or simply “claus- trum,” and the endopiriform nucleus, which is in turn divided into dorsal and ventral components (Paxinos et al., 2012). In other primate species, as well as in cats, the majority of con- nections from sensory and association cortex are confined to the insular region of the claustrum, while the endopiriform nucleus is largely connected with olfactory and entorhinal cortex, along with limbic subcortical nuclei. Our data in the Cebus conform to this pattern, with the overwhelming majority of projections to With the exception of an isolated FB neuron from an injec- tion in area 9 (case FR04-FB), retrogradely labeled neurons were Frontiers in Systems Neuroscience July 2014 | Volume 8 | Article 123 | 6 www.frontiersin.org www.frontiersin.org www.frontiersin.org Claustrum-prefrontal connections Reser et al. FIGURE 6 | Summary of claustrum-prefrontal projections. Regions of the Cebus claustrum as defined by Gattass et al. (this volume) are schematically displayed as color coded regions in (A,B). (C) illustrates the smoothed outline of the maximum extent of each patch of labeled cells within the claustrum for each of the prefrontal cortex injections included in this study. Scale bar = 4 mm in (A). of the maximum extent of each patch of labeled cells within the claustrum for each of the prefrontal cortex injections included in this study. Scale bar = 4 mm in (A). FIGURE 6 | Summary of claustrum-prefrontal projections. Regions of the Cebus claustrum as defined by Gattass et al. (this volume) are schematically displayed as color coded regions in (A,B). (C) illustrates the smoothed outline restricted to the ipsilateral claustrum. This is inconsistent with the pattern of interhemispheric connections observed in the rat, e.g., between claustrum and the frontal eye field (Smith and Alloway, 2014), and other prefrontal areas (Sloniewski et al., 1986; Smith and Alloway, 2010). This difference is unlikely to be related to the directionality of the tracers employed, as both FB and DY were employed by Slownieski et al., and resulted in bilateral labeling. In primates, interhemispheric claustral con- nections have been reported in the mouse lemur (Park et al., 2012), using high resolution diffusion tensor imaging, and in humans, using constrained spherical deconvolution tractogra- phy (Milardi et al., 2013). Frontiers in Systems Neuroscience RELATIONSHIP OF CLAUSTRUM-PREFRONTAL PROJECTIONS TO CLAUSTRUM CONNECTIONS WITH SENSORY AND ASSOCIATION AREAS y Our data show that prefrontal areas which are part of the salience network (area 12) and areas which are not (9, 10) receive input from the same region of the claustrum (the rostral and ven- tral region), though the precise topography of inputs requires more detailed investigation. Specifically, it will be necessary in future studies to determine if individual claustrum cells project to multiple areas of prefrontal or other cortex, i.e., whether they could provide input to multiple cortical functional networks. The overlap in topography of input from the claustrum to these areas suggests to us that the circuitry of the claustrum-prefrontal con- nection would ideally position the claustrum as a modulator or “switch” that could desynchronize or terminate correlated activa- tion of DMN-related areas when external cues require activation of the various task-positive networks. Indeed, the time-series analysis of Seeley et al. (2007) showed that the component cor- tical areas of the salience network exhibited weak correlation over time, suggesting that the temporal structure of network activity could be dictated by one or a very small number of hub areas. The claustrum is ideally positioned, in terms of connectivity and anatomy, to act in this capacity. Additional anatomical data which would be required to assess this hypothesis includes mapping of claustrum connections with other known network hubs, which include (for the DMN) ventromedial prefrontal (Damoiseaux et al., 2008) and subgenual anterior cingulate cortex (Mantini et al., 2011), the precuneus, and especially posterior cingulate cor- tex (Damoiseaux et al., 2008; Belcher et al., 2013). Extensive study will be required to assess the hypothesized involvement of the claustrum in DMN and/or other cortical networks, and to deter- mine whether the claustrum acts in isolation or in concert with other cortical or subcortical structures. Previous tracing studies of claustral projections in primates have shown localized sensory cortical connections within the body of the claustrum (Reviewed in Druga, 2014; visual cortex- Tigges et al., 1982; Doty, 1983; Baizer et al., 1997; Gattass et al., 2014; somatosensory cortex- Pearson et al., 1982; Minciacchi et al., 1991; auditory cortex- Pearson et al., 1982; Smiley et al., 2007; Reser et al., 2009). As mentioned above, it is currently impos- sible to draw complete homologies of the claustrum anatomy of primate species, though some general patterns have emerged. Projections to visual areas are largely confined to the caudal and mid-dorsal regions of the claustrum. HYPOTHESIS: POSSIBLE CLAUSTRUM INVOLVEMENT IN SWITCHING BETWEEN RESTING STATE NETWORKS in association with schizophrenia and impaired working memory (Barch et al., 2003). The dense projection we observed from the rostral and ventral claustrum to area 9 suggests a possible focus for future investigations of claustrum involvement in prefrontal function in both normal and pathological function, and the sim- ilar topography of this projection across primate species suggests that widely used laboratory primate species could be effective models of both of these states. As discussed below, there are intriguing parallels between the observed anatomical connectivity of the claustrum and the pre- frontal components of several of the known cortical resting state networks. Here we introduce the hypothesis that one function of the primate claustrum may involve mediation or modulation of resting state network activity. Activity in ventrolateral prefrontal cortex, which includes area 12 (according to Carmichael and Price, 1996; note that this region overlaps with area 47 in other nomenclatures Petrides and Pandya, 2002; Paxinos et al., 2012), is also associated with retrieval of information from memory, but not with maintenance or mon- itoring of that information post-retrieval, which is associated with areas 9 and 9/46 (Cadoret et al., 2001). Thus it is likely that the functional interaction between the claustrum and prefrontal cortex overlaps both working memory- and retrieval- dependent processes. The identification of synchronously oscillating patterns of regional blood flow and synaptic activity across cortico-cortical and subcortical-cortical networks in recent years has forced a re-examination of what occurs in the brain during periods of presumed inactivity. Approximately a dozen resting state cortical networks (Mantini et al., 2011; Van Den Heuvel and Sporns, 2013) have been identified in primates, including: the default mode network (DMN; Greicius et al., 2003; reviewed in Buckner et al., 2008); the central executive network (Damoiseaux et al., 2008); the fronto-parietal control network (Dosenbach et al., 2007; Vincent et al., 2008); and the salience network (Downar et al., 2002; Seeley et al., 2007). DISCUSSION Area 10 is a cortical region that has expanded significantly across primate species, including humans (Semendeferi et al., 2001), The distribution of labeled neurons in claustrum following the area 9 injection was largely consistent with previous studies of the macaque (Pearson et al., 1982; Saleem et al., 2014) and mar- moset. Damage or hypoactivation of this area is often reported July 2014 | Volume 8 | Article 123 | 7 www.frontiersin.org www.frontiersin.org Reser et al. Claustrum-prefrontal connections RELATIONSHIP OF CLAUSTRUM-PREFRONTAL PROJECTIONS TO CLAUSTRUM CONNECTIONS WITH SENSORY AND ASSOCIATION AREAS In contrast, motor and somatosensory projections are heavily concentrated in the dor- sal and dorsolateral portions of the claustrum, with virtually no overlap between the areas of somato-motor connectivity (Pearson et al., 1982; Minciacchi et al., 1991) and the distribution of pre- frontal label we observed. Auditory connections are somewhat more difficult to characterize. We have observed sparse auditory cortex connections in the marmoset (Reser et al., 2009), and other groups have reported claustrum projections to auditory areas in the macaque (Smiley et al., 2007). Where topographic informa- tion has been provided, auditory connections were restricted to the ventral claustrum (Pearson et al., 1982). Thus, it appears that there is relatively little overlap among the major sensory corti- cal areas and PFC projections. This roughly concords with the description of claustrum connections in the human as reported by Fernandez-Miranda et al. (2008), allowing for differences in claustrum topology across species. Pearson et al. (1982) reported that labeled cells from injections in area 22 (non-primary audi- tory cortex) in the macaque were concentrated along the ventral portion of the middle and caudal claustrum. Based on the demar- cation of the injection zone in that report, it is likely that the target tissue included part of the temporal lobe polymodal association cortex. The precise relationship of claustrum projections to asso- ciation areas and respectively, auditory and visual sensory areas along the primate temporal lobe, remains to be determined. Frontiers in Systems Neuroscience REFERENCES Fernandez-Miranda, J. C., Rhoton, A. L. Jr., Alvarez-Linera, J., Kakizawa, Y., Choi, C., and De Oliveira, E. P. (2008). 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A surface-based analysis of hemispheric asymmetries and folding of cere- bral cortex in term-born human infants. J. Neurosci. 30, 2268–2276. doi: 10.1523/JNEUROSCI.4682-09.2010 Belcher, A. M., Yen, C. C., Stepp, H., Gu, H., Lu, H., Yang, Y., et al. (2013). Large- scale brain networks in the awake, truly resting marmoset monkey. J. Neurosci. 33, 16796–16804. doi: 10.1523/JNEUROSCI.3146-13.2013 Buckner, R. L., Andrews-Hanna, J. R., and Schacter, D. L. (2008). The brain’s default network: anatomy, function, and relevance to disease. Ann. N.Y. Acad. Sci. 1124, 1–38. doi: 10.1196/annals.1440.011 Hoover, W. B., and Vertes, R. P. (2007). Anatomical analysis of afferent projections to the medial prefrontal cortex in the rat. Brain Struct. Funct. POSSIBLE LIMITATIONS OF THIS STUDY There are several aspects of this study which must be considered in evaluation of our results and conclusions. First, the homol- ogy between brain areas of different primate species is difficult to establish, especially as the size and function of the various regions is known to have changed across primate evolution (Semendeferi July 2014 | Volume 8 | Article 123 | 8 www.frontiersin.org www.frontiersin.org www.frontiersin.org Reser et al. Claustrum-prefrontal connections et al., 2001; Chaplin et al., 2013), with a general trend toward segregation between areas and networks with increasing corti- cal size (Changizi and Shimojo, 2005). In both body mass and brain volume, the Cebus monkey is at least 10 times larger than the species we have studied most recently, the marmoset, so it is reasonable to assume that some functional changes across pre- frontal areas have occurred. A second key consideration is our poor understanding of the functional architecture of the claus- trum itself, especially in primates. Although recent advances have been made in identification of anatomical and neurochemical markers of the claustrum (Arimatsu et al., 2009; Mathur et al., 2009), this approach has not yet yielded reliable results in pri- mates. Thus, it remains difficult to infer claustrum functions from compartmentalization or topographic organization of cor- tical connections. Finally, testing hypotheses regarding claustrum involvement in cortical functional networks will require a more precise survey of which cortical areas are components of spe- cific networks, and reconciliation of the anatomical definitions of those areas with areas of increased or decreased activity in func- tional studies, which will likely require intensive future study and revisitation of existing datasets. Burman, K. J., and Rosa, M. G. (2009). Architectural subdivisions of medial and orbital frontal cortices in the marmoset monkey (Callithrix jacchus). J. Comp. 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Neurol. 522, 1641–1690. doi: 10.1002/cne.23498 Conflict of Interest Statement: The authors declare that the research was con- ducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Sallet, J., Mars, R. B., Noonan, M. P., Neubert, F. X., Jbabdi, S., O’Reilly, J. X., et al. (2013). The organization of dorsal frontal cortex in humans and macaques. J. Neurosci. 33, 12255–12274. doi: 10.1523/JNEUROSCI.5108-12.2013 Seeley, W. W., Menon, V., Schatzberg, A. F., Keller, J., Glover, G. H., Kenna, H., et al. (2007). Dissociable intrinsic connectivity networks for salience processing and executive control. J. Neurosci. 27, 2349–2356. doi: 10.1523/JNEUROSCI.5587- 06.2007 Received: 15 March 2014; accepted: 10 June 2014; published online: 03 July 2014. Citation: Reser DH, Richardson KE, Montibeller MO, Zhao S, Chan JMH, Soares JGM, Chaplin TA, Gattass R and Rosa MGP (2014) Claustrum projections to pre- frontal cortex in the capuchin monkey (Cebus apella). Front. Syst. Neurosci. 8:123. doi: 10.3389/fnsys.2014.00123 Received: 15 March 2014; accepted: 10 June 2014; published online: 03 July 2014. Citation: Reser DH, Richardson KE, Montibeller MO, Zhao S, Chan JMH, Soares JGM, Chaplin TA, Gattass R and Rosa MGP (2014) Claustrum projections to pre- Selemon, L. D., and Goldman-Rakic, P. S. (1988). Common cortical and subcortical targets of the dorsolateral prefrontal and posterior parietal cortices in the rhesus monkey: evidence for a distributed neural network subserving spatially guided behavior. J. Neurosci. 8, 4049–4068. frontal cortex in the capuchin monkey (Cebus apella). Front. Syst. Neurosci. 8:123. doi: 10.3389/fnsys.2014.00123 f y This article was submitted to the journal Frontiers in Systems Neuroscience. Copyright © 2014 Reser, Richardson, Montibeller, Zhao, Chan, Soares, Chaplin, Gattass and Rosa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). REFERENCES 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. Semendeferi, K., Armstrong, E., Schleicher, A., Zilles, K., and Van Hoesen, G. W. (2001). Prefrontal cortex in humans and apes: a comparative study of area 10. Semendeferi, K., Armstrong, E., Schleicher, A., Zilles, K., and Van Hoesen, G. W. (2001). Prefrontal cortex in humans and apes: a comparative study of area 10. Am. J. Phys. Anthropol. 114, 224–241. doi: 10.1002/1096-8644(200103)114:3 p p y Am. J. Phys. 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Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells
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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 Permanent link http://nrs.harvard.edu/urn-3:HUL.InstRepos:4728514 Citation Wu, Erxi, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger, Hongbing Zhang, and Isaac S. Kohane. 2008. Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells. PLoS ONE 3(11): e3794. Wu, Erxi, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger, Hongbing Zhang, and Isaac S. Kohane. 2008. Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells. PLoS ONE 3(11): e3794. Published Version doi:10.1371/journal.pone.0003794 Abstract Despite the growing understanding of PDGF signaling, studies of PDGF function have encountered two major obstacles: the functional redundancy of PDGFRa and PDGFRb in vitro and their distinct roles in vivo. Here we used wild-type mouse embryonic fibroblasts (MEF), MEF null for either PDGFRa, b, or both to dissect PDGF-PDGFR signaling pathways. These four PDGFR genetically defined cells provided us a platform to study the relative contributions of the pathways triggered by the two PDGF receptors. They were treated with PDGF-BB and analyzed for differential gene expression, in vitro proliferation and differential response to pharmacological effects. No genes were differentially expressed in the double null cells, suggesting minimal receptor-independent signaling. Protean differentiation and proliferation pathways are commonly regulated by PDGFRa, PDGFRb and PDGFRa/b while each receptor is also responsible for regulating unique signaling pathways. Furthermore, some signaling is solely modulated through heterodimeric PDGFRa/b. Citation: Wu E, Palmer N, Tian Z, Moseman AP, Galdzicki M, et al. (2008) Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells. PLoS ONE 3(11): e3794. doi:10.1371/journal.pone.0003794 itor: Suzannah Rutherford, Fred Hutchinson Cancer Research Center, United States of America Editor: Suzannah Rutherford, Fred Hutchinson Cancer Research Center, United States of Americ ceived July 21, 2008; Accepted October 29, 2008; Published November 24, 2008 Received July 21, 2008; Accepted October 29, 2008; Published November 24, 2008 Received July 21, 2008; Accepted October 29, 2008; Published November 24, 2008 Copyright:  2008 Wu 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. Copyright:  2008 Wu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by National Institutes of Health training grant 2 Ta5 LM 07092-11. The funder had no role in study design, data collection and analysis, decision to publish, and preparation of the manuscript Competing Interests: The authors have declared that no competing interests exist. * E-mail: isaac_kohane@harvard.edu . These authors contributed equally to this work. . These authors contributed equally to this work. Share Your Story The Harvard community has made this article openly available. Please share how this access benefits you. Submit a story . Accessibility Abstract inhibition of cancer growth when PDGF-PDGFR signaling is activated: (a) direct targeting of tumor cells in which PDGF signaling is activated, and (b) indirect inhibition of tumors by targeting pericytes to block tumor angiogenesis independently of PDGF activity. A PDGFR inhibitor, imatinib mesylate (Gleevec, STI-571), has benefited patients with myeloid malignancies, GIST and DFSP [8]. PI3K-AKT-mTOR cascade is one of the most frequently deregulated pathway in cancers [9,10,11]. Recently we have found that the PDGF receptors are critical for the PI3K/ AKT activation and negatively regulated by mTOR. This negative feedback mechanism is important in the prevention of aberrant cell proliferation/growth such as tumor formation and has significant implication in the targeted inhibition of this pathway for cancer treatment [12,13]. Erxi Wu1,2., Nathan Palmer3., Ze Tian1, Annie P. Moseman1, Michal Galdzicki1, Xuetao Wang1, Bonnie Berger3,4, Hongbing Zhang5, Isaac S. Kohane1,2* Erxi Wu1,2., Nathan Palmer3., Ze Tian1, Annie P. Moseman1, Michal Galdzicki1, Xuetao Wang1, Bonnie Berger3,4, Hongbing Zhang5, Isaac S. Kohane1,2* 1 Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America, 2 Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 3 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 4 Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 5 Department of Physiology & Pathophysiology, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing, China Introduction The distinct phenotypes of mice lacking either PDGFRa or PDGFRb suggest that PDGFRs might have unique effectors and/or distinct spatial and temporal expression pattern in vivo. Introduction Platelet-derived growth factor (PDGF) is the principal mitogen in serum for mesenchymal cells and consists of a family of A, B, C, and D polypeptides which promote cell migration, proliferation, and survival by binding to their cognate homo- or heterodimeric tyrosine kinase receptors, PDGFRa and PDGFRb[1,2,3]. En- hanced signaling of PDGF has been implicated in the pathogenesis of atherosclerosis, balloon injury induced restenosis, pulmonary fibrosis, angiogenesis, and tumorigenesis [4]. Tumor growth can be promoted by PDGF via autocrine stimulation of malignant cells, by overexpression or overactivation of PDGFRs, or by PDGF stimulation of angiogenesis within the tumor. Constitutive activation of PDGFRa or PDGFRb is seen in myeloid malignancies as a consequence of fusion to diverse partner genes, and activating mutations of PDGFRa are seen in gastrointestinal tumors (GISTs). Active PDGFRa was also found in non-small cell lung cancer[5]. Autocrine signaling as a consequence of PDGF overexpression has been implicated in the pathogenesis of dermatofibrosarcoma protruberans (DFSP) and overexpression of PDGFRs and/or their ligands has been described in many other solid tumors such as medulloblastomas and malignant gliomas [6,7]. Therefore, PDGFRs have increas- ingly become targets for anticancer therapeutics and antirestenosis agents. Two main approaches have been taken toward the Despite the growing understanding of PDGF signaling, studies of PDGF function have met two obstacles. First, PDGF stimulates a very similar set of cellular responses and signaling events in cultured cells expressing only PDGFRa or PDGFRb. Because of their functional redundancy or compensation of the receptors with respect to one another in vitro, the signaling events of PDGFRa or PDGFRb cannot be readily analyzed and differentiated. Second, in contrast to in vitro studies, PDGFRa and PDGFRb have dramatically different roles in vivo. The mechanism of PDGFR signaling during development is poorly understood because deletion of either the PDGFRa or PDGFRb leads to early PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 1 PDGF-PDGFR Signaling PDGF-PDGFR Signaling differentially expressed in this particular comparison). The complete list of genes affected by treatment in each cell line can be found in the Supplemental Material (see Table S1 Diff-Genes- PDGF-BB-Treatment.xls). embryonic lethality. While PDGFRb null embryos are only deficient in smooth muscle cells, particularly vascular smooth muscle cells and pericytes, a large number of different mesenchy- mal cells are affected in PDGFRa null embryos. Gene set (pathway) analysis In addition to the differential expression analysis, we used sigPathway [15] to identify functional groups of genes (e.g., pathways) that exhibited significantly different behavior between the various conditions. As with the differential expression analysis, we first identified gene sets by comparing the treatment to the non- treatment condition for each of the cell lines. We then compared the pathways identified for each cell line to one another in order to determine which functionality could be attributed most strongly to stimulation of each combination of receptors. The double null data was not included in this analysis because our differential expression analysis indicated that there was no significant change in transcriptional activity that resulted from treatment of the double null cell line. Table 1 lists the gene sets identified as responding to treatment in the various cell lines. ( g ) Furthermore, PDGF-PDGFR is a known trigger of at least two pathways: the PI3K-AKT and MAPK pathways. To investigate the ability of PDGF to stimulate these pathways in our system, we treated cells with 50 ng/ml of PDGF-BB for various durations. For 10 min post treatment, ERK protein in PDGFRb null, PDGFRa null, and WT cell lines was extensively phosphorylated, compared with the no treatment by PDGF-BB (Figure 1C). The phosphorylation of AKT protein at various time points showed a similar pattern to ERK phosphorylation and decreased after 24 h. However, in the PDGFRa and PDGFRb double null cell line, neither ERK nor AKT phosphorylation was increased after the PDGF-BB stimulation. Gene Ontology (GO) terms associated with differentially expressed genes In this study we employed a panel of PDGFR genetically defined cell lines as a platform that allows us to examine the relative contributions of the two receptors to PDGF signaling. We studied the gene expression profile and in vitro proliferation assays of the four different genotypes of PDGF receptors: PDGFRa/b double null, PDGFRb null, PDGFRa null or WT PDGFRa/b in MEF cells. These profiles were then dissected analytically using gene set oriented techniques and complementary data from protein interaction databases. The genes identified in this analysis were then investigated further via protein expression and phosphorylation status analyses. Their functional relevance was then studied. In order to identify functional similarities among the genes that were differentially expressed in one or more of the treatment conditions, we identified GO terms that were statistically overrepresented in each list of genes as described in Materials and Methods. Figure 3 shows the GO Molecular Function terms that were enriched for each cell line. Lists enumerating all of the enriched GO terms for each cell line can be found in the Supplemental Material (see Table S2 GO-Enrichment-PDGF-BB- Treatment.xls). The GO terms characterizing the WT alone (in green) cover transcriptional control and apoptotic programs. Examination of which genes are responsible for this enrichment reveals central ‘‘actors’’ in proliferation, differentiation and apoptosis such as: HES1, BHLHB2, JunB, FOSL1, SRF, SKIL, EGR1, NAB2, FOSB, NR4A1, CCL2 and SERPINE1. The PDGFRa null cell line but not the PDGFRb null or WT showed differential expression of GDP signaling genes (i.e. required the PDGFRb isoform, but may be repressed by activity of the PDGFRa isoform). Conversely, the differentially expressed GO sets particular to the PDGFRb null and WT cell lines (i.e. requiring the PDGFRa isoform) characterize ketosteroid metab- olism (colored magenta). Red nodes represent those sets that were found to be differentially expressed in all but the double (a/b) null cell lines, and include the MAP kinase pathway, prostaglandin signaling pathways and several other signaling pathways. Characterization of PDGFR knockout cell lines To investigate the role of PDGFRs in cellular proliferation in response to PDGF stimulation, cells were grown in serum free Cellgro COMPLETETM medium with or without PDGF. In the absence of PDGF, the proliferation rates of all four PDGFR genetically defined cell lines were found to be similar. However, with the addition of PDGF-BB, PDGFRb null, PDGFRa null and WT cells proliferate faster than the PDGFRa/b double null cells (Figure 1A). In addition, we examined the role that each of the PDGF receptors plays in promoting cell migration and invasion. PDGFRa, PDGFRb and heterodimeric PDGFRa/b were dem- onstrated to promote cell migration and also PDGFRb and heterodimeric PDGFRa/b to enhance cell invasion (Figure 1B). Differentially Expressed Genes Several pathways were ranked highly for all three cell lines in this analysis, indicating that these pathways were activated by all of the receptors after PDGF-BB stimulation, including cAMP/Ca signaling and G-protein coupled receptor signaling. In addition, many pathways were highly-ranked in only a strict subset of the cell lines. For example, the IL6 and NFkB signaling pathways were both stimulated in the WT cell line; C21-steroid hormone biosynthesis was stimulated in the PDGFRb null cell line; angiogenesis and epidermal growth factor receptor signaling pathway were both stimulated in the PDGFRa null cell line. To study the role of PDGFRs in PDGF mediated transcription, cells were treated with or without PDGF-BB for 1 h. Analysis of the microarray expression data yielded lists of transcripts that were differentially expressed (responded to PDGF-BB) with high statistical confidence in each of the four cell lines. As described in the Experimental Procedures section, the Significance Analysis of Microarrays (SAM) [14] method was used to identify differentially expressed genes with a false discovery rate ,0.05. By comparing these lists, we identified genes that responded to PDGF-BB treatment uniquely in each cell line, and also genes that responded to treatment in multiple cell lines. For example, Figure 2 shows a heatmap describing the transcriptional activity of the genes that were identified in common among the PDGFRb null, PDGFRa null and WT cell lines (genes such as Txnip, Fos, Egr1, Egr2, Fra-1 (FOSL1), ATF-3, and NR4A1 were all identified as Results Characterization of PDGFR knockout cell lines November 2008 | Volume 3 | Issue 11 | e3794 All PDGF signaling is PDGFR-dependent None of the mRNA targets probed by the microarrays exceeded our differential expression threshold in the double null cell line, indicating that transcriptional response to PDGF-BB ligand is mediated entirely through activation of one or both of the PDGF November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 2 PDGF-PDGFR Signaling ONE | www.plosone.org 3 November 2008 | Volu PLoS ONE | www.plosone.org 3 November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 3 November 2008 | Volume 3 | Issue 11 | e3794 November 2008 | Volume 3 | Issue 11 | e3794 November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 3 PLoS ONE | www.plosone.org PDGF-PDGFR Signaling Figure 1. Characterization of four PDGFR genetically defined MEF cell lines. A: PDGF-BB promotes cell proliferation through PDGFR. 16105 cells were plated at Day 0 and then counted each day for next consecutive three days. Dot lines: cells grown in FBS-free Cellgro Complete medium. Solid lines: cells grown in FBS-free Cellgro Complete medium with PDGF-BB (50 ng/ml). B: PDGFR is required for PDGF mediated cell migration and invasion. Cell migration and invasion were measured by a 24-well chamber-based assay. 2.56104 cells were seeded in the upper chamber in FBS free Cellgro Complete medium. The lower chamber was filled with Cellgro Complete medium with no FBS, 10% FBS or PDGF-BB (50 ng/ml). After 24 h, the cells in the lower chamber were labeled with Calcein AM and detached. The detached labeled cells were then measured for fluorescence. Upper panel: Migration assay. Lower panel: Invasion assay. C: PDGF-mediated PI3K and MAP kinase signalings are absent in PDGFRa and PDGFRb double deficient cell lines. Four cell lines were treated with PDGF-BB (50 ng/ml) for 10 min, 1 hour (h), 4 h, 8 h and 24 h. The harvested lysates were immunoblotted for PDGFRa, PDGFRb, p-ERK (Tyr 204), ERK, p-AKT (Ser473), and AKT. Data shown is one of the representative experiments. doi:10.1371/journal.pone.0003794.g001 stimulation. PDGFRb may have some effects during longer treatment. To confirm this result, we also performed Western blotting with a different ligand (PDGF-AA, 50 ng/ml) to assess the level of Txnip protein expression. The results showed that Txnip was down-regulated in the cell lines containing PDGFRa and heterodimeric PDGFRa/b (Figure 5A). Pathway validation by protein level y y As described above, we employed the sigPathway method [15] to identify functional groups of genes that exhibited significantly different behavior between the various conditions. We used Western blotting to validate components of one of the pathways, IL6, identified as up-regulated significantly (p,0.05) in the WT cell line in response to PDGF stimulation (Figure 6 A and B). In this IL6 pathway, the genes Fos, Cebpb (NF-IL6), Jun and IL6 were significantly upregulated (p,0.05). As shown in Figure 6C, a few key component genes such as Cebpb (NF-IL6), Fos and Jun in the IL6 pathway were demonstrated as up-regulated by Western blotting. Fos and Jun were up-regulated with PDGF-BB treatment for 1 h while Cebpb (NF-IL6) was little changed. In the absence of PDGF-BB treatment, Jun expression was slightly higher in the PDGFRb null and WT cell lines than in the others. PDGF-independent PDGFR function In order to study the function of the two receptors independent of their activation state, we sought genes whose transcription levels changed between the PDGFRa null, PDGFRb null and WT samples when compared to the untreated double null samples. We then repeated this analysis using the treated samples (i.e., which genes were differentially expressed in the treated PDGFRa null/ PDGFRb null/WT vs. the treated double null cells). We identified those genes whose expression changes were conserved between the untreated and PDGF-BB treated cells. We suggest that these genes are regulated by the presence or absence of a particular receptor, rather than by activation of a receptor through growth factor ligation. Please see Supplemental Material (see Table S3 PDGF- Independent-Gene-Lists.xls) for complete lists of these transcripts. Protein expression of Nurr1 (Nr4a2) and Nur77 (Nr4a1) are altered only in the PDGFR WT cell line post 10 min stimulation of PDGF-BB. This is consistent with the microarray data, where production of mRNA for Nurr1 was induced only in the WT cell line, and production of mRNA for Nur77 was induced most drastically in the WT cell line, and less so in the PDGFRb null and PDGFRa null cell lines (Figure 2). EGR1 is an early response gene and its protein expression is up-regulated in the PDGFRb null, PDGFRa null and WT cell lines, but not in the PDGFR double null cell line at 1 h treatment with PDGF-BB. This is also consistent with the microarray data. ATF-3 is up-regulated in the PDGFRb null, PDGFRa null and WT cell lines, but not in the PDGFR double null cell line, even at 24 h treatment with PDGF- BB. In the PDGFRa null cell line, protein levels of ATF-3 gradually increase at all time points. This is somewhat different from the PDGFRb null and WT cell lines where ATF-3 protein levels are increased at early time points and gradually decrease thereafter. This indicates that ATF-3 is regulated differently by PDGFRa, PDGFRb and heterodimeric PDGFRa/b. These results again agree with the microarray analysis (Figure 2). Protein level validation of microarray results through selected protein level assays of the PDGFRa and PDGFRb systems Immunoblotting was used to examine the effect of PDGF-BB treatment at the protein-level for several of the genes identified by the microarray analysis. As per mRNA expression data, Txnip (thioredoxin-interacting protein) was identified as one of the most significantly down-regulated mRNA transcripts. As shown in Figures 2 and 5, protein expression of Txnip is mainly suppressed by PDGFRa, since Txnip is reduced in the presence of PDGFRa and diminished with the activation of PDGFRa by PDGF All PDGF signaling is PDGFR-dependent In the regular medium , Txnip was also down regulated in the PDGFRa (PDGFRb null cell line) and WT cell line (Figure 5B). PDGF is one of main growth factors in FBS and thus is sufficient to suppress Txnip in PDGFRa and WT cell line. Txnip gene expression was further validated by real time-PCR (Figure 5c). receptors. Pearson correlation coefficients were computed between the mRNA expression fold-change vectors for each cell line (Table 2). This analysis revealed that transcriptional responses to PDGF-BB in the PDGFRa null and PDGFRb null cells are more similar to the expression response of the WT cells than they are to one another, or the double null cells. The double null cell line’s response to PDGF-BB was essentially uncorrelated with that of the other three cell lines. Interactome of dissected pathways of PDGFR reveals central processes We constructed a protein-interaction network based on the annotations present in the HPRD database. We included all interactions where both proteins were the products of genes that were differentially expressed in at least one cell line. Figure 4 shows this network, with each gene labeled by color to indicate the cell lines where it was differentially expressed. Interpretation of this network must be cautious; at the very least because there is significant bias of protein-interaction databases towards those pathways that are better characterized. Nonetheless, we identified significantly enriched pathways (i.e. hypergeometric p value, corrected for multiple hypothesis testing, ,0.05) among the various combinations of receptor systems. For example, A2B adenosine receptor related processes were identified among the dark blue nodes (see Table S4 GO-Enrichment-for-PPI-Figure.xls in Supplementary Materials for all pathways). Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 STI-571 (imatinib mesylae, Gleevec, Novartis, Basel, Switzer- land) inhibits phosphorylation of both PDGFRa and PDGFRb and their downstream targets ERK and AKT [16,17]. In this November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 4 PDGF-PDGFR Signaling Figure 2. Representative PDGFR dependent differential gene expression in respons each cell line were treated with or without PDGF-BB for 1 h. mRNA expression profiles for the treatment group for all of the cell lines, except for double knockout. Expression levels of the pr differentially expressed in the PDGFRb2/2 (beta null), PDGFRa2/2 (alpha null), and WT heatmap. Each column represents a sample, each row a gene. Column labels indicate the cell lin PDGF-BB, U for untreated samples) for each sample. Each probe set’s expression has been ind green shading indicates an expression level below the gene-wise mean, bright red indicates an indicate expression levels closer to the mean intensity. Lower panel: four cell lines were treate lysates were immunoblotted for ATF-3, Txnip, Fra-1, Nurr1, Nur77, TF, and EGR1 (PDGF treatm regarded as a spotting control in this system, the same for the following experiments in th validate findings from the mRNA expression analysis (upper panel). Expression levels of prob shown in the heatmap above the western blot figure. Figure 2. Representative PDGFR dependent differential gene expression in response to PDGF treatment. Upper panel: triplicate sets of each cell line were treated with or without PDGF-BB for 1 h. mRNA expression profiles for the probe sets identified as differentially expressed in the treatment group for all of the cell lines, except for double knockout. Expression levels of the probe sets interrogating the genes that were commonly differentially expressed in the PDGFRb2/2 (beta null), PDGFRa2/2 (alpha null), and WT (PDGFRa+/+ PDGFRb+/+) cell lines are shown in the heatmap. Each column represents a sample, each row a gene. Column labels indicate the cell line and treatment condition (T for samples treated with PDGF-BB, U for untreated samples) for each sample. Each probe set’s expression has been independently normalized across the experiments. Bright green shading indicates an expression level below the gene-wise mean, bright red indicates an expression level above the mean, while darker shades indicate expression levels closer to the mean intensity. Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 Lower panel: four cell lines were treated with PDGF-BB (50 ng/ml) for various times and their lysates were immunoblotted for ATF-3, Txnip, Fra-1, Nurr1, Nur77, TF, and EGR1 (PDGF treatment does not influence the total Erk, therefore Erk was regarded as a spotting control in this system, the same for the following experiments in the MEF cell lines with genetically defined PDGFRs) to validate findings from the mRNA expression analysis (upper panel). Expression levels of probe sets interrogating the genes for these proteins are shown in the heatmap above the western blot figure. doi:10.1371/journal.pone.0003794.g002 Figure 2. Representative PDGFR dependent differential gene expression in response to PDGF treatment. Upper panel: triplicate sets of each cell line were treated with or without PDGF-BB for 1 h. mRNA expression profiles for the probe sets identified as differentially expressed in the treatment group for all of the cell lines, except for double knockout. Expression levels of the probe sets interrogating the genes that were commonly differentially expressed in the PDGFRb2/2 (beta null), PDGFRa2/2 (alpha null), and WT (PDGFRa+/+ PDGFRb+/+) cell lines are shown in the heatmap. Each column represents a sample, each row a gene. Column labels indicate the cell line and treatment condition (T for samples treated with PDGF-BB, U for untreated samples) for each sample. Each probe set’s expression has been independently normalized across the experiments. Bright green shading indicates an expression level below the gene-wise mean, bright red indicates an expression level above the mean, while darker shades indicate expression levels closer to the mean intensity. Lower panel: four cell lines were treated with PDGF-BB (50 ng/ml) for various times and their lysates were immunoblotted for ATF-3, Txnip, Fra-1, Nurr1, Nur77, TF, and EGR1 (PDGF treatment does not influence the total Erk, therefore Erk was regarded as a spotting control in this system, the same for the following experiments in the MEF cell lines with genetically defined PDGFRs) to validate findings from the mRNA expression analysis (upper panel). Expression levels of probe sets interrogating the genes for these proteins are shown in the heatmap above the western blot figure. doi:10.1371/journal.pone.0003794.g002 November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 5 PDGF-PDGFR Signaling PDGF-PDGFR Signaling Figure 3. Categories within the Molecular Function GO hierarchy that were overrepresented among the genes that responded to PDGF-BB treatment. PLoS ONE | www.plosone.org Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 Red nodes represent GO terms that were overrepresented among the genes identified as responding to PDGF-BB treatment in the PDGFRa null, PDGFRb null and WT cell lines Magenta nodes represent GO terms that were thin the Molecular Function GO hierarchy that were overrepresented among the genes that responded to PDGF-BB treatment. Red nodes represent GO terms d among the genes identified as responding to PDGF-BB treatment in the PDGFRa null, PDGFRb null and WT cell lines. Magenta nodes represent GO terms that were he genes that responded in the PDGFRb null and WT cell lines, but not in the PDGFRa null cell line. Dark blue nodes represent GO terms that were overrepresented among the y in the PDGFRa null cell line. Green nodes represent GO terms that were overrepresented among the genes responding in only the WT cell line. GO categories associated with to illustrate context within the GO hierarchy, and were not overrepresented among any of the cell lines. Solid lines represent direct relationships between parent and child nodes ed lines represent long branches of the GO tree containing nodes that were not identified in this analysis. 003794 003 PLoS ONE | www.plosone.org PDGF-PDGFR Signaling Table 1. Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 Pathways identified in each of the PDGFR-defined cell lines Cell Lines Source Gene Set Wild Type Only GO:0030182 neuron differentiation GO:0042417 dopamine metabolism BioCarta Cadmium induces DNA synthesis and proliferation in macrophages BioCarta IL 6 signaling pathway GO:0001942 hair follicle development BioCarta NFAT and Hypertrophy of the heart (Transcription in the broken heart) GO:0042133 neurotransmitter metabolism GO:0051239 regulation of organismal physiological process GO:0008083 growth factor activity mousepaths NFkB Signaling Pathway GO:0030282 bone mineralization GO:0045664 regulation of neuron differentiation GO:0030574 collagen catabolism GO:0007566 embryo implantation GO:0009888 histogenesis GO:0030522 intracellular receptor-mediated signaling pathway GO:0030518 steroid hormone receptor signaling pathway GO:0045638 negative regulation of myeloid cell differentiation GO:0043154 negative regulation of caspase activation GO:0001719 inhibition of caspase activation GO:0001502 cartilage condensation GO:0007565 pregnancy GO:0006309 DNA fragmentation during apoptosis GO:0006921 disassembly of cell structures during apoptosis GO:0030262 apoptotic nuclear changes Beta Null Only KEGG Synthesis_and_degradation_of_ketone_bodies BioCarta SREBP control of lipid synthesis GO:0008207 C21-steroid hormone metabolism GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer GO:0016229 steroid dehydrogenase activity GO:0003918 DNA topoisomerase (ATP-hydrolyzing) activity GO:0000123 histone acetyltransferase complex GO:0000777 condensed chromosome kinetochore GO:0006700 C21-steroid hormone biosynthesis BioCarta Granzyme A mediated Apoptosis Pathway GO:0005694 chromosome GO:0050728 negative regulation of inflammatory response GO:0000278 mitotic cell cycle GO:0030529 ribonucleoprotein complex GO:0006281 DNA repair GO:0009613 response to pest, pathogen or parasite GO:0050877 neurophysiological process GO:0043207 response to external biotic stimulus BioCarta The information-processing pathway at the IFN-beta enhancer BioCarta Regulation of MAP Kinase Pathways Through Dual Specificity Phosphatases GO:0008217 regulation of blood pressure KEGG Cytokine-cytokine_receptor_interaction GO:0006974 response to DNA damage stimulus GO:0001584 rhodopsin-like receptor activity BioCarta Transcription Regulation by Methyltransferase of CARM1 BioCarta Mechanism of Acetaminophen Activity and Toxicity PLoS ONE | www.plosone.org 7 November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 7 PDGF-PDGFR Signaling Table 1. Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 cont Cell Lines Source Gene Set GO:0016070 RNA metabolism BioCarta Platelet Amyloid Precursor Protein Pathway GO:0004930 G-protein coupled receptor activity GO:0015268 alpha-type channel activity GO:0015267 channel or pore class transporter activity GO:0004709 MAP kinase kinase kinase activity GO:0007186 G-protein coupled receptor protein signaling pathway Alpha Knockout Only mousepaths Th1-Th2-Th3 GO:0006692 prostanoid metabolism GO:0006693 prostaglandin metabolism BioCarta Eicosanoid Metabolism GO:0007173 epidermal growth factor receptor signaling pathway GO:0001525 angiogenesis GO:0048514 blood vessel morphogenesis GO:0001508 regulation of action potential GO:0045670 regulation of osteoclast differentiation GO:0046456 icosanoid biosynthesis GO:0006690 icosanoid metabolism GO:0030316 osteoclast differentiation KEGG Prostaglandin_and_leukotriene_metabolism GO:0030224 monocyte differentiation GO:0007205 protein kinase C activation Beta Knockout and Wild Type GO:0016126 sterol biosynthesis GO:0006695 cholesterol biosynthesis Alpha Knockout and Wild Type BioCarta Neuropeptides VIP and PACAP inhibit the apoptosis of activated T cells mousepaths Ca _ NFAT Signaling Pathways mousepaths Breast Cancer _ Estrogen Receptor Signaling mousepaths Signal Transduction in Cancer mousepaths Cardiovascular Disease mousepaths Signal Transduction PathwayFinder mousepaths Nitric Oxide mousepaths Tumor Metastasis mousepaths Autoimmune and Inflammatory Response mousepaths Angiogenesis mousepaths Endothelial Cell Biology GO:0008015 circulation GO:0008016 regulation of heart contraction rate GO:0042552 myelination GO:0042553 cellular nerve ensheathment GO:0007272 ionic insulation of neurons by glial cells GO:0008366 nerve ensheathment Alpha Knockout and Beta Knockout GO:0045765 regulation of angiogenesis GO:0046457 prostanoid biosynthesis GO:0001516 prostaglandin biosynthesis GO:0016525 negative regulation of angiogenesis GO:0006955 immune response GO:0006952 defense response GO:0000279 M phase November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 8 PDGF-PDGFR Signaling Cell Lines Source Gene Set GO:0007067 mitosis GO:0000087 M phase of mitotic cell cycle GO:0003735 structural constituent of ribosome GO:0005840 ribosome KEGG Ribosome Alpha Knockout, Beta Knockout and Wild Type mousepaths cAMP _ Ca Signaling PathwayFinder mousepaths G-Protein Coupled Receptors Signaling PathwayFinder doi:10.1371/journal.pone.0003794.t001 Table 1. cont doi:10.1371/journal.pone.0003794.t001 study we examined the downstream effects of the drug on the PDGF-PDGFR pathway by inhibiting the different isoforms of the receptor. The dosage 5 mM of STI-571 was selected to inhibit PDGFRa and PDGFRb efficiently [18]. results with protein-level validation and pharmacological response studies. We have confirmed some of the genes previously implicated in the PDGF-PDGFR pathway, such as FOS, NR4A1, ZFP36, EGR2, NR4A2, EGR3, FOSB, ATF3, JUN, IER3, ADRB2, DUSP6, MCL1, RGS2, MYC, F3, BHLHB2, GEM, EGR1, LIF and CEBPB [19,20]. We also identified the involvement of Axud1, MCl1, Tiparp and Txnip in the PDGF-PDGFR system as previously identified by Chen et al. [21] using a microarray- coupled gene-trap mutagenesis method. Pharmacological dissection of the PDGF-PDGFR signaling pathways with STI-571 Furthermore we have been able to add more genes to the list such as PTGS2, ERRFI1, JUNB, FOSL1, ERRFI1, EREG, HBEGF, CH25H, HOMER1, PHLDA1, FOS, KLF10, FOSB, SERPINE1, DUSP5, EREG, GEM, HOMER1, HBEGF, TRIB1, CCL2, NFIL3, LBH, IER2, MMP13, GS2, AREG, RSBN1, LIF, TNFRSF11B, CXCL1, NFKBIZ, DUSP4, CCL7, RSBN1, RGS2, IER3, ARL5B, BTG2, ADAMTS1, BTG2, IER5, HES1, RGS2, AXUD1, MMP3, PTGER4 etc. As in Figure 6D, p-AKT was inhibited in PDGFRb null, PDGFRa null and WT cell lines, while p-ERK was mainly inhibited in PDGFRa containing cells upon the STI-571 treatment. C-Fos was moderately inhibited in PDGFRb null and PDGFRa null while its expression was strongly inhibited in WT cells by the drug. ATF3 was not inhibited in PDGFRb null, PDGFRa null and WT cell lines by STI-571 alone, but was inhibited in PDGFRb null, PDGFRa null and WT cell lines by STI-571 in the presence of both PDGF-BB. Fra-1 (FOSL1) expression did not change significantly in the PDGFRb null, PDGFRa null and WT cell lines by STI-571 while its expression was increased in the PDGFRb null, PDGFRa null and WT cell lines in the presence of both PDGF-BB and STI-571. It is notable that PDGF-BB stimulation could not reverse the STI-571 inhibition effect on some genes’ expression even though PDGFR-BB moderately increased the expression of C-Fos and Fra-1 as compared to STI-571 inhibition alone. PDGFRa and PDGFRb activate many overlapping signaling pathways. All of the receptors activate the same pathways such as cAMP/Ca+ signaling and G-protein coupled receptor signaling after the PDGF-BB stimulation. However, some signaling pathways are exclusively or predominantly activated by one receptor but not the other. Here, we demonstrated that 33 gene sets were activated by PDGFRa only and 15 genes sets by PDGFRb only. 25 genes sets were specifically activated by PDGFRa/b heterodimers. For example, PDGFRa/b activated components of the NFkB and IL6 signaling pathways, PDGFRa activated C21-steroid hormone biosynthesis; and PDGFRb activated the angiogenesis and epidermal growth factor receptor signaling pathways. Previous investigations of the pathways regulated by PDGFRs were done one pathway at a time[22]; here we used a bioinformatics approach to comprehensively analyze ,multiple pathways. Nonetheless, the earlier study suggested the Ca++ fluxes pathway is regulated by both PDGFRa and PDGFRb [22] and angiogenesis is only transduced by PDGFRb [22,23]. Our current study is agreement with the previous study (Table 1). Discussion In this study, we have demonstrated a first ‘‘cut’’ dissection exercise of the PDGFR signaling systems by using the gene expression profile of the four states of PDGF receptors in the PDGFR genetically defined MEF cells and complemented these Table 2. Pearson correlation between the vectors of fold change values (all probe sets, treated v.s. untreated conditions) for the four cell lines Pearson Correlation Double null Alpha null Beta null WT Double null 1.000 0.0712 20.034 0.041 Alpha null 0.071 1.000 0.719 0.780 Beta null 20.035 0.719 1.000 0.770 WT 0.0417 0.780 0.770 1.000 Notice that the responses of both the PDGFRb knock out cell line and PDGFRa null cell line to PDGF-BB treatment are more similar to that of the WT cell line than any of the others. The response of the double null cell line is essentially uncorrelated with the response of the other three cell lines. doi:10.1371/journal.pone.0003794.t002 Txnip was identified here to be highly suppressed by PDGFRa. It is identical to VDUP1 (Vitamin D3 up-regulated protein 1) [24,25]. Txnip/VDUP1 is a known tumor suppressor, cell cycle inhibitor and a factor contributing to P27kip1 stability [26,27,28,29]. Recently, PDGF has been shown to suppress VDUP1 at the mRNA level [30]. We have confirmed that Txnip is down-regulated by PDGF at both the mRNA level and protein level. Furthermore, we identified PDGFRa as the suppressor of Txnip in response to PDGF signaling (Figure 2 and Figure 5). Notice that the responses of both the PDGFRb knock out cell line and PDGFRa null cell line to PDGF-BB treatment are more similar to that of the WT cell line than any of the others. The response of the double null cell line is essentially uncorrelated with the response of the other three cell lines. doi:10.1371/journal.pone.0003794.t002 November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 9 NR4A1/Nur77 and NR4A2/Nurr1 genes are two members of nuclear hormone receptor family (including Nur77, Nurr1 and Nor-1 or NR4A1-3) [31]. It has been demonstrated that the constitutive expression of Nur77 may induce apoptosis while transient expression does not [31]. With addition of PDGF, Nurr1 and Nur77 protein levels are transiently up-regulated in 10 min, which may protect cells against apoptosis. This occurs only in the presence of PDGFRa with PDGF stimulation It also has been Figure 4. Protein interaction map for differentially expressed genes. Discussion The HPRD database was searched for records that reference genes that were differentially expressed in one or more of the PDGFR defined cell lines after stimulation with PDGF-BB ligand. The network shown here represents all of the records in HPRD where both interacting proteins were among the differentially expressed genes. Red nodes represent genes that were differentially expressed in the alpha null, beta null and WT cell lines. Cyan nodes represent genes that were differentially expressed in the alpha null and WT cell lines, but not in the beta null. Dark blue nodes represent genes that were differentially expressed only in the alpha nullcell line. Green nodes represent genes that were differentially expressed only in the WT (heterodimer) cell line. doi:10.1371/journal.pone.0003794.g004 PDGF-PDGFR Signaling PDGF-PDGFR Signaling Figure 4. Protein interaction map for differentially expressed genes. The HPRD database was searched for records that reference genes that were differentially expressed in one or more of the PDGFR defined cell lines after stimulation with PDGF-BB ligand. The network shown here represents all of the records in HPRD where both interacting proteins were among the differentially expressed genes. Red nodes represent genes that were differentially expressed in the alpha null, beta null and WT cell lines. Cyan nodes represent genes that were differentially expressed in the alpha null and WT cell lines, but not in the beta null. Dark blue nodes represent genes that were differentially expressed only in the alpha nullcell line. Green nodes represent genes that were differentially expressed only in the WT (heterodimer) cell line. doi:10 1371/journal pone 0003794 g004 Figure 4. Protein interaction map for differentially expressed genes. The HPRD database was searched for records that reference genes that were differentially expressed in one or more of the PDGFR defined cell lines after stimulation with PDGF-BB ligand. The network shown here represents all of the records in HPRD where both interacting proteins were among the differentially expressed genes. Red nodes represent genes that were differentially expressed in the alpha null, beta null and WT cell lines. Cyan nodes represent genes that were differentially expressed in the alpha null and WT cell lines, but not in the beta null. Dark blue nodes represent genes that were differentially expressed only in the alpha nullcell line. Green nodes represent genes that were differentially expressed only in the WT (heterodimer) cell line. doi:10.1371/journal.pone.0003794.g004 transient expression does not [31]. PLoS ONE | www.plosone.org Discussion With addition of PDGF, Nurr1 and Nur77 protein levels are transiently up-regulated in 10 min, which may protect cells against apoptosis. This occurs only in the presence of PDGFRa with PDGF stimulation. It also has been NR4A1/Nur77 and NR4A2/Nurr1 genes are two members of nuclear hormone receptor family (including Nur77, Nurr1 and Nor-1 or NR4A1-3) [31]. It has been demonstrated that the constitutive expression of Nur77 may induce apoptosis while PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 November 2008 | Volume 3 | Issue 11 | e3794 10 Figure 5. Activation of PDGFRa suppresses Txnip expression. Txnip was downregulated in PDGFRb null (beta KO) and WT cell line PDGF-BB and AA treatments (A) and (C) or with regular medium (10% FBS containing DMEM) (B). A: Immunoblotting for Txnip and ERK in fo lines treated with PDGF-BB (50 ng/ml) and PDGF-AA (50 ng/ml) for 10 min and 1 h. B: Immunoblotting for Txnip and ERK from the same cells in regular medium. C: RNA was extracted from 4 cell lines (double KO, Beta KO, Alpha KO and WT) treated without or with PDGF-BB (50 ng/ 1 h. Txnip gene expression was assessed by reverse transcription-quantitative PCR and normalized using GAPDH as the internal control. The r one representative of three independent experiments. doi:10.1371/journal.pone.0003794.g005 PDGF-PDGFR Sig PDGF-PDGFR Signaling Figure 5. Activation of PDGFRa suppresses Txnip expression. Txnip was downregulated in PDGFRb null (beta KO) and W PDGF-BB and AA treatments (A) and (C) or with regular medium (10% FBS containing DMEM) (B). A: Immunoblotting for Txnip an lines treated with PDGF-BB (50 ng/ml) and PDGF-AA (50 ng/ml) for 10 min and 1 h. B: Immunoblotting for Txnip and ERK from the in regular medium. C: RNA was extracted from 4 cell lines (double KO, Beta KO, Alpha KO and WT) treated without or with PDGF- 1 h. Txnip gene expression was assessed by reverse transcription-quantitative PCR and normalized using GAPDH as the internal con Figure 5. Activation of PDGFRa suppresses Txnip expression. Txnip was downregulated in PDGFRb null (beta KO) and WT cell lines with PDGF-BB and AA treatments (A) and (C) or with regular medium (10% FBS containing DMEM) (B). A: Immunoblotting for Txnip and ERK in four cell lines treated with PDGF-BB (50 ng/ml) and PDGF-AA (50 ng/ml) for 10 min and 1 h. PLoS ONE | www.plosone.org Discussion B: Immunoblotting for Txnip and ERK from the same cells grown in regular medium. C: RNA was extracted from 4 cell lines (double KO, Beta KO, Alpha KO and WT) treated without or with PDGF-BB (50 ng/ml) for 1 h. Txnip gene expression was assessed by reverse transcription-quantitative PCR and normalized using GAPDH as the internal control. The result is one representative of three independent experiments. doi:10.1371/journal.pone.0003794.g005 demonstrated that Nur77 is a survival effecter protein in the context of TNF alpha mediated signaling [31]. The mechanism for Nur77 as a survival effecter protein needs to be further investigated. A very recent study showed that the third member in the nuclear hormone receptor family NR4A orphan nuclear receptor NOR1 is induced by PDGF and mediates vascular smooth muscle cell proliferation [32].This finding suggests that the nuclear hormone receptor family are therapeutic targets for some diseases in which PDGFRs are overexpressed. reveal the downstream interplay of the signaling events brought about by the activation of each of the two receptors, indicating the biological effect of receptor/ligand specificity. Furthermore, in this study, we have demonstrated that transcriptional response to PDGF-BB ligand is mediated entirely through activation of one or both of its receptors and suggest that PDGF ligand, PDGF-BB in this study, does not bind any other receptors. Similar to the stimulation of PDGF, the responsiveness of PDGF receptors to pharmacological inhibition is also complex. While STI-571 inhibits AKT activation through either PDGFRa or PDGFRb, it blocks ERK activation mainly through PDGFRa These results are illustrative of the combinatorial richness of PDGF receptor/ligand-mediated signaling. Our results begin to PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 11 PDGF-PDGFR Signaling gure 6. PDGFR regulates IL6 pathway and the signaling pathways modulated by STI-571. A and B: Triplicate sets of each cell line were eated with or without PDGF-BB (50 ng/ml) for 1 h. Expression levels of the genes in the IL6 pathway in the WT cell line are shown in panel A. pression values are summarized over multiple probe sets for each gene, and a standard Student’s T-test p-value indicates the strength of the fference-of-the-means between the treatment groups. In panel B, the expression patterns (across all cell lines) of a few selected genes from the IL6 thway are shown along with their respective Western blot results in panel C. Discussion In both heatmaps, bright green shading indicates an expression level November 2008 | Volume 3 | Issue 11 | e3794 PLoS ONE | www.plosone.org 12 PDGF-PDGFR Signaling PDGF-PDGFR Signaling below the gene-wise mean, bright red indicates an expression level above the mean, while darker shades indicate expression levels closer to the mean intensity. The mean and standard deviation for each (log-reduced) gene are shown to the right of each gene name. C: Four cell lines were treated with PDGF-BB (50 ng/ml) for 10 min, 1 h. Cell lysates were immunoblotted for Jun, Cebpb, Fos and ERK (lower panel). D: Four cell lines were pretreated with STI-571 (5 mM) for 90 minutes and then stimulated with PDGF-BB (50 ng/ml) for 1 h. The harvested lysates were immunoblotted for PDGFRa, PDGFRb, AKT, p-AKT (Ser473), p-ERK (Tyr 204), ERK, EGR1, c-Jun, c-Fos, ATF-3, Fra-1, and b-actin (b-actin as internal control). doi:10.1371/journal.pone.0003794.g006 below the gene-wise mean, bright red indicates an expression level above the mean, while darker shades indicate expression levels closer to the mean intensity. The mean and standard deviation for each (log-reduced) gene are shown to the right of each gene name. C: Four cell lines were treated with PDGF-BB (50 ng/ml) for 10 min, 1 h. Cell lysates were immunoblotted for Jun, Cebpb, Fos and ERK (lower panel). D: Four cell lines were pretreated with STI-571 (5 mM) for 90 minutes and then stimulated with PDGF-BB (50 ng/ml) for 1 h. The harvested lysates were immunoblotted for PDGFRa, PDGFRb, AKT, p-AKT (Ser473), p-ERK (Tyr 204), ERK, EGR1, c-Jun, c-Fos, ATF-3, Fra-1, and b-actin (b-actin as internal control). doi:10.1371/journal.pone.0003794.g006 Transcript Labeling Kit (Enzo, New York, NY). The labeled cRNA target (20 mg each) was then fragmented into 35–200 base pair fragments and hybridized to each Affymetrix GeneChipH Mouse Genome 430 2.0 array according to Affymetrix Eukaryotic Target Hybridization Protocol. Following a 16-h incubation the microarrays were washed and scanned using the EukGE-WS2v4 fluidics protocol. (Figure 6). Therefore, this PDGFR platform may help us to further understand the molecular mechanism of therapeutic inhibition on PDGF-PDGFR signaling and identify additional critical molecular targets for the intervention of cancer and other diseases. The studies presented here are prone to many well-known limitations, such as the noisiness of expression microarrays, the frequent lack of concordance of gene and protein expression, and the post-translational signaling systems that are at most only faintly echoed in gene expression levels. Comparison of genes lists Once lists of genes and pathways whose mRNA expression responded to PDGF-BB treatment were assembled by the above methods, we compared the lists to see which genes had responded to treatment uniquely in one of the nulls or wild type, or common to two or more of the null and wild type conditions. Differential expression analysis Microarray data were normalized, background corrected and summarized using the robust multi-array average (RMA2) method [35]. We identified individual genes that exhibited statistically significant differential expression as a result of PDGF treatment in each null experiment (i.e., genes induced or repressed in the a2/ 2 b2/2, a+/+ b2/2, a2/2b+/+, a+/+ b+/+ cells when treated with PDGF-BB) using SAM method [14]. In each comparison we selected a value for SAM’s D parameter to specify a median false discovery rate less than 0.05, and we consider the genes reported at this threshold to be differentially expressed between the treatment and non-treatment conditions. In summary, we have taken advantage of the experimental platform presented by PDGFR double null cells, PDGFRa, PDGFRb and PDGFR WT cell lines (where dimers PDGFRa/a, PDGFRb/b, PDGFRa/b co-exist) and used a bioinformatics approach to dissect the gene sets/pathways that are controlled by two PDGFR isoforms with PDGF-BB ligand stimulation. Our study also provides a reproducible approach to the dissection of the contributions of a heteromeric receptor signaling system. While minimal PDGF receptor-independent signaling was found, we identified the signals commonly regulated by PDGFRa, PDGFRb and PDGFRa/b, specifically triggered by each of the two PDGF receptors as well as the heterodimeric PDGFRa/b. Gene set analysis To identify functional groups of genes from each cell line with RNA expression profiles that were affected by PDGF-BB treatment, we used Tian et al’s [15] sigPathway method Gene set annotations were assembled from Gene Ontology [36], KEGG [37], BioCarta (biocarta.com), BioCyc [38] and custom data. This method identifies significantly enriched gene sets by testing two related null hypotheses: 1) The pattern of expression for the genes in a particular gene set is the same as all the other genes, and 2) the gene set does not contain genes with expression profiles that are correlated with treatment. We picked out gene sets that were distinguished by both statistics by ranking the sets by the sum of the ranks of their two statistics. All of the gene sets presented here had a false discovery rate below 0.05 for at least one statistic. Cells and viruses PDGFRa/b double null (double KO) (a2/2b2/2), PDGFR beta null (PDGFRa/b double null cells infected with PDGFRa expressing retro-viruses), and PDGFR alpha null (PDGFRa/b double null cells infected with PDGFRb expressing retro-viruses) MEFs were gifts from Dr. Andrius Kazlauskas (Schepens Eye Research Institute) [33]. Wild-type PDGFRa and PDGFRb MEFs [PDGFRa+/+ b+/+] were generated as follows. Human PDGFRb cDNA was amplified from hPDGFRb in pEF6 (Invitrogen, Carlsbad, CA) with primers (all primer sequences available upon request) using proof-reading Pfu polymerase (Stratagene, La Jolla, CA). The PCR products were digested with Not I and Cla I (NEB Biolab, Ipswich, MA) and inserted into a retroviral vector pIRES-hygromycin [34]. The plasmids were transfected with Lipofectamine 2000 (Invitrogen, Carlsbad, CA) into the retroviral packaging cell line PT67 (Clontech, Palo Alto, CA). Filtered medium containing viruses carrying PDGFRb was used to infect PDGFRa+/+ b2/2 MEF. Infected cells were then selected with 100 mg/ml hygromycin B (Clontech, Palo Alto, CA). All cells were cultured in DMEM with or without 10% FBS in 5% CO2 at 37uC. We identified statistically over-represented Gene Ontology (GO) terms for the lists of differentially expressed genes by computing a hypergeometric p-value for each GO annotation associated with a given gene list. The resulting p-values were corrected for multiple hypothesis testing using the FRD method [39]. An FDR below 0.05 was regarded as indicating significant over-representation. Discussion We have attempted to minimize these limitations by employing rigorous statistical techniques, focusing on pathways as much as on individual genes, using protein interaction data to corroborate co-expression findings and using selected protein measurements, including previously impli- cated post-translational modifications. Discussion In both heatmaps, bright green shading indicates an expression level PDGF-PDGFR Signaling Figure 6. PDGFR regulates IL6 pathway and the signaling pathways modulated by STI-571. A and B: Triplicate sets of each cell line were treated with or without PDGF-BB (50 ng/ml) for 1 h. Expression levels of the genes in the IL6 pathway in the WT cell line are shown in panel A. Expression values are summarized over multiple probe sets for each gene, and a standard Student’s T-test p-value indicates the strength of the difference-of-the-means between the treatment groups. In panel B, the expression patterns (across all cell lines) of a few selected genes from the IL6 pathway are shown along with their respective Western blot results in panel C. In both heatmaps, bright green shading indicates an expression level Figure 6. PDGFR regulates IL6 pathway and the signaling pathways modulated by STI-571. A and B: Triplicate sets of each cell line were treated with or without PDGF-BB (50 ng/ml) for 1 h. Expression levels of the genes in the IL6 pathway in the WT cell line are shown in panel A. Expression values are summarized over multiple probe sets for each gene, and a standard Student’s T-test p-value indicates the strength of the difference-of-the-means between the treatment groups. In panel B, the expression patterns (across all cell lines) of a few selected genes from the IL6 pathway are shown along with their respective Western blot results in panel C. In both heatmaps, bright green shading indicates an expression level Figure 6. PDGFR regulates IL6 pathway and the signaling pathways modulated by STI-571. A and B: Triplicate sets of each cell line were treated with or without PDGF-BB (50 ng/ml) for 1 h. Expression levels of the genes in the IL6 pathway in the WT cell line are shown in panel A. Expression values are summarized over multiple probe sets for each gene, and a standard Student’s T-test p-value indicates the strength of the difference-of-the-means between the treatment groups. In panel B, the expression patterns (across all cell lines) of a few selected genes from the IL6 pathway are shown along with their respective Western blot results in panel C. PLoS ONE | www.plosone.org References 1. Heldin CH, Johnsson A, Wennergren S, Wernstedt C, Betsholtz C, et al. (1986) A human osteosarcoma cell line secretes a growth factor structurally related to a homodimer of PDGF A-chains. Nature 319: 511–514. 12. Zhang H, Bajraszewski N, Wu E, Wang H, Moseman AP, et al. (2007) PDGFRs are critical for PI3K/Akt activation and negatively regulated by mTOR. J Clin Invest 117: 730–738. 1. Heldin CH, Johnsson A, Wennergren S, Wernstedt C, Betsholtz C, et al. (1986) A human osteosarcoma cell line secretes a growth factor structurally related to a homodimer of PDGF A-chains. Nature 319: 511–514. 13. Zhang H, Cicchetti G, Onda H, Koon HB, Asrican K, et al. (2003) Loss of Tsc1/Tsc2 activates mTOR and disrupts PI3K-Akt signaling through downregulation of PDGFR. J Clin Invest 112: 1223–1233. 2. Li X, Ponten A, Aase K, Karlsson L, Abramsson A, et al. (2000) PDGF-C is a new protease-activated ligand for the PDGF alpha-receptor. Nat Cell Biol 2: 302–309. g 14. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116–5121. 3. Ross R, Glomset J, Kariya B, Harker L (1974) A platelet-dependent serum factor that stimulates the proliferation of arterial smooth muscle cells in vitro. Proc Natl Acad Sci U S A 71: 1207–1210. 4. Levitzki A (2004) PDGF receptor kinase inhibitors for the treatment of PDGF driven diseases. Cytokine Growth Factor Rev 15: 229–235. 15. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 102: 13544–13549. 5. Rikova K, Guo A, Zeng Q, Possemato A, Yu J, et al. (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131: 1190–1203. 16. Carroll M, Ohno-Jones S, Tamura S, Buchdunger E, Zimmermann J, et al. (1997) CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins. Blood 90: 4947–4952. 6. MacDonald TJ, Brown KM, LaFleur B, Peterson K, Lawlor C, et al. (2001) Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. Nat Genet 29: 143–152. 17. McGary EC, Weber K, Mills L, Doucet M, Lewis V, et al. (2002) Inhibition of platelet-derived growth factor-mediated proliferation of osteosarcoma cells by the novel tyrosine kinase inhibitor STI571. Cell proliferation, migration and invasion assays TM p , g y Cells were cultured in Cellgro COMPLETETM with L- glutamine & phenol red (40-101-CV, Mediatech, Herndon, VA) in the presence or absence of growth/proliferation factor. Cell numbers were counted every day in triplicates using Trypan Blue dye exclusion method for cell viability (Vi-Cell, Beckman Coulter, Fullerton, CA). Migration and invasion assays were performed using 24-well chamber-based plates (BD Biosciences, Bedford, MA). FBS or PDGF-BB was used as chemo-attractants. Acknowledgments We thank Dr. Andrius Kazlauskas for some MEF lines. We wish to extend our thanks to Dr. Arthur Pardee, Dr. Mengsheng Qiu and Dr. Zoltan Szallasi for critical reading of the manuscript. We thank Dr. Andrius Kazlauskas for some MEF lines. We wish to extend our thanks to Dr. Arthur Pardee, Dr. Mengsheng Qiu and Dr. Zoltan Szallasi for critical reading of the manuscript. Western blot analysis The cells were starved for two days, then left unstimulated, or simulated with 50 ng/ml PDGF-BB (Sigma-Aldrich, Saint Louis, MO) in six well plates in serum-free medium for specific time points. Cell lysates were prepared and proteins were separated by electrophoresis. The electroblotted nitrocellulose membranes were probed with antibodies. Correlation analysis Total RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA) from cells that were treated or untreated with or without 50 ng/ml PDGF-BB for 1 h. Five mg RNA of each sample was used for double-stranded cDNA synthesis. In vitro transcription was carried out using the Enzo BioArray High Yield RNA In order to evaluate how similar each of the four cell lines’ transcriptional responses to PDGF-BB ligand stimulation were to one another, Pearson correlation coefficients were computed between all pairs of cell lines. The SAM software package for R was used to compute fold change values (PDGF-BB treated PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 13 PDGF-PDGFR Signaling PDGF-PDGFR Signaling volume. 2 ml of the diluted cDNA was used as the template in the quantitative PCR reaction. Amplification was done using iQ SYBR Green Supermix on an iCycler (Bio-Rad, Hercules, CA) (primer sequences for Txnip and GAPGH available upon request). expression values vs. untreated expression values) for all genes present in the normalized microarray data, for each cell line. Thus, four vectors of fold change estimates were obtained (one for double null, one for alpha null, one beta null and one for wild type) representing each cell line’s response to ligand stimulation. Pearson correlations between each pair of these vectors were computed using R. Statistical analysis Hypergeometric p-values were used to evaluate GO term enrichment. The raw p-values were corrected for multiple hypothesis testing using the FRD method [39] to compute q- values. Any q-value below 0.05 was considered significant. Reverse transcription-quantitative PCR Conceived and designed the experiments: EW HZ ISK. Performed the experiments: EW ZT AM MG XW HZ ISK. Analyzed the data: EW NP Conceived and designed the experiments: EW HZ ISK. Performed the One mg of RNA from each sample was reverse transcribed using iScript cDNA Synthesis Kit (Bio-Rad Laboratories, Hercules, CA) according to the instructions of the manufacturer. The original cDNA reaction mixture was diluted to one-tenth of the reaction experiments: EW ZT AM MG XW HZ ISK. Analyzed the data: EW NP ZT BB HZ ISK. Contributed reagents/materials/analysis tools: EW NP BB HZ ISK. Wrote the paper: EW NP ZT BB HZ ISK. Supporting Information Table S1 Diff-Genes-PDGF-BB-Treatment Found at: doi:10.1371/journal.pone.0003794.s001 (0.06 MB XLS) Antibodies were obtained from: PDGFRa (C-20), ERK (K-23), p-ERK (E-4), Fra-1 (R-20), Nurr1 (M-196), Nur77 (M-210),TF (I- 20), Egr3 (C-24), ATF-3 (C-19), c-Fos (4), Cebpb (H-7) (Santa Cruz Biotech, CA); PDGFRb (Upstate, Temecula, CA); p-AKT (Ser473), AKT, EGR1 and c-jun (Cell Signaling Technology, Beverly, MA); Txnip (MBL International, Woburn, MA). Secondary antibodies were anti-mouse IgG, anti-rabbit IgG and anti-goat IgG HRP (Santa Cruz Biotech, CA). Table S2 GO-Enrichment-PDGF-BB-Treatment Found at: doi:10.1371/journal.pone.0003794.s002 (0.06 MB XLS) Table S3 PDGF-Independent-Gene-Lists Found at: doi:10.1371/journal.pone.0003794.s003 (0.08 MB XLS) Table S4 GO-Enrichment-for-PPI-Figure Found at: doi:10.1371/journal.pone.0003794.s004 (0.12 MB XLS) References Vrekoussis T, Stathopoulos EN, Kafousi M, Navrozoglou I, Zoras O (2007) Expression of endothelial PDGF receptors alpha and beta in breast cancer: up- regulation of endothelial PDGF receptor beta. Oncol Rep 17: 1115–1119. n of endothelial PDGF receptor beta. Oncol Rep 17: 1115–1119. regulation of endothelial PDGF receptor beta. Oncol Rep 17: 1115 33. Andrews A, Balciunaite E, Leong FL, Tallquist M, Soriano P, et al. (1999) Platelet-derived growth factor plays a key role in proliferative vitreoretinopathy. Invest Ophthalmol Vis Sci 40: 2683–2689. 24. Chen KS, DeLuca HF (1994) Isolation and characterization of a novel cDNA from HL-60 cells treated with 1,25-dihydroxyvitamin D-3. Biochim Biophys Acta 1219: 26–32. 24. Chen KS, DeLuca HF (1994) Isolation and characterization of a novel cDNA 34. El-Hashemite N, Zhang H, Walker V, Hoffmeister KM, Kwiatkowski DJ (2004) Perturbed IFN-gamma-Jak-signal transducers and activators of transcription signaling in tuberous sclerosis mouse models: synergistic effects of rapamycin- IFN-gamma treatment. Cancer Res 64: 3436–3443. 25. Nishiyama A, Matsui M, Iwata S, Hirota K, Masutani H, et al. (1999) Identification of thioredoxin-binding protein-2/vitamin D(3) up-regulated protein 1 as a negative regulator of thioredoxin function and expression. J Biol Chem 274: 21645–21650. 35. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249–264. 26. Ohta S, Lai EW, Pang AL, Brouwers FM, Chan WY, et al. (2005) Downregulation of metastasis suppressor genes in malignant pheochromocyto- ma. Int J Cancer 114: 139–143. p 36. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25–29. 27. Han SH, Jeon JH, Ju HR, Jung U, Kim KY, et al. (2003) VDUP1 upregulated by TGF-beta1 and 1,25-dihydorxyvitamin D3 inhibits tumor cell growth by blocking cell-cycle progression. Oncogene 22: 4035–4046. 37. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354–357. 28. Shin KH, Kang MK, Kim RH, Christensen R, Park NH (2006) Heterogeneous nuclear ribonucleoprotein G shows tumor suppressive effect against oral squamous cell carcinoma cells. Clin Cancer Res 12: 3222–3228. 38. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. References Clin Cancer Res 8: 3584–3591. 7. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, et al. (2004) Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 18: 629–640. 18. Li L, Blumenthal DK, Masaki T, Terry CM, Cheung AK (2006) Differential effects of imatinib on PDGF-induced proliferation and PDGF receptor signaling in human arterial and venous smooth muscle cells. J Cell Biochem 99: 1553–1563. 8. Jones AV, Cross NC (2004) Oncogenic derivatives of platelet-derived growth factor receptors. Cell Mol Life Sci 61: 2912–2923. factor receptors. Cell Mol Life Sci 61: 2912–2923. 9. Hay N (2005) The Akt-mTOR tango and its relevance to cancer. Cancer Cell 8: 179–183. 19. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM (2004) Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem 279: 20167–20177. 10. Hennessy BT, Smith DL, Ram PT, Lu Y, Mills GB (2005) Exploiting the PI3K/ AKT pathway for cancer drug discovery. Nat Rev Drug Discov 4: 988– 1004. 20. Antipova AA, Stockwell BR, Golub TR (2008) Gene expression-based screening for inhibitors of PDGFR signaling. Genome Biol 9: R47. 11. Samuels Y, Ericson K (2006) Oncogenic PI3K and its role in cancer. Curr Opin Oncol 18: 77–82. PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 November 2008 | Volume 3 | Issue 11 | e3794 14 PDGF-PDGFR Signaling PDGF-PDGFR Signaling muscle cell proliferation through interaction with thioredoxin. Circ Res 91: 689–695. muscle cell proliferation through interaction with thioredoxin. Circ Res 91: 689–695. 21. Chen WV, Delrow J, Corrin PD, Frazier JP, Soriano P (2004) Identification and validation of PDGF transcriptional targets by microarray-coupled gene-trap mutagenesis. Nat Genet 36: 304–312. 31. Hsu HC, Zhou T, Mountz JD (2004) Nur77 family of nuclear hormone receptors. Curr Drug Targets Inflamm Allergy 3: 413–423. g 22. Claesson-Welsh L (1994) Platelet-derived growth factor receptor signals. J Biol Chem 269: 32023–32026. 32. Nomiyama T, Nakamachi T, Gizard F, Heywood EB, Jones KL, et al. (2006) The NR4A orphan nuclear receptor NOR1 is induced by platelet-derived growth factor and mediates vascular smooth muscle cell proliferation. J Biol Chem 281: 33467–33476. 23. References Nucleic Acids Res 33: 6083–6089. 29. Jeon JH, Lee KN, Hwang CY, Kwon KS, You KH, et al. (2005) Tumor suppressor VDUP1 increases p27(kip1) stability by inhibiting JAB1. Cancer Res 65: 4485–4489. 39. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57: 289–300. 30. Schulze PC, De Keulenaer GW, Yoshioka J, Kassik KA, Lee RT (2002) Vitamin D3-upregulated protein-1 (VDUP-1) regulates redox-dependent vascular smooth PLoS ONE | www.plosone.org November 2008 | Volume 3 | Issue 11 | e3794 15
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Multi-choice stochastic transportation problem involving general form of distributions
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1 Introduction 1 Introduction The transportation problem is one of the oldest appli- cations of Linear Programming Problem (LPP). The standard form of the transportation problem was first for- mulated along with the constructive method of solution by Hitchcock (1941). In a classical transportation prob- lem, a product is to be transported from m sources to n destinations. The availability of the product at ith source is denoted by ai, where i = 1, 2, . . . , m and the demand required at jth destination is bj where j = 1, 2, . . . , n. The penalty cij is the cost coefficient of the objective function which can represent transportation cost, delivery time etc. In many real world situations the availability ai and demand bj are not certainly known to Decision Maker (DM). One way to deal such uncertainty is to describe the availability ai and demand bj parameters as random variables rather than the deterministic one. These random variables ai and bj are assumed to follow a given prob- ability distribution or its probability distribution may be estimated. This type of transportation problem is known as “Stochastic Transportation Problem” (STP). Further- more, suppose that there exist k routes for transporting *Correspondence: abdulquddoos.or.amu@gmail.com Department of Statistics and Operations Research AMU, Aligarh, India © 2014 Quddoos et al.; licensee Springer. T Attribution License (http://creativecommon in any medium, provided the original work The transportation problem is one of the oldest appli- cations of Linear Programming Problem (LPP). The standard form of the transportation problem was first for- mulated along with the constructive method of solution by Hitchcock (1941). In a classical transportation prob- lem, a product is to be transported from m sources to n destinations. The availability of the product at ith source is denoted by ai, where i = 1, 2, . . . , m and the demand required at jth destination is bj where j = 1, 2, . . . , n. The penalty cij is the cost coefficient of the objective function which can represent transportation cost, delivery time etc. In many real world situations the availability ai and demand bj are not certainly known to Decision Maker (DM). One way to deal such uncertainty is to describe the availability ai and demand bj parameters as random variables rather than the deterministic one. © 2014 Quddoos et al.; licensee Springer. 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. Multi-choice stochastic transportation problem involving general form of distributions Abdul Quddoos*, Md Gulzar ull Hasan and Mohammad Masood Khalid Abstract Many authors have presented studies of multi-choice stochastic transportation problem (MCSTP) where availability and demand parameters follow a particular probability distribution (such as exponential, weibull, cauchy or extreme value). In this paper an MCSTP is considered where availability and demand parameters follow general form of distribution and a generalized equivalent deterministic model (GMCSTP) of MCSTP is obtained. It is also shown that all previous models obtained by different authors can be deduced with the help of GMCSTP. MCSTP with pareto, power function or burr-XII distributions are also considered and equivalent deterministic models are obtained. To illustrate the proposed model two numerical examples are presented and solved using LINGO 13.0 software package. Keywords: General form of distributions; Multi-choice programming; Stochastic transportation problem; Transformation technique the product from ith source to jth destination and the cost of transporting a unit of product via kth route is denoted by Ck ij. Thus DM have multiple (i.e. ‘k’) route choices for shipping the product from ith source to jth destination and he has to identify exactly one among k routes in such a manner that the combination of choices should minimize the overall transportation cost. With the above discussed objective the STP becomes ‘Multi Choice Stochastic Transportation Problem’ (MCSTP) in which the cost coefficient Cij are multi-choice and availability ai and demand bj are random variables. Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Quddoos et al. SpringerPlus 2014, 3:565 a SpringerOpen Journal a SpringerOpen Journal *Correspondence: abdulquddoos.or.amu@gmail.com Department of Statistics and Operations Research AMU, Aligarh, India 1 Introduction These random variables ai and bj are assumed to follow a given prob- ability distribution or its probability distribution may be estimated. This type of transportation problem is known as “Stochastic Transportation Problem” (STP). Further- more, suppose that there exist k routes for transporting j MCSTP has been extensively studied by many researchers. Roy et al. (2012) presented an equivalent deterministic model of MCSTP by assuming that both availability ai and demand bj as random variables fol- lowing exponential distribution. Biswal and Samal (2013) obtained an equivalent deterministic model of MCSTP in which they considered that both ai and bj follow Cauchy distribution. Mahapatra (2014) also given equivalent deterministic model of MCSTP involving Weibull distri- bution. Mahapatra et al. (2013) considered the MCSTP involving Extreme value distribution. Barik et al. (2011) presented a stochastic transportation model involving Pareto distribution. *Correspondence: abdulquddoos.or.amu@gmail.com Department of Statistics and Operations Research AMU, Aligarh, India Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 2 of 9 These random variables ai and bj may also be consid- ered to follow Burr-XII or Power Function distributions. Burr-XII may be used in place of normal distribution when data shows some positive skewness. Since ai and bj are the physical quantities so it is advisable to use Burr-XII instead of Normal distribution. When upper bound of availability and demand is known, Power Function distri- bution would be most suitable distribution to fit. In this paper we considered general form of MCSTP, where ai and bj are assumed to follow ‘General classes of distribu- tion’ and obtained a generalised equivalent deterministic model (GMCSTP). All the models discussed above by many authors have been deduced by using the proposed GMCSTP. Three new equivalent deterministic models of MCSTP have also been obtained by considering that both ai and bj follow Pareto, Power Function and Burr-XII distribution (only one at a time). An equivalent deter- ministic GMCSTP has also been obtained by considering that ai follows any one distribution among Exponential, Weibull, Cauchy, Exterme Value, Pareto, Power Function or Burr-XII and bj follows any other distribution except that of distribution of ai. To illustrate the proposed mod- els two numerical examples are taken and solved by using transformation technique given by Biswal and Acharya (2009). Lingo 13.0 software has been used for obtaining the optimal solution. 3 Mathematical model of multi-choice stochastic transportation problem (MCSTP) In this section a mathematical model of multi-choice transportation problem involving general form of distri- butions (2.1 or 2.2) is considered. The general form of MCSTP is: 2 General classes of distributions Let us consider a random variable y following any of the two general classes of distributions with distribution function (df ) F(y) as follows: j The following cases are to be considered: (i) Only ai, i = 1, 2, . . . , m follows general form of distribution. (i) Only ai, i = 1, 2, . . . , m follows general form of distribution. F(y) = 1 −F(y) = 1 −  ph(y) + q r , y ∈(ξ, φ) (2.1) F(y) = 1 −F(y) = 1 −  ph(y) + q r , y ∈(ξ, φ) (2.1) distribution. (ii) Only bj, j = 1, 2, . . . , n follows general form of distribution. F(y) = 1 −F(y) = 1 −  ph(y) + q r , y ∈(ξ, φ) (2.1) (ii) Only bj, j = 1, 2, . . . , n follows general form of distribution. (ii) Only bj, j = 1, 2, . . . , n follows general form of distribution. (ii) Only bj, j = 1, 2, . . . , n follows general form of distribution. and (iii) Both ai, i = 1, 2, . . . , m and bj, j = 1, 2, . . . , n follow general form of distribution. (iii) Both ai, i = 1, 2, . . . , m and bj, j = 1, 2, . . . , n follow general form of distribution. F(y) = 1 −F(y) = e−ph(y) p ̸= 0, y ∈(ξ, φ) (2.2) (2.2) subject to, Pr ⎡ ⎣ n  j=1 xij ≤ai ⎤ ⎦≥1 −αi, i = 1, 2, . . . , m (3.2) Pr m  i=1 xij ≥bj ≥1 −βj, j = 1, 2, . . . , n (3.3) Pr ⎡ ⎣ n  j=1 xij ≤ai ⎤ ⎦≥1 −αi, i = 1, 2, . . . , m (3.2) (3.2) (3.3) xij ≥0 ∀iand j (3.4) (3.4) where 0 < αi < 1, ∀i and 0 < βj < 1, ∀j, are the aspiration levels. where 0 < αi < 1, ∀i and 0 < βj < 1, ∀j, are the aspiration levels. p It is assumed that ai, i = 1, 2, . . . , m, bj, j = 1, 2, . . . , n are random variables following general form of distribu- tion,  C1 ij, C2 ij, . . . , Ck ij  k = 1, 2, . . . , K are multi-choice parameters and xij are deterministic decision variables. MCSTP1: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (3.1) Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 3.1 Only ai i = 1, 2, . . . , m follows (2.1) or (2.2) where h(y) is a monotonic and differentiable function of y and p, q, r and h(y) are chosen such that F(y) in (2.1) and (2.2) are df over (ξ, φ). It is considered that ai, i = 1, 2, . . . , m are independent random variable which follows any of two general form of distributions as defined in (2.1) and (2.2) consider the probabilistic constraint (3.2), Differentiating (2.1) and (2.2) with respect to y the probability density function (pdf ), f (y) may be obtained respectively as, respectively as, f (y) = −prh′(y)  ph(y) + q r−1 (2.3) f (y) = −ph′(y)e−ph(y) (2.4) where F(ξ)=0 and F(φ)=1. Pr ⎡ ⎣ n  j=1 xij ≤ai ⎤ ⎦≥1 −αi, i = 1, 2, . . . , m or Pr ⎡ ⎣ai ≥ n  j=1 xij ⎤ ⎦≥1 −αi, i = 1, 2, . . . , m (3.5) f (y) = −prh′(y)  ph(y) + q r−1 (2.3) (2.3) f (y) = −ph′(y)e−ph(y) f (y) = −ph′(y)e−ph(y) (3.5) Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 3 of 9 the above inequality (3.5) can be represented as the above inequality (3.5) can be represented as the above inequality (3.11) can be represented as φi n j=1 xij f (ai)dai ≥1 −αi φi n j=1 xij d dai  −F(ai)  dai ≥1 −αi −F(ai)|φn j=1 xij ≥1 −αi − ⎡ ⎣F(φi) −F ⎛ ⎝ n  j=1 xij ⎞ ⎠ ⎤ ⎦≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi (3.6) φi n j=1 xij f (ai)dai ≥1 −αi φi n j=1 xij d dai  −F(ai)  dai ≥1 −αi −F(ai)|φn j=1 xij ≥1 −αi − ⎡ ⎣F(φi) −F ⎛ ⎝ n  j=1 xij ⎞ ⎠ ⎤ ⎦≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi (3.6) m i=1 xij ξ f (bj)dbj ≥1 −βj, j = 1, 2, . . . , n m i=1 xij ξ d dbj  −F(bj)  dbj ≥1 −βj, j = 1, 2, . . . , n −F(bj)| m i=1 xij ξ ≥1 −βj j = 1, 2, . . . , n − ⎡ ⎣F ⎛ ⎝ m  j=i xij ⎞ ⎠−1 ⎤ ⎦≥1 −βj j = 1, 2, . 3.2 Only bj, j = 1, 2, . . . , n follows (2.1) or (2.2) 3.2 Only bj, j = 1, 2, . . . , n follows (2.1) or (2.2) It is considered that ai (i = 1, 2, . . . , m) and bj, j = 1, 2, . . . , n are independent random variable which follows any of two general form of distributions as defined in (2.1) and (2.2). It is considered that bj, i = 1, 2, . . . , n are independent random variable which follows any of two general form of distributions as defined in (2.1) and (2.2) consider the probabilistic constraint (3.3), In view of (3.6) and (3.12) we may obtain a multi-choice deterministic model GMCSTP as follows: Pr m  i=1 xij ≥bj ≥1 −βj, j = 1, 2, . . . , n r Pr bj ≤ m  i=1 xij ≥1 −βj, j = 1, 2, . . . , n (3.11) Pr m  i=1 xij ≥bj ≥1 −βj, j = 1, 2, . . . , n MCSTP 3: MCSTP 3: Thus, we obtained a multi-choice deterministic model MCSTP 2 as follows: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K ( MCSTP 2: i=1 j=1 (3.13) (3.13) min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K subject to, subject to, subject to, (3.7) (3.7) n  j=1 xij ≤ai i = 1, 2, . . . , m (3.14) (3.14) subject to, F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi, i = 1, 2, . . . , m (3.8) m j F  m  i=1 xij  ≥1 −βj j = 1, 2, . . . F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi, i = 1, 2, . . . , m (3.8) m F  m  i=1 xij  ≥1 −βj j = 1, 2, . . . , n (3.15) 3.8) F  m  i=1 xij  ≥1 −βj j = 1, 2, . . . , n (3.15) (3.8) (3.15) m  i=1 xij ≥bj j = 1, 2, . . . , n m  xij ≥bj j = 1, 2, . . . , n (3.9) (3.9) xij ≥0 ∀i and j (3.16) xij ≥0 ∀i and j (3.16) where m i=1 ai ≥n j=1 F−1(1−βj) (feasibility condition). xij ≥0 ∀i and j (3.10) (3.10) 3.3 Both ai (i = 1, 2, . . . , m) and bj (j = 1, 2, . . . , n) follow (2.1) or (2.2) 3.3 Both ai (i = 1, 2, . . . , m) and bj (j = 1, 2, . . . , n) follow (2.1) or (2.2) where m i=1 F−1(αi) ≥n j=1 bj (feasibility condition). 3.1 Only ai i = 1, 2, . . . , m follows (2.1) or (2.2) . . , n F  m  i=1 xij  ≥1 −βj j = 1, 2, . . . , n (3.12) φi n j=1 xij d dai  −F(ai)  dai ≥1 −αi j −F(ai)|φn j=1 xij ≥1 −αi − ⎡ ⎣F(φi) −F ⎛ ⎝ n  j=1 xij ⎞ ⎠ ⎤ ⎦≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≥1 −αi F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi F  m  i=1 xij  ≥1 −βj j = 1, 2, . . . , n (3.12) (3.12) 3.6) Thus, we obtained a multi-choice deterministic model MCSTP 3 as follows: ) Thus, we obtained a multi-choice deterministic model MCSTP 3 as follows: xij ⎞ ⎠≤αi (3.6) Thus, we obtained a multi-choice deterministic model MCSTP 3 as follows: F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi (3.6) Thus, we obtained a multi-choice deterministic model MCSTP 3 as follows: (3.6) MCSTP 3: 4.3 When ai and bj follow general form of distribution defined in (2.1) and (2.2) respectively or vice-versa 4.3 When ai and bj follow general form of distribution defined in (2.1) and (2.2) respectively or vice-versa 4.1 When ai and bj both follow general form of distribution defined in (2.1) j defined in (2.1) and (2.2) respectively or vice-ver Consider a case when ai follows any one of general form of distributions defined in (2.1) and (2.2) and bj follows any one of general form of distribution defined in (2.2) and (2.1) respectively, then in view of GMCSTP 1 and GMCSTP 2 we have, Let us consider that ai and bj follows general form of dis- tribution of the form defined in (2.1) i.e F(y) = 1−F(y) = 1−[ ph(y) + q]r , p ̸= 0, y ∈(ξ, φ). [ p (y) q] p ̸ y (ξ φ) Putting F n j=1 xij  = 1 −  pih n j=1 xij  + qi ri in (3.18) of GMCSTP and F m i=1 xij  = 1 − ′ Putting F n j=1 xij  = 1 −  pih n j=1 xij  + qi ri in (3.18) of GMCSTP and F m i=1 xij  = 1 − ′ GMCSTP 3:  p′ jg m i=1 xij  + q′ j r′ j in (3.19) of GMCSTP, we get, min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K  p′ jg m i=1 xij  + q′ j r′ j in (3.19) of GMCSTP, we get, subject to, subject to, GMCSTP: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K or Pr bj ≤ m  i=1 xij ≥1 −βj, j = 1, 2, . . . , n (3.11) (3.17) Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 4 of 9 4 Different cases of GMCSTP 4 Different cases of GMCSTP Consider the following three cases of GMCSTP 1 −e −pih n j=1 xij  ≥1 −αi, i = 1, 2, . . . , m (4.6) e−p′ jg( m i=1 xij) ≥1 −βj, j = 1, 2, . . . , n (4.7) xij ≥0 ∀i and j (4.8) 1 −e −pih n j=1 xij  ≥1 −αi, i = 1, 2, . . . , m (4.6) (4.6) Consider the following three cases of GMCSTP (a) when ai and bj both follow general form of distribution defined in (2.1). e−p′ jg( m i=1 xij) ≥1 −βj, j = 1, 2, . . . , n (4.7) (4.7) (b) when ai and bj both follow general form of distribution defined in (2.2). xij ≥0 ∀i and j (4.8) xij ≥0 ∀i and j (4.8) (c) when ai and bj follow general form of distribution defined in (2.1) and (2.2) respectively or vice-versa. (c) when ai and bj follow general form of distribution defined in (2.1) and (2.2) respectively or vice-versa. 1 − p′ jg  m  i=1 xij  + q′ j r′ j ≥1 −βj, j = 1, 2, . . . , n (4 GMCSTP 2: MCSTP 2: in: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K xij ≥0 ∀i and j (3.20) where m i=1 F−1(αi) ≥n j=1 F−1(1 −βj) (feasibility condition). (4.5) 4.2 When ai and bj both follow general form of distribution defined in (2.2) subject to, F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi, i = 1, 2, . . . , m F  m  i=1 xij  ≥1 −βj, j = 1, 2, . . . , n F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi, i = 1, 2, . . . , m (3.18) F  m  i=1 xij  ≥1 −βj, j = 1, 2, . . . , n (3.19) distribution defined in (2.2) Let us consider that ai and bj in (2.2) i.e F(y) = 1−F(y) = e−ph(y) p ̸= 0, y ∈(ξ, φ). Putting F n j=1 xij  = e −pih n j=1 xij  in (3.18) of GMC- STP and F m i=1 xij  = e−p′ jg( m i=1 xij) in (3.19) of GMC- STP, we get, F ⎛ ⎝ n  j=1 xij ⎞ ⎠≤αi, i = 1, 2, . . . , m (3.18) F  m  i=1 xij  ≥1 −βj, j = 1, 2, . . . , n (3.19) Let us consider that ai and bj in (2.2) i.e F(y) = 1−F(y) = e−ph(y) p ̸= 0, y ∈(ξ, φ). Putting F n j=1 xij  = e −pih n j=1 xij  in (3.18) of GMC- STP and F m i=1 xij  = e−p′ jg( m i=1 xij) in (3.19) of GMC- STP, we get, e p (y) p ̸= 0, y ∈(ξ, φ). Putting F n j=1 xij  = e −pih n j=1 xij  in (3.18) of GMC- STP and F m i=1 xij  = e−p′ jg( m i=1 xij) in (3.19) of GMC- STP, we get, F  m  i=1 xij  ≥1 −βj, j = 1, 2, . . . , n GMCSTP 1: (4.9) min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (4.1 subject to, subject to, min: Z =  i=1  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (4.1) subject to, ⎡ ⎣pih ⎛ ⎝ n  j=1 xij ⎞ ⎠+ qi ⎤ ⎦ ri ≥1 −αi, i = 1, 2, . . . , m (4.2) 1 − p′ jg  m  i=1 xij  + q′ j r′ j ≥1 −βj, j = 1, 2, . . . , n (4.3) subject to, ⎧ ⎨ ⎩ ⎡ ⎣pih ⎛ ⎝ n  j=1 xij ⎞ ⎠+ qi ⎤ ⎦ ri⎫ ⎬ ⎭or ! 1 −e −pih n j=1 xij " ≥1 −αi, i = 1, 2, . . . , m (4.10)  e−p′ jg( m i=1 xij) or ⎧ ⎨ ⎩1 − p′ jg  m  i=1 xij  + q′ j r′ j ⎫ ⎬ ⎭≥1 −βj, j = 1, 2, . . . , n (4.11) (4.1) (4.1) subject to, j ⎡ ⎣pih ⎛ ⎝ n  j=1 xij ⎞ ⎠+ qi ⎤ ⎦ ri ≥1 −αi, i = 1, 2, . . . , m (4.2) 1 − p′ jg  m  i=1 xij  + q′ j r′ j ≥1 −βj, j = 1, 2, . . . , n (4.3) ! 1 −e −pih n j=1 xij " ≥1 −αi, i = 1, 2, . . . , m (4.10)  e−p′ jg( m i=1 xij) or ⎧ ⎨ ⎩1 − p′ jg  m  i=1 xij  + q′ j r′ j ⎫ ⎬ ⎭≥1 −βj, j = 1, 2, . . . , n (4.11) (4.10) (4.3) (4.11) (4.11) xij ≥0 ∀i and j (4.4) xij ≥0 ∀i and j (4.4) xij ≥0 ∀i and j (4.12) xij ≥0 ∀i and j (4.4) xij ≥0 ∀i and j (4.12) xij ≥0 ∀i and j xij ≥0 ∀i and j (4.12) Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 5 of 9 5.1 Deductions using GMCSTP 1 and GMCSTP 2 xij ≥0 ∀i and j xij ≥0 ∀i and j (5.8) xij ≥0 ∀i and j (5.8) where m i=1 e  lnδi+ 1 γi ln{−ln(1−αi)}  ≥n j=1 e lnδ ′ j + 1 γ ′ j ln{−ln(βj)} (feasibility condition) and ai ≥0, bj ≥0 and {γi, γ ′ j } > 0 and {δi, δ′ j} > 0 are shape and scale parameters. 5.1.1 When ai and bj follows exponential distribution Let us consider that both ai and bj follow exponential dis- tribution. In order to deduce the model obtained by S.K. y Roy et al, we set pi = 1, qi = 0, ri = θi ki , h n j=1 xij  = e−ki n j=1 xij and p′ j = 1, q′ j = 0, r′ j = θ′ j k′ j , g m i=1 xij  = Roy et al, we set pi = 1, qi = 0, ri = θi ki , h n j=1 xij  = e−ki n j=1 xij and p′ j = 1, q′ j = 0, r′ j = θ′ j k′ j , g m i=1 xij  = j The above MCSTP 5 is same as obtained by Mahapatra (2014). e−k′ j m i=1 xij in GMCSTP 1 and get, MCSTP 5: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K In this section we deduce some previous results with the help of GMCSTP 1 and GMCSTP 2. Since GMCSTP 1 and 2 has been modelled with the assump- tion that both ai and bj are random variable. So we are considering only GMCSTP 1 and 2 throughout the paper. One can also consider MCSTP 2 or/and MCSTP 3 accord- ing to requirement. Many previous models proposed by Roy et al. (2012), Mahapatra (2014), Biswal and Samal (2013) and Mahapatra et al. (2013) can be deduced from GMCSTP 1 and GMCSTP 2 by setting different values of pi, p′ j, qi, q′ j, ri, r′ j, h n j=1 xij  and g m i=1 xij  . (5.5) (5.5) subject to: n  j 1 xij ≤e  lnδi+ 1 γi ln{−ln(1−αi)}  i = 1, 2 . . . m. (5.6) (5.6) m  i=1 xij ≥e lnδ ′ j + 1 γ ′ j ln{−ln(βj)} j = 1, 2 . . . n. (5.7) (5.7) MCSTP 4: j Biswal and Samal (2013) proposed MCSTP model by con- sidering that ai and bj follow Cauchy distribution. On min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K j Setting pi = −1 π , qi = 1 2, ri = 1, h n j=1 xij  = tan−1 n j=1 xij−lai sai and p′ j = −1 π , q′ j = 1 2, r′ j = 1, g m i=1 xij  = tan−1 m i=1 xij−lbj sbj in GMCSTP 1, we get, (5.1) subject to, n  j=1 xij ≤−θiln(1 −αi), i = 1, 2 . . . m. (5.2) m  i=1 xij ≥−θ ′ j ln(βj), j = 1, 2 . . . n. (5.3)  MCST min: Z subject n  j 1 xij ≤−θiln(1 −αi), i = 1, 2 . . . m. (5.2) MCSTP 6: (5.2) (5.2) MCS (5.2) MCSTP 6: (5.2) MCSTP 6: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K m  i 1 xij ≥−θ ′ j ln(βj), j = 1, 2 . . . n. (5.3) i=1 j (5.3) (5.9) subject to: n  j=1 xij ≤lai + saitan  παi −π 2  , i = 1, 2, . . . , m (5.10) m  i=1 xij ≥lbj + sbjtan π 2 −πβj  , j = 1, 2, . . . , n (5.11) xij ≥0 ∀i and j (5.4) (5.4) xij ≥0 ∀i and j where m i=1{−θiln(1 −αi)} ≥n j=1{−θ′ j ln(βj)} (feasi- bility condition) and ai ≥0, bj ≥0 and {θi, θ′ j } > 0 are the parameters of exponential distribution. The above MCSTP 4 is same as obtained by Roy et al. (2012). xij ≥0 ∀i and j xij ≥0 ∀i and j (5.23) xij ≥0 ∀i and j xij ≥0 ∀i and j (5.24) (5.24) MCSTP 8: pj = −θ′ j , h m i=1 xij  = ln ' m i=1 xij d′ j ( in GMCSTP 2, we get, MCSTP 8: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.17) pj = −θ′ j , h m i=1 xij  = ln ' m i=1 xij d′ j ( in GMCSTP 2, we 5.2 Some new results using GMCSTP 1, GMCSTP 2 and GMCSTP 3 ⎣ ⎦ sibility condition) and ai ≥0, bj ≥0 and {θi, θ′ j } > 0 and {ki, k′ j} > 0 are shape parameters of Burr-XII distribution. y g p i q −θi ki , h n j=1 xij  = n j=1 xij ki and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ j , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 1, we get, 5.1.2 When ai and bj follows Weibull distribution SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 6 of 9 5.1.4 When ai and bj follows extreme value distribution Setting p = 1, h n j=1 xij  = e− n j=1 xij−γi  δi and p′ = 1, g m i=1 xij  = e − m i=1 xij−γ ′ j  δ′ j in GMCSTP 2 it deduces to, 5.2.2 When ai and bj follow Burr-XII distribution Setting p = θi, q = 1, r = −ki, h n j=1 xij  = n j=1 xij δi and p ′ = θ ′ j , q ′ = 1, r ′ = −k ′ j, g m i=1 xij  = m i=1 xij δ ′ j in GMCSTP 1 we get, 5.1.4 When ai and bj follows extreme value distribution 5.2.2 When ai and bj follow Burr-XII distribution 5.2.2 When ai and bj follow Burr-XII distribution j Setting p = 1, h n j=1 xij  = e− n j=1 xij−γi  δi and p′ = 1 g m x  e − m i=1 xij−γ ′ j  δ′ j in GMCSTP 2 it deduces Setting p n j=1 xij   δ Setting p = θi, q = 1, r = −ki, h n j=1 xij  = n j=1 xij δi and p ′ = θ ′ j , q ′ = 1, r ′ = −k ′ j, g m i=1 xij  = ′ m i=1 xij δ ′ j in GMCSTP 1 we get, to, 5.2 Some new results using GMCSTP 1, GMCSTP 2 and GMCSTP 3 5.2.1 When ai and bj follow Pareto distribution Let us consider the MCSTP in which ai and bj follow P t di t ib ti B tti d−ki 0 5.2.1 When ai and bj follow Pareto distribution Let us consider the MCSTP in which ai and bj follow Pareto distribution. By setting pi = d−ki i , qi = 0, ri = −θi ki , h n j=1 xij  = n j=1 xij ki and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ j , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 1, we get, 5.2.1 When ai and bj follow Pareto distribution Let us consider the MCSTP in which ai and bj follow Pareto distribution. By setting pi = d−ki i , qi = 0, ri = −θi ki , h n j=1 xij  = n j=1 xij ki and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ j , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 1, we get, 5.2.1 When ai and bj follow Pareto distribution Let us consider the MCSTP in which ai and bj follow k i j Pareto distribution. By setting pi = d−ki i , qi = 0, ri = Pareto distribution. By setting pi = d ki i , qi = 0, ri = −θi ki , h n j=1 xij  = n j=1 xij ki and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 1, ⎣ ⎦ sibility condition) and ai ≥0, bj ≥0 and {θi, θ′ j } > 0 and {ki, k′ j} > 0 are shape parameters of Burr-XII distribution. ⎣ ⎦ sibility condition) and ai ≥0, bj ≥0 and {θi, θ′ j } > 0 and {ki, k′ j} > 0 are shape parameters of Burr-XII distribution. 5.2.3 When ai and bj follow power function distribution ' ( Setting pi = −θi, h n j=1 xij  = ln ' n j=1 xij di ( and pj = −θ′ j , h m i=1 xij  = ln ' m i=1 xij d′ j ( in GMCSTP 2, we get, we get, MCSTP 7: m MCSTP 7: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.13) subject to: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.21) (5.21) subject to: subject to: n  j=1 xij ≤γi −δi [ln{−ln(αi)}] , i = 1, 2, . . . , m (5.14) m  i=1 xij ≥γ ′ j −δ′ j  ln{−ln(βj)}  , j = 1, 2, . . . , n (5.15) xij ≥0 ∀i and j (5.16) where m i=1 [γi −δi[ ln{−ln(αi)}] ] ≥n j=1  γ ′ j −δ′ j[ ln{−ln(βj)}]  (feasibility condition) and −∞< ai < +∞, −∞<bj < + ∞and {γi, γ ′ j } > 0 and {δi, δ′ j} > 0 are location and scale parameters of extreme value distribution, which is same as obtained by Mahapatra et al. (2013). subject to n  j=1 xij ≤ m  i=1 xij ≥ n  j=1 xij ≤γi −δi [ln{−ln(αi)}] , i = 1, 2, . . . , m (5.14) m  i=1 xij ≥γ ′ j −δ′ j  ln{−ln(βj)}  , j = 1, 2, . . . , n (5.15) xij ≥0 ∀i and j (5.16) where m i=1 [γi −δi[ ln{−ln(αi)}] ] ≥n j=1  γ ′ j −δ′ j[ ln{−ln(βj)}]  (feasibility condition) and −∞< ai < +∞, −∞<bj < + ∞and {γi, γ ′ j } > 0 and {δi, δ′ j} > 0 are location and scale parameters of extreme value distribution, which is same as obtained by Mahapatra et al. (2013). subject to: n  j=1 xij ≤ ⎡ ⎣(1 −αi)−1 ki −1 θi ⎤ ⎦ 1 δi , i = 1, 2, . . . , m (5.22) m  i=1 xij ≥ ⎡ ⎢⎢⎢⎣ β −1 k′ j j −1 θ ′ j ⎤ ⎥⎥⎥⎦ 1 δ′ j , j = 1, 2, . . . , n (5.23) (5.14) (5.15) (5.16) −ln(βj)}]  <bj < + and scale h is same subject to: n  j=1 xij ≤ ⎡ ⎣(1 −αi)−1 ki −1 θi ⎤ ⎦ 1 δi , i = 1, 2, . . . 5.1.2 When ai and bj follows Weibull distribution xij ≥0 ∀i and j (5.12) xij ≥0 ∀i and j (5.12) xij ≥0 ∀i and j xij ≥0 ∀i and j (5.12) Mahapatra (2014) presented a model by considering both ai and bj follow weibull distribution which can be obtained where m i=1 lai + saitan  παi −π 2  ≥ n j=1 lbj + sbjtan  π 2 −πβj  (feasibility condition) and −∞< ai < + ∞, −∞< bj < +∞and lai, lbj > 0 and sai, sbj > 0 are the location and scale parameter of ai and bj, respectively, Which is a multi-choice approach of the model proposed by Biswal and Samal (2013). where m i=1 lai + saitan  παi −π 2  ≥ n j=1 lbj + sbjtan  π 2 −πβj  (feasibility condition) and −∞< ai < + ∞, −∞< bj < +∞and lai, lbj > 0 and sai, sbj > 0 are the location and scale parameter of ai and bj, respectively, Which is a multi-choice approach of the model proposed by Biswal and Samal (2013). by setting pi = 1, qi = 0, ri = δ−γi i ki , h n j=1 xij  = e −ki n j=1 xij γi and p′ j = 1, q′ j = 0, r′ j = δ′ j −γ ′ j k′ j , g m i=1 xij  = ′ e−k′ j( m i=1 xij) γ ′ j in GMCSTP 1, as follows: Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Quddoos et al. MCSTP 7: m , m (5.22) m  i=1 xij ≥ ⎡ ⎢⎢⎢⎣ β −1 k′ j j −1 θ ′ j ⎤ ⎥⎥⎥⎦ 1 δ′ j , j = 1, 2, . . . , n (5.23) n  j=1 xij ≤γi −δi [ln{−ln(αi)}] , i = 1, 2, . . . , m (5.14) m  i=1 xij ≥γ ′ j −δ′ j  ln{−ln(βj)}  , j = 1, 2, . . . , n (5.15) xij ≥0 ∀i and j (5.16) subject to: n  j=1 xij ≤ ⎡ ⎣(1 −αi)−1 ki −1 θi ⎤ ⎦ 1 δi , i = 1, 2, . . . , m (5.22) ⎡ 1 ⎤1 ′ m  i=1 xij ≥ ⎡ ⎢⎢⎢⎣ β −1 k′ j j −1 θ ′ j ⎤ ⎥⎥⎥⎦ 1 δ′ j , j = 1, 2, . . . , n (5.23) 6.1 Illustration 1 Let us consider that we have three known parame- ters of availability a1, a2, a3 follow Burr-XII distribution. The specified probability levels and shape parameters of a1, a2, a3 are given in Table 2. Extreme value distribution Setting pi = θi, qi = 1, ri = −ki, h n j=1 xij  = n j=1 xij δi and p′ j = 1, g m i=1 xij  = e − m i=1 xij−γ ′ j  δ′ j in GMCSTP 3 we get, in Further, consider that we have four known parameters of demand b1, b2, b3, b4 follow extreme value distribution. The specified probability levels and location and scale parameters of b1, b2, b3, b4 are given in Table 3. MCSTP 10: subject to: n  j=1 xij ≤ di (1 −αi) 1 θi , i = 1, 2, . . . , m (5.18) m  i=1 xij ≥ d ′ j (β ) 1 θ′ j , j = 1, 2, . . . , n (5.19) min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.25) subject to: n 1 n  j=1 xij ≤ di (1 −αi) 1 θi , i = 1, 2, . . . , m (5.18) m  i=1 xij ≥ d ′ j (βj) 1 θ′ j , j = 1, 2, . . . , n (5.19) xij ≥0 ∀i and j (5.20) where m i=1  di (1−αi) 1 θi  ≥n j=1 ⎛ ⎜⎝ d ′ j (βj) 1 θ′ j ⎞ ⎟⎠ (feasibility d ) d d d′ d ′ l d min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.25) subject to: n  j=1 xij ≤diα 1 θi i , i = 1, 2, . . . , m (5.26) m  i=1 xij ≥d′ j(1 −βj) 1 θ′ j , j = 1, 2, . . . , n (5.27) (5.25) (5.19) (βj) j xij ≥0 ∀i and j (5.20) where m i=1  di (1−αi) 1 θi  ≥n j=1 ⎛ ⎜⎝ d ′ j (βj) 1 θ′ j ⎞ ⎟⎠ (feasibility  j=1 xij ≤diα 1 θi i , i = 1, 2, . . . , m (5.26) m  i=1 xij ≥d′ j(1 −βj) 1 θ′ j , j = 1, 2, . . . , n (5.27) (5.27) ⎝ j ⎠ condition) and {di, d′ j} > 0 and {θi, θ′ j } > 0 are scale and shape parameters respectively and ai ≥di and bj ≥d′ j. xij ≥0 ∀i and j (5.28) (5.28) Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 7 of 9 Page 7 of 9 p g http://www.springerplus.com/content/3/1/565 where m i=1 ' diα 1 θi i ( ≥n j=1  d′ j(1 −βj) 1 θ′ j  (feasibility 6 Numerical illustrations We consider the numerical example taken by (Mahapatra et al. 2013). Data for multi-choice cost Ck ij are appended below in Table 1.   condition) and {di, d′ j} > 0 and {θi, θ′ j } > 0 are the scale and shape parameters of ai ≥0 and bj ≥0 respectively. 5.2.5 When ai follows power function distribution and bj follows Pareto distribution ' n ( (6.2) follows Pareto distribution Setting pi = −θi, h m i=1 xij  = ln ' n j=1 xij di ( and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ j , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 3. (6.3) GMCSTP 3. Table 1 Multi-choice transportation cost for route xij Table 1 Multi-choice transportation cost for route xij MCSTP 12: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.33) subject to: n  j=1 xij ≤diαi 1 θi , i = 1, 2, . . . , m (5.34) m  i=1 xij ≥ d ′ j (βj) 1 θ′ j , j = 1, 2, . . . , n (5.35) xij ≥0 ∀i and j (5.36) where m i=1 ' diα 1 θi i ( ≥ n j=1 ⎛ ⎝ d′ j (βj) 1 θ′ j ⎞ ⎠ (feasibility condition). Table 1 Multi-choice transportation cost for route xij SI. no. Route: xij Transportation cost(in Rupees) Ck ij : per unit (1 unit = 10 kg) 1 (1, 1): x11 10 or 11 or 12 2 (1, 2): x12 15 or 16 3 (1, 3): x13 21 or 22 or 23 or 24 4 (1, 4): x14 21 or 23 or 25 5 (2, 1): x21 15 or 17 or 19 or 21 or 23 or 25 6 (2, 2): x22 10 or 12 or 14 or 16 or 18 or 20 7 (2, 3): x23 9 or 10 or 11 8 (2, 4): x24 18 or 19 9 (3, 1): x31 20 or 21 or 22 or 23 or 24 or 25 or 26 10 (3, 2): x32 10 or 11 or 12 or 13 or 14 or 15 or 16 or 17 11 (3, 3): x33 20 or 22 or 25 12 (3, 4): x34 15 or 20 MCSTP 11: , n nd j (5.32) subject to, (5.32) subject to, subject to, (5.32) s xij ≥0 ∀iand j (5.32) subject to, (5.32) xij ≥0 ∀iand j xij ≥0 ∀iand j xij ≥0 ∀iand j ij j ( ) where m i=1 (1−αi) −1 ki −1 θi 1 δi ≥n j=1  γ ′ j −δ′ j[ ln{−ln(βj)}]  . 5.2.5 When ai follows power function distribution and bj follows Pareto distribution Setting pi = −θi, h m i=1 xij  = ln ' n j=1 xij di ( and p ′ j = d ′ j −k ′ j , q ′ j = 0, r ′ i = − θ ′ j k′ j , g n j=1 xij  = n j=1 xij k ′ j in GMCSTP 3. 4  j=1 x1j ≤967.544404 (6.1) 4  j=1 x2j ≤762.934875 (6.2) 4  j=1 x3j ≤612.817850 (6.3)  . = in 4  j=1 x1j ≤967.544404 (6.1) 4  j=1 x2j ≤762.934875 (6.2) 4  j=1 x3j ≤612.817850 (6.3) where m i=1 (1−αi) −1 ki −1 θi 1 δi ≥n j=1  γ ′ j −δ′ j[ ln{−ln(βj)}]  . 4  j=1 x1j ≤967.544404 (6.1) where m i=1 (1−αi) −1 ki −1 θi 1 δi ≥n j=1  γ ′ j −δ′ j[ ln{−ln(βj)}]  . (6.1) 5.2.5 When ai follows power function distribution and bj follows Pareto distribution ' ( MCSTP 11: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.29) Using the data provided in Tables 1, 2 and 3 the follow- ing equivalent multi-choice deterministic transportation problem is formulated with the help of GMCSTP 3 as: Subject to: min:z = {10, 11, 12}x11 + {15, 16}x12 + {21, 22, 23, 24}x13 + {21, 23, 25}x14 + {15, 17, 19, 21, 23, 25}x21 + {10, 12, 14, 16, 18, 20}x22 + {9, 10, 11}x23 + {18, 19}x24 + {20, 21, 22, 23, 24, 25, 26}x31 + {10, 11, 12, 13, 14, 16, 17}x32 + {20, 22, 25}x33 + {15, 20}x34 Subject to: n  j=1 xij ≤ ⎡ ⎣(1 −αi)−1 ki −1 θi ⎤ ⎦ 1 δi , i = 1, 2, . . . , m (5.30) m  i=1 xij ≥γ ′ j −δ′ j[ ln{−ln(βj)}] , j = 1, 2, . . . , n (5.31) min:z = {10, 11, 12}x11 + {15, 16}x12 + {21, 22, 23, 24}x13 + {21, 23, 25}x14 + {15, 17, 19, 21, 23, 25}x21 + {10, 12, 14, 16, 18, 20}x22 + {9, 10, 11}x23 + {18, 19}x24 + {20, 21, 22, 23, 24, 25, 26}x31 + {10, 11, 12, 13, 14, 16, 17}x32 + {20, 22, 25}x33 + {15, 20}x34 Subject to: n  j=1 xij ≤ ⎡ ⎣(1 −αi)−1 ki −1 θi ⎤ ⎦ 1 δi , i = 1, 2, . . . , m (5.30) m  i=1 xij ≥γ ′ j −δ′ j[ ln{−ln(βj)}] , j = 1, 2, . . . , n (5.31) min:z = {10, 11, 12}x11 + {15, 16}x12 + {21, 22, 23, 24}x13 + {21, 23, 25}x14 + {15, 17, 19, 21, 23, 25}x21 + {10, 12, 14, 16, 18, 20}x22 + {9, 10, 11}x23 + {18, 19}x24 + {20, 21, 22, 23, 24, 25, 26}x31 + {10, 11, 12, 13, 14, 16, 17}x32 + {20, 22, 25}x33 + {15, 20}x34  i 1 xij ≥γ ′ j −δ′ j[ ln{−ln(βj)}] , j = 1, 2, . . . MCSTP 12: Now using the transformation technique proposed by Biswal and Acharya (2009), we obtain the following multi- choice deterministic transportation problem: t32 = 10z1 32z2 32z3 32  + 11  1 −z1 32  z2 32z3 32 + 12z1 32  1 −z2 32  z3 32 + 13z1 32z2 32   1 −z3 32  + 14  1 −z1 32   1 −z2 32  z3 32 + 15z1 32  1 −z2 32   1 −z3 32  + 16  1 −z1 32  z2 32  1 −z3 32  + 17  1 −z1 32   1 −z2 32   1 −z3 32  t33 = 20z1 33z2 33 + 22z1 33  1 −z2 23  + 25  1 −z1 33  z2 33 t34 = 15z1 34 + 20  1 −z1 34  min: z = t11x11 + t12x12 + t13x13 + t14x14 + t21x21 + t22x22 + t23x23 + t24x24 + t31x31 + t32x32 + t33x33 + t34x34 subject to, (6.1)-(6.7) subject to, (6.1)-(6.7) where, t11 = 10z1 11z2 11 + 11z1 11  1 −z2 11  + 12  1 −z1 11  z2 11 t12 = 15z1 12 + 16  1 −z1 12  t13 = 21z1 13z2 13 + 22z1 13  1 −z2 13  + 23  1 −z1 13  z2 13 + 24  1 −z1 13   1 −z2 13  t14 = 21z1 14z2 14 + 23z1 14(1 −z2 14 + 25  1 −z1 14  z2 14 1 ≤z1 11 + z2 11 ≤2 1 ≤z1 14 + z2 14 ≤2 1 ≤z1 21 + z2 21 + z3 21 ≤2 1 ≤z1 22 + z2 22 + z3 22 ≤2 1 ≤z1 23 + z2 23 ≤2 1 ≤z1 31 + z2 31 + z3 31 ≤2 1 ≤z1 33 + z2 33 ≤2 where, xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. Table 3 Specified probability levels,location and scale parameters of bj Table 3 Specified probability levels,location and scale parameters of bj Random Specified Location Scale parameters bj probability levels parameters parameters b1 0.04 600 5 b2 0.05 500 4 b3 0.06 400 3 b4 0.07 300 2 where, xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. MCSTP 12: t31 = 20  1 −z1 31   1 −z2 31   1 −z3 31  + 21z1 31  1 −z2 31   1 −z3 31  + 22  1 −z1 31  z2 31  1 −z3 31  + 23  1 −z1 31   1 −z2 31   1 −z3 31  + 24z1 31z2 31  1 −z3 31  + 25z1 31  1 −z2 31  z3 31 + 26  1 −z1 31  z2 31z3 31 (6.7) xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. MCSTP 12: min: Z = m  i=1 n  j=1  C1 ij, C2 ij, . . . , Ck ij  xij, k = 1, 2, . . . , K (5.33) subject to: n  j=1 xij ≤diαi 1 θi , i = 1, 2, . . . , m (5 m  i=1 xij ≥ d ′ j (βj) 1 θ′ j , j = 1, 2, . . . , n (5 xij ≥0 ∀i and j Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 8 of 9 Table 2 Specified probability levels and shape parameters of ai Random Specified Shape Shape parameters ai probability levels parameters 1 parameters 2 a1 0.01 0.002 0.73 a2 0.02 0.004 0.76 a3 0.03 0.006 0.79 3  i=1 xi1 ≥615.992671 (6.4) 3  i=1 xi2 ≥511.880781 (6.5) 3  i=1 xi3 ≥408.347897 (6.6) 3  i=1 xi4 ≥305246388 (6.7) xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. MCSTP 12: t21 = 15z1 21  1 −z2 21   1 −z3 21  + 17  1 −z1 21  z2 21  1 −z3 21  + 19  1 −z1 21   1 −z2 21  z3 21 + 21z1 21z2 21  1 −z3 21  + 23  1 −z1 21  z2 21z3 21 + 25z1 21  1 −z2 21  z3 21 t22 = 10z1 22  1 −z2 22   1 −z3 22  + 12  1 −z1 22  z2 22  1 −z3 22  + 14z1 22z2 22  1 −z3 22  + 16  1 −z1 22   1 −z2 22  z3 22 + 18z1 22  1 −z2 22  z3 22 + 20  1 −z1 22  z2 22z3 22 t23 = 9z1 23z2 23 + 10z1 23  1 −z2 23  + 11  1 −z1 23  z2 23 t24 = 18z1 24 + 19  1 −z1 24  t31 = 20  1 −z1 31   1 −z2 31   1 −z3 31  + 21z1 31  1 −z2 31   1 −z3 31  + 22  1 −z1 31  z2 31  1 −z3 31  + 23  1 −z1 31   1 −z2 31   1 −z3 31  + 24 1 2  1 3  + 25 1  1 2  3 Table 2 Specified probability levels and shape parameters of ai Random Specified Shape Shape parameters ai probability levels parameters 1 parameters 2 a1 0.01 0.002 0.73 a2 0.02 0.004 0.76 a3 0.03 0.006 0.79 3  i=1 xi1 ≥615.992671 (6.4) 3  i=1 xi2 ≥511.880781 (6.5) 3  i=1 xi3 ≥408.347897 (6.6) 3  i=1 xi4 ≥305246388 (6.7) xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. Table 2 Specified probability levels and shape parameters of ai Table 2 Specified probability levels and shape parameters of 3  i=1 xi1 ≥615.992671 (6.4) 3  i=1 xi2 ≥511.880781 (6.5) 3  i=1 xi3 ≥408.347897 (6.6) 3  i=1 xi4 ≥305246388 (6.7) xij ≥0, i = 1, 2, 3; j = 1, 2, 3, 4. Acknowledgement g The authors would like to thank the Section Editor ‘Prof. Lakhmi C Jain’ and the anonymous reviewers for their suggestions which have led to an improvement in both the quality and clarity of the paper. The authors are also thankful to Dr. S. K. Roy for his support. The first author is thankful to University Grant Commission, New Delhi, India for providing Maulana Azad National Fellowship to carry out this research work. Received: 28 May 2014 Accepted: 22 September 2014 Published: 27 September 2014 Authors’ contributions Table 5 Specified probability levels, scale and shape parameters of bj Random Specified Scale Shape parameters bj probability levels parameters parameters b1 0.04 350 5 b2 0.05 300 6 b3 0.06 270 7 b4 0.07 230 8 Table 5 Specified probability levels, scale and shape parameters of bj 6.2 Illustration 2 Mahapatra DR, Roy SK, Biswal MP (2013) Multi-choice stochastic transportation problem involving extreme value distribution. Appl Math Model 37:2230–2240 Again consider, in the above illustration 1 the availability a1, a2, a3 are supposed to follow Power Function distribu- tion and the demand b1, b2, b3, b4 are assumed to follow Pareto distribution. The specified probability levels, scale and shape parameters of a1, a2, a3 are given in Table 4 and of b1, b2, b3, b4 are given in Table 5 respectively. Roy SK, Mahapatra DR, Biswal MP (2012) Multi-choice stochastic transportation problem with exponential distribution. JUS 6:200–213 Roy SK, Mahapatra DR, Biswal MP (2012) Multi-choice stochastic transportation problem with exponential distribution. JUS 6:200–213 doi:10.1186/2193-1801-3-565 Cite this article as: Quddoos et al.: Multi-choice stochastic transportation problem involving general form of distributions. SpringerPlus 2014 3:565. Solving this in the similar manner optimal solutions are obtained as x11 = 666.2789, x22 = 352.9524, x23 = 403.5651, x32 = 141.3123, x34 = 320.6938 and rest of the xij are zero. The minimum transportation cost is 20047.93 obtained by choosing multi-choice cost as follows: xij : x11 x12 x13 x14 x21 x22 x23 x24 x31 x32 x33 x34 value of Ck ij : 10 15 23 21 21 10 9 18 25 10 20 15 References Barik SK, Biswal MP, Chakravarty D (2011) Stochastic programming problems involving pareto distribution. J Interdiscip Math 14:39–56 Biswal MP, Acharya S (2009) Transformation of multi-choice linear programming problem. Appl Math Comput 210:182–188 Biswal MP, Samal HK (2013) Stochastic transportation problem with cauchy random variables and multi choice parameters. J Phy Sci 17:117–130 Hitchcock FL (1941) The distribution of a product from several sources to numeral localities. J Math Phys 20:224–230 transportation cost is 19532.56 obtained by choosing multi-choice cost as follows: transportation cost is 19532.56 obtained by choosing multi-choice cost as follows: xij : x11 x12 x13 x14 x21 x22 x23 x24 x31 x32 x33 x34 value of Ck ij : 10 15 21 23 15 10 9 18 22 10 22 15 y Mahapatra DR (2014) Multi-choice stochastic transportation problem involving Weibull distribution. IJOCTA 4:45–55 MCSTP 12: The above non-linear mixed integer programming prob- lem is solved by using LINGO 13.0 software package and the optimal solution is obtained as: x11 = 615.9927, x22 = 382.1037, x23 = 408.3469, x32 = 129.7771, x34 = 305.2464 and rest of the xij are zero. The minimum Quddoos et al. SpringerPlus 2014, 3:565 http://www.springerplus.com/content/3/1/565 Page 9 of 9 Table 4 Specified probability levels, scale and shape parameters of ai Random Specified Scale Shape parameters ai probability levels parameters parameters a1 0.01 1000 100 a2 0.02 800 70 a3 0.03 700 60 Table 4 Specified probability levels, scale and shape parameters of ai cost parameters are considered because we were much concerned about random parameters. In further studies extended multi-choice parameters may also be taken into account. Authors’ contributions The first author AQ performed calculations involved in the manuscript. All authors read and approved the final manuscript. Authors’ contributions The first author AQ performed calculations involved in the manuscript. All authors read and approved the final manuscript. 7 Conclusion Submit your manuscript to a journal and benefi t from: 7 Convenient online submission 7 Rigorous peer review 7 Immediate publication on acceptance 7 Open access: articles freely available online 7 High visibility within the fi eld 7 Retaining the copyright to your article Submit your next manuscript at 7 springeropen.com In this paper we have considered a MCSTP where cost coefficient of objective function are assumed to be of multi-choice type and random availability and demand of product are assumed to follow general form of dis- tributions. With this generalized formulation of MCSTP the DM becomes capable to fit any distribution among exponential, weibull, cauchy, extreme value, power func- tion, burr-XII and pareto according to the nature of data. Thus the present model can be applied in several sit- uations of transportation problems when demand and availability are restricted to follow a particular probability distribution. Here, only upto eight choices of multi-choice
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Organization and dynamics of the SpoVAEa protein, and its surrounding inner membrane lipids upon germination of <i>Bacillus subtilis</i> spores
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Citation for published version (APA): Wen, J., Vischer, N. O. E., de Vos, A. L., Manders, E. M. M., Setlow, P., & Brul, S. (2022). Organization and dynamics of the SpoVAEa protein and its surrounding inner membrane lipids, upon germination of Bacillus subtilis spores. Scientific Reports, 12(1), Article 4944. https://doi.org/10.1038/s41598-022-09147-3 Juan Wen1, Norbert O. E. Vischer1, Arend L. de Vos1, Erik. M. M. Manders2, Peter Setlow3 & Stanley Brul1* Juan Wen1, Norbert O. E. Vischer1, Arend L. de Vos1, Erik. M. M. Manders2, Peter Setlow Stanley Brul1* Juan Wen1, Norbert O. E. Vischer1, Arend L. de Vos1, Erik. M. M. Manders2, Peter Setlow3 & Stanley Brul1* The SpoVA proteins make up a channel in the inner membrane (IM) of Bacillus subtilis spores. This channel responds to signals from activated germinant receptors (GRs), and allows release of ­Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the IM complex formed by all GRs termed the germinosome. However, while the GRs’ spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. It seems possible that this movement may be a means of communicating germination signals from the germinosome to the IM SpoVA channel, thus stimulating CaDPA release in germination. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, and the loss of fluorescence of the IM with fluorescent dyes, as well as the appearance of peak SpoVAEa-SGFP2 fluorescent intensity occurred in parallel. These observed events were highly related to spores’ rapid phase darkening, which is considered as due to rapid ­Ca2+DPA release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40–80 °C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80 °C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events. Bacillus subtilis, the model Gram-positive bacterium, has multiple complex responses to environmental stress and nutrient depletion. Notably, it can generate different subsets of cells, such as persisters, spores, and biofilms to promote survival in harsh environmental ­conditions1. Spores in particular are capable of maintaining meta- bolic dormancy for very long times by protecting their chromosomal DNA through its location in the low water environment of the spore core and its surrounding by multiple protective macromolecular ­layers2. UvA-DARE (Digital Academic Repository) UvA-DARE (Digital Academic Repository) Citation for published version (APA): Wen, J., Vischer, N. O. E., de Vos, A. L., Manders, E. M. M., Setlow, P., & Brul, S. (2022). Organization and dynamics of the SpoVAEa protein and its surrounding inner membrane lipids, upon germination of Bacillus subtilis spores. Scientific Reports, 12(1), Article 4944. https://doi.org/10.1038/s41598-022-09147-3 General rights 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), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Disclaimer/Complaints regulations UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:24 Oct 2024 www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports/ the latter is complete the core water content has returned to the levels observed in vegetative ­cells2,8. Multiple signals can trigger the opening of the SpoVA channel, including activated germinant receptors (GRs), hydrolysis of the cortex PG and high hydrostatic ­pressure2. The SpoVA channel has seven subunits, A, B, C, D, Eb, Ea and ­F6,9. SpoVAA, -B, -C, -Eb and -F are transmembrane IM proteins, one of which, SpoVAC, is a pressure-sensitive membrane channel ­protein6,7,10,11. SpoVAD and -Ea are hydrophilic proteins, located on the outer surface of the IM. Somehow there must be signal transduction from activated GRs to the SpoVA channel, but while there is some evidence for physical interaction between GRs and some SpoVA ­proteins6,12, how signal transduction takes place is not clear. B. subtilis spores have an estimated level of ~ 7000 molecules of SpoVA proteins, which is 7–10 times higher than the level of ­GRs13. Notably, all GRs in spores are in a complex in the IM that is generally present in only one or two immobile spots/spore termed ­germinosomes14–17. In contrast, by averaging hundreds of consecutive images, previous work indicated that SpoVAEa seems uniformly distributed throughout the ­IM17. In the current work, we created a SpoVAEa-SGFP2 reporter protein. The fusion protein was expressed in B. subtilis from the native spoVAEa locus and super resolution rescan confocal microscopy (RCM) was used to analyze SpoVAEa-SGFP2 location in spores. As mentioned above, GRs are present in foci in the dormant spore IM, and our previous work found that B. subtilis spores’ GerKB-SGFP2 foci, the gerKB gene encodes the B subunit of the GerK GR, reached peak fluores- cence intensity around the ‘time to germination’, followed by the dispersion of the spots in a short time window in germinated ­spores18. The ‘time to germination’ was defined as the time needed for the spore to complete half of its rapid decline in phase brightness. The rapid decline of phase brightness is due to the refractility change of spores induced by ­Ca2+DPA release and water uptake, and results in the change of a phase bright spore (dormant spore) into a phase dark spore (germinated spore) upon examination under a phase contrast microscope. The molecular basis of GR functioning in spore germination is still not resolved. Results L i Location and the dynamics of SpoVAEa protein in dormant spores. While previous analyses had indicated for SpoVAEa-SGFP2 no discrete fluorescence foci in spores expressing the fusion ­protein17, our wide- field microscopy indicated that the spore surface area did not have a uniform level of SpoVAEa-SGFP2 (data not shown). Possibly the different microscopical magnifications used as well as the use of an SGFP reporter rather than GFP lead to these differing results. Next, we employed Rescan Confocal Microscopy (RCM) with a scanning time of 2 s per frame to obtain more detailed structural ­information21. Surprisingly, clusters of GFP fluorescence were observed, which clearly stood out from the background in dormant PS832 (wild-type) Spo- VAEa-SGFP2 spores (Fig. 1A, left panel). By enlarging one of the spores, two spots were observed in the spore labelled ‘a’ (Fig. 1A, right panel). The full width at half maximum (FWHM) of the pronounced spot of spore ‘a’ was 220 nm (Fig. 1C). Due to the fact that the visualization of germination proteins can be interfered with by heavy ­autofluorescence17,22 from the spore coat, we also imaged SpoVAEa-SGFP2 in spores with a severely defec- tive ­coat23. Similar fluorescent spot structures were found in the coat defective double mutant PS4150 SpoVAEa- SGFP2 spores (Fig. 1B,C). These spots were, however, not more pronounced indicating that our observations in wild-type spores were not majorly obscured by coat layers. Two obvious questions about the results with spores carrying the spoVAEa-SGFP2 fusion are: (1) could the fact that the fusion eliminates spoVAF expression modulate the effects of the fusion protein; and (2) is fusion protein functional? It seems most likely that the answer to question 1 is “very unlikely”, since a spoVAF mutation has no effect on AGFK ­germination6. However, the answer to question 2 is “yes”, since a spoVAEa deletion mutation decreases rates of AGFK germination ~ ­threefold6, and the spores with the SpoVAEa-SGFP2 fusion germinated identically to wild-type spores with AGFK (data not shown and see “Materials and methods”). Previously, we showed that GerKB-SGFP2 proteins, one class of GRs, also presented themselves as 1–3 spots per ­spore18. These spots ‘oscillated’ at high frequency, but were confined only to a small area of the ­IM18. Here, the crucial question is whether SpoVAEa-SGFP2 is also at least somewhat mobile in the IM. www.nature.com/scientificreports/ However, we speculated that the increased GerKB-SGFP2 fluorescence is due to a relatively ‘dramatic’ environmental change in the physical state of the IM near the fusion ­protein18. Because both GRs and SpoVA proteins are IM proteins, we were curious to assess the dynamic response of SpoVAEa-SGFP2 fluorescence to the environmental changes occurring during germination. Time-lapse imaging was used to track both the refractility change of spores, and the dynamics of SpoVAEa-SGFP2 fluorescence during GR-triggered germination using phase contrast and widefield micros- copy. The IM is undergoing dramatic modifications during spore germination, including a 1.3 fold increase in its encompassed volume and the restoration of its full lipid ­mobility2,19. Consequently, we also tracked changes in the IM during germination. In addition, because previous ­work20 showed that 40–80 °C heat treatments of B. subtilis dormant spores resulted in spore heat activation of germination at temperatures ≤ 65 °C, caused a combination of heat activation and heat damage at 70–75 °C, and led to full heat inactivation at 80 °C, we also studied thermal effects on SpoVAEa-SGFP2 and membrane dye related fluorescence. Juan Wen1, Norbert O. E. Vischer1, Arend L. de Vos1, Erik. M. M. Manders2, Peter Setlow3 & Stanley Brul1* From the outside in, these spore layers are the coat, outer membrane (OM), peptidoglycan (PG) cortex, germ cell wall, inner membrane (IM) and ­core2. Despite their potential long period of dormancy, these spores can be revived or germinated by many environmental cues, primarily small molecules termed germinants that signal the presence of a growth friendly environment, and they then resume cell ­growth2.hh g y y g The SpoVA channel is located in the IM, and has a crucial role in spore ­germination3–7. This channel functions to release the large pool of the 1:1 complex of ­Ca2+ and dipicolinic acid ­(Ca2+-DPA) from the spore core during ­germination5,8. Upon release of the ­Ca2+-DPA, water is taken up and hydrolysis of the PG cortex begins. When 1Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH  Amsterdam, The Netherlands. 2Confocal.Nl B.V., Science Park 106, 1098 XG Amsterdam, The Netherlands. 3Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030‑3305, USA. *email: s.brul@uva.nl | https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 www.nature.com/scientificreports/ Results L i The spore in the inset ‘a’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (B) The RCM fluorescence image of PS4150 SpoVAEa-SGFP2 spores. The spore in the inset ‘b’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (C) The plot profiles of the pronounced SpoVAEa-SGFP2 spot of spores ‘a’ and ‘b’. (D) The RCM high frequency time-lapse images (22.2 ms/frame) of a PS832 SpoVAEa-SGFP2 dormant spore. The presented images represent frames in which the strong SpoVAEa-SGFP2 spot appears during the high frequency time-lapse track. The relative FWHM of the SpoVAEa-SGFP2 spot in each frame is indicated at the bottom of each image. Figure 1. Organization of SpoVAEa-SGFP2 in dormant spores in a region of increased fluorescence (a fluorescent ‘spot’). (A) The RCM fluorescence image of PS832 SpoVAEa-SGFP2 spores. The spore in the inset ‘a’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (B) The RCM fluorescence image of PS4150 SpoVAEa-SGFP2 spores. The spore in the inset ‘b’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (C) The plot profiles of the pronounced SpoVAEa-SGFP2 spot of spores ‘a’ and ‘b’. (D) The RCM high frequency time-lapse images (22.2 ms/frame) of a PS832 SpoVAEa-SGFP2 dormant spore. The presented images represent frames in which the strong SpoVAEa-SGFP2 spot appears during the high frequency time-lapse track. The relative FWHM of the SpoVAEa-SGFP2 spot in each frame is indicated at the bottom of each image. surface of the ­IM6. Moreover, we cannot exclude that there are some ‘free’ SpoVAEa proteins distributed over the IM outside of the spot. surface of the ­IM6. Moreover, we cannot exclude that there are some ‘free’ SpoVAEa proteins distributed over the IM outside of the spot. Dynamics of SpoVAEa in the IM of B. subtilis spores during GR‑triggered spore germina- tion. Previously, we found that during spore germination GerKB-SGFP2 spots gradually increased in fluores- cence ­intensity18. This phenomenon is potentially related to the change of the spore’s physical state in general and the IM in particular upon germination, because no new protein synthesis was ­observed18. It could be linked, for instance, to the increase in core water content and core pH due to the release of ­Ca2+-DPA and cortex hydrolysis. Results L i Here we used widefield microscopy to track the overall mean intensity of SpoVAEa-SGFP2 in spores during germination via GerB and GerK GRs by supplying the AGFK nutrient germinant cocktail (l-asparagine, glucose, fructose, and potassium chloride).hl , p ) The phase brightness and SpoVAEa-SGFP2 fluorescence history of a single spore is shown in the time-lapse image montage in Fig. 2A,C. By analyzing the brightness and fluorescence profiles of this spore, we observed that the peak fluorescence intensity of SpoVAEa-SGFP2 was reached before the appearance of the phase dark spore, followed by a slow decline of fluorescence intensity in the phase dark spore (Fig. 2A–D). The initiation of SpoVAEa-SGFP2 fluorescence increase was at the same time as the start of the spore’s brightness rapid decline, which is considered as the start of rapid ­Ca2+-DPA release (Fig. 2B,D,E). In order to confirm the observed dynamics in the population, we synchronized SpoVAEa-SGFPs fluorescence profiles by defining the t = 0 as the ‘time to germination’, which is the time needed for the spore to complete half of its rapid decline in phase brightness (Fig. 2E). In the averaged trace of 418 germinating spores, the SpoVAEa-SGFP2 intensity increased sharply and the peak was around the ‘time to germination’ (Fig. 2F), while no SpoVAEa-SGFP2 synthesis was detected by western blot analysis (Fig. S1). Two independent batches of spores were analysed in this experi- ment. Thus, the increase of SpoVAEa-SGFP2 fluorescence intensity during germination is correlated with the rapid release of ­Ca2+-DPA. Western blot analysis in the current work, as well as previous work, did not detect a significant decrease of SpoVAEa level in germinated spores compared to dormant spores (Fig. S1), however, a decrease of SpoVAEa-SGFP2 fluorescence was observed in germinated spores (Fig. 2D,F)6. Subsequently, we found that photobleaching had a role in the observed fluorescence decrease (Figs. S2, S3), and photochemical alteration of both spore coat and SGFP2 potentially contributed to the photobleaching. A spore coat defective strain with no autofluorescence will likely be necessary in the future to study the dynamics of SpoVAEa-SGFP2 in germinated ­spores22,23. Changes in IM structure upon triggering spore germination via GRs. It is known that lipids in the B. subtilis dormant spore IM are largely ­immobile2,19. Still, this IM is capable of increasing its surface area ~ 1.3 fold upon the spore swelling due to spore core water uptake and cortex ­hydrolysis2. Results L i To address this query, RCM microscopy was applied for high frequency imaging with a scanning time of 22.2 ms per frame. Even more surprisingly, a single spot, traveling around the IM, i.e. not confined to a small area, was observed in the PS832 SpoVAEa-SGFP2 dormant spores when the spore was tracked for 1000 frames and imaged at very high time resolution, and the movement of the SpoVAEa-SGFP2 fluorescent spot in the spore appeared in dif- ferent random positions. Figure 1D shows eight frames with a pronounced fluorescent spot, and the location differs in each frame. The measured Fluorescence Width at Half Maximum (FWHM) of the spot in different frames varied from 96 to 263 nm. Hence, the observed high frequency movement with longer exposure time, could explain why not all the spores in Fig. 1A,B, showed a spot structure, as well as the uniform distribution of SpoVAE, most likely SpoVAEa, in previous ­work17. It is, however, not clear how SpoVAEa is able to move at such a high frequency in an otherwise ‘rigid’ inner ­membrane19,24, although SpoVAEa appears to be on the outer https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 1. Organization of SpoVAEa-SGFP2 in dormant spores in a region of increased fluorescence (a fluorescent ‘spot’). (A) The RCM fluorescence image of PS832 SpoVAEa-SGFP2 spores. The spore in the inset ‘a’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (B) The RCM fluorescence image of PS4150 SpoVAEa-SGFP2 spores. The spore in the inset ‘b’ is the enlarged view of the spore indicated by the grey arrow in the left panel. (C) The plot profiles of the pronounced SpoVAEa-SGFP2 spot of spores ‘a’ and ‘b’. (D) The RCM high frequency time-lapse images (22.2 ms/frame) of a PS832 SpoVAEa-SGFP2 dormant spore. The presented images represent frames in which the strong SpoVAEa-SGFP2 spot appears during the high frequency time-lapse track. The relative FWHM of the SpoVAEa-SGFP2 spot in each frame is indicated at the bottom of each image. Figure 1. Organization of SpoVAEa-SGFP2 in dormant spores in a region of increased fluorescence (a fl ‘ ’) (A) Th RCM fl i f PS832 S VAE SGFP2 Th i h Figure 1. Organization of SpoVAEa-SGFP2 in dormant spores in a region of increased fluorescence (a fluorescent ‘spot’). (A) The RCM fluorescence image of PS832 SpoVAEa-SGFP2 spores. Results L i As shown in the schematic, upon germination commitment, slow leakage of ­Ca2+DPA from the spore core begins, followed by the rapid release of the remaining ­Ca2+DPA and then spore cortex ­hydrolysis25. The latter two events result in the rapid decline in the brightness of spores in phase contrast microscopy. Here, SporeTrackerB_06K detected the ­TStartRelease (time of initiation of the rapid decline in spore brightness) and ­TPhaseDark (time of completion of spore brightness rapid decline) in the brightness profile, and further calculated the ‘time to germination’ for presenting data for the population. Here, the ‘time to germination’ is defined as the time needed for the spore to complete half of its rapid decline in phase brightness. The magenta arrow here and in (A) indicates the ‘time to germination’. (F) Average of 418 synchronized single SpoVAEa-SGFP2 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 613 spores were tracked by microscopy for 90 min and 68.2% of them completed germination. mobility of the IM lipids. To that end, the IM of PS832 spores was stained with either the carbocyanine dye ­DiIC12 or the styryl dye FM5-95, which were added to a sporulating culture and hence incorporated into the IM upon the formation of the forespore, as has been shown in previous ­studies16,19. Any lipid probe present in the OM could be removed by extensive washing during spore ­purification19.ihl mobility of the IM lipids. To that end, the IM of PS832 spores was stained with either the carbocyanine dye ­DiIC12 or the styryl dye FM5-95, which were added to a sporulating culture and hence incorporated into the IM upon the formation of the forespore, as has been shown in previous ­studies16,19. Any lipid probe present in the OM could be removed by extensive washing during spore ­purification19.ihl i We again used widefield microscopy to track the change in IM staining during germination. The fluorescence intensity of ­DiIC12 and FM5-95 stained spores dropped dramatically upon the start of the rapid decline in spore brightness, and the drop was completed around the ‘time to germination’ (Figs. 3, 4). In a word, just as with the dynamics of SpoVAEa-SGFP2, the change of the IM during germination is also highly correlated with the rapid ­Ca2+-DPA release and cortex hydrolysis, which lead to the increase of spore core pH, and water ­content26,27. Results L i As indicated above, Spo- VAEa-SGFP2 fluorescence reached peak intensity around ‘time to germination’. Consequently, we decided to probe for a putative correlation between the SpoVAEa-SGFP2 peak fluorescence intensity and the change in https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 2. Dynamic behaviour of SpoVAEa-SGFP2 during spore germination. Spore germination was triggered by (10 mM each) AGFK without heat activation treatment. (A) Phase contrast time lapse images of a single PS832 SpoVAEa-SGFP2 spore. (B) The brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the same spore shown in panel (A). (D) The SpoVAEa- SGFP2 fluorescence intensity profile corresponding to images in panel (C). (E). Parameters detected by SporeTrackerX, and their corresponding positions in spore germination. As shown in the schematic, upon germination commitment, slow leakage of ­Ca2+DPA from the spore core begins, followed by the rapid release of the remaining ­Ca2+DPA and then spore cortex ­hydrolysis25. The latter two events result in the rapid decline in the brightness of spores in phase contrast microscopy. Here, SporeTrackerB_06K detected the ­TStartRelease (time of initiation of the rapid decline in spore brightness) and ­TPhaseDark (time of completion of spore brightness rapid decline) in the brightness profile, and further calculated the ‘time to germination’ for presenting data for the population. Here, the ‘time to germination’ is defined as the time needed for the spore to complete half of its rapid decline in phase brightness. The magenta arrow here and in (A) indicates the ‘time to germination’. (F) Average of 418 synchronized single SpoVAEa-SGFP2 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 613 spores were tracked by microscopy for 90 min and 68.2% of them completed germination. Figure 2. Dynamic behaviour of SpoVAEa-SGFP2 during spore germination. Spore germination was triggered by (10 mM each) AGFK without heat activation treatment. (A) Phase contrast time lapse images of a single PS832 SpoVAEa-SGFP2 spore. (B) The brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the same spore shown in panel (A). (D) The SpoVAEa- SGFP2 fluorescence intensity profile corresponding to images in panel (C). (E). Parameters detected by SporeTrackerX, and their corresponding positions in spore germination. Results L i subtilis spores at 40–65 °C promotes spore germination in a positive time/temperature depend- ent manner, higher heat temperatures resulted in both heat activation and heat damage, and eventually led to heat inactivation at 80 °C20. The germination proteins and their surrounding IM are potential targets of the heat treatments. Here we studied whether heat treatments change the states of the spore’s, SpoVAEa and the IM after 5 h of heat treatment at 40–80 °C.i Significant drops of spore’s absorbance at the population (Figs. 5A, 7A,E) and refractive index at single spore level (Figs. 5C,E, 7C,G) were detected in spores treated at 80 °C, and in some cases also in 75 °C treated spores. Spores treated at 40–70 °C morphologically looked similar upon the microscopical examination. Hence, we only present images of 65, 75, and 80 °C heated spores as representative images (Figs. 6, 8). As shown in the phase contrast images (Figs. 6, 8), a subpopulation of phase-grey-like spores appeared in 80 °C treated groups. These phase-grey-like spores are potentially spores that have lost ­Ca2+-DPA, as reported ­previously28,29.l p g y p p y p p p y Heat treatments at 40–80 °C led to a decrease of fluorescence intensity of coat defective PS4150 SpoVAEa- SGFP2 spores (Figs. 5F, 6D). However, we cannot exclude the possibility that the decreased SpoVAEa-SGFP2 spore fluorescence was caused by heat denaturation of ­SGFP230. This denaturation seems reversible at tempera- tures ≤ 65 °C, due to the fact that 65 °C treated PS832 SpoVAEa-SGFP2 spores still exhibited similar fluorescence profiles as untreated spores during spore germination (Figs. 2, S2). However, it is not clear how spores maintain functionally active channel proteins during the heat activation process. Clearly, a pH and thermal stable fluores- cent reporter will be important for future spore related ­research31–33. Notably, we tested the response of SpoVAEa- SGFP2 to heat in coat defective spores, because the change of SpoVAEa-SGFP2 fluorescence was masked by the enhanced green autofluorescence of the spore coat (Figs. 5, 6). The increase of autofluorescence had a positive correlation with the heat treatment temperature. We speculate the enhanced autofluorescence is likely related to coat protein denaturation, since studies showed that a lethal thermal treatment induced significant protein denaturation in B. subtilis, B. cereus, and B. megaterium ­spores28,29, but there could also be reorganization of coat surface proteins. Results L i The FM5-95 stained spore also had a fluorescent spot, whereas ­DiIC12 spores had relative uniform staining (Figs. 3C, 4C). Regarding the fact that the FM5-95 dye was almost invisible in the germinated spore (Fig. 4C), we note that the hydrophobicity and affinity of FM5-95 for the IM lipids seems lower than that of DiIC12. This implies also that FM5-95 prefers to bind in lipid domains with higher fluidity. Hence, the FM5-95 spot area could well be a fluid membrane domain, instead of the compressed IM. The disappearance of the FM5-95 spot in the phase dark spore, suggests that this region might be a germination related functional membrane microdomain (Fig. 4C). https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 3. Dynamic behavior of the ­DiIC12 stained wild-type spore IM during germination. Spore germination was triggered by (10 mM each) AGFK as described in “Materials and methods”. (A) Phase brightness of a PS832 ­(DiIC12) spore; the magenta triangle denotes the ‘time to germination’. (B) The spore brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the spore shown in panel (A). (D) The ­DiIC12 stained IM intensity profile corresponding to images in panel (C); the magenta arrow indicates the ‘time to germination’. (E) Average of 170 synchronized single ­DiIC12 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 289 spores were tracked by microscopy for 90 min, and 58.8% of them completed germination. Figure 3. Dynamic behavior of the ­DiIC12 stained wild-type spore IM during germination. Spore germination was triggered by (10 mM each) AGFK as described in “Materials and methods”. (A) Phase brightness of a PS832 ­(DiIC12) spore; the magenta triangle denotes the ‘time to germination’. (B) The spore brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the spore shown in panel (A). (D) The ­DiIC12 stained IM intensity profile corresponding to images in panel (C); the magenta arrow indicates the ‘time to germination’. (E) Average of 170 synchronized single ­DiIC12 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 289 spores were tracked by microscopy for 90 min, and 58.8% of them completed germination. Response of SpoVAEa and probe stained IM to thermal treatments. Our previous work showed that heating B. Results L i Indeed, the observed increased autofluorescence in PS4510 spores treated at 80 °C is considered due to the response of either the residual outer coat or the inner coat layers to heat (Fig. 6C). y g Compared to the untreated (ut) ­DiIC12 labeled spores, spores heated at 40–80 °C exhibited slightly decreased fluorescence intensity (Figs. 7B,D, 8A). However, no correlation was detected between the drop of the phase contrast image brightness and changes in ­DiIC12 fluorescence (Table S2). In contrast, FM5-95 stained spores showed a continuous fluorescence decrease upon treatment at 70, 75, and 80 °C (Figs. 7F,H, 8B). The FM5-95 https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 4. Dynamic behavior of the FM5-95 stained IM during wild-type spore germination. Spore germination was triggered by (10 mM each) AGFK as described in “Materials and methods”. (A) Phase brightness of a PS832 (FM5-95) spore; the magenta arrow denotes the ‘time to germination’. (B) The spore brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the same spore shown in panel (A). (D) The FM5-95 stained IM intensity profile corresponding to images in the panel (C); the magenta arrow indicates the ‘time to germination’. (E) Average of 277 synchronized single FM5-95 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 369 spores were tracked by microscopy for 90 min, and 75.1% of them completed germination. Figure 4. Dynamic behavior of the FM5-95 stained IM during wild-type spore germination. Spore germination was triggered by (10 mM each) AGFK as described in “Materials and methods”. (A) Phase brightness of a PS832 (FM5-95) spore; the magenta arrow denotes the ‘time to germination’. (B) The spore brightness profile corresponding to the images shown in panel (A). (C) The fluorescence time lapse images of the same spore shown in panel (A). (D) The FM5-95 stained IM intensity profile corresponding to images in the panel (C); the magenta arrow indicates the ‘time to germination’. (E) Average of 277 synchronized single FM5-95 spore fluorescence intensity traces. Synchronization defines t = 0 min as the ‘time to germination’. 369 spores were tracked by microscopy for 90 min, and 75.1% of them completed germination. Results L i fluorescence had a positive correlation with the spore brightness of 70 and 75 °C heated spores (Table S2), Pearson correlation coefficients of 0.54 and 0.76, respectively, and it was minimal in spores heated at 80 °C. As mentioned above, we speculate that spores with decreased brightness are potentially spores that have lost ­Ca2+-DPA. Hence, the decrease of FM5-95 intensity presumably correlated with the release of ­Ca2+-DPA, and the subsequent physi- cal state changes in spores. Discussion O k h Changes in SpoVAEa-SGFP2 dormant spore refractility and fluorescence intensity at populatio and single spore levels after 5 h of heat treatment at various temperatures. (A) The change in OD at 600 nm of a PS832 SpoVAEa-SGFP2 dormant spore population measured by a plate reader. Untreated PS832 spor were used as control. (B) The corresponding fluorescence intensity of spores in panel (A). (C) The change brightness of PS832 SpoVAEa-SGFP2 dormant spores at the single spore level measured by phase contras microscopy. Here, PS832 spores with different heat treatments were employed as controls and ≥ 444 spores were examined in each group. (D) The corresponding intensity of spores in panel (C) measured by widefie microscopy. (E) The brightness of PS4150 SpoVAEa-SGFP2 dormant spores at the single spore level. Here PS4150 spores with different treatments were employed as control and ≥ 937 spores were examined in each group. (F) The corresponding fluorescence intensity of spores in panel (E). The number of spores detected microscopy is presented in Table S1. Figure 5. Changes in SpoVAEa-SGFP2 dormant spore refractility and fluorescence intensity at population and single spore levels after 5 h of heat treatment at various temperatures. (A) The change in OD at 600 nm of a PS832 SpoVAEa-SGFP2 dormant spore population measured by a plate reader. Untreated PS832 spores were used as control. (B) The corresponding fluorescence intensity of spores in panel (A). (C) The change of brightness of PS832 SpoVAEa-SGFP2 dormant spores at the single spore level measured by phase contrast microscopy. Here, PS832 spores with different heat treatments were employed as controls and ≥ 444 spores were examined in each group. (D) The corresponding intensity of spores in panel (C) measured by widefield microscopy. (E) The brightness of PS4150 SpoVAEa-SGFP2 dormant spores at the single spore level. Here, PS4150 spores with different treatments were employed as control and ≥ 937 spores were examined in each group. (F) The corresponding fluorescence intensity of spores in panel (E). The number of spores detected by microscopy is presented in Table S1. IM surrounded area takes place without new lipid synthesis, and a recent electron microscopy study revealed an intracellular membrane structure in dormant spores below the ­IM19,34. This membrane structure, which contains at least one SpoVA protein, disappears upon spore core hydration, most likely due to integration with the ­IM34. Discussion O k h Our work shows that at least one SpoVA subunit SpoVAEa, clustered in the IM as a spot undergoing high fre- quency movement in dormant B. subtilis spores. A germination related microdomain with higher fluidity was also observed in the spore IM. The rapid phase darkening of IM labeled spores, caused by the rapid release of ­Ca2+DPA and by cortex hydrolysis, is accompanied by the loss of fluorescence in the IM, the disappearance of the IM fluid microdomain, and an increase in SpoVAEa-SGFP2 fluorescence intensity. Heat treatment at 65–80 °C resulted in a temperature dependent increase in green autofluorescence, potentially caused by the degradation of coat proteins. Dormant spores heat treated at 80 °C have a sub-population of phase-grey-like spores. As mentioned above, a FM5-95 stained microdomain was observed in dormant spores, and this domain disappeared upon the appearance of the phase dark germinated spore. In addition, the microdomain likely has higher fluidity compared to the rest of the IM, and remains in a confined location in the IM before dispersing upon germination. This immobile behavior is likely in line with the ‘germinosome’ spot, in which GRs and their scaffold protein GerD are clustered together and are ­immobile17. In addition, our previous work showed that following spore germination the ‘germinosome’ agglomerates and diffuses in the same location of the IM, and gradually ­disperses15,18. Hence, there is a potential link between the germinosome and the fluid microdomain. To better understand this germination related membrane domain, efforts can take aim at answering the follow- ing questions. (1) Is the ‘germinosome’ spot truly located in the microdomain? (2) Does GerD have a function in recruiting the specific disordered lipids into this microdomain, as it does play such a role in maintaining the ‘germinosome’ spot? (3) When and how does the fluid microdomain form during sporulation? f h d h h lf ll O k ll g pl g p Except for the microdomain in the IM, the spore IM itself still remains mysterious. Our current work, as well as previous publications showed that there is an expansion of the IM surrounded area and a reduced staining by lipid dyes in the IM during ­germination19. Notably, it has long been known that this dramatic increase of the https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 5. Discussion O k h The integration of the IM lipids during germination might have a role in the decline of the dye staining in the IM. A technique with better temporal and spatial resolution might reveal the specifics of the integration. Current work showed that SpoVAEa clusters in the IM as a spot, and is capable of moving in the ‘gel state’ IM randomly with high frequency. This movement of the SpoVAEa spot might facilitate a physical interaction with both the immobile GR spots as well as the entire SpoVA protein channel, and thus communicate signals from the germinosome to the SpoVA CaDPA release channel. However, it is not clear how the SpoVA channel proteins interact with GRs, nor whether this interaction requires the integration of all SpoVA proteins either in the spot or dissociated in the IM, or even from the intracellular membrane structure. In addition, SpoVA channel pro- teins, synthesized in the developing forespores, are also crucial for import of ­Ca2+-DPA during ­sporulation6,35. Revealing the mechanism of SpoVA spot formation in the forespore will contribute to the knowledge of both ­Ca2+-DPA uptake and release processes, as well as perhaps to an understanding of signal transduction between the germinosome and SpoVA channels. https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 6. The effect of 5 h of heat-treatment on PS832 SpoVAEa-SGFP2 spores. The phase contrast (PC) and widefield fluorescence (Fluo) images of spores of wild type strain PS832 (A), PS832 SpoVAEa-SGFP2 (B), PS4150 (C), and PS4150 SpoVAEa-SGFP2 (D) after different heat treatments. (A,B) are the images corresponding to Fig. 5C,D. (B,C) are the images corresponding to Fig. 5E,F. The fluorescent image intensity display range for each strain is the same. Figure 6. The effect of 5 h of heat-treatment on PS832 SpoVAEa-SGFP2 spores. The phase contrast (PC) and widefield fluorescence (Fluo) images of spores of wild type strain PS832 (A), PS832 SpoVAEa-SGFP2 (B), PS4150 (C), and PS4150 SpoVAEa-SGFP2 (D) after different heat treatments. (A,B) are the images corresponding to Fig. 5C,D. (B,C) are the images corresponding to Fig. 5E,F. The fluorescent image intensity display range for each strain is the same. We also made efforts to check the response of SpoVAEa-SGFP2 and the dye stained IM to heat treatments, which induced either heat activation or heat inactivation to spores. The thermal inactivation resulted in the appearance of phase-grey-like spores. Discussion O k h However, no clear changes were observed in spores treated at heat acti- vation temperatures (40–65 °C). Interestingly, the green autofluorescence, related to the proteinaceous coat, increased with the elevated heat temperatures. We speculate this phenomenon likely relates to coat protein’ denaturation. Studying spore proteins’ thermal stability profile on the proteome scale might provide a way to understand heat activation and inactivation at the molecular level. Materials and methods Bacterial strains, and culture conditions. B. subtilis PS832 is a prototrophic 168 laboratory strain. Strain PS4150 is derived from PS832, carries cotE and gerE deletion mutations and is a coat defective mutant with greatly reduced coat ­autofluorescence23. Strains PS832 SpoVAEa-SGFP2 and PS4150 SpoVAEa-SGFP2 were derived from PS832 and PS4150, respectively. These two strains contain a SpoVAEa-C-terminal SGFP2 fusion, integrated at the spoVAEa locus, and expressed under the control of the spoVA operon′s promoter essen- tially as previously described for the germinant receptor GerKB-SGFP218,36. In short, primers were designed to separately amplify spoVAEa-GCA​GGT​ sGFP2 and kanR. Then by overlap extension PCR the construct spo- VAEa-GCA​GGT​-sGFP2_kanR was amplified. The full construct was then ligated into a T-vector to create pFL- XS spoVAEa-GCA​GGT​-sGFP2_kanR. The GCA​GGT​ triplets encode alanine-glycine which we used as a short linker between spoVAEa and the fluorescent reporter protein. The resulting vector was propagated in E. coli XL-1 and transformed by selection for ­Kmr into B. subtilis PS832 and PS4150 for genomic integration at the spoVAEa locus by a single cross-over event. The latter was confirmed by sequencing of the region. Note that the integration event will separate the spoVAEa-SGFP2 locus from the intact spoVAEa spoVAF genes by the plasmid sequence as well as the kanR gene, almost certainly eliminating the expression of these two genes in developing spores. Spores of all strains were prepared in 2 × SG sporulation medium at 37 °C as described ­previously37. If required, the fluorescent dyes ­DiIC12 (1 μg/ml, ThermoFisher) or FM5-95 (2 μg/mL, ThermoFisher) were added to the sporulating culture, when it reached the peak optical density at 600 nm ­(OD600). Spores were harvested and purified, including centrifugation through HistodenZ as described ­previously16. Spores ­(OD600 ~ 60, in MIl- liQ water) used in the current work had ≥ 98% dormant spores, and were essentially free of germinated spores, cells or cell debris as verified by phase contrast microscopy. Measuring the fluorescence of SpoVAEa‑SGFP2 and the dye stained IM in heated spore popu- lations. Spores (OD600 =  ~ 1, in MIlliQ water) were heated for 5 h at 40, 50, 60, 65, 70, 75 or 80 °C, followed by cooling in a water–ice bath (≥15 min). Spores ­(OD600 =  ~ 1, 150 µl/well) were added to a 96-well flat-bottomed https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 7. Materials and methods The change of lipid probe stained dormant spore refractility and fluorescence in and single spore levels after 5 h of treatment at various temperatures. (A) The change in ­OD dormant spore populations measured by a plate reader. Untreated PS832 spores were used corresponding fluorescence intensity of spores in panel (A). (C) The change of individual P brightness measured by a phase contrast microscopy  ≥ 612 spores were examined in each g corresponding fluorescence intensity of spores in panel (C). (E) The brightness of individua dormant spores  ≥ 932 spores were examined in each group. (F) The corresponding fluoresc spores in panel (E). The numbers of individual spores examined by microscopy are given in l Figure 7. The change of lipid probe stained dormant spore refractility and fluorescence int and single spore levels after 5 h of treatment at various temperatures. (A) The change in ­OD dormant spore populations measured by a plate reader. Untreated PS832 spores were used corresponding fluorescence intensity of spores in panel (A). (C) The change of individual P brightness measured by a phase contrast microscopy  ≥ 612 spores were examined in each g corresponding fluorescence intensity of spores in panel (C). (E) The brightness of individua dormant spores  ≥ 932 spores were examined in each group. (F) The corresponding fluoresc spores in panel (E). The numbers of individual spores examined by microscopy are given in Figure 7. The change of lipid probe stained dormant spore refractility and fluorescence intensity at population and single spore levels after 5 h of treatment at various temperatures. (A) The change in ­OD600 of PS832 ­(DiIC12) dormant spore populations measured by a plate reader. Untreated PS832 spores were used as control. (B) The corresponding fluorescence intensity of spores in panel (A). (C) The change of individual PS832 ­(DiIC12) spores’ brightness measured by a phase contrast microscopy  ≥ 612 spores were examined in each group. (D) The corresponding fluorescence intensity of spores in panel (C). (E) The brightness of individual PS832 (FM5-95) dormant spores  ≥ 932 spores were examined in each group. (F) The corresponding fluorescence intensity of spores in panel (E). The numbers of individual spores examined by microscopy are given in Table S2. microtiter plate (black wall, Greiner Bio-One), and the optical density and fluorescence intensity were measured by a BioTek plate reader. Data were collected from at least two independent tests, each of them had three biologi- cal repeats. Materials and methods microtiter plate (black wall, Greiner Bio-One), and the optical density and fluorescence intensity were measured by a BioTek plate reader. Data were collected from at least two independent tests, each of them had three biologi- cal repeats. Imaging and image analysis. In current work, two microscopes were employed for imaging. The wide- field microscope had a Nikon Ti Microscope, a NA1.45 plan Apo λ 100 × Oil Ph3 DM objective, and the rescan confocal microscope was equipped with a Nikon Ti Microscope and a NA1.49 SR Apo TIRF 100 × objective. Spores were stabilized on a 1.5% agarose pad sealed in an air containing chamber as described ­previously38. If https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | www.nature.com/scientificreports/ Figure 8. The effect of 5 h of heat-treatment on the fluorescence intensity of IM probe stained spores. The phase contrast (PC) and widefield fluorescence (Fluo) images of wild type PS832 spores stained by ­DiIC12 (A), and FM5-95 (B) after different heat treatments: (A) images corresponding to Fig. 7C,D; and (B) images corresponding to Fig. 7G,H. The fluorescence images displayed for ­DiIC12 spores are all in the same range, whereas, the FM5-95 fluorescence images displayed are in different ranges due to the big decline in brightness at higher temperatures. Figure 8. The effect of 5 h of heat-treatment on the fluorescence intensity of IM probe stained spores. The phase contrast (PC) and widefield fluorescence (Fluo) images of wild type PS832 spores stained by ­DiIC12 (A), and FM5-95 (B) after different heat treatments: (A) images corresponding to Fig. 7C,D; and (B) images corresponding to Fig. 7G,H. The fluorescence images displayed for ­DiIC12 spores are all in the same range, whereas, the FM5-95 fluorescence images displayed are in different ranges due to the big decline in brightness a higher temperatures. necessary, spores were heated for 5 h at 40, 50, 60, 65, 70, 75 and 80 °C, followed by cooling in a water–ice bath (≥ 15 min). In case of tracking spores’ germination, HEPES buffer (25 mM) supplemented with AGFK (l-aspar- agine, glucose, fructose, and potassium chloride, 10 mM each) were provided in the agarose pad. The time lapse images were captured once every 1.5 min for 90 min. Time lapse images were analyzed by the ImageJ macro ­SporeTrackerB_06k39. In brief, spores were detected and marked in the first-time frame of the phase contrast images. Materials and methods For each spore, a phase contrast and a fluores- cence montage stack were created to present the phase contrast brightness history, and the fluorescent dynamics of this spore (Fig. 2A,C). The phase contrast brightness profile and fluorescent profile of the spore were detected and stored by SporeTrackerB_06k for display and further analysis (Fig. 2B,D). Subsequently, the time of start ­(TRapidRelease) and ­(TPhaseDark) end of the rapid decline in the brightness profile were detected, and further the ‘time to germination’ was calculated for presenting the averaged fluorescence profile in the population (Fig. 2E)22. Here, the ‘time to germination’ = 1/2 × ­(TRapidRelease + ­TPhaseDark). In order to present the fluorescent profile of the population, each spore’s fluorescence profile was synchronized by defining t = 0 min as the ‘time to germination’. Eventually, averaged fluorescence traces vs time relative to germination were created to show the fluorescence profile in the population (Fig. 2F). Two channel images (phase contrast and fluorescent image) with single time frames were analyzed by ImageJ macro SporeAnalyzer. Spores were detected and marked in the phase contrast channel, followed by the detection of spore brightness and fluorescence intensity of each spore. Both macro runs in the background of ImageJ plugin ObjectJ. Western blot analysis. B. subtilis PS832 SpoVAEa-SGFP2 spores were heat activated for 30 min at 70 °C, followed by cooling in a water–ice bath (≥ 15 min). Subsequently, spore germination (OD600 =  ~ 30, 100 µl) was triggered by l-asparagine, glucose, fructose, and potassium chloride, 10 mM each (AGFK) in 5 ml MOPS medium. Spores were collected after incubation at 37 °C for 0, 15, 30, and 60 min with continuous rotation at 200 rpm. Spore lysates were obtained by the procedure of Troiano et al.15. Proteins from equal aliquots of the same amounts of spores were run on a Tricine-SDS-PAGE gel, and probed with rabbit polyclonal anti-GFP anti- body (Abcam) and HRP-conjugated goat anti-rabbit IgG H&L (Abcam) on a PDVF ­membrane40. Received: 1 February 2022; Accepted: 17 March 2022 www.nature.com/scientificreports/ Stage-specific fluorescence intensity of GFP and mCherry during sporulation In Bacillus subtilis. BMC Res. Notes. 3, 303 (2010). 4. Laue, M., Han, H.-M., Dittmann, C. & Setlow, P. Intracellular membranes of bacterial endospores are reservoirs for spore core membrane expansion during spore germination. Sci. Rep. 8, 11388 (2018). 5. Ramírez-Guadiana, F.H., Meeske, A.J., Rodrigues, C.D.A., Barajas-Ornelas, R.D.C., Kruse, A.C. & et al. A two-step transpor pathway allows the mother cell to nurture the developing spore in Bacillus subtilis. PLoS Genet. 13, e1007015 (2017).l p y p g p 36. Kremers, G-J, Goedhart, J., van den Heuvel, D.J., Gerritsen, H.C. & Gadella, T.W.J. 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Protoc. 1, 16–22 (200 Acknowledgements g We thank the Van Leeuwenhoek Centre for Advanced Microscopy (LCAM) at the University of Amsterdam for the use of the widefield microscope, and the Confocal.nl for the use of the RCM microscope. We thank Ronald Breedijk from LCAM for the assistance for imaging. We thank Jeroen Kole from Confocal.nl for the RCM imag- ing. Juan Wen acknowledges the China Scholarship Council for a PhD fellowship. www.nature.com/scientificreports/ et al. Heat activation and inactivation of bacterial spores. Is there an overlap? Appl. Environ. Microbiol. (2022); in press. pp p 1. De Luca, G. M. R. et al. Re-scan confocal microscopy: scanning twice for better resolution. Biomed. Opt. Express. 4, 2644–2656 (2013). 22. Magge, A., Setlow, B., Cowan, A. E. & Setlow, P. Analysis of dye binding by and membrane potential in spores of Bacillus species. J. Appl. Microbiol. 106, 814–824 (2009). pp 23. Ghosh, S. et al. Characterization of spores of Bacillus subtilis that lack most coat layers. J. Bacteriol. 190, 6741–6748 (2008). l f f l b f ll l l / 24. Loison, P. et al. Direct investigation of viscosity of an atypical inner membrane of Bacillus spores: a molecular rotor/FLIM study. Biochim. Biophys. Acta. 1828, 2436–2443 (2013). Biochim. Biophys. Acta. 1828, 2436–2443 (2013). 25. Wang, S., Setlow, P. & Li, Y-Q. Slow leakage of Ca-dipicolinic acid from individual Bacillus spores during initiation of spore ger- mination. J. Bacteriol. 197, 1095–1103 (2015).il 6. van Beilen, J. W. A. & Brul, S. Compartment-specific pH monitoring in Bacillus subtilis using fluorescent sensor proteins: a too to analyze the antibacterial effect of weak organic acids. Front. Microbiol. 4, 157 (2013). yf g 7. Setlow, B. & Setlow, P. Measurements of the pH within dormant and germinated bacterial spores. Proc. Natl. Acad. Sci. 77 2474–2476 (1980). 28. Coleman, W. H., Chen, D., Li, Y.-Q., Cowan, A. E. & Setlow, P. How moist heat kills spores of Bacillus subtilis. J. Bacteriol. 189, 8458–8466 (2007). 9. Coleman, W. H., Zhang, P., Li, Y.-Q. & Setlow, P. Mechanism of killing of spores of Bacillus cereus and Bacillus megaterium by we heat. Lett. Appl. Microbiol. 50, 507–514 (2010).f pp 0. Alkaabi, K. M., Yafea, A. & Ashraf, S. S. Effect of pH on thermal- and chemical-induced denaturation of GFP. Appl. Biochem Biotechnol. 126, 149–156 (2005).l 1. Cava, F. et al. Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology. Environ. Microbiol. 10, 605–613 (2008). p gy 2. Frenzel, E., Legebeke, J., van Stralen, A., van Kranenburg, R. & Kuipers, O. P. In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. Biotechnol. Biofuels. 11, 1–19 (2018).il y y p p f 3. Doherty, G. P., Bailey, K. & Lewis, P. J. www.nature.com/scientificreports/ www.nature.com/scientificreports/ 9. Fort, P. & Errington, J. Nucleotide sequence and complementation analysis of a polycistronic sporulation operon, spoVA Bacillus subtilis. J. Gen. Microbiol. 131, 1091–1105 (1985). 10. Wang, G., Yi, X., Li, Y.-Q. & Setlow, P. Germination of individual Bacillus subtilis spores with alterations in the GerD and Sp proteins, which are important in spore germination. J. Bacteriol. 193, 2301–2311 (2011). p p p g 11. Velásquez, J., Schuurman-Wolters, G., Birkner, J. P., Abee, T. & Poolman, B. Bacillus subtilis spore protein SpoVAC functions as a mechanosensitive channel. Mol. Microbiol. 92, 813–823 (2014). 2. Vepachedu, V. R. & Setlow, P. Analysis of interactions between nutrient germinant receptors and SpoVA proteins of Bacillus subtilis spores. FEMS Microbiol. Lett. 274, 42–47 (2007). p y spores. FEMS Microbiol. Lett. 274, 42–47 (2007) p 3. Stewart, K.-A.V. & Setlow, P. Numbers of individual nutrient germinant receptors and other germination proteins in spores of Bacillus subtilis. J. Bacteriol. 195, 3575–3582 (2013). ( ) 14. Wang, Y., de Boer, R., Vischer, N., van Haastrecht, P., Setlow, P. & et al. Visualization of germination proteins in putative Bacillus cereus germinosomes. Int. J. Mol. Sci. 21, 5198 (2020). g 5. Troiano, A. J. Jr., Zhang, J., Cowan, A. E., Yu, J. & Setlow, P. Analysis of the dynamics of a Bacillus subtilis spore germination protein complex during spore germination and outgrowth. J. Bacteriol. 197, 252–261 (2015). 15. Troiano, A. J. Jr., Zhang, J., Cowan, A. E., Yu, J. & Setlow, P. Analysis of the dynamics of a Bacillu complex during spore germination and outgrowth. J. Bacteriol. 197, 252–261 (2015). 6. Wen, J., Pasman, R., Manders, E.M.M., Setlow, P. & Brul, S. Visualization of germinosomes and the inner membrane in Bacillus subtilis spores. J. Vis. Exp. e59388. (2019).fi p p 7. Griffiths, K. K., Zhang, J., Cowan, A. E., Yu, J. & Setlow, P. Germination proteins in the inner membrane of dormant Bacillus subtilis spores colocalize in a discrete cluster. Mol. Microbiol. 81, 1061–1077 (2011). p 8. Breedijk, R. M. P. et al. A live-cell super-resolution technique demonstrated by imaging germinosomes in wild-type bacteria spores. Sci. Rep. 10, 5312 (2020). p p 19. Cowan, A.E., Olivastro, E.M., Koppel, D.E., Loshon, C.A., Setlow. B. et al. Lipids in the inner membrane of dormant spores of Bacillus species are largely immobile. Proc. Natl. Acad. Sci. 101, 7733–7738 (2004). p g y 0. Wen, J., Smelt, J.P.P.M., Vischer, N.O.E., de Vos, A.L. References References 1. Lopez, D., Vlamakis, H. & Kolter, R. Generation of multiple cell types in Bacillus subtilis. FEMS Microbiol. Rev. 33, 152–163 (2009). 2. Setlow, P., Wang, S. & Li, Y-Q. Germination of spores of the orders Bacillales and Clostridiales. Annu. Rev. Microbiol. 71, 459–477 (2017). t al. Bacillus subtilis spore inner membrane proteome. J. Proteome ( ) 3. Zheng, L. et al. Bacillus subtilis spore inner membrane proteome. J. Proteome. Res. 15, 585–594 (2016). ( ) 3. Zheng, L. et al. Bacillus subtilis spore inner membrane proteome. J. Proteome. Res. 15, 585–594 (2016). 4. Korza, G. & Setlow, P. Topology and accessibility of germination proteins in the Bacillus subtilis spore inner membrane. J. Bacteriol 195, 1484–1491 (2013). 5. Francis, M.B. & Sorg, J.A. Dipicolinic acid release by germinating spores occurs through a mechanosensing mechanism. mSphere 1, e00306–16 (2016) 5. Francis, M.B. & Sorg, J.A. Dipicolinic acid release by germinating spores occurs through a mechanosensing mechanism. mSphere. 1, e00306–16 (2016) ( ) 6. Perez-Valdespino, A. et al. Function of the SpoVAEa and SpoVAF proteins of Bacillus subtilis spores. J. Bacteriol. 196, 2077–2088 (2014). 6. Perez-Valdespino, A. et al. Function of the SpoVAEa and SpoVAF proteins of Bacillus subtilis spores. J. Bacteriol. 196, 2077–2088 (2014). ( ) 7. Vepachedu, V. R. & Setlow, P. Localization of SpoVAD to the inner membrane of spores of Bacillus subtilis. J. Bacteriol. 87 5677–5682 (2005). ( ) 8. Vepachedu, V. R. & Setlow, P. Role of SpoVA proteins in release of dipicolinic acid during germination of Bacillus subtilis spores triggered by dodecylamine or lysozyme. J. Bacteriol. 189, 1565–1572 (2007). https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 | Author contributions J.W. (data analysis and interpretation, manuscript writing), N.O.E.V. (image analysis), A.D.V. (data analysis and interpretation), E.M.M.M. (RCM microscopy), P.S. (data interpretation and manuscript editing) and S.B. (data analysis, manuscript interpretation, editing and project supervision). Fundingh Funding This article was funded by China Scholarship Council, Universiteit van Amsterdam, Confocal.nl, UConnHealth. ng cle was funded by China Scholarship Council, Universiteit van Amsterdam, Confocal.nl, UConnHealth. g This article was funded by China Scholarship Council, Universiteit van Amsterdam, Confocal.nl, UConnHealth Scientific Reports | (2022) 12:4944 | https://doi.org/10.1038/s41598-022-09147-3 www.nature.com/scientificreports/ Competing interests  The authors declare no competing interests. Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​09147-3. Correspondence and requests for materials should be addressed to S.B. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. © The Author(s) 2022 Competing interests  The authors declare no competing interests. Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​09147-3. Correspondence and requests for materials should be addressed to S.B. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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. Fundingh 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/. © The Author(s) 2022 Competing interests  The authors declare no competing interests. Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​09147-3. Correspondence and requests for materials should be addressed to S.B. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and nstitutional affiliations. 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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. © The Author(s) 2022 https://doi.org/10.1038/s41598-022-09147-3 Scientific Reports | (2022) 12:4944 |
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Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014)
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Palavras-chave Satisfação com a Democracia; Avaliação de Governo; Responsividade; Instituições Democráticas; Economia. Resumo Resumo Com base na análise de resultados do Estudo Eleitoral Brasileiro (ESEB) de 2002 a 2014, e a partir das respostas à pergunta: “De uma maneira geral, o(a) sr.(a) está muito satisfeito(a), satisfeito(a), pouco satisfeito(a) ou nada satisfeito(a) com o funcionamento da democracia no Brasil?” e de seus correlatos atitudinais e socioeconômicos, o artigo descreve a satisfação com a democracia como medida de responsividade do regime aos olhos dos cidadãos e, como tal, como fenômeno multifacetado, que envolve não apenas a avaliação de resultados e conteúdos substantivos das políticas democráticas, como também aspectos institucionais e normativos da democracia representativa. Os resultados sugerem que, embora multifacetado, o fenômeno da satisfação com a democracia no país tem correlatos razoavelmente consistentes através do tempo em termos de avaliação de autoridades e de normas democráticas. Sugerem também que, embora a dimensão econômica seja importante, ela nem sempre é determinante para a satisfação com a democracia no país. Satisfaction with democracy among Brazilians in the recent scenario (2002-2014) Fabíola Brigante Del Porto Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) Satisfaction with democracy among Brazilians in the recent scenario (2002-2014) Abstract Based on the Brazilian Electoral Study Data Analysis (ESEB) from 2002 to 2014 and from the answers to the question "On the whole, are you very satisfied, rather satisfied, not very satisfied or not at all satisfied with the way democracy is developing in Brazil?" and its attitudinal and socioeconomic correlates, the article describes the satisfaction with democracy as a measure of responsiveness of the regime to the citizens’ view, and, as such, as a multifaceted phenomenon involving not only the evaluation of results and substantial content of the democratic politics, as well as institutional and regulatory aspects of representative democracy. The results suggest that although multifaceted, the phenomenon of satisfaction with democracy in the country has fairly consistent correlates over time in terms of evaluating authorities and democratic norms. They also suggest that, although the economic dimension is important, it is not always determinant to the satisfaction with democracy in the country. 1 Este artigo é parte do projeto de pesquisa "O que sabemos sobre a (in)satisfação com a democracia no Brasil? Orientações avaliativas do regime democrático segundo os brasileiros no período democrático recente (2002-2014)" desenvolvido pela autora com o apoio da Fundação de Amparo à Pesquisa do Estado de São Paulo (Processo Fapesp nº 2016/05619-7). Uma versão anterior e parcial deste artigo foi apresentada no XXXIV Congresso Internacional da Associação de Estudos da América Latina (LASA), realizado em Nova York, entre os dias 27 e 30 de maio de 2016. Agradeço à Jana Morgan (University of Tenessee), Dinorah Azpuru (Wichita State University) e Elisa Castro (Purdue University) pelos comentários na ocasião. 2 O ESEB é estudo vinculado ao projeto internacional Comparative Study of Electoral Systems (CSES), da Universidade de Michigan (www.cses.org), e, no Brasil, realizado pelo CESOP-UNICAMP sob a coordenação da Profa. Dra. Rachel Meneguello (Departamento de Ciência Política), da Universidade Estadual de Campinas, desde seu início (2002). O ESEB é survey nacional pós-eleitoral, realizado logo após as eleições presidenciais. O questionário aplicado pelo ESEB contém um módulo que é comum a todos os países integrantes do CSES e outro que é desenhado por pesquisadores brasileiros. Keywords y Satisfaction with Democracy; Evaluation of Government; Responsiveness; Democratic Institution; Economy. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] 84 | Fabíola Brigante Del Porto 84 1 Este artigo é parte do projeto de pesquisa "O que sabemos sobre a (in)satisfação com a democracia no Brasil? Orientações avaliativas do regime democrático segundo os brasileiros no período democrático recente (2002-2014)" desenvolvido pela autora com o apoio da Fundação de Amparo à Pesquisa do Estado de São Paulo (Processo Fapesp nº 2016/05619-7). Uma versão anterior e parcial deste artigo foi apresentada no XXXIV Congresso Internacional da Associação de Estudos da América Latina (LASA), realizado em Nova York, entre os dias 27 e 30 de maio de 2016. Agradeço à Jana Morgan (University of Tenessee), Dinorah Azpuru (Wichita State University) e Elisa Castro (Purdue University) pelos comentários na ocasião. 2 O ESEB é estudo vinculado ao projeto internacional Comparative Study of Electoral Systems (CSES), da Universidade de Michigan (www.cses.org), e, no Brasil, realizado pelo CESOP-UNICAMP sob a coordenação da Profa. Dra. Rachel Meneguello (Departamento de Ciência Política), da Universidade Estadual de Campinas, desde seu início (2002). O ESEB é survey nacional pós-eleitoral, realizado logo após as eleições presidenciais. O questionário aplicado pelo ESEB contém um módulo que é comum a todos os países integrantes do CSES e outro que é desenhado por pesquisadores brasileiros. Introdução1 Em artigo sobre as bases da avaliação do regime democrático brasileiro, Meneguello (2010) encontra uma dissociação entre a satisfação com a democracia, a atuação das instituições e os resultados de políticas públicas, sugerindo que, para os cidadãos, essas dimensões não se relacionam diretamente. Segundo a autora, para a necessidade de “[...] um estudo aprofundado sobre o conceito de satisfação com a democracia no país” (MENEGUELLO, 2010, p. 143). Este artigo propõe um estudo exploratório dos fatores que impulsionam a satisfação com a democracia no cenário brasileiro recente, com base na análise longitudinal de medidas de nível individual, obtidas de pesquisas de opinião por amostragem, que fazem parte do Estudo Eleitoral Brasileiro (ESEB) de 2002 a 20142. Partindo-se do suposto de que o grau de qualidade da democracia, em termos de procedimentos, conteúdos e resultados, influencia as atitudes e percepções acerca do regime democrático (DIAMOND; MORLINO, 2005; RENNÓ et al., 2011; MOISÉS, 2013), procura-se compreender a satisfação com a democracia como medida de responsividade do regime democrático aos olhos dos cidadãos e, nesse sentido, como fenômeno multifacetado que envolve fatores de curto e longo prazo de avaliação ou, nos termos de Easton (1965 e 1975), dimensões de apoio específico (resposta às autoridades diante da satisfação com desempenho ou resultados percebidos) e difuso (avaliação do que os objetos políticos são ou representam) da democracia. A análise dos fatores que favorecem a satisfação com a democracia é importante para compreender o cenário de “déficit democrático” que perpassa grande parte das democracias atuais (NORRIS, 2011). Estudos têm mostrado que os [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 85 85 insatisfeitos com o regime são menos propensos a aderir à democracia em termos normativos e, quando o fazem, tendem a escolher modelos deficitários de democracia – sem partidos e sem congresso (MOISÉS e CARNEIRO, 2008; SARSFIELD e ECHEGARAY, 2005). A insatisfação política também pode deter o envolvimento político dos cidadãos e comprometer comportamentos de conformidade política necessários ao contrato social subjacente à democracia, como a submissão voluntária à lei (DALTON, 2004; NORRIS, 2011). Introdução1 Para Norris, a percepção do “déficit democrático” resultaria de processos culturais – como a modernização social e a mobilização cognitiva – e da racionalidade dos indivíduos, que aumentariam as demandas dos cidadãos por mais e diferentes direitos, assim como os capacitaria a julgar o desempenho do regime não só quanto à sua política substantiva geral, como quanto aos procedimentos institucionais. A esses processos, acrescenta a autora o impacto que a divulgação e o acesso a notícias negativas sobre o desempenho governamental têm sobre as visões dos cidadãos sobre os governos democráticos (NORRIS, 2011). Nessa perspectiva, a construção do “déficit democrático” baseia-se na percepção de que o desempenho do regime é falho. Se essa relação parece óbvia, os critérios com os quais os indivíduos avaliam o funcionamento do regime são complexos. Para Dalton (2004), nesta avaliação, os cidadãos misturam avaliações dos incumbentes políticos e julgamentos das normas e procedimentos do regime. Este artigo procura contribuir com essa discussão, analisando correlatos e conteúdos da satisfação com a democracia, a partir da análise do cenário brasileiro recente. Para tanto, na próxima seção, o artigo apresenta os aspectos teóricos subjacentes à análise da qualidade da democracia e as percepções de legitimidade e efetividade do regime que embasam esta discussão. Em seguida, o cenário brasileiro é apresentado a partir dos resultados do Estudo Eleitoral Brasileiro e as análises estatísticas são realizadas com o intuito de explorar o construto da satisfação com a democracia entre os cidadãos brasileiros no período recente. Perspectivas teóricas para a análise da satisfação com a democracia no Brasil O tema da (in)satisfação com o regime democrático “realmente existente” e está em pauta no país desde o início da experiência brasileira de democracia recente, chamando atenção para o fato de que os cidadãos percebem que a promessa democrática parece não ser realizável (MOISÉS, 1995 e 2010). Não obstante, ainda [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 86 não se produziu uma reflexão sistemática e longitudinal sobre as dimensões da satisfação com a democracia no país. Os estudos têm se voltado a compreender seus correlatos em termos de avaliação de resultados de políticas democráticas e têm apontado que o nível de satisfação com a democracia é afetado negativamente, entre outros fatores, pela percepção de que a renda é insuficiente, pelas percepções e experiências de corrupção, de criminalidade e discriminação e pela avaliação da capacidade do governo de gerir a economia (MOISÉS e CARNEIRO, 2008; RENNÓ et al., 2011). As análises sobre a satisfação com a democracia no país não consideram, porém, o aspecto dinâmico desta e têm como pontos de partida variáveis um pouco distintas. Por exemplo, enquanto Moisés e Carneiro (2008) incluem percepções sobre a economia, Rennó et al. (2011) utilizam recursos que os cidadãos dispõem para cumprir seu papel no processo democrático (por exemplo, o acesso à informação). Essas dimensões devem ser articuladas para uma compreensão ampliada de como os cidadãos se relacionam com a democracia em termos práticos no país, além da necessidade de considerá-las em termos longitudinais. Em adição, também é necessário considerar: 1. Qual o impacto da avaliação das instituições representativas como instrumentos que fazem a intermediação dos interesses dos cidadãos com o regime, no julgamento que os indivíduos fazem do desempenho da democracia? 2. Como as percepções dos cidadãos sobre normas e procedimentos da democracia representativa articulam-se às percepções sobre os resultados do regime e sobre a atuação dos governantes do momento na produção de níveis de satisfação com a democracia no Brasil? Para avançar no entendimento da satisfação com a democracia no país nesse sentido, o artigo segue Meneguello (2010 e 2013) e inclui, no construto da satisfação com o regime, as avaliações das instituições, dos serviços, das políticas públicas, da economia e dos governantes do momento. 3 A bibliografia sobre as premissas normativas da democracia é bastante extensa e sujeita a interpretações distintas. Ver, por exemplo, Schumpeter (1984), Bobbio (1986), Dahl (1997), O´Donnell (2010). 3 A bibliografia sobre as premissas normativas da democracia é bastante extensa e sujeita a interpretações distintas. Ver, por exemplo, Schumpeter (1984), Bobbio (1986), Dahl (1997), O´Donnell (2010). 4 Mensurar a responsividade é, de fato, tarefa desencorajadora, dada a complexidade dos conceitos e as disputas normativas e teóricas que são postas em questão e a necessidade de estabelecer e verificar a corrente de mecanismos causais que se estabelecem no processo democrático responsivo. A esse respeito ver Powell (2005). 5 Easton (1975, p.447) já chamara a atenção para esse aspecto ao mencionar que a satisfação com o desempenho do regime representaria a satisfação dos cidadãos não só com os resultados das ações das autoridades, mas com os próprios processos que levariam a tais resultados. Há, portanto, nessa perspectiva, uma dimensão normativa e difusa na satisfação com o funcionamento do regime, a qual é incluída na presente análise. 5 Easton (1975, p.447) já chamara a atenção para esse aspecto ao mencionar que a satisfação com o desempenho do regime representaria a satisfação dos cidadãos não só com os resultados das ações das autoridades, mas com os próprios processos que levariam a tais resultados. Há, portanto, nessa perspectiva, uma dimensão normativa e difusa na satisfação com o funcionamento do regime, a qual é incluída na presente análise. Perspectivas teóricas para a análise da satisfação com a democracia no Brasil No entanto, ampliando esse entendimento, agrega à análise as percepções dos cidadãos sobre a eficácia de normas e procedimentos da democracia representativa que, segundo Aarts e Thomassen (2008), em diferentes cenários institucionais, afetam a satisfação com a democracia. Em termos teóricos, essa perspectiva também se baseia em Diamond e Morlino (2005), que avaliam a democracia em termos de sua qualidade quanto a: 1. Procedimentos (se mecanismos tais como eleições e instituições governamentais sustentam um governo responsivo e de acordo com o primado da lei); 2. Conteúdos (se os cidadãos e associações gozam de amplas liberdades e igualdade política); e 3. Resultados (se as expectativas cidadãs quanto ao cumprimento dos objetivos da [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 87 87 democracia são satisfeitas). Nessa perspectiva, uma democracia de qualidade configura-se como um sistema de oito dimensões: cinco procedimentais (primado da lei, participação, competição e accountability vertical e horizontal); duas substantivas (respeito às liberdades civis e políticas e progressiva implantação de maior igualdade política) e uma dimensão de resultados, a responsividade. Essa última relaciona as dimensões procedimentais às dimensões substantivas, permitindo mensurar a extensão na qual as ações governamentais e as políticas democráticas correspondem às expectativas, demandas e preferências dos cidadãos. O conceito de democracia3 como um sistema de qualidades implica que essas oito dimensões estejam inter-relacionadas e que a melhora em uma dimensão pode ter consequências sobre as outras (DIAMOND e MORLINO, 2005). Enquanto o primado da lei é base para o desenvolvimento das demais dimensões, a exigência de contínua responsividade dos governos às preferências dos cidadãos também é central para definir uma democracia de qualidade. Para os autores, as percepções sobre a responsividade do regime democrático podem ser medidas de modo indireto, perguntando aos indivíduos por sua satisfação com o modo como a democracia trabalha4. Sendo a responsividade a dimensão da democracia que articula procedimentos e conteúdos, os cidadãos estarão satisfeitos com o regime não apenas quando perceberem que os governos estabelecem políticas que atendam a suas demandas, mas também quando avaliarem positivamente o próprio processo democrático e os procedimentos associados (POWELL, 2005)5. Norris (2011) retoma essa questão quando aborda o “déficit democrático”. p ç p p p O´Donnell (2010). 4 Mensurar a responsividade é, de fato, tarefa desencorajadora, dada a complexidade dos conceitos e as disputas normativas e teóricas que são postas em questão e a necessidade de estabelecer e verificar a corrente de mecanismos causais que se estabelecem no processo democrático responsivo. A esse respeito ver Powell (2005). Perspectivas teóricas para a análise da satisfação com a democracia no Brasil Apontando que a satisfação com a democracia resulta do modo como as pessoas experienciam o processo democrático, a autora detalha que a satisfação com o regime 5 Easton (1975, p.447) já chamara a atenção para esse aspecto ao mencionar que a satisfação com o desempenho do regime representaria a satisfação dos cidadãos não só com os resultados das ações das autoridades, mas com os próprios processos que levariam a tais resultados. Há, portanto, nessa perspectiva, uma dimensão normativa e difusa na satisfação com o funcionamento do regime, a qual é incluída na presente análise. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 88 diz respeito não apenas às avaliações de seus resultados e do fato de os serviços públicos serem efetivos, como também às avaliações das práticas democráticas (procedimentos como a justeza, transparência e regularidade das eleições, que garantem a rotatividade democrática do poder, honestidade e probidade dos representantes eleitos e servidores públicos, que fazem parte de modo efetivo da política democrática). Trata-se, portanto, de uma medida avaliativa da democracia, que, baseada em expectativas culturais e racionais dos cidadãos, lida com normas e procedimentos e expressa a frustração quando se compara o que se tem e o que se deveria ter (GUNTHER e MONTERO, 2003; BLAIS e GÉLINEAU, 2007; MOISÉS e CARNEIRO, 2008). No entanto, não apenas o desempenho do governo e os valores culturais são importantes correlatos da avaliação do sistema democrático e de seus resultados, mas o próprio formato das instituições políticas afeta a satisfação dos indivíduos com o funcionamento da democracia6. Isso implica, por exemplo, que os apoiadores do partido no poder verão o funcionamento da democracia em seu país de modo mais positivo do que aqueles cujo partido esteja fora do poder (FUCHS, GUIDOROSSI e SVENSSON, 1995; NORRIS, 1999 e 2011; GUNTHER e MONTERO, 2003; DIAMOND e MORLINO, 2005; BLAIS e GÉLINEAU, 2007). Todavia, enquanto as eleições democráticas necessariamente produzem perdedores e ganhadores, a democracia baseia-se na premissa de que os perdedores consentem sua perda e aceitam que a democracia trabalha bem, apesar do resultado eleitoral (BLAIS e GÉLINEAU, 2007). 6 Anderson e Guillory (1997) e Aarts e Thomassen (2008) mostram que diferentes desenhos institucionais do regime democrático, por exemplo, sistemas proporcionais ou majoritários, têm diferentes efeitos sobre a satisfação dos cidadãos com o funcionamento do regime democrático. Essa discussão, no entanto, foge aos objetivos deste artigo. Perspectivas teóricas para a análise da satisfação com a democracia no Brasil De todo modo, embora os governos democráticos devam ser continuamente responsivos às preferências e demandas de seus cidadãos, nas democracias atuais, com tantos e distintos interesses em disputa, a responsividade governamental é fenômeno complexo, e os perdedores ficarão temporariamente insatisfeitos, mas deverão consentir sua perda, na medida em que acreditem que as regras do jogo garantem a rotatividade do poder e permitem que o partido que endossam possa ser eleito em outra ocasião. Dessa forma, a satisfação com o funcionamento do regime também deve correlacionar-se com medidas de apoio específico, como a aprovação do Executivo e a preferência partidária, e com as [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 89 percepções da capacidade de influência do voto e de representação do sistema (BLAIS e GÉLINEAU, 2007; AARTS e THOMASSEN, 2008). Essas questões apontam para a complexidade do fenômeno da satisfação com o funcionamento do regime democrático, que remonta a “um apoio político de nível intermediário, que é frequentemente difícil de captar” (NORRIS, 1999, p. 11; 2011, p. 28). Diante dessa dificuldade estabeleceu-se um debate, ainda não resolvido, sobre a medida clássica7 de satisfação com a democracia e sobre o modo de apreender as percepções cidadãs acerca do desempenho do regime democrático (CANACHE, MONDAK e SELIGSON, 2001; LINDE e EKMAN, 2003). Quanto à primeira questão, enquanto alguns autores tratam o indicador de satisfação com a democracia como medida de apoio a autoridades (DALTON, 1999), outros a tratam como apoio às normas constitucionais da democracia “em operação”, ou avaliação do funcionamento do regime em contraste aos ideais do governo democrático (FUCHS, GUIDOROSSI e SWENSSON, 1995; MOISÉS, 2011). Outros, ainda (FUCHS e KLINGEMANN, 1995; TÓKA, 1995; MISHLER e ROSE, 1999 e 2002), abordam a satisfação com a democracia como equivalente à legitimidade política. Para resumir o debate, usando os termos de Easton (1965 e 1975), as definições sobre o conceito, de um lado, e sobre os usos da medida de satisfação com a democracia, de outro, oscilariam entre o apoio específico e o apoio difuso. 7 Trata-se da pergunta "De uma maneira geral, o(a) sr.(a) está muito satisfeito(a), satisfeito(a), pouco(a) satisfeito(a) ou nada satisfeito(a) com o funcionamento da democracia no país?" A pergunta tem sido incluída em diferentes instrumentos de pesquisa de opinião internacionais: Eurobarometer, Latinobarômetro, Comparative Study of Electoral Systems (CSES), Latin American Public Opinion Project (Lapop) e New Democracies Barometer (este último realizado nos países ex-comunistas do Leste Europeu). 8 Segundo a perspectiva aqui adotada, a base dessa possível ambiguidade, mais do que na forma e medida de mensuração do desempenho do regime, baseia-se na própria definição dessa dimensão do apoio político, que tem sido abordada de modo inespecífico, por exemplo, “satisfação simbólica com os processos pelos quais o país é governado” (EASTON, 1975, p. 447), ou ainda “satisfação com os trabalhos do regime” (NORRIS, 1999, p. 10). Como definir os processos e trabalhos do regime? Para Dalton (2004), que prefere chamar essa dimensão como “normas e procedimentos” (do regime), trata- se das avaliações do desempenho do sistema, que podem ser captadas por avaliações de direitos políticos e das normas de participação, além da própria medida de satisfação com o funcionamento da democracia. Essa questão aponta que o próprio conceito de desempenho do regime precisa de estudos adicionais, tema que será abordado em outra etapa da pesquisa que origina este artigo. Perspectivas teóricas para a análise da satisfação com a democracia no Brasil Enquanto a mensuração de quaisquer das dimensões do apoio político não é tarefa fácil, sendo difícil estabelecer distinções teóricas finas entre dimensões e objetos de apoio político com base em itens de surveys, a sobreposição de dimensões seria particularmente problemática na medida de satisfação com a democracia, uma vez que ela deixa em aberto que critérios ou objetos políticos o respondente deve utilizar para respondê-la (NORRIS, 1999; CANACHE, MONDAK e SELIGSON, 2001). Dessa forma, os indivíduos podem referir-se aos governantes do momento e a seus resultados, a aspectos práticos do regime democrático em oposição a seus princípios ou a um misto dessas dimensões. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] 90 | Fabíola Brigante Del Porto 9 Com relação à amostragem, as quatro pesquisas são amostras nacionais representativas dos eleitores com 16 anos ou mais, do tipo probabilística estratificada em estágios (municípios, setores censitários e domicílios) e com um último estágio de estratificação segundo cotas dentro dos setores, definidas de acordo com o perfil de idade, escolaridade e população economicamente ativa cruzadas por sexo. 10 Todas as bases de dados do ESEB estão disponíveis no Banco de Dados de Pesquisa de Opinião do CESOP/UNICAMP. 90 | Fabíola Brigante Del Porto 90 | Fabíola Brigante Del Porto Por considerarem a medida de satisfação com a democracia ambígua8, Booth e Seligson (2009) utilizam, em seu lugar, indicadores sociotrópicos de avaliação da economia para mensurar as percepções sobre o desempenho do regime, justificando que “[...] o desempenho da economia é um fator crítico na avaliação cidadã do governo” (BOOTH e SELIGSON, 2009, p. 43). No entanto, ao restringir o desempenho do regime a seu aspecto econômico, essa perspectiva não leva em conta que os cidadãos também podem estar atentos a aspectos políticos do regime quando respondem à pergunta sobre o funcionamento da democracia. Nesse sentido, McAllister (1999), Montero, Gunther e Torcal (1997), Mishler e Rose (1999, 2001 e 2002) e Bratton e Mattes (2001), analisando cenários distintos, como os países da Europa Ocidental, do Sul e do Leste e da África, têm demonstrado que bens políticos, como as avaliações dos cidadãos sobre as liberdades e os direitos humanos em seus países, podem ser até mais importantes que os bens econômicos na avaliação do desempenho do regime. Este artigo pretende contribuir para a reunião de subsídios empíricos, a partir do estudo do caso brasileiro, para a análise da proposição teórica de Diamond e Morlino (2005) de que a satisfação com a democracia diz respeito à percepção de responsividade do regime ao articular as dimensões ‘instituições’ e ‘procedimentos’ aos ‘resultados’ do regime. No plano dos resultados do regime, o intuito é também observar o lugar da dimensão da economia na avaliação do desempenho do regime, face às dimensões normativas da democracia no cenário brasileiro. Acompanhando as referências que apontam que a satisfação com o desempenho do regime diz respeito a fenômeno multifacetado, a expectativa é de que, embora a dimensão econômica seja importante, o construto do desempenho do regime transcenda sua avaliação. Na próxima seção, são destacados os resultados do ESEB que são utilizados na discussão da natureza da avaliação do regime democrático, segundo os brasileiros, nesse sentido. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 91 Eleitoral Brasileiro (ESEB) e questões analisadas ( ) q O ESEB baseia-se em entrevistas individuais face a face, realizadas logo após as eleições presidenciais, e sua primeira onda foi aplicada em 2002. Seus dados permitem explorar de forma longitudinal a evolução da relação dos cidadãos brasileiros com o funcionamento do sistema democrático representativo. As informações básicas das 4 ondas do ESEB estão descritas na Tabela 19: Tabela 1 – Informações do Estudo Eleitoral Brasileiro (ESEB)10 Onda Data das entrevistas Universo Tamanho da amostra 2002 31 de outubro a 28 de dezembro de 2002 População brasileira com 16 anos ou mais 2513 2006 17 a 27 de dezembro de 2006 1000 2010 4 a 20 de novembro de 2010 2000 2014 1 a 19 de novembro de 2014 3136 Fonte: ESEB (2002, 2006, 2010 e 2014). Em países de democracia recente como o Brasil, o apoio político democrático resulta, sobretudo, das experiências institucionais recentes dos indivíduos (EASTON, 1975; MISHLER e ROSE, 2001 e 2002). Nesses cenários, o apoio democrático é, em grande medida, contingente ao desempenho do regime, além da consideração por parte dos cidadãos de seus aspectos normativos. Assim, a avaliação do desempenho da democracia é fenômeno complexo: os cidadãos avaliam não apenas a capacidade de as autoridades proverem os bens econômicos almejados, mas também os resultados de outras políticas públicas, como a segurança, o bem-estar e a igualdade. Avaliam também a accountability e a responsividade dos políticos e instituições (BRATTON e MATTES, 2001; FARAH, BARNES e HEUNKS, 1979; POWELL, 2005). Ainda, a satisfação com a democracia remonta não apenas à avaliação que os cidadãos fazem [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 92 dos resultados que recebem dos governos e políticas democráticas, como também aos processos políticos que os embasam (EASTON, 1975; NORRIS, 2011). Cinco conjuntos de questões foram definidos para analisar o fenômeno da satisfação com a democracia no país: 1. Avaliação de instituições representativas (partidos, congresso, justiça e polícia); 2. Avaliação de serviços e políticas públicas (qualidade da educação e saúde, acesso à justiça, controle da criminalidade, diminuição do desemprego e diminuição das desigualdades sociais); 3. Avaliação retrospectiva da gestão da economia; 4. Avaliação dos governantes do momento (incumbentes políticos); e 5. 11 Na ausência de um indicador melhor de percepção da representação pelo regime democrático, como já apontado na nota 9 deste artigo, a pergunta “Existe algum partido que representa a maneira como o senhor pensa?”, presente em todas as ondas do ESEB, é utilizada como medida de sentimento de representação pelo sistema. Trata-se de indicador imperfeito, mas é a informação disponível no conjunto dos dados que mais se aproxima da percepção de representatividade do regime. 12 Apenas a título de referência, no ESEB 2010, 56,2% dos entrevistados avaliavam a situação econômica do país como ‘boa’ ou ‘ótima’ e 28,6% a avaliavam como ‘regular’. Em torno de 80% avaliavam, então, a economia de modo positivo ou regular. Infelizmente, para os ESEB 2014, não há a variável de avaliação da situação econômica do momento para dimensionar de quanto foi, de fato, a Eleitoral Brasileiro (ESEB) e questões analisadas Percepções normativas da democracia - preferência democrática em comparação a outros regimes, percepção do voto como mecanismo de influência no sistema político democrático (proxy de norma de accountability vertical, seguindo Arts e Thomassen (2008)) e sentimento de representação pelo sistema (ter identificação partidária)11. A distribuição das respostas positivas para o período entre 2002 e 2010 (Tabelas 2 e 3) mostra a convivência da crítica às instituições representativas e aos resultados de políticas públicas e das percepções positivas sobre a democracia em termos normativos, reiterando cenários paradoxais já relatados desde o início da experiência democrática brasileira recente (MOISÉS, 1995 e 2010a; BAQUERO, 1994 e 2012) e comum a outros países de democracia recente e longamente estabelecida (BOOTH e SELIGSON, 2009; NORRIS, 1999 e 2011). Dessa forma, no que diz respeito às percepções normativas da democracia, os dados da Tabela 2 mostram que, mesmo com a queda na preferência pela democracia em 2014, a crença na legitimidade democrática é elevada. Ao seu lado, a percepção do voto como mecanismo que exerce influência no que acontece no país também é majoritária no período. Na leitura desses dados, há que se considerar os efeitos dos momentos de realização das pesquisas: conjunturas eleitorais têm efeitos politizadores que podem influenciar positivamente a percepção dos mecanismos democráticos (MOISÉS, 1995; BLAIS e GÉLINEAU, 2007; ROSE, 2007). Por outro lado, não mais do que 40%, declaram que algum partido representa seu modo de pensar em todo o período (percentual que oscila para baixo em 2006 e 2014). [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 93 Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 93 93 O cenário também é menos positivo quando se olha para as avaliações do congresso, dos partidos e da justiça: em todo o período, as somas das avaliações positivas são bastante modestas e apresentam, inclusive, uma trajetória descendente. Por último, a satisfação com a democracia, dimensão avaliativa do apoio político, ainda que esteja bastante aquém da preferência pelo regime democrático, segue uma trajetória similar a esta enquanto tendência entre 2002 e 2014 - aumento entre 2002 e 2010 e queda em 2014 (Tabela 2): Tabela 2 – Variáveis de percepção normativa da democracia e avaliação do desempenho do regime (%) Variáveis 2002 2006 2010 2014 Voto influencia o que acontece no Brasil (soma dos graus influencia muito e influencia) 78,8 77,6 83,9 79,6 Algum partido representa a maneira como o eleitor pensa (sim) 40,7 29,4 40,4 28,1 A democracia é sempre melhor do que qualquer outra forma de regime 69,3 77,2 85,4 77,9 Satisfação com o funcionamento da democracia no país (muito satisfeito + satisfeito) 30,7 44,7 50,2 40,7 Avaliação do governo/presidente (bom + muito bom) 41,0 76,2 93,9 45,9 Avaliação Congresso (ótima + boa) 40,4 27,0 25,3 16,8 Avaliação Partidos 37,3 26,5 20,9 15,5 Avaliação Justiça 42,4 41,3 29,5 23,7 Avaliação Polícia 52,5 51,7 33,4 25,7 Obs: somente respostas válidas. Fonte: ESEB (2002, 2006, 2010 e 2014). Tabela 2 – Variáveis de percepção normativa da democracia e l d d h d ( ) Os dados para o ESEB 2010 e 2014 permitem visualizar ainda as percepções de alguns resultados do regime democrático (Tabela 3). Com relação à avaliação da economia, enquanto em 2010 mais da metade dos entrevistados viam a situação econômica do país como melhor do que a de 2009, em 2014, apenas 24,7% acreditavam que ela estivesse melhor em comparação ao ano anterior12. O cenário [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 94 também aponta para a insatisfação acentuada dos cidadãos com relação a políticas e serviços públicos. piora na avaliação da situação econômica “atual” em 2014 comparativamente a 2010, segundo os entrevistados. 13 A satisfação com a democracia é mensurada através da pergunta: “De uma maneira geral, o(a) sr(a) está muito satisfeito(a), satisfeito(a), pouco satisfeito(a) ou não está satisfeito (a) com o funcionamento da democracia no Brasil?”. A variável foi tratada como dicotômica: satisfeitos (soma das respostas “muito satisfeito” e “satisfeito”) e não satisfeitos (soma das respostas “pouco satisfeitos” e “nada satisfeitos”). As respostas “nem satisfeito nem insatisfeito”, “não sabe” e “não respondeu” foram incluídas na categoria “não satisfeitos”). As análises foram então realizadas em relação à categoria “satisfeitos” com o funcionamento do regime. Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 93 A quantidade de notas 7 a 10 para todos esses serviços são minoritárias e, ademais, decrescentes no período: Tabela 3 – Satisfação com a situação econômica e com políticas públicas (%) Variáveis 2010 2014 Situação econômica em comparação aos 12 meses anteriores (melhor) 55,1 24,7 Controle da criminalidade (soma das respostas de 7 a 10, onde 10= “totalmente satisfeito”) 6,8 5,4 Diminuição das desigualdades sociais 14,5 9,7 Acesso do cidadão comum à justiça 17,8 10,5 Qualidade do ensino público 26,0 15,4 Acesso aos serviços de atendimento médico 12,5 8,1 Diminuição do desemprego 23,9 12,8 Obs: somente respostas válidas. Fonte: ESEB (2002, 2006, 2010 e 2014). Com o intuito de avançar na compreensão de quais dimensões mais se relacionam à satisfação com o funcionamento do regime democrático, os dados para 2010 e 2014 foram selecionados para os procedimentos estatísticos apresentados na sequência. Em trabalho anterior, com base nesses mesmos dados (DEL PORTO, 2016), a execução de técnicas de análise de componentes principais mostrou que a dimensão da legitimidade democrática (apoio normativo e voto) articula-se às avaliações dos resultados do regime e de suas autoridades e instituições no construto multidimensional de avaliação do funcionamento da democracia no Brasil. Embora esses resultados ainda necessitem de testes adicionais, em seu conjunto, eles sugeriram que aspectos normativos do regime importam para essa avaliação, confirmando achados de Aarts e Thomassen (2008) para outros contextos. Trata-se, aqui, ainda de modo descritivo, de explorar os fatores que fomentam a satisfação com a democracia no país no cenário recente. Qual o impacto da percepção da efetividade das normas do regime sobre a satisfação com a democracia em comparação aos efeitos de seus resultados? Características demográficas, socioeconômicas e culturais dos indivíduos (sexo, cor, idade, região e escolaridade, [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 95 95 hábito de leitura de jornais e assistência a telejornais com notícias nacionais) correlacionam-se à percepção do desempenho da democracia brasileira? Para tratar dessas questões, foram realizados modelos de regressão logística, tendo sido a satisfação com a democracia caracterizada como variável dependente binomial13. As variáveis independentes também foram definidas como dicotômicas - a codificação das variáveis está no Anexo -, possibilitando uma comparação direta dos seus efeitos sobre a satisfação com democracia. g g Variável dependente: satisfação com o funcionamento da democracia no país. das amostras (Tabela 1) devido aos missing cases contidos na variável dependente. Nota: Nos 2 anos, os números das amostras dos modelos são menores do que os totais Fonte: Elaboração própria a partir do ESEB (2010 e 2014). 14 Embora avaliação do governo/presidente e satisfação com o funcionamento do regime refiram-se a construtos distintos, poderia haver alguma colinearidade entre os dois indicadores (as correlações entre ambos, medidas pelo “kendall´s tau-b” e “spearman”, foram, respectivamente: para 2010= ,209 e ,233; para 2014= ,264 e ,309 (todas com nível de significância de ,01)). No entanto, a retirada da variável “avaliação do governo” dos modelos para os 2 anos não alterou significativamente a capacidade explicativa dos mesmos. Diante disso, e dada a relevância analítica desse construto, ele foi mantido nas análises aqui apresentadas. A distinção entre satisfação com a democracia e a avaliação dos governos do momento é uma discussão importante aos estudos de apoio político no cenário brasileiro, a qual será abordada em outra etapa da pesquisa, referenciada na nota 1 deste artigo. Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 93 A Tabela 4 apresenta as razões de chance (coeficientes OR- Exp(B)) de ocorrência da satisfação com o funcionamento da democracia segundo os modelos especificados: [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] 96 | Fabíola Brigante Del Porto Tabela 4 – Preditores da Satisfação com o Funcionamento da Democracia Variáveis independentes 2010 2014 Avaliação do governo/presidente 2,514** 2,007** Avaliação da economia comparada aos 12 meses anteriores ,771 2,347** Avaliação do Congresso Nacional 1,181 ,912 Avaliação dos Partidos Políticos 1,250 1,435* Avaliação do Poder Judiciário 1,067 1,870** Avaliação da Polícia 1,237 1,004 Satisfação com redução da criminalidade ,930 ,723* Satisfação com redução das desigualdades sociais ,674** ,822 Satisfação com acesso do cidadão comum à justiça ,934 1,024 Satisfação com diminuição do desemprego 1,044 1,026 Satisfação com serviço de saúde pública 1,046 ,759 Satisfação com serviço de educação pública ,619** ,959 Sentimento de representação por partido político 1,529** 1,652** Percepção de influência do voto 1,359* 1,122 Prefere a democracia 3,257** 1,562** Costuma ler jornais ,813 ,868 Assistiu telejornais com notícias nacionais na semana 1,354 1,259 Escolaridade ,838 1,035 Idade ,702* 1,062 Sexo 1,595** 1,125 Cor 1,115 1,195 Região ,658 1,029 R²Nagelkerke ,203 ,189 N 1091 2521 * sig. a ,01; **sig. a ,05. Fonte: Elaboração própria a partir do ESEB (2010 e 2014). [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 97 Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 97 Nos dois anos, a avaliação dos governos aparece como o principal correlato da satisfação com a democracia, apontando para o papel dos fatores de curto prazo, ou apoio específico, sobre ela14. O apoio normativo ao regime democrático, assim como ter uma identificação partidária, variáveis de longo prazo ou apoio difuso, também aumentam de modo expressivo as chances de satisfação com a democracia nos dois anos. Para além dessas três variáveis, as demais variáveis de avaliação das instituições, das políticas, da situação econômica e do voto têm efeitos menos expressivos, e em apenas um ou outro dos anos – demonstrando efeitos contextuais sobre a satisfação com a democracia no país. Nesse terreno, o primeiro resultado que deve ser destacado diz respeito à avaliação retrospectiva da situação econômica, que, embora em 2014 tenha apresentado o mais forte efeito sobre a satisfação com a democracia, não havia alcançado impacto significativo em 2010. Embora esse resultado ainda demande testes adicionais, isso sugere que nem sempre a dimensão econômica explica a avaliação que os cidadãos fazem do funcionamento do regime democrático. Pode-se supor, nesse caso, que a percepção da economia seja significativa para a avaliação da democracia em momentos de conjunturas mais desfavoráveis. Ademais, como, em 2010, a avaliação da gestão do presidente Lula era extremamente positiva, ela pode ter concentrado os efeitos positivos sobre a satisfação com a democracia. Os dados aqui utilizados não permitem, no entanto, avançar a discussão nesse sentido. Os efeitos de alguns resultados do regime sobre a satisfação com seu funcionamento também parecem variar de acordo com as conjunturas: no âmbito das políticas públicas, enquanto, em 2010, as avaliações da diminuição das desigualdades sociais e da qualidade da educação pública impactaram a satisfação com a democracia, em 2014, sobressai o efeito da percepção de diminuição da criminalidade sobre a satisfação com a democracia. As eventuais diferenças na conjuntura econômica e [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 98 social do país entre os dois momentos, mais positiva em 2010 do que em 2014, podem ter contribuído para esses resultados. 15 Uma análise deste pleito pode ser encontrada em Amaral e Ribeiro (2015). Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 97 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 99 tendo em vista que, no início do período democrático recente, desigualdades socioeconômicas e culturais colocavam as mulheres, os mais jovens, os menos escolarizados, os mais marginalizados e excluídos como mais satisfeitos com a democracia “realmente existente”, embora menos aderidos a ela em termos normativos (MOISÉS, 1995). Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 97 No que se refere à percepção dos mecanismos e instituições da democracia representativa, os resultados são mistos: por um lado, quanto às instituições, chama a atenção o fato de que, em 2010, a avaliação de nenhuma das instituições afete a satisfação com a democracia no país. Em 2014, por sua vez, avaliar positivamente os partidos políticos e a justiça aumentam a satisfação com o desempenho do regime. Os efeitos apenas pontuais tanto da avaliação de instituições como de serviços sobre a satisfação com o funcionamento da democracia no país adicionam evidências às considerações de Meneguello (2010) de que, no mapa dos cidadãos brasileiros, a satisfação com o funcionamento do regime não está articulada diretamente às avaliações de instituições e de serviços públicos. Os modelos aqui definidos para 2010 e 2014, aliás, com capacidade explicativa de cerca de 20% da satisfação com a democracia no Brasil, sugerem que o fenômeno é, de fato, mais complexo do que as dimensões possíveis de serem definidas com base nos dados aqui utilizados. Ainda com relação aos mecanismos democráticos, chama atenção que, em 2014, aqueles que acreditam no voto como mecanismo de accountability vertical não estão mais satisfeitos com o funcionamento da democracia no país. Esse resultado, em desacordo com as expectativas teóricas, pode dever-se ao contexto da eleição presidencial de 2014, a mais disputada no período democrático recente15, mas ainda são necessárias novas análises para melhor qualificar esse cenário. Foi notável que a satisfação com o funcionamento da democracia não tenha se associado à escolaridade nem aos hábitos de ler jornais ou assistir a telejornais com notícias nacionais, o que também contraria a expectativa de que os mais mobilizados cognitivamente mostrar-se-iam mais insatisfeitos e críticos com o funcionamento do regime (NORRIS, 2011). Com relação ao impacto das variáveis sociodemográficas, apenas no primeiro desses anos, os mais jovens e as mulheres mostravam menos chances de estarem satisfeitos com o funcionamento da democracia, resultados que, associados aos efeitos também negativos das avaliações das políticas de redução da desigualdade e qualidade do ensino público, sugerem que jovens e mulheres estavam menos satisfeitos com essa gestão do cotidiano naquele momento. Fora esse resultado, o impacto das variáveis socioeconômicas e demográficas sobre a satisfação com a democracia é quase nulo nos dados aqui explorados. Esse resultado, de todo modo, não deixa de ser significativo, [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. Considerações finais No cenário latino-americano recente, Seligson e Smith (2010) apontam para os efeitos da percepção da crise econômica sobre os valores democráticos, entre os quais a satisfação com a democracia. Os resultados dos autores apontam que, mais do que a percepção da gravidade da crise, os cidadãos estão atentos e avaliam o modo como essa é gerida pelos governantes do momento, e essa percepção tem impacto importante sobre o nível de satisfação com a democracia. Em certo sentido, os resultados do ESEB aqui explorados também parecem apontar nessa direção: enquanto, em 2010, a visão positiva retrospectiva da economia não esteve entre os correlatos da satisfação com a democracia, em 2014, ela emerge como o mais importante fator para explicar a avaliação do regime. Na leitura desses resultados, há que se considerar a diferença dos cenários econômicos dos dois momentos: mesmo que, em 2014, o país ainda não atravessasse uma crise política e econômica como a iniciada em 2015, a percepção do cenário já era bem menos positiva do que em 2010, tanto em termos econômicos e sociais como em relação à avaliação de seus governantes. Nos dois anos, de todo modo, as avaliações dos executivos federais são centrais para explicar quão satisfeitos os cidadãos estão com a democracia. Ou seja, tal como nos resultados relatados por Seligson e Smith (2010), as percepções que os cidadãos têm sobre o modo como as autoridades dirigem o país e lidam com a diversidade de questões percebidas como socialmente prioritárias, entre as quais a gestão da economia e da crise, estão no âmago da avaliação do desempenho do regime democrático. Por outro lado, tendo em vista os resultados de Meneguello (2010), que apontaram para a dissociação entre a avaliação das instituições representativas e a satisfação com a democracia, o artigo buscou explorar os efeitos das primeiras como mecanismos que fazem a intermediação dos cidadãos com o regime democrático sobre a satisfação com o seu funcionamento. Ao seguir nessa direção, este estudo incorporou um aspecto ainda não mensurado nas análises sobre o desempenho do regime democrático no país, qual seja, a percepção sobre a dimensão normativa da [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] | Fabíola Brigante Del Porto 100 democracia representativa. Tendo em vista a experiência recente dos brasileiros com a democracia, explorar essa relação parece fundamental. Considerações finais Os resultados, embora ainda exploratórios, sugerem que medidas de apoio normativo à democracia adicionam capacidade explicativa à satisfação com o regime democrático. Nesta, além do apoio ao regime, chama atenção que ter uma identidade partidária esteja entre os fatores institucionais que mais se correlacionem com a chance de satisfação com a democracia através do tempo, o que deve ser explorado em estudos posteriores à luz das teorias da democracia representativa. 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[REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 103 103 MONTERO, José Ramon; GUNTHER, Richard; TORCAL, Mariano. Actitudes hacía la democracia en España: legitimidad, descontento y desafección. Revista Española de Investigaciones Sociológicas, v. 83, Sept. 1998. NORRIS, Pippa (org.). Critical citizens: global support for democratic governance. Oxford: Oxford University Press, 1999. Democratic Deficit: critical citizens revisited. Cambridge University Press, 2011. ______. Democratic Deficit: critical citizens revisited. Cambridge University Press, 2011. O’DONNELL, Guillermo. Democracia, agência e estado: teoria com intenção comparativa. São Paulo ______. Democratic Deficit: critical citizens revisited. Cambridge University Press, 2011. O’DONNELL, Guillermo. Democracia, agência e estado: teoria com intenção comparativa. São Paulo: Paz e Terra, 2011. f g y O’DONNELL, Guillermo. 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Vanderbilt University, 2010. HUMPETER, Joseph. Capitalismo, socialismo e democracia. Rio de Janeiro: Zahar, 1984. TÓKA, Gábor. Texto recebido em 15 de setembro de 2016. Aprovado em 15 de novembro de 2016. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Anexo Anexo 102 | Fabíola Brigante Del Porto Political support in East-Central Europe. In: KLINGEMANN, Hans-Dieter; FUCHS, Dieter (org.). Citizens and the State. Cambridge University Press, 1995. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] 104 104 | Fabíola Brigante Del Porto Definição das variáveis independentes utilizadas nas análises de regressões logísticas Os graus 1 e 2 foram recodificados na resposta ‘influencia’ e os graus 3 a 5 como ‘mais ou menos ou não influencia’. Em 2014, o 1 significa que o nosso voto NÃO influencia nada no que acontece no Brasil e 5 significa que o voto influencia muito no que acontece no Brasil. O que o senhor acha? Os graus 1 a 3 foram recodificados na resposta ‘mais ou menos ou não influencia’ e os graus 4 e 5 como ‘influencia’. Em 2014, o 1 significa que o nosso voto NÃO influencia nada no que acontece no Brasil e 5 significa que o voto influencia muito no que acontece no Brasil. O que o senhor acha? Em 2014, o 1 significa que o nosso voto NÃO influencia nada no que acontece no Brasil e 5 significa que o voto influencia muito no que acontece no Brasil. O que o senhor acha? Os graus 1 a 3 foram recodificados na resposta ‘mais ou menos ou não influencia’ e os graus 4 e 5 como ‘influencia’. Os graus 1 a 3 foram recodificados na resposta ‘mais ou menos ou não influencia’ e os graus 4 e 5 como ‘influencia’. 5. Apoio normativo à democracia Na sua opinião: 1.A democracia é sempre melhor que qualquer outra forma de governo; OU 2.Em algumas situações é melhor uma ditadura do que uma democracia. As categorias de resposta incluem ainda a opção espontânea “Tanto faz / Nenhuma das duas é melhor”. As respostas foram recodificadas em: ‘prefere democracia’ e ‘outras respostas’ (incluindo Ditadura, Tanto faz, Não sabe e Não respondeu). 6. Representação por partidos Existe algum partido que representa a maneira como o senhor pensa? Variável original dicotômica: ‘sim’ e ‘não’. 6. Representação por partidos Existe algum partido que representa a maneira como o senhor pensa? Variável original dicotômica: ‘sim’ e ‘não’. 7. Avaliação da situação econômica do país O sr. considera que a situação econômica atual do país está melhor, igual ou pior que há 12 meses? As respostas foram recodificadas em: ‘melhor’ e ‘igual/pior.’ 7. Avaliação da situação econômica do país O sr. considera que a situação econômica atual do país está melhor, igual ou pior que há 12 meses? As respostas foram recodificadas em: ‘melhor’ e ‘igual/pior.’ 8. Definição das variáveis independentes utilizadas nas análises de regressões logísticas Todas as variáveis independentes foram recodificadas como categóricas binárias (dummies), conforme descrição abaixo: 1. Avaliação do Governo/Executivo Federal Na sua opinião, de uma maneira geral o Governo XXX nos últimos 4 anos foi muito bom, bom, ruim ou péssimo? As respostas foram recodificadas nas respostas ‘avaliação positiva’(muito bom, bom) e ‘avaliação negativa’ (ruim, péssima). A resposta ‘regular’ (espontânea) foi considerada como positiva. 2. Avaliação das instituições representativas Para os três anos a variável é: Eu vou falar o nome de várias instituições e gostaria que o senhor dissesse se avalia a atuação de cada uma como ótima, boa, ruim ou péssima? (Instituições utilizadas na análise: Polícia; Justiça; Partidos políticos; Congresso). As respostas foram recodificadas nas respostas ‘avaliação positiva’(muito bom, bom) e ‘avaliação negativa’ (ruim, péssima). A resposta ‘regular’ (espontânea) foi considerada como positiva. 3. Avaliação de políticas e serviços públicos Vou citar algumas políticas e gostaria que o sr. dissesse o quanto está satisfeito com cada uma delas.(Políticas utilizadas na análise: "Controle da criminalidade"; "Diminuição das desigualdades sociais"; "Acesso do cidadão comum à justiça"; "Qualidade do ensino público"; "Acesso aos serviços de atendimento médico"; "Diminuição do desemprego". As respostas foram assim recodificadas: notas 0 a 4 - avaliação negativa e notas 5 a 10 – avaliação regular/ positiva. 3. Avaliação de políticas e serviços públicos Vou citar algumas políticas e gostaria que o sr. dissesse o quanto está satisfeito com cada uma delas.(Políticas utilizadas na análise: "Controle da criminalidade"; "Diminuição das desigualdades sociais"; "Acesso do cidadão comum à justiça"; "Qualidade do ensino público"; "Acesso aos serviços de atendimento médico"; "Diminuição do desemprego". As respostas foram assim recodificadas: notas 0 a 4 - avaliação negativa e notas 5 a 10 – avaliação regular/ positiva. 4. Percepção da accountability vertical Algumas pessoas dizem que o nosso voto influencia muito no que acontece no Brasil, outras dizem que o nosso voto NÃO influencia nada no que acontece no Brasil. Gostaria que o senhor desse uma nota de 1 a 5. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] Satisfação com a democracia entre os brasileiros no cenário recente (2002-2014) | 105 105 Em 2010, o 1 significa que o nosso voto influencia muito, e o 5 significa que o nosso voto NÃO influencia nada no que acontece no Brasil. O que o senhor acha? Definição das variáveis independentes utilizadas nas análises de regressões logísticas Grau de instrução Variável categorizada em diferentes níveis nos vários anos foi recodificada em: ‘Baixa/média escolaridade’=até Ensino Médio incompleto e ‘Elevada escolaridade’= pelo menos Ensino Médio completo. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] 106 | Fabíola Brigante Del Porto 106 | Fabíola Brigante Del Porto 106 | Fabíola Brigante Del Porto 9. Faixa etária A variável original ‘idade’ (contínua) foi categorizada em dois grupos: ‘até 29 anos (inclusive)’ e ‘30 anos ou mais’. 9. Faixa etária A variável original ‘idade’ (contínua) foi categorizada em dois grupos: ‘até 29 anos (inclusive)’ e ‘30 anos ou mais’. 10. Região Variável original REGIÃO categórica com 5 categorias de resposta - Norte,. Nordeste, Centro-Oeste, Sudeste e Sul - foi dicotomizada em ‘Região sudeste’ e ‘Outras’. 10. Região Variável original REGIÃO categórica com 5 categorias de resposta - Norte,. Nordeste, Centro-Oeste, Sudeste e Sul - foi dicotomizada em ‘Região sudeste’ e ‘Outras’. 10. Região 11. Cor Variável original COR categórica com 5 categorias de resposta - Branco, Preto, Pardo/Moreno, Amarelo, Indígena - foi dicotomizada em ‘Branco’ e ‘Não branco’. 11. Cor Variável original COR categórica com 5 categorias de resposta - Branco, Preto, Pardo/Moreno, Amarelo, Indígena - foi dicotomizada em ‘Branco’ e ‘Não branco’. [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016] [REVISTA DEBATES, Porto Alegre, v. 10, n. 3, p. 83-106, set.-dez. 2016]
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New insights into mechanisms of enhanced synaesthetic memory: Benefits are synaesthesia-type-specific
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New insights into mechanisms of enhanced synaesthetic memory: Benefits are synaesthesia-type-specific Katrin Lunke, Beat Meier* Institute of Psychology, University of Bern, Bern, Switzerland Katrin Lunke, Beat Meier* * beat.meier@psy.unibe.ch RESEARCH ARTICLE a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Lunke K, Meier B (2018) New insights into mechanisms of enhanced synaesthetic memory: Benefits are synaesthesia-type-specific. PLoS ONE 13(9): e0203055. https://doi.org/ 10.1371/journal.pone.0203055 Citation: Lunke K, Meier B (2018) New insights into mechanisms of enhanced synaesthetic memory: Benefits are synaesthesia-type-specific. PLoS ONE 13(9): e0203055. https://doi.org/ 10.1371/journal.pone.0203055 Editor: Lutz Ja¨ncke, University of Zurich, SWITZERLAND Abstract a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 The goal of this study was to test the nature of the memory advantage in synaesthesia. We compared four different types of synaesthetes (27 grapheme-colour, 21 sound-colour-, 25 grapheme-colour-and-sound-colour- and 24 sequence-space synaesthetes) to their matched controls. Recognition memory for three types of stimuli (music, words, colour) was tested. We anticipated a general advantage in memory for synaesthetes and potentially additional synaesthesia-specific benefits. The results showed a general advantage for synaesthesia. Further, a benefit for colour stimuli resulted for grapheme-colour syn- aesthetes and a benefit for music stimuli resulted for grapheme-colour-and-sound-colour synaesthetes, indicating synaesthesia-type specific effects. These results suggest different mechanisms for the explanation of the memory benefit for different types of synaesthesia such as synaesthesia-related colour expertise for grapheme-colour synaesthesia and addi- tional encoding opportunities for grapheme-colour-and-sound-colour synaesthesia. OPEN ACCESS Citation: Lunke K, Meier B (2018) New insights into mechanisms of enhanced synaesthetic memory: Benefits are synaesthesia-type-specific. PLoS ONE 13(9): e0203055. https://doi.org/ 10.1371/journal.pone.0203055 Inducer-specific advantage According to dual-coding theory the opportunity to encode a stimulus via two pathways increases the chances of remembering it compared to a stimulus that was coded only via one pathway [5]. The additional memory code (i.e., the synaesthetic concurrent) results in a stron- ger representation, additional retrieval cues, and accordingly, in a performance advantage for synaesthetes compared to non-synaesthetes. Naturally, different types of synaesthesia would have benefits in different tasks according to their inducer. Several group studies do support the hypothesis of an inducer-specific benefit. Simner, Mayo and Spiller [3] found superior mem- ory for inducer-related autobiographical and public dates in time-space synaesthetes. Rad- vansky, Gibson and McNerney [7] found superior memory performance for inducer-related words in grapheme-colour synaesthesia. In contrast, Rothen and Meier [8] did not find an inducer-related memory advantage in grapheme-colour synaesthetes in a free recall test of digit matrices. As, these studies did exclusively test memory for inducer-specific material in one single type of synaesthesia, they cannot inform whether potential benefits would occur for types of synaesthesia with different inducers. Introduction Synaesthesia is a rare phenomenon in which the perception of ordinary stimuli (referred to as inducers) triggers untypical experiences (referred to as concurrents). Many different types of inducer-concurrent pairings exist. For example, in grapheme-colour synaesthesia a digit (e.g., “5”) may trigger a specific colour experience (e.g., “blue). In sound-colour synaesthesia, music, tones and sounds trigger colour experiences. In sequence-space synaesthesia, sequences like days of the week or months elicit visuospatial representations. In case- and group studies grapheme-colour synaesthetes have shown cognitive benefits in many memory tasks (for reviews see [1, 2]). Copyright: © 2018 Lunke, Meier. 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. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. However, only very few studies have considered memory in other types of synaesthesia, and no study so far has used inducer- and concurrent-specific as well as synaesthesia-unrelated material [3],[4]. The goal of the present study was to systematically compare different types of synaesthesia with different inducer-concurrent pairings regarding a general, an inducer- and a concurrent-related advantage in memory. Theoretically, several mechanisms might lead to a synaesthetic memory advantage and these might differ in different types of synaesthesia. A Funding: This project was supported by the Swiss National Science Foundation, grant # 100014_149692. Competing interests: The authors have declared that no competing interests exist. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 1 / 17 Memory advantage for synaesthesia memory advantage for material related to the inducer would be consistent with dual-coding theory as the concurrent experience leads to an encoding via two pathways [5]. Another possi- ble explanation is the experience-driven expertise for materials of the synaesthetic domain that should be reflected in a memory advantage for stimuli related to inducer and/or concurrent. A third possibility is a general memory advantage through a broader and more connected semantic network in which information can be easily integrated [2],[6]. In the following we outline these three possible mechanisms and the evidence supporting each. Domain-specific advantage Another possible explanation for an advantage in memory for both inducer- and concurrent- related material is the specific expertise for the synaesthetic domain. Synaesthetes might bene- fit from easier encoding and processing of synaesthesia-related stimuli such as colours, or more generally, visually presented stimuli [6], [4], [9]. Additionally, according to the implicit bi-directionality of synaesthesia, an association also exists between the concurrent and the inducer. This association might provide additional retrieval cues on an implicit level for con- current-related stimuli as well [10], [11], [12], [13],[6], [14]. Such a domain-specific account is in line with results by Yaro and Ward [9], who found that grapheme-colour synaesthetes out- performed their control participants in the inducer-related Rey auditory-verbal learning task and in concurrent-related colour perception and colour recognition tasks. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 General advantage Neither dual-coding, implicit bi-directionality, nor domain-expertise can account for a benefit for materials completely unrelated to synaesthesia [15],[16],[17]. It is possible, that the richer world of experiences with cascadically triggered associations in a broader semantic network accounts for this seemingly independent benefit, cf. [18], [19]. Such an explanation would be consistent with evidence from structural brain imaging suggesting a different, hyper-con- nected network-organization [20] and complemented by findings of general differences in cognitive style [21]. Accordingly, the memory advantage in synaesthesia would not necessarily directly be related to inducer and concurrent but rather to wider changes in the synaesthetic brain, related to perception and encoding in general [22], [23], [6]. This theory is in line with several group studies. Rothen and Meier [17] for instance found that grapheme-colour synaesthetes outperformed their control participants in inducer- and concurrent-related as PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 2 / 17 Memory advantage for synaesthesia well as synaesthesia-unrelated tasks of the Wechsler Memory Scale. Gross, Neargarder, Cald- well-Harris and Cronin-Golomb[24] on the other hand found an advantage for grapheme-col- our synaesthetes only for a part of the inducer-related verbal and synaesthesia-unrelated tasks. These results rather support a general benefit but indicate that a benefit may only occur under certain circumstances. Pritchard, Rothen, Coolbear and Ward [16] tested recognition memory for shape-colour-location combinations. Grapheme-colour synaesthetes outperformed their control participants overall, strongest though when colour was the critical feature. This sup- ports a concurrent expertise explanation. Bankieris and Aslin [15] compared grapheme-colour synaesthetes performance in learning colour-shape pairings. Synaesthetes outperformed con- trols which supports a more general memory advantage. However, neither Pritchard et al. [16] nor Bankieris and Aslin [15] included any inducer-related tasks. Finally, Ward, Hovard, Jones and Rothen [4] used inducer-related, concurrent-related, and synaesthesia-unrelated memory tasks, based on words, non-words, scenes and abstract pic- tures (with and without colours), to compare grapheme-colour and lexical-gustatory synaesthetes. Grapheme-colour synaesthetes outperformed controls in all tasks, strongest for non-coloured fractals. Lexical-gustatory synaesthetes did not show any benefit. This speaks strongly against an inducer-specific benefit and supports a general advantage, but only for grapheme-colour synaesthetes. Further, it supports a mechanism related to coloured concur- rents that appears to boost visual perception. Most importantly, it suggests that different types of synaesthesia have different memory advantages. This is consistent with the observation that different types of synaesthetes show preferences for different cognitive styles [21]. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 General advantage To summarize, the reviewed results support a memory advantage for grapheme-colour and for time-space synaesthesia [3], [4]. However, they also implicate different benefits for differ- ent types of synaesthesia. At this point, no conclusion can be drawn which type of synaesthesia benefits from which of the aforementioned mechanisms–inducer-, concurrent- or domain- specificity or a general advantage. First of all, there is evidence that types of synaesthesia differ. Moreover, it is likely that types tested as grapheme-colour synaesthetes so far have been het- erogeneous as well. While some studies did not describe their sample further, other authors included grapheme-colour synaesthetes with colour experiences for auditory graphemes or such with colour experiences for printed graphemes. Still others tested synaesthetes with col- our experiences for sequential words like months [25], [26],[7], [9]. Some synaesthetes do asso- ciate their visual concurrents like colours or spatial arrangements and some do project them into space [27]. Additionally, many synaesthetes do not only show one distinct type of synaes- thesia but also other, partly less pronounced types. Synaesthetes with coloured concurrents show for instance a significantly higher prevalence for sequence-space synaesthesia [28], [29]. It is thus particularly difficult to create homogenous and distinctive groups of synaesthesia types to detect the possible source of an advantage through the material. Second, so far no study has included inducer-specific, concurrent-specific and unrelated material in a comparable way for different types of synaesthesia. In the present study, we thus compared four types of synaesthesia and matched controls for inducer-related, concurrent- related and synaesthesia-unrelated material in a recognition memory task. Grapheme-colour synaesthetes can be considered as the standard type of synaesthesia, sound-colour synaesthetes are based on a different inducer and grapheme-colour-and-sound-colour synaesthetes repre- sent a multiple type of synaesthesia with different modalities. Additionally, we included sequence-space synaesthetes who have neither graphemes nor sound as inducer, but sequences, and no coloured concurrents, but spatial representations. All participants com- pleted three episodic recognition memory tests, that is, one for words, one for music, and one for colour stimuli. Fig 1 illustrates the extent of the expected advantage compared to matched controls according to the three theories described above. As evidence for an inducer-specific PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 3 / 17 Memory advantage for synaesthesia Fig 1. Note. GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Verbal IQ was tested with a standardized vocabulary test [31]. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 https://doi.org/10.1371/journal.pone.0203055.t001 Participants We recruited 102 synaesthetes who had completed the Synaesthesia-Check on our website (www.synaesthesie.unibe.ch) previously, and who had reported consistent colours for words, digits, letters, musical tones, instruments or melodies and/or spatial representations for digits, days, months or years. 102 healthy control-participants matched for age, gender and education were recruited, cf. [30]. The study was approved by the Ethics committee of the Human Sci- ences Faculty of the University of Bern (#2013-1-272903). Five participants experienced tech- nical problems during different tasks and were therefore eliminated together with their matched controls resulting in a sample size of 97 synaesthetes and 97 control participants. Of the synaesthetes, 27 were grapheme-colour synaesthetes (25 female and 2 male), 21 were sound-colour- (14 female and 7 male), 25 were grapheme-colour-and-sound-colour (21 female and 4 male) and 24 sequence-space synaesthetes (23 female and 1 male). Nine synaesthetes and nine controls were left handed. Table 1 shows the demographic characteristic of all groups. One-factorial ANOVAs showed no difference between synaesthetes and controls for age, F (1, 192) = 0.04, MSE = 288.90, p = .853, ηp 2 < .01 and years of primary education F(1, 192) = 1.34, MSE = 2.50, p = .248, ηp 2 < .01. However, there was an effect of Verbal IQ which was due to sequence-space synaesthetes who showed a higher score than their matched controls (t(46) = 2.29, SE = 2.72, p = .014). Prior to participation in the laboratory, participants with colour experiences for graphemes filled out an on-line measurement of consistency. They were presented with 36 black on white graphemes (A-Z, 0–9) in a random order and instructed to choose a colour out of 13 (black, dark blue, brown, dark green, grey, pink, purple orange, red, white, light blue, light green, yel- low) or indicate no colour [32], [29]. The mean number of consistent digits and letters was M = 25.19 (SD = 6.97) which is above the cut-off of 20 used by Simner et al. [29] and Rothen and Meier [32]. Two participants did not fill out the on-line measurement. Six of the 52 partic- ipants with grapheme-colour synaesthesia scored lower than 20 consistent digits and letters. Notably, three of the remaining six participants had only digit-colour or word-colour synaes- thesia. However, we did not exclude any participant as we relied on the subjective experiences of the participants. General advantage Expected results for the three possible mechanisms as mean differences between synaesthetic performance and performance of matched controls: a) an inducer-specific, b) a domain-specific and c) a general memory advantage of synaesthetes. GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound- colour synaesthetes; SS = Sequence-Space synaesthetes. Fig 1. Expected results for the three possible mechanisms as mean differences between synaesthetic performance and performance of matched controls: a) an inducer-specific, b) a domain-specific and c) a general memory advantage of synaesthetes. GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound- colour synaesthetes; SS = Sequence-Space synaesthetes. https://doi.org/10.1371/journal.pone.0203055.g001 advantage we expected a higher performance for grapheme-colour and grapheme-colour-and- sound-colour synaesthetes regarding word stimuli and for sound-colour synaesthetes and grapheme-colour-and-sound-colour synaesthetes regarding musical stimuli. As evidence for a advantage we expected a higher performance for grapheme-colour and grapheme-colour-and- sound-colour synaesthetes regarding word stimuli and for sound-colour synaesthetes and grapheme-colour-and-sound-colour synaesthetes regarding musical stimuli. As evidence for a Table 1. Age, education and verbal intelligence of each type of synaesthesia and the respective control group. Synaesthetes Controls M (SD) M (SD) age 42.22 (17.81) 42.78 (18.56) GC years of primary education 11.93 (1.54) 12.07 (1.85) verbal IQ 111.04 (9.09) 107.82 (11.12) age 36.43 (19.11) 37.38 (20.16) SC years of primary education 12.48 (1.21) 12.95 (1.72) verbal IQ 111.76 (10.07) 109.90 (9.54) age 32.44 (13.34) 32.80 (13.29) GCSC years of primary education 11.46 (1.68) 12.54 (1.54) verbal IQ 106.92 (6.56) 107.52 (7.54) age 34.46 (15.56) 34.46 (15.97) SS years of primary education 12.71 (1.30) 12.06 (1.34) verbal IQ 113.17 (9.09) 106.96 (9.71) Table 1. Age, education and verbal intelligence of each type of synaesthesia and the respective control group. 4 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Memory advantage for synaesthesia domain-specific advantage we expected a higher performance for grapheme-colour-, sound- colour- and grapheme-colour-and-sound-colour synaesthetes regarding coloured stimuli and for their inducing stimuli respectively. If synaesthesia would show a general memory advan- tage, we expected higher performance in all types of stimuli. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Participants Notably, a re-analysis without these three participants gave the same pat- tern of results. For sound-colour synaesthesia, we originally considered using the Eagleman battery [33]. However, we noticed that in this battery, using a simple strategy (low tones/big instrument -> dark colours; high tones/small instruments -> bright colours) leads to a high consistency score (passing synaesthesia criterion). Moreover, sound-colour synaesthesia is a very heteroge- neous phenomenon in which for some people pitch relates to colours, for others timbre relates to colours, for others tone intervals relate to colours, etc.. Thus, we decided to rely on the sub- jective self-reported experiences. For sequence space synaesthesia, participants who experienced spatial representations for sequences were instructed to draw these representations once at the beginning and once at the end of the experiment on-site (about 2h later). Drawings were categorized by an independent rater regarding consistency and complexity to confirm synaesthesia. One synaesthete was PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 5 / 17 Memory advantage for synaesthesia rated as inconsistent. However, this participant had indicated where variations occur in her experiences and was consistent in some other. We thus did not exclude her. At the beginning of the laboratory session, both synaesthetes and control participants were asked again whether they experienced any kind of synaesthesia. If any synaesthetic experiences were reported in addition to those described in the questionnaire, participants were–if possi- ble–tested for consistency and either reassigned or excluded. If several types of synaesthesia were present, participants were asked which they would describe as the main type of synaes- thesia. Of the grapheme-colour synaesthetes, thirteen reported having additional types of syn- aesthesia (sequence-space, other: person-smell and situation-smell). One grapheme-colour synaesthete was recategorised as grapheme-colour-and-sound-colour synaesthete. One control participant was recategorised as grapheme-colour synaesthete. Of the sound-colour synaesthetes, thirteen reported additional types of synaesthesia (sequence-space, grapheme- colour, other: ticker-tape, touch-colour, smell-form, two person/memory-colour, taste-colour/ pictures). Three grapheme-colour-and-sound-colour synaesthetes were recategorised as sound-colour synaesthetes. Moreover, one control participant was recategorised as sound-col- our synaesthete. Of the grapheme-colour-and-sound-colour synaesthetes, fourteen reported additional types of synaesthesia in the laboratory (sequence-space, other: ticker-tape, daytime- feeling, pain-colour, scene-taste/smell, sound-haptic). Three grapheme-colour synaesthetes were recategorised as grapheme-colour-and-sound-colour synaesthetes. Of the sequence- space synaesthetes, three reported additional types of synaesthesia in the laboratory (one grapheme-colour, one grapheme-colour-and-sound-colour, one person/experience-colour). One grapheme-colour and one grapheme-colour-and-sound-colour synaesthete were recate- gorised as sequence-space synaesthetes. Four control participants were recategorised as sequence-space synaesthetes. Participants To obtain a medium effect size as reported in previous research, e.g. [17], for a repeated measures ANOVA with a three-levels within-subjects factor and 1-β = .80, the GPower analy- sis proposed 19.13 participants per group [34]. We aspired to test at least 20 participants per group. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Procedure Participants received a brief information about synaesthesia and signed a consent form. In the course of the acquisition of demographic data, synaesthetes who experience spatial representa- tions for sequences sketched their representations. In the study phase, participants were first presented with a list of words on the screen one at the time. In addition to each word, a colour palette with 13 different colours was presented and the participant was instructed to select the colour that goes best with the particular word. Words were presented in randomized order for each participant. After a colour was selected the next word appeared immediately. For the music study phase, participants were asked to put on headphones. They were presented with short pieces of music for 10 sec each and were instructed to rate on a seven-point scale how much they liked it. They were also asked whether they knew this particular piece of music immediately after each stimulus. Musical pieces were presented in randomized order for each participant. For the colour study phase, participants were presented with coloured patterns for 3 seconds each and they were asked to rate how much they liked each pattern on a seven-point Likert scale. Colour patterns were presented in randomized order for each participant. The three study phases were always fulfilled in the same order: words–music–pictures. After a filled retention interval of approximately 60 minutes, including the vocabulary test [31], the memory test phase began. In the word recognition test phase, words were presented, one at the time, in randomized order for each participant at the center of the screen, in black on a white background. Participants were informed that some of the words were old words from the study phase and some were new words not presented before. They were instructed to indicate whether the word was old or new. After a “new” decision, the next word appeared immediately. An “old” decision was given by pressing “b” and a “new” decision by pressing “n”. After an “old” decision, participants were immediately asked to give a Remember/Know judgement. They were instructed to give a “remember” response when they were able to recol- lect the word from the study phase and to give a “know” response when they were not able to recollect the word, but nevertheless believed that they had seen it in the study phase. Apparatus On-site, participants were tested under controlled light conditions with an 85lux/watt lamp with 6400 calvin colour temperature and two standard interior lamps. Stimuli were presented with E-prime 1.2 (https://www.pstnet.com) on a standard 17 inch flat screen. Answers were given on a standard keyboard and sound was delivered via standard Sennheiser stereo head- phones. Audio output was set at a comfortable level for the participant and remained unchanged during data collection. For one participant headphones were replaced by speakers due to her sensitivity of the ears. Material The pictures were presented cen- tred on a white screen (50% height x 50% width) in the study as well as the recognition phase. Verbal intelligence. To assess verbal intelligence, a standardized vocabulary test was used. It consists of 42 trials, each composed of one target word and five distractor pseudo-words and the participant has to select the real world [31]. Material Word recognition. The word material was composed according to an earlier study [35] and consisted of high-frequency and low-frequency words, all concrete nouns selected from the vocabulary database of the University of Leipzig (http://wortschatz.uni-leipzig.de/). Two counter-balanced study and test lists were constructed. Twenty-four words of each frequency category were used in the study list together with 19 filler words (days and months), the remaining 24 words of each category were used as lures in the recognition test. Mean word- length was 5.42 letters. In the study phase, words were presented in a 32 point black Arial font on a white rectangle. A chart of colours was presented with every word. Each consisted of the 10 colours red, navy, yellow, green, black, white, light blue, purple, pink and brown, illustrated as 2x1.2cm big squares, arranged in an upright rectangle. In the recognition phase, words were presented in an 18 point courier new font centred on a white background. Music recognition. Each piece of music was selected from unfamiliar, rare recordings. They comprised music styles such as Classic, Jazz, Rock, Pop, Metal, Chinese, Indian, and Swiss folklore. Ten sec wav-files were cut. Two counter-balanced study and test lists were con- structed. Twenty-four pieces were used in the study list, 24 additional pieces were used as lures in the recognition test. Loudness was set to a comfortable level for the participants. Colour recognition. Colour patterns were selected for colour recognition. Half were selected from a synaesthesia catalogue (International Congress on Synesthesia, Science and PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 6 / 17 Memory advantage for synaesthesia Art, Granada, 2009) and half of the patterns were Mondrian style pictures, each consisting of four differently coloured squares. Two counter-balanced study and test lists were constructed. Twenty-four patterns (twelve of each category) were used in the study list, 24 patterns (twelve of each category) were used as lures in the recognition test. The pictures were presented cen- tred on a white screen (50% height x 50% width) in the study as well as the recognition phase. Art, Granada, 2009) and half of the patterns were Mondrian style pictures, each consisting of four differently coloured squares. Two counter-balanced study and test lists were constructed. Twenty-four patterns (twelve of each category) were used in the study list, 24 patterns (twelve of each category) were used as lures in the recognition test. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Memory advantage for synaesthesia stimulus and key 2 whenever they had the feeling they remembered the stimulus. After a response was made, the next word appeared. In the music recognition test phase, participants were again asked to put on headphones. They were played pieces of music for 10 sec each and they were informed that some of the pieces had been played before in the study phase (old pieces) and some not (new pieces). The pieces were presented in randomized order for each participant. They were instructed to indi- cate whether a piece was old or new. Immediately after an “old” decision, participants were asked to give a Remember/Know judgement similar as in the word-recognition phase. In the colour recognition test, coloured patterns were presented, one at the time, in ran- domized order at the center of the screen. Participants were informed that some of the patterns were old patterns from the study phase and some were new patterns not presented before. Col- our patterns were presented in randomized order for each participant. They were instructed to indicate whether a pattern was old or new. Immediately after an “old” decision, participants were asked to give a Remember/Know judgement as in the word-recognition phase. After the three tests were completed, sequence-space synaesthetes were asked to draw their sequences for a second time. Statistical analysis Alpha was set at .05 for all analyses. Analyses were primarily performed in SPSS [36]. If homo- geneity of variances was violated Greenhouse-Geisser corrected values are reported. In order to be able to interpret non-significant effects between synaesthetes and controls, Bayesian sta- tistics was calculated using JASP [37]. Between-subject factors were synaesthesia (yes/no) with two levels and type of synaesthesia (grapheme-colour, sound-colour, grapheme-colour-and-sound-colour, sequence-space) with four levels. Within-subjects factor was type of stimuli (words, music, colours) with three levels. Age differed between types of synaesthesia and was thus included as a covariate. To assess recognition for words, music and colours, hits and false alarms were assessed and the proportions of recognition (Pr) were computed by individually subtracting false alarms from hits. This score reflects the two-high-threshold model of recognition in which old items are correctly categorised as old when they exceed the recognition threshold and new items are wrongly categorised as old when they exceed the recognition threshold [38]. For an additional visualisation of performance differences between synaesthetes and non-synaesthetes, we z- transformed Pr scores for each type of synaesthesia and their controls separately and then sub- tracted scores of controls from scores of synaesthetes in order to provide a depiction that is comparable to the expected results in Fig 1. As measurement of response bias, C was computed as -0.5  (zHits + zFalseAlarms) [39]. Remember/Know judgements were analysed as estimates of recollection and familiarity according to the formula: Recollection = [(Remember old −Remember new)/(1 −Remember new)]; Familiarity = [z(Familiarity old) −z(Familiarity new)], with Familiarity old = [Know old/(1 −Remember old)] and Familiarity new = [Know new/(1 −Remember new)] by Yoneli- nas, Kroll, Dobbins, Lazzara and Knight [40]. Extreme values in hits and false alarms (e.g. 0, 24, 48) were adjusted by adding 0.5 to values of 0 and substracting 0.5 from values of 24 or 48 respectively before the proportion was calculated [41]. Procedure They were instructed to press key 1 after each response they had felt they exactly remembered the PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 7 / 17 Sound-colour synaesthetes No main effect resulted for synaesthesia (yes/no), F(1, 39) = 1.22, MSE = .04, p = .276, ηp 2 = .03 and no interaction between synaesthesia (yes/no) and type of stimuli F(2, 78) = 0.32, MSE = .03, p = .726, ηp 2 = .01. The covariate age produced a main effect, F(1, 39) = 21.18, MSE = .04, p < .001, ηp 2 = .35 but did not interact. Bayesian t-tests confirmed these results by showing evi- dence for the null hypothesis for musical stimuli, BF10 = 0.31. For colour stimuli, BF10 = 0.75 and word stimuli, BF10 = 0.39 results were inconclusive. General memory performance The results are presented in Fig 2. We conducted a 2x4x3 repeated measures ANCOVA with the between-subject factors synaesthesia (yes/no), type of synaesthesia and the within-subjects PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 8 / 17 Memory advantage for synaesthesia PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 9 / 17 Memory advantage for synaesthesia Fig 2. Recognition memory performance (Pr) for musical stimuli, word stimuli and colour stimuli. GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Error bars display standard errors. https://doi.org/10.1371/journal.pone.0203055.g002 factor type of stimuli. Age was included as covariate. Dependent variable was memory perfor- mance calculated as Pr. A significant main effect of synaesthesia (yes/no) F(1, 185) = 5.87, MSE = .03, p = .016, ηp 2 = .03 occurred as well as a two-way interaction between type of synaesthesia and type of stimuli, F(5.66, 349.28) = 2.21, MSE = .03, p = .046, ηp 2 = .04 and a three-way inter- action between synaesthesia (yes/no), type of synaesthesia and type of stimuli F(5.66, 349.28) = 3.14, MSE = .03, p = .006, ηp 2 = .05. The covariate age produced a main effect, F(1, 185) = 65.29, MSE = .03, p < .001, ηp 2 = .26 and interacted with type of stimuli, F(1.89, 349.28) = 6.17, MSE = .03, p = .003, ηp 2 = .03. We addressed the three-way interaction between synaesthesia (yes/no), type of synaesthesia and type of stimuli by separating the analysis for type of synaesthe- sia which also allowed us to see for synaesthesia specific differences in stimuli that act as inducer or concurrent. Four separate ANCOVAs including synaesthesia (yes/no) as between- subject factor, type of stimuli as within-subject factor and age as covariate were conducted. In order to specifically illustrate the effects of synaesthesia, we plotted the difference of z- transformed on recognition memory performance in Fig 3 to provide a direct opportunity for visual comparison for the theoretical predictions outlined in Fig 1. An analysis including intel- ligence as a covariate is provided in the supporting information. Grapheme-colour synaesthetes No main effect resulted for synaesthesia (yes/no), F(1, 51) = 0.60, MSE = .03, p = .441, ηp 2 = .01. An interaction occurred between synaesthesia (yes/no) and type of stimuli F(2, 102) = 6.81, MSE = .02, p = .002, ηp 2 = .12. The covariate age produced a main effect, F(1, 51) = 18.08, MSE = .03, p < .001, ηp 2 = .26 but did not interact. Post-hoc tests showed that grapheme-colour synaesthetes had an advantage for colour stimuli, t(52) = 2.32, SE = .04, p = .012, d = 0.63 and for music, t(52) = 1.69, SE = .05, p = .049, d = 0.46 and a disadvantage for words, t(40.29) = -1.85, SE = .05, p = .036, d = -0.50. Grapheme-colour-and-sound-colour synaesthetes No main effect resulted for synaesthesia (yes/no), F(1, 47) = 1.74, MSE = .04, p = .194, ηp 2 = .04. An interaction occurred between synaesthesia (yes/no) and type of stimuli F(1.68, 78.70) = 3.70, MSE = .03, p = .036, ηp 2 = .07. The covariate age produced a main effect, F(1, 47) = 12.59, MSE = .04, p = .001, ηp 2 = .21 but did not interact. Post-hoc tests showed that grapheme-col- our-and-sound-colour synaesthetes had a significant advantage for music stimuli, t(48) = 2.48, SE = .05, p = .009, d = 0.70 but not for words, t(48) = 1.14, SE = .07, p = .131, d = 0.32 or col- ours, t(48) = -1.41, SE = .04, p = .082, d = -0.40. Results of Bayesian t-tests regarding colour sti- muli, BF10 = 0.64 and word stimuli, BF10 = 0.48 were inconclusive. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 10 / 17 Memory advantage for synaesthesia Fig 3. Difference of z-transformed recognition (Pr) of synaesthetes and controls. Sound-colour- and sequence- space synaesthetes show a general advantage. Grapheme-colour-and-sound-colour synaesthetes show an inducer- specific advantage. Grapheme-colour synaesthetes show rather a concurrent-related advantage. GC = Grapheme- colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Error bars display standard errors. Fig 3. Difference of z-transformed recognition (Pr) of synaesthetes and controls. Sound-colour- and sequence- space synaesthetes show a general advantage. Grapheme-colour-and-sound-colour synaesthetes show an inducer- specific advantage. Grapheme-colour synaesthetes show rather a concurrent-related advantage. GC = Grapheme- colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Error bars display standard errors. https://doi.org/10.1371/journal.pone.0203055.g003 Sequence-space synaesthetes No main effect resulted for synaesthesia (yes/no), F(1, 45) = 2.51, MSE = .03, p = .120, ηp 2 = .05 and no interaction between synaesthesia (yes/no) and type of stimuli F(2, 90) = 0.06, MSE = .02, p = .938, ηp 2 < .01. The covariate age produced a main effect, F(1, 45) = 12.47, MSE = .03, p = .001, ηp 2 = .22 and interacted with type of stimuli, F(2, 90) = 11.30, MSE = .02, p < .001, ηp 2 = .20. Bayesian t-tests gave inconclusive results for colour stimuli, BF10 = 0.56, for word stimuli, BF10 = 0.50 and for musical stimuli, BF10 = 0.34. Note. GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Sound-colour- and sequence-space synaesthetes show a general advantage. https://doi.org/10.1371/journal.pone.0203055.t002 https://doi.org/10.1371/journal.pone.0203055.t002 Response bias To assess whether synaesthetes differ in their general tendency to respond yes, response bias was computed as C and included as dependent variable in a mixed ANCOVA with between- subjects factors synaesthesia (yes/no) and type of synaesthesia [39]. The within-subjects factor was type of stimuli and the covariate age. No main effect occurred for synaesthesia (yes/no), F (1, 185) = 0.07, MSE = .92, p = .792, ηp 2 < .01 and type of synaesthesia, F(3, 185) = 0.31, MSE = .92, p = .819, ηp 2 < .01 and no interaction between the two, F(3, 185) = 1.07, MSE = .92, p = .362, ηp 2 = .02 or between synaesthesia (yes/no) and type of synaesthesia and type of stimuli, F (6, 370) = 0.15, MSE = .44, p = .990, ηp 2 < .01. A main effect occurred for type of stimuli, F(2, 370) = 11.29, MSE = .44, p < .001, ηp 2 = .06. Type of stimuli interacted with the covariate age, F (2, 370) = 13.71, MSE = .44, p < .001, ηp 2 = .07. Bayesian t-tests gave evidence for the null hypothesis for grapheme-colour synaesthetes regarding all types of stimuli, all BF10 between 0.27 and 0.32 and for sound-colour synaesthetes regarding music, BF10 = 0.33 and colours, BF10 = 0.31. All other results were inconclusive, all BF10 between 0.34 and 0.67. Table 2. Estimates of recollection and familiarity for each type of synaesthesia and stimuli. GC Controls SC Controls GCSC Controls SS Controls M (SD) M (SD) M (SD) M (SD) M (SD) M (SD) M (SD) M (SD) music recollection 0.33 (0.21) 0.29 (0.16) 0.38 (0.16) 0.24 (0.21) 0.40 (0.22) 0.32 (0.21) 0.33 (0.19) 0.28 (0.18) familiarity 0.36 (1.24) -0.17 (1.16) -0.26 (1.41) -0.14 (1.78) 0.29 (1.15) -0.35 (0.84) 0.11 (1.25) 0.07 (1.15) words recollection 0.47 (0.26) 0.58 (0.16) 0.69 (0.20) 0.63 (0.15) 0.58 (0.27) 0.58 (0.28) 0.68 (0.18) 0.62 (0.21) familiarity -0.22 (1.21) -0.10 (0.74) 0.16 (1.32) -0.09 (1.25) 0.32 (0.93) -0.16 (1.03) 0.13 (0.75) 0.00 (0.88) colours recollection 0.51 (0.16) 0.45 (0.13) 0.53 (0.18) 0.40 (0.15) 0.47 (0.17) 0.49 (0.17) 0.51 (0.14) 0.48 (0.15) familiarity 0.38 (1.07) -0.12 (0.92) -0.06 (1.11) -0.37 (1.00) -0.12 (1.16) 0.21 (0.97) 0.17 (1.00) -0.19 (0.93) Table 2. Estimates of recollection and familiarity for each type of synaesthesia and stimuli. Note. Recollection and familiarity To assess whether synaesthetes differ in retrieval strength we analysed recollection and famil- iarity as suggested by Yonelinas et al. [40]. We conducted two separate repeated measures ANCOVAs–one for recollection and one for familiarity–with between-subject factors synaes- thesia (yes/no) and type of synaesthesia (Table 2). The within-subjects factor was type of stimuli and the covariate age. For estimates of recollection, a main effect occurred for synaesthesia (yes/no), F(1, 185) = 5.41, MSE = .05, p = .021, ηp 2 = .03 but not for type of synaesthesia, F(3, 185) = 0.44, MSE = .05, p = .725, ηp 2 < .01 and no interaction between the two, F(3, 185) = 1.53, MSE = .05, p = .207, ηp 2 = .02. An interaction occurred between type of synaesthesia and type of stimuli, F(5.23, 322.73) = 2.92, MSE = .03, p = .012, ηp 2 < = .05. The covariate age, pro- duced a main effect, F(1, 185) = 21.74, MSE = .05, p < .001, ηp 2 = .11 and interacted with type of stimuli, F(1.74, 322.72) = 5.99, MSE = .03, p = .004, ηp 2 = .03. Post-hoc tests showed for grapheme-colour synaesthetes significantly higher recollection for colours, t(52) = 1.74, SE = .04, p = .044, d = 0.47 and lower recollection for words, t(43.26 = -1.81, SE = .06, p = .04, d = -0.49. For sound-colour synaesthetes they showed a significantly higher recollection for colour stimuli, t(40) = 2.40, SE = .05, p = .011, d = 0.74 and music, t(40) = 2.44, SE = .06, p = .010, d = 0.75. Bayesian t-tests showed that for grapheme-colour synaesthetes the results for music were inconclusive, BF10 = 0.35. For sound-colour synaesthetes the result for words was incon- clusive, BF10 = 0.51. For grapheme-colour-and-sound-colour synaesthetes evidence for the null hypothesis occurred regarding words, BF10 = 0.28 and colours, BF10 = 0.30. Results regarding music were inconclusive, BF10 = 0.52. For sequence-space synaesthetes results were inconclusive, all BF10 between 0.40 and 0.47. For familiarity, a main effect occurred for synaesthesia (yes/no), F(1, 185) = 4.28, MSE = 1.55, p = .040, ηp 2 = .02 and none for type of synaesthesia, F(3, 185) = 0.80, MSE = 1.55, p = .497, ηp 2 = .01 and no interaction between the two, F(3, 185) = 0.13, MSE = 1.55, p = .945, ηp 2 < .01 (Table 2). Response bias GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space synaesthetes. Sound-colour- and sequence-space synaesthetes show a general advantage. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 11 / 17 Memory advantage for synaesthesia Recollection and familiarity The covariate age, produced a main effect, F(1, 185) = 20.19, MSE = 1.55, p < .001, ηp 2 = .10 and interacted with type of stimuli, F(2, 370) = 7.30, MSE = .94, p = .001, ηp 2 = .04. Post-hoc t-tests showed a significantly higher familiarity for grapheme-colour synaesthetes regarding colours, t(52) = 1.87, SE = .27, p = .034, d = 0.51 and for grapheme-col- our-and-sound-colour synaesthetes regarding music, t(43.79) = 2.24, SE = .28, p = .015, d = 0.63 and words, t(48) = 1.72, SE = .28, p = .047, d = 0.49. Bayesian t-tests showed for graph- eme-colour synaesthetes evidence for the null hypothesis regarding words, BF10 = 0.30 and inconclusive results regarding music, BF10 = 0.80. For sound-colour synaesthesia there was evi- dence for the null hypothesis regarding music, BF10 = 0.31 and inconclusive results for words, BF10 = 0.35 and colours, BF10 = 0.44. For grapheme-colour-and-sound-colour synaesthetes there was inconclusive evidence for the effects of synaesthesia (yes/no) regardingr colours, BF10 = 0.46. For sequence-space synaesthetes there was evidence for the null hypothesis regarding musical stimuli, BF10 = 0.29 and words, BF10 = 0.32. Results were inconclusive regarding colours, BF10 = 0.58. General advantage Across types of stimuli, synaesthetes showed higher recognition memory than the respective control groups. This general advantage was small but consistent for all types of synaesthesia. A general advantage would be in line with earlier research that found a memory advantage for synaesthesia-unrelated material, e.g. [24], [7], [17]. Overall synaesthetes did show significantly higher estimates of recollection based responses. This indicates richer memory traces and more retrieval strength for synaesthetes, [35], [42] and is in line with findings by Chin and Ward who found significantly more recollection for autobiographic memories in grapheme- colour synaesthetes [43]. These results support the hypothesis that not (only) the synaesthetic experience itself is boosting memory, but a more general cognitive difference expressed also in cognitive style and neural connectivity. Synaesthetes are supposed to have a broader, more connected semantic network. These differences are related to more efficient integration, prop- agation and processing of information. They are hypothesized to having a more associative semantic memory with richer representations and easier access. This accounts for an advan- tage beyond synaesthesia related material, [20], [2], [21], [44]. Discussion The goal of this study was to test the nature of the memory advantage in synaesthesia. Towards this goal, recognition memory performance of four different types of synaesthesia (grapheme- colour, sound-colour, grapheme-and-sound-colour, sequence-space) were compared to matched controls for three different types of stimuli, that is, inducer- or concurrent-specific or synaesthesia-unrelated. The results support an advantage for grapheme-colour synaesthetes for concurrent-related colour stimuli, also reflected in significantly higher recollection. In con- trast, grapheme-colour-and-sound-colour synaesthetes showed a significant benefit for PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 12 / 17 Memory advantage for synaesthesia inducer specific sound-stimuli. These results suggest that different types of synaesthesia, regardless of overlapping inducer-concurrent pairings, rely on different mechanisms that sup- port their specific memory advantage. PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Conclusion Overall, this study shows a general memory advantage for different types of synaesthesia. An inducer-specific benefit was present for grapheme-colour-and-sound-colour synaesthetes, possibly through elevated activation in the semantic network. A concurrent-specific benefit was present for grapheme-colour synaesthetes, based on higher recollection, possibly related to enhanced expertise in colour processing. Interestingly, no evidence for a domain-specific benefit emerged in any condition. The fact that the memory benefit of different types of synaesthesia is due to different mech- anisms implicates strongly that it is important to investigate further types of synaesthesia in order to advance our understanding rather than generalize from one specific type. Moreover, it is also necessary to distinguish monotypic (e.g., sound-colour) from multiple types (e.g. grapheme-colour-and-sound-colour synaesthetes). Memory advantage for synaesthesia is in line with Ward et al. [4] who found an advantage for grapheme-colour but not lexical-gus- tatory synaesthetes. That any other type of synaesthesia showed an advantage is partly in line with findings by Simner et al. [3] who found that sequence-space synaesthetes showed advan- tages only for stimuli related to their type of synaesthesia. The difference between grapheme-colour-and-sound-colour synaesthetes and grapheme- colour synaesthetes may be due to the higher co-occurrence of several types of synaesthesia. Previous studies have revealed that subsamples with multiple types of synaesthesia differed from those with fewer or only one type. Meier and Rothen [21], for example, found that synaesthetes with multiple types differed in their cognitive style. Ward, Thompson-Lake, Ely and Kaminski [44] found that the number of types of synaesthesia correlated positively with convergent creative thinking. Especially the latter finding supports the view of a broader semantic network which is crucial for creative thinking and was also anticipated with inducer- specific memory benefits [6, 47].The inducer-specific advantage for musical stimuli in graph- eme-colour-and-sound-colour synaesthetes could therefore imply that multiple types of syn- aesthesia do show the broader kind of semantic network hypothesized for synaesthetes in general [19]. However, this would suggest that monotypic types of synaesthesia or those for whom inducer and concurrent activate the same modality do not show this broader network activation but rely on other mechanisms such as enhanced colour processing. As stated in the participant section, a clear division between types of synaesthesia is very hard to obtain and our sample of monotypic synaesthetes contains participants who stated other, presumably less prominent types of synaesthesia when asked in the laboratory. However, in our sample, graph- eme-colour-and-sound-colour synaesthetes are those with multiple synaesthetic experiences involving different modalities. In sum, these results support synaesthesia specific stronger memory advantages which are related to inducer or concurrent depending on the type of syn- aesthesia. Furthermore, the result that no type showed a significant advantage for words is in line with Teichmann, Nieuwenstein and Rich [14], who suggested that additional synaesthetic information only aids memory if it is less abstract than the stimulus to be learned. Alike many other studies on synaesthesia, we cannot rule out a motivational difference between synaesthetes and controls. However, we used an incidental study phase to reduce this possibility. Moreover, the particular pattern of results does not suggest a motivational bias. Specific advantage We also found an interaction between synaesthesia (yes/no), type of synaesthesia and type of sti- muli, indicating an inducer-specific benefit for musical stimuli in grapheme-colour-and-sound- colour synaesthetes and a significant concurrent-specific benefit for colour stimuli in grapheme- colour synaesthetes. These results speak against a domain-specific or a general advantage. They are partly in line with earlier research that found differences between different types of synaesthe- sia [4]. However, we had rather expected consistent inducer- and/or concurrent-specific benefits for those types of synaesthetes who share a certain concurrent. Thus, if any, we anticipated the same specific benefits for grapheme-colour-, for sound-colour and for grapheme-colour-and- sound-colour synaesthetes, for instance, an advantage for visually presented word and colour sti- muli. However, word stimuli led to the smallest and statistically non-significant benefit. Further, we had expected a possible colour-specific advantage would be present in all colour-synaesthetes, but only grapheme-colour synaesthetes showed a benefit. These are interesting findings as they indicate different mechanisms for different types of synaesthesia. The enhanced recognition memory performance of grapheme-colour synaesthetes for col- our stimuli occurred together with significantly higher recollection. This result may indicate that their memory traces were richer and retrieval strength was higher compared to their matched controls. Recollection is generally linked to learning of novel items and associations including context information [45], [46], [42]. According to models of recollection and famil- iarity it reflects storage in the episodic memory [42]. Thus, our results may imply that enhanced processing of colour stimuli leads to more efficient, controlled encoding, stronger memory traces in episodic memory and higher retrieval strength. This would be in line with findings by Pritchard et al. [16] who found a certain expertise for visual stimuli and with Yaro and Ward [9] and Rothen and Meier [17] who found better encoding and retention for visual stimuli. It would also be congruent with findings by Bankieris and Aslin, [15, 25] who found an enhanced ability to form stable colour associations. The results show that significant advantages were only present for synaesthetes with graph- eme-colour inducer-concurrent pairings and only for some synaesthesia-related stimuli. This PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 13 / 17 Project administration: Beat Meier. Supervision: Beat Meier. Supervision: Beat Meier. Writing – original draft: Katrin Lunke, Beat Meier. Writing – review & editing: Beat Meier. Acknowledgments We would like to thank Elisabeth Zeller and Rebecca Ovalle Fresa for recruitment and testing of participants and Nicolas Rothen for helpful comments on a former version of this manuscript. Supporting information S1 Table. Proportions of hits and false alarms and C for each type of synaesthesia and sti- muli. Note. Fa = false alarms; GC = Grapheme-colour synaesthetes; SC = Sound-colour synaesthetes; GCSC = Grapheme-and-Sound-colour synaesthetes; SS = Sequence-Space 14 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0203055 September 5, 2018 Memory advantage for synaesthesia synaesthetes. Sound-colour- and sequence-space synaesthetes show a general advantage. (DOCX) Author Contributions Conceptualization: Beat Meier. Methodology: Beat Meier. Project administration: Beat Meier. Supervision: Beat Meier. 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Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States
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Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States James Johndrow1 Patrick Ball2 Maria Gargiulo2,3 Kristian Lum2,4 1Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, 2Human Rights Data Analysis Group, San Francisco, California, United States of America, 3Department of Sociology, University of Oxford, Oxford, England, United Kingdom, 4Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America The MIT Press Published on: Nov 23, 2020 DOI: https://doi.org/10.1162/99608f92.7679a1ed License: Creative Commons Attribution 4.0 International License (CC-BY 4.0) Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances mes Johndrow1 Patrick Ball2 Maria Gargiulo2,3 Kristian Lum2 James Johndrow1 Patrick Ball2 Maria Gargiulo2,3 Kristian Lum2,4 1Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, 2Human Rights Data Analysis Group, San Francisco, California, United States of America, 3Department of Sociology, University of Oxford, Oxford, England, United Kingdom, 4Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America The MIT Press Published on: Nov 23, 2020 DOI: https://doi.org/10.1162/99608f92.7679a1ed License: Creative Commons Attribution 4.0 International License (CC-BY 4.0) ABSTRACT Knowledge of the number of individuals who have been infected with the novel coronavirus SARS-CoV-2 and the extent to which attempts for mitigation by executive order have been effective at limiting its spread are critical for effective policy going forward. Directly assessing prevalence and policy effects is complicated by the fact that case counts are unreliable. In this article, we present a model for using death-only data—in our opinion, the most stable and reliable source of COVID-19 information—to estimate the underlying epidemic curves. Our model links observed deaths to a susceptible-infected-removed (SIR) model of disease spread via a likelihood that accounts for the lag in time from infection to death and the infection fatality rate. We present estimates of the extent to which confirmed cases in the United States undercount the true number of infections, and analyze how effective social distancing orders have been at mitigating or suppressing the virus. We provide analysis for four states with significant epidemics: California, Florida, New York, and Washington. Keywords: COVID-19, SARS-CoV-2, compartmental model, SIR model, Bayesian The MIT Press Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States 1. Introduction The coronavirus SARS-CoV-2, which causes the disease COVID-19, has already changed the lives of billions of people globally. Many people have been ordered to stay in their homes, and economies worldwide have largely come to a halt. Thousands have died and at least several million have been infected. In the United States, social distancing policies began being implemented in mid-March, as states such as Washington, California, and New York saw a sharp rise in the number of hospitalizations attributable to the virus. The coronavirus SARS-CoV-2, which causes the disease COVID-19, has already changed the lives of billions of people globally. Many people have been ordered to stay in their homes, and economies worldwide have largely come to a halt. Thousands have died and at least several million have been infected. In the United States, social distancing policies began being implemented in mid-March, as states such as Washington, California, and New York saw a sharp rise in the number of hospitalizations attributable to the virus. Government response has been hindered by an insufficient supply of materials needed for testing, and by the large proportion of infected individuals who are asymptomatic and therefore are unlikely to seek testing even if it is available. These factors make it difficult to know the true size of the infected population. Because effective surveillance has not been possible, policymakers have instead turned to social distancing policies as the best available tool to slow the spread of the virus. Government response has been hindered by an insufficient supply of materials needed for testing, and by the large proportion of infected individuals who are asymptomatic and therefore are unlikely to seek testing even if it is available. These factors make it difficult to know the true size of the infected population. Because effective surveillance has not been possible, policymakers have instead turned to social distancing policies as the best available tool to slow the spread of the virus. Here, we seek to address two key questions: (1) How many people are actually infected or have ever been infected with SARS-CoV-2?; and (2) Are the social distancing policies currently in place effective at suppressing the virus? That is, can they be expected to lead to a decrease in the number of infections? Media Summary Our analysis offers two findings. First, we estimate that the true number of COVID-19 infections is likely 6 to 10 times larger than the number of confirmed, officially reported cases as of late March. Second, we find that the first round of executive orders for social distancing had mixed effects across states. While in New York the effective reproductive number (a measure of the spread of the virus) dropped low enough to suppress the spread of the virus, this was less clear in states like Florida, where our estimates suggest that the executive orders caused the infection rate only to plateau rather than decrease. Our model offers two technical improvements, in addition to these findings. First, we use what we believe is the most reliable, or least unreliable, source of data about the pandemic: reported deaths. Next, we build a Bayesian model that accounts for the time lag between infection and death. We model the transmission of the virus (creating new infections) by a susceptible-infected-removed (SIR) model, a mechanistic description of the spread of infectious disease. Based on prior research, we assume an infection fatality rate of 1%. The true infection fatality rate is still contested, even among experts, so we provide results for infection fatality rates covering a range of plausible scenarios. Our work is motivated by the problem that official data about confirmed COVID-19 infections drastically understates the true extent of the disease. Many people who have been infected have not sought testing or have not succeeded in being tested due to restrictive policies delineating who is eligible for testing. As testing capabilities in the United States have ramped up, larger proportions of infected individuals have been recorded 2 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States as infected in the data. This has even made comparative statements across time based on case counts unreliable. Subsequent declines in testing further complicate the use of the reported cases. as infected in the data. This has even made comparative statements across time based on case counts unreliable. Subsequent declines in testing further complicate the use of the reported cases. These findings offer insights into the true scale of the pandemic. 1. Introduction Effectively addressing these questions requires innovative modeling due to severe limitations in commonly used sources of data for tracking the spread of the virus (Angelopoulos et al., 2020). Media Summary Furthermore, with estimated infection rates that correct for underreporting bias, these findings enable comparisons among regions and over time. A measure of the magnitude and pattern of the infections is an essential input to health care planning, public policy about distancing, and public communication about the progress of the pandemic. 1.1. (Limitations of) Data on COVID-19 Ideally, to address these questions we would use data on the number of confirmed cases to understand the prevalence of the disease and assess policy measures. However, we view confirmed case counts for COVID-19 to be unreliable and ill-suited to this type of analysis for a number of reasons. Media reports have made clear that testing is more available in some regions than others, and so case counts are primarily an indication of where testing is most comprehensive.1 In fact, there may be as much as a 20-fold difference in case detection between countries, leading to incomparable numbers (Golding et al., 2020). Evidence for the insufficiency of case counts within the United States can also be seen in the large observed difference in test-positive rates—the proportion of positives among all tests performed—across states. For example, as of May 17, 2020, California has conducted 1.24 million tests and enumerated about 80,000 3 3 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States confirmed cases, for a test positive rate of about 6.5%. By contrast, New York has conducted 1.41 million tests and enumerated about 350,000 confirmed cases, for a test positive rate of close to 25%. For case counts to represent an accurate count of the number of infections in both locations, one would need to believe that testing policies and test-seeking behavior in New York are much more likely to identify individuals who have the disease while simultaneously not missing infected people at a higher rate than in California, a highly dubious prospect. One way such large discrepancies in test positive rates could arise is through random testing. If people were tested at random in both states, we would expect to see higher test positive rates in locations with higher prevalence, such as New York. 1.1. (Limitations of) Data on COVID-19 While the prevalence likely does vary between the states, outside of limited designed experiments accounting for a tiny fraction of the total number of tests, testing is not administered to a random sample of people. Instead, tests are administered mainly to symptomatic individuals and people who seek testing. Rather, the most likely explanation for this disparity in test positive rates is that in locations like New York—where the epidemic is large—the number of people infected has persistently outstripped the capacity to test, while in California—where the epidemic is much smaller—this is less true. Thus, the case counts likely do not accurately reflect even the relative size of the infected population across states. It is even more questionable that they could accurately reflect the absolute size of the infected population across states. Furthermore, even within a single administrative boundary, case counts from earlier in the epidemic cannot meaningfully be compared with more recent case counts. Early in the epidemic, tests were administered only to people meeting strict criteria that likely excluded many sick individuals (Johnson & McGinley, 2020, March 7). In some cases, these criteria were chosen due to shortages of testing resources, such as reagents (Cavitt, 2020, April 12). Over time, shortages of key components of testing have slowly resolved, and the administrative rules and guidelines have themselves changed. For example, according to the Centers for Disease Control’s (CDC) website, several revisions to the official guidance on which patients should be tested have been made, including a March 4, 2020, revision that modified the criteria for testing to expand the pool of eligible people (Centers for Disease Control and Prevention, 2020). Thus, some of the trends in cases we observe over time within a given location are likely attributable to changes in test availability and criteria for test eligibility rather than purely to changes in prevalence of the disease. This makes case data of questionable value for modeling, even if model results are not compared across different locations. Another, potentially more reliable, data source is hospitalizations. Unfortunately, these data have become universally available only fairly recently. For example, the Johns Hopkins COVID-19 database provides hospitalization data by state beginning only on April 14, 2020—more than two months after the epidemic began in New York, Washington, and California. 1.1. (Limitations of) Data on COVID-19 High-quality data on the size of the epidemic in the early days are critical to fitting epidemiological models, which tend to be sensitive to initial conditions, and thus a partial time series lacks information that is critical for obtaining the best estimates. Moreover, even if the data source as it currently exists had been available since the beginning of the outbreak, it is a measure of total hospitalizations by day. Without supplementary information on the length of stay for each patient, it is not 4 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States possible to calculate the number of new hospital admissions over time, which is much more useful from the perspective of modeling the total number of infected individuals. Thus, while this could be useful as an additional data source, particularly in the future as the length of the available time series grows, at the moment it is not adequate for our purposes. possible to calculate the number of new hospital admissions over time, which is much more useful from the perspective of modeling the total number of infected individuals. Thus, while this could be useful as an additional data source, particularly in the future as the length of the available time series grows, at the moment it is not adequate for our purposes. This brings us to data on deaths attributable to COVID-19. Death data have been recorded since the earliest days of the epidemic and are universally available across states. Because gravely ill patients who die from severe disease are more likely than the average infected person to be hospitalized and tested, we believe death data are the most complete and representative data source available on a timely basis that could be used to estimate the number of SARS-CoV-2 infections. Even so, death data are imperfect. Excess mortality calculations suggest that the death-only data will miss some people who died of COVID-19 but whose cause of death was not listed as such on their death certificates (Weinberger et al., 2020). Why, then, not use excess mortality data? Excess mortality estimates offer an invaluable approach to evaluating the disease’s overall impact. 1.1. (Limitations of) Data on COVID-19 However, excess mortality almost certainly overcounts actual deaths directly attributable to COVID- 19, since some of the excess mortality is a result of people with other health conditions avoiding hospitals and clinics, cancellation of procedures to reduce hospital census, and so forth. Such second-order effects of the disease don’t fit into traditional models of the spread of infectious disease that are built around the assumption that people who die from the disease were at some point themselves infectious. Thus, while approaches based on excess mortality are incredibly useful for revealing the total effect of the epidemic on mortality, we find them less suitable for fitting models of the spread of the virus. As a result, we fit our model to the data that we believe are best suited for modeling the spread of the virus and have a reasonable chance of being accurate, or —more precisely—are likely the least inaccurate of available measures of the extent of COVID-19 infections: death data. Notably, several other influential COVID-19 modeling efforts have come to the same conclusion and have turned to death data to fit or calibrate their models (Altieri et al., 2020; Ferguson et al., 2020, March 16; Flaxman et al., 2020; Golding et al., 2020). 1.2. Our Modeling Approach A common approach in the statistical epidemiological literature focuses on fitting or calibrating ordinary differential equation (ODE) models to observed data, and this underpins our approach as well (Hethcote, 2000). However, because we build our model using death-only data, we propose modifications to the standard approaches that rely on case data. In order to do this, the observed deaths need to be linked to the underlying state variables of the ODE model via a sensible, scientifically motivated likelihood. We do this by means of a distribution for the time from infection to death, and an assumption about the infection fatality rate (IFR), that is, the proportion of infected individuals who will eventually die of COVID-19. Using death-only data in the early stage of the epidemic, these parameters and the parameters of the underlying ODE model are not separately identifiable. For this reason, the time to death distribution and IFR are assumptions of our model. 5 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States There exist external estimates of the time to death distribution based on high-quality data. For the IFR, precisely because of the difficulty outlined above in establishing the true number of infections, there remains considerable uncertainty about its true value. Because the IFR is such an important assumption of our model, we perform analysis for five scenarios with different values of the IFR that span the (relatively small) range of plausible values. Our model assumes that the IFR is constant over the time period considered. While we believe this is a useful approximation to the truth, in reality there may be drift over time. For example, as physicians and researchers gain more insight into the most efficacious treatments for the disease, outcomes for seriously ill patients may improve over time, leading to a lower rate of death given infection later in the epidemic. 1.2. Our Modeling Approach It has also been speculated that the demographics of who becomes infected may change the IFR.2 However, because our focus is on the first months of the pandemic during which we believe the IFR was likely close to constant, we do not incorporate a time-varying IFR in our model. Conditional on these assumptions and a sampling model for deaths given infections, we fit the parameters of an underlying ODE model of epidemic dynamics to the observed death data. We emphasize that our analysis should be read as ‘if the infection fatality rate is X, then the following would be true,’ rather than primarily as advocating for a particular value of the IFR over others. As a side-effect of fitting epidemic curves and evaluating the impact of interventions, our model allows us to make projections for the likely trajectory of infections and deaths. However, exact projections is not the primary goal of this work. A model focused more on precise predictions would likely include location-specific measures of containment and treatment efficacy, as well as age- and comorbidity-specific infection fatality rates. In order to minimize the prediction error, it would also account for reporting artifacts, such as delays in recording of deaths in quickly updated records over weekends or holidays. It would also account for increased mortality if the sick overwhelm hospital systems. It would also emphasize finding external data sources that provide strong leading indicators of future deaths. This kind of information could be included in a more prediction-optimized version of the model. Our focus here is to outline a modeling approach using minimal but relatively reliable data that are described by a likelihood and priors that incorporate our understanding of the data-generating process, is fitted to data, and is underpinned by a widely used epidemiological model that is designed to approximate the real dynamics of disease spread. It also turns out that this model predicts reasonably well over a two-week time horizon—the only prediction that we assess here. The remainder of this article is organized as follows. In section 2 we review related work. In section 3 we introduce our model and explain how the model can be used to infer the number of infections and the effect of executive orders for social distancing. In section 4 we describe an Markov chain Monte Carlo (MCMC) algorithm for fitting our model. In section 5 we give results. 2. Related Work Several previous studies have attempted to model the dynamics of the pandemic in various geographic locations and with varying goals. Several of these have provided some analysis or estimate of the amount by which confirmed cases undercount the true number of infections. For example, R. Li et al. (2020) propose that in the first month of the epidemic in China, 82–90% of infections were undocumented. Riou et al. (2020) use a susceptible-exposed-infected-removed (SEIR) model, an epidemiological ordinary differential equation (ODE) model, and calibrate their model to the time series of reported deaths and reported infections. By modeling the underreporting of symptomatic cases, and by assuming that approximately half of infections lead to symptomatic cases, they estimate the infected population in Hubei, finding that approximately 30% of infections were documented. Perkins et al. (2020) estimate directly that in the United States, more than 90% of infections have been undocumented by tests using Chinese data and initial reports in the United States. The first wave of a random sampling design in Indiana conducted by researchers at the University of Indiana and the Indiana State Department of Health concluded in a preliminary report that the number of positive tests undercounted the number of people ever infected by a factor of 9.6 (Menachemi et al., 2020). Ferguson et al. (2020, March 16) model the effect of transmission between susceptible and infectious individuals using a microsimulation model built on synthetic populations designed to mimic the populations of the United Kingdom and United States. They assume a fixed time-to-onset and a range of values from 2.0– 2.6, and they assume symptomatic cases to be 50% more infectious than asymptomatic cases. Having calibrated their model to the cumulative number of deaths, they estimate deaths and hospital loads under different nonpharmaceutical interventions involving social distancing and isolation. This analysis was arguably the most influential in triggering the adoption of social distancing policies in the United States, as it indicated that without social distancing measures in place, there would likely be around 2.2 million deaths, and hospitals nationwide would be completely overwhelmed. They also predicted that social distancing measures could reduce the number of deaths substantially and prevent exceedance of hospital resources, but only if they were dynamically turned ‘on and off’ by triggering mechanisms based on the current number of COVID-19 patients. 1.2. Our Modeling Approach In section 6 we conduct a sensitivity analysis. Section 7 concludes. 6 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States 2. Related Work The report envisioned social distancing remaining in place for roughly 18 months, the amount of time they think it will take for a vaccine to become available. R0 The CHIME app (Weissman et al., 2020) is an online tool created by researchers at the University of Pennsylvania to help hospitals anticipate the number of incoming COVID-19 patients and their needs. The CHIME model uses the current number of COVID-19 hospitalizations to ‘back out’ the total number of cases based on a user-provided hospitalization rate conditional on infection. Similar to our work, their model does not rely on the case counts. They make forward projections for the number of hospital admissions, ICU admissions, and ventilators needed over the coming weeks. They allow the user to specify the parameters of their underlying epidemiological model as inputs in terms of the doubling time for the infected population. 7 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States The model given in Murray (2020) has a goal similar to CHIME (hospital use planning). This model takes a different approach by fitting parametric curves to observed cumulative death rates. They use a hierarchical model on the parameters of the parametric curve. The model essentially projects that the future course of the cumulative death rate curve in the United States will follow a path similar to that observed in other locations that are farther along in the course of their epidemics. There is no underlying model of epidemic dynamics, but there is a sampling model for death rates, which allows them to give confidence intervals. The research team developing this model has updated the details of their estimation procedure several times since their model was made public. Instead of an arbitrary curve-fitting procedure, the current version as of writing fits an underlying SEIR model (Institute for Health Metrics & Evaluation, 2020). 2. Related Work The New York Times online tool allows the user to specify inputs to understand how those inputs affect likely infections, hospital loads, and deaths; infections are a side-effect of the rest of the model. Flaxman et al. (2020) take a similar approach to ours to evaluate the effect of social distancing orders across countries in Europe. They define a likelihood for death-only data and incorporate mitigation efforts in the model. They build a hierarchical model to estimate the number of infections and effects of mitigation across countries in Europe. The overall approach is similar, but their analysis is done for Europe, whereas here we consider the United States. Lewnard et al. (2020) similarly evaluate the effect of mitigation efforts. They observe reductions in estimates of the effective reproduction number for patients in three hospital systems in Northern California, Southern California, and Washington State as a consequence of the implementation of nonpharmaceutical interventions, like social distancing. Song et al. (2020) describe a statistical software package that can be used to estimate the impact of quarantine protocols on the spread of COVID-19, and they apply their method to data from China. 3. Model r =s D(r) ⊥⊥D(s) ∣p, θ, ν X(t, t ) ∣ ′ p, θ, ν ∼ t Binomial(ν , pθ ) t (t−t ) ′ νt νt pθs ν Poisson(pθ ν) s Binomial(ν, pθ ) s and for , . This defines our likelihood. The use of a Poisson distribution in specifying our model may seem unnatural compared to the specification r =s D(r) ⊥⊥D(s) ∣p, θ, ν and for , . This defines our likelihood. The use of a Poisson distribution in specifying our model may seem unnatural compared to the specification r =s D(r) ⊥⊥D(s) ∣p, θ, ν and for , . This defines our likelihood. The use of a Poisson distribution in specifying our model may seem unnatural compared to the specification . The Poisson specification allows to take real values as opposed to integer values, as would be required for a Binomial distribution. This allows us to use simpler, deterministic models for the underlying epidemiological curves defining the s, simplifying computation. Fortunately, in cases where is small and is large—precisely the situation in which we find ourselves after the very early days of the epidemic— is a good approximation to . r =s D(r) ⊥⊥D(s) ∣p, θ, ν X(t, t ) ∣ ′ p, θ, ν ∼ t Binomial(ν , pθ ) t (t−t ) ′ νt νt pθs ν Poisson(pθ ν) s Binomial(ν, pθ ) s and for , . This defines our likelihood. The use of a Poisson distribution in specifying our model may seem unnatural compared to the specification . The Poisson specification allows to take real values as r =s D(r) ⊥⊥D(s) ∣p, θ, ν X(t, t ) ∣ ′ p, θ, ν ∼ t Binomial(ν , pθ ) t (t−t ) ′ νt The observed number of deaths are linked to a compartmental epidemiological model via the total number of newly infected individuals on day , . 3. Model Let be the number of new infections on day of the epidemic, and let denote the infection fatality rate, that is, the probability of death given infection. We denote the day of the first infection by . Let be the set of probabilities defining the discrete time-to-death distribution, where denotes the probability that, for those who die, death from COVID-19 occurs days after the initial infection. Let denote the number of individuals newly infected on day who die on day . Our death model is νt t p T0 θ = {θ : s s = 0, 1, ..., m} θs s X(t, t ) ′ t t′ (3.1)    X(t,t ) ∣ ′ p,θ,ν ∼ t Poisson(pν θ ). t (t −t) ′ The observed deaths on day are thus given by r The observed deaths on day are thus given by r The observed deaths on day are thus given by r (3.2)    D(r) = X(t,r), t=1 ∑ r Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infectio Mitigation Policie Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Inf Mitigation P p Unprecedented Challenges and Chances g Mitigation Policie the sum over all previous days of the number of individuals infected on that day who went on to die on day . The distribution of marginal of is given by r D(r) X (3.3)    D(r) ∣p,θ,ν ∼Poisson p ν θ , ( t=1 ∑ r t (r−t)) and for , . This defines our likelihood. The use of a Poisson distribution in specifying our model may seem unnatural compared to the specification . The Poisson specification allows to take real values as opposed to integer values, as would be required for a Binomial distribution. This allows us to use simpler, deterministic models for the underlying epidemiological curves defining the s, simplifying computation. Fortunately, in cases where is small and is large—precisely the situation in which we find ourselves after the very early days of the epidemic— is a good approximation to . 3. Model To generate realistic curves, we use a SIR model of epidemic dynamics, with state evolution given by the following ODE: D t νt νt (3.4)     dt dst dt dit dt drt = {−βs i t t −ϕβs I t t t < T1 t ≥T1 = {βs i −γi t t t ϕβs i −ηγi t t t t < T1 t ≥T1 = , {γit ηγit t < T1 t ≥T1 (3.4)     dt dst dt dit dt drt = {−βs i t t −ϕβs I t t t < T1 t ≥T1 = {βs i −γi t t t ϕβs i −ηγi t t t t < T1 t ≥T1 = , {γit ηγit t < T1 t ≥T1 where is the proportion of susceptible individuals at time , is the number of infected individuals at time , is the number of removed individuals at time , and is the time at which social distancing orders were issued. The variables on which our likelihood is conditioned can be extracted directly from this model. The number of new infections that occurred during day is simply the difference in the size of the compartment at time and multiplied by . This is because, under this model, individuals may leave the susceptible compartment only by becoming infected, so the number of new infections that occurred in any time period is precisely the reduction in the number susceptible in that same period. st t it t rt t T1 νt t S t t + 1 N Up to time , these equations represent a standard SIR model with parameters ; postmitigation, it is a SIR model with parameters . 3. Model In a SIR model with parameters , infected individuals are all T1 {β, γ} {ϕβ, ηγ} {β, γ} 9 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States considered contagious, and the mean time between infection and removal (the end of the contagious period) is given by . is given by —this is the number of people who are infected by a single infected individual in a population in which everyone is susceptible. The quantity represents the percent reduction in the rate of infection that occurred following implementation of mitigation policies; the quantity represents the increase in the rate at which infected individuals cease to be contagious— whether by recovery, death, self-isolation, or medical quarantine—following the implementation of mitigation policies. γ−1 R0 βγ−1 (1 −ϕ) ∈(0, 1) η > 1 The SIR model is a stylized mathematical model of the spread of infectious disease, and—like any model of a complex process—is an approximation of a more complicated reality. In particular, there are several ways in which its compartments only approximately represent distinct subpopulations in the real world. For example, although the compartment is typically conceptualized as containing people who have been ‘removed’ from the population of infectious people due to recovery or death, reality is not so simple. Quarantine or R The SIR model is a stylized mathematical model of the spread of infectious disease, and—like any model of a complex process—is an approximation of a more complicated reality. In particular, there are several ways in which its compartments only approximately represent distinct subpopulations in the real world. For example, although the compartment is typically conceptualized as containing people who have been ‘removed’ from the population of infectious people due to recovery or death, reality is not so simple. 3. Model The series of s has roughly the same shape as the s, D D ν D ν 10 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances though it lags it by about 25 days. This lag is due to the shape of the time from infection to death distribution , which we describe following. The bottom panel gives the standard view of the SIR model, showing the total number of susceptible, infected, and removed at any given time point. θ Figure 1. One realization of our modified SIR models. The top two panels are displayed on the scale of counts. The bottom panel, which shows our underlying SIR model, is given on the scale of proportion of the population. Figure 1. One realization of our modified SIR models. The top two panels are displayed on the scale of counts. The bottom panel, which shows our underlying SIR model, is given on the scale of proportion of the population. 3. Model Quarantine or hospitalization may largely ‘remove’ an individual from the population of infectious people because the rate of transmission for isolated people is substantially reduced; indeed, that is the point of quarantine. Although some models explicitly include a quarantine compartment (e.g., Song et al., 2020), we allow the postinfection quarantines to be subsumed by the removed compartment. This more expansive definition of the compartment justifies the increase in the rate of removal from to following the promulgation of mitigation policies. As awareness and fear of the virus grows, individuals become more likely to self-isolate or seek care when they begin to show symptoms. One further consequence of this simplification is that the number of individuals who die on the th day is not directly comparable with the number of people who enter the compartment during that period because many of the individuals who died at that time could have been effectively removed at an earlier time. R R γ ηγ t R These limitations notwithstanding, we elect to use the SIR model to underpin our likelihood because it is among the simplest options that generate epidemic simulations incorporating the key facets of an epidemic. Specifically, the SIR model manifests herd immunity, rapid growth in the early phase, and is constrained to produce a finite number of infections (Hethcote, 2000). The main purpose of incorporating a compartmental model into our method is to have a realistic, low-dimensional generative model of the new infection curves, , on which our likelihood is based. Because of its simplicity, ease of interpretability, and well-understood properties, we find the SIR model to be an appealing choice. However, the framework we have defined for creating a sensible likelihood-based model of death-only data could easily be extended to embed more elaborate compartmental models or any other generative model of new infections. νt Figure 1 shows one realization of our SIR model. The top panel shows one draw of the daily number of deaths. Notice that this is not a smooth curve. When fitting our model, these s will be our data and will be the only thing we observe directly. The other panels are what we will infer from the s. The middle panel of the figure shows the s, the number of daily new infections. 3.1. Fixed Model Parameters Due to identifiability constraints, we do not estimate all of the parameters of the model. Rather, we fix those parameters for which there exists relatively higher quality information on reasonable values applicable in the context studied here. By and large, this includes those parameters pertaining more to the biology of the disease than to the social dynamics of its spread, which we expect to vary more widely across cultural and geographic contexts.3 These include and . θ p For , we draw from two studies. Zhou et al. (2020) reports that in Wuhan, China, the time from symptom onset to death had a median of 18.5 days with an interquartile range of 15 to 22 days. A Gamma mixture of Poisson distributions (henceforth referred to as the ‘Poisson-Gamma’ distribution) with parameters matches the reported quantiles well. Lauer et al. (2020) estimate the incubation period of the disease, also using data from China. They report a median incubation time of 5.1 days with an θ {a, b} = {27.75, 1.5} 11 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States estimated 97.5th percentile of 11.5 days and a 99th percentile of 14 days. The quantiles of a Poisson-Gamma distribution with parameters match these reported quantiles well. We compute numerically the mass function of the distribution of the total time from infection to death by generating 100,000 samples from the distribution of the incubation period and the distribution of the time from symptom onset to death that were just described. The time to death is the sum of these two numbers. We truncate the maximum time to death from infection to be the 99th percentile of the generated samples; we call this maximum time to death . The parameter is a length vector giving the probability that death occurs days after infection given that death occurs. The probability of death days after infection (marginal of death occurring) is given by . This time to death distribution is shown in Figure 2. 3.1. Fixed Model Parameters {a, b} = {5.5, 1.1} m θ m + 1 θs s pθs Figure 2. Distribution of time (in days) from infection to death. Figure 2. Distribution of time (in days) from infection to death. Because of its importance in the undercount analysis and the considerable uncertainty surrounding the value of the infection fatality rate , most of our results are given for five different values of . To set this range of values for , we rely on several external data points. Russell et al. (2020) use data from individuals on the Diamond Princess cruise ship to estimate an infection fatality rate of 1.2% (95% CI: 0.38%-2.7%) after adjusting for delays between infection confirmation and death. The ship was a closed population: We know who was on the ship and therefore who to test, so we have confidence in the denominator (all individuals infected with COVID-19 were identified because all people on the ship could be tested). We base the upper end of the range of values we consider for on the upper end of the confidence interval given by Russell et al. (2020). p p p p We base the lower bound of values considered on data from the United States. As of May 18, 2020, the New York City Health website reported 20,806 deaths for which the deceased tested positive for COVID-19 or COVID-19 was listed as the cause of death on their death certificate. Compared with an estimated population of about 8.4 million people, this gives an overall mortality rate of about 0.25%. Given that each day there are more reported COVID-19 deaths in New York City, and that it is unlikely that every person in New York City 12 Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances has already been infected, this offers a compelling lower bound on the infection fatality rate in the United States. This range of values is consistent with other external sources of information. One high-quality source is reported case fatality rates in countries that have done aggressive testing and contact tracing, including testing asymptomatic individuals. In these places, the case numbers may approach the true number of infections, so case fatality information in these locations provides a reasonably tight upper bound on infection fatality rates. 3.1. Fixed Model Parameters Here, we look to South Korea, which has done the most testing per capita. As of a May 17, 2020 press release from the Korea Centers for Disease Control and Prevention (Korea Centers for Disease Control and Prevention, 2020, May 17), there were 11,050 confirmed positive cases and 262 deaths in South Korea. This gives a naive estimate of the case fatality rate of 2.4%. For each of these data sources, differences in underlying age and income structure, comorbidities, and other risk factors could limit the generalizability of these estimates to the United States at large. For example, the age distribution on the Diamond Princess cruise ship skews considerably older than the U.S. population in general with about 58% of its passengers 60 years of age or older, while only about 16% of the U.S. population is 62 years of age or older.4 The Diamond Princess IFR might be higher than the IFR for the U.S. population in general, as older age is a known risk factor for COVID-19 (Zhou et al., 2020). However, the fact that the people on the Diamond Princess were able to travel may indicate that these people suffer fewer other comorbidities on average than their similarly aged U.S. cohort. IFR estimates from other geographic regions, such as South Korea, may be limited by similar demographic and risk-factor differences relative to the United States. Additionally, the IFR is influenced by the quality and availability of medical care. Data from locations where medical care is unavailable or inadequate, or where the health care system has been overwhelmed by a surge of COVID-19 patients, may overestimate the IFR relative to situations where quality care is available to anyone who needs it. Such factors are difficult to adjust for, since data on risk factors is preliminary and limited and health care availability can change dramatically if the number of infections in an area explodes. The differences between the context from which we draw our estimates of and the population to which they are applied notwithstanding, we believe that the comparison is still useful in providing a range of rough estimates. Indeed, there are many similarities as well. The Diamond Princess cruise ship had a large American population—about 400 of the 3,700 total passengers and crew on board were U.S. citizens. South Korea’s healthcare system has not been overwhelmed by COVID-19 cases. 3.1. Fixed Model Parameters This is similar to the United States where, although hospitals in New York City were very full, health care providers have not reached a situation where they have had to ration ventilators. p With all of these qualifications, we cannot be certain that any given value of is correct when applied in our context. We also do not think that it is possible to precisely estimate the IFR for this virus with the currently available data. However, we believe these external estimates are useful in providing a range of possible values. Thus, because the infection fatality rate is arguably the most important parameter in our model that cannot be p 13 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States learned from the data, we consider five different scenarios that cover the spectrum of plausible values put forth above: 0.2%, 0.5%, 1.0%, 1.5%, and 2.5%. We focus on the 1.0% case in some figures because we consider values of in this range to be most likely. p 3.2. Estimated Model Parameters The parameters we estimate in our model are , , , , and . We base our prior for the infectious period on previously published studies. Ferguson et al. (2020, March 16) give a mean generation time ( in the SIR model) of 6.4 days; Prem et al. (2020) assume an infectious period of 3 or 7 days in their simulations with an incubation period of about 6 days. While these aren’t directly comparable due to differences in the model—as described above, people can actually move to the R compartment while still infected with the virus—we use these as rough guidance. We choose the prior , corresponding to an infectious period that ranges from about 1 to 15 days. The value of 1 day would be consistent with a situation in which most symptomatic people rapidly self-isolate, and asymptomatic people are uncommon. Rather than specifying a prior on , we choose a prior on , which induces a prior on . Using the reported confidence interval in Q. Li et al. (2020) to establish rough upper and lower bounds on , we specify the prior . We place a uniform prior on between January 1, 2020, and February 20, 2020. γ β ϕ η T0 γ−1 γ ∼ −1 Uniform(1, 15) β R = 0 βγ−1 β R0 R ∼ 0 Uniform(1, 4) T0 We place a prior on , allowing it to encompass the possibility that mitigation policies had significant effect ( small) and that the policy had a very limited effect ( large). This prior rules out the possibility that the mitigation policies, in fact, increased the transmissibility. This prior is consistent with information on the University of Maryland COVID-19 Impact Analysis Platform, which calculates several social distancing-relevant metrics as a function of mobility data. In each of the states considered, the percent of people not staying home according to this data was roughly 60-80% post-executive orders as it was prior. We do not expect that decreases in mobility perfectly map to decreases in transmissions, as other behaviors that likely changed in tandem with social distancing policies, such as mask wearing or not shaking hands, also have an effect. However, from this data it is clear that we should expect that there was some effect, as there was a significant increase in the proportion of the population staying home. 4. Computation We carry out computation by MCMC using the adaptive Metropolis algorithm (Haario et al., 2001). The algorithm produces samples from the Bayesian posterior distribution of the parameters of our model, . Specifically, we update by proposing a new set of parameters, from , with the time-inhomogeneous covariance computed using the method of Haario et al. (2001). In brief, during a pre-adaptation phase, proposals are made from the usual multivariate Gaussian random-walk, that is, ξ = {β, γ, T , ϕ, η} 0 ξ ξ∗ N(ξ, Σ) Σ (4.1)    ξ ∼ ∗ N(ξ,c Σ ), 0 0 where is an initial estimate of the posterior covariance, and is a scalar tuning parameter. After adaptation begins, the proposal becomes Σ0 c0 where is an initial estimate of the posterior covariance, and is a scalar tuning parameter. After adaptation begins, the proposal becomes Σ0 c0 (4.2)    ξ ∼ t ∗ N(ξ,c ), 1Σ^ t (4.2)    ξ ∼ t ∗ N(ξ,c ), 1Σ^ t where is the usual time-averaging estimate of the posterior covariance based on the Markov path up until step . For details, see Haario et al. (2001). Once a new state is proposed, we solve the SIR model with these parameters using the Runge-Kutta (4,5) method. We then calculate the sequence from the sequence. We accept or reject the proposed using the usual Metropolis acceptance probability, with target density proportional to Σ^t t −1 ξ∗ νt ∗ st η∗ (4.3)    ℓ(ν(ξ),ξ) = p(D(t) ∣ t=1 ∑ T ν) + log(π(ξ)), where is the Poisson probability mass function implied by (3.3), and represents the prior density. Notice that, because is a deterministic function of , both terms in (4.3) depend on the values of these parameters. The tuning parameters of the adaptive Metropolis algorithm are chosen to give acceptance rates between about .2 and .4. p(D(t) ∣ν) π() ν ξ where is the Poisson probability mass function implied by (3.3), and represents the prior density. Notice that, because is a deterministic function of , both terms in (4.3) depend on the values of these parameters. The tuning parameters of the adaptive Metropolis algorithm are chosen to give acceptance rates between about .2 and .4. p(D(t) ∣ν) π() ν ξ To obtain the initial value of the proposal covariance , we compute an estimate of the sampling covariance of the maximum likelihood estimator using a parametric bootstrap. 3.2. Estimated Model Parameters Furthermore, based on this, we also believe that transmissions were not completely eliminated, as there still remain a significant proportion of the population interacting outside of their homes. Uniform(0.2, 0.9) ϕ ϕ ϕ Finally, we use a prior on , allowing the rate at which people are removed from the infectious population to increase after the implementation of social distancing policies. A value of substantially larger than 1 would indicate that after social distancing measures and other policies were promulgated, symptomatic people more rapidly self-isolated or otherwise ‘removed’ themselves from human contact after becoming symptomatic. This would be consistent with increasing awareness of the virus due to persistent messaging from media and the authorities resulting in greater individual efforts to self-isolate. On the other hand, values near 1 would indicate that symptomatic people did not change their behavior much with regard to self-isolation after social distancing policies went into effect. Uniform(1, 4) η η 14 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Im Mitigation Policies in the Unite Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States p Unprecedented Challenges and Chances Unprecedented Challenges and Chances 5.1. Model Fit and Projections Figure 3 shows model fit for each of the states for . The gray bands show point-wise 95% posterior predictive intervals; the black line shows the posterior mean. The red lines show a 7-day moving average of the daily deaths, while the gray lines show the raw daily reported deaths. We include the moving average for reference because we believe some of the variability in the daily raw data is likely due to delays in reporting rather than inherent variability in the timing of deaths. Despite the low-dimensionality of the free parameters in our model, it fits the data reasonably well. On several occasions, the true values exhibit large spikes or valleys that stray outside of the intervals. This suggests that perhaps a negative binomial or other overdispersed count distribution be considered for future models, though of course one expects to occasionally see values outside of a pointwise 95% interval. We also believe that some of the extremes of day-to-day variation in the raw data are recording artifacts. For example, there is a persistent trend of reported deaths temporarily falling on weekends and spiking early in the week. There is no obvious way to reallocate the data to weekend days, and since our model is not very sensitive to variation on the scale of a few days, we do not attempt to do so. The comparison of the posterior mean to the 7-day moving average provides another way to visualize the performance of the model that is not as sensitive to recording artifacts. p = .01 Figure 3 includes data through May 13, 2020, the last 13 days of which were not used for training. The values shown after April 30, 2020 (marked with a vertical line in Figure 3) are projections from the model and associated 95% pointwise posterior credible intervals. For Florida, New York, and Washington, the projections are fairly accurate over this 2-week time span and the moving average largely falls within the intervals. For California, the model predicts a slowly moving increase in deaths, whereas the data in that time period appear to have reached a plateau. This discrepancy could occur if the true time to death distribution were slightly longer than that indicated by our chosen . If that were true, the model would ‘expect’ changes to the trajectory of deaths to show up in the data before they actually do. 5. Results We fit our model to the daily number of deaths for several states in the United States: California, Florida, New York, and Washington. We use the state-level data compiled by the New York Times. The last date in our training data is April 30, 2020. We base the state populations on 2018 US state population estimates from World Population Review, which pulls data from the U.S. Census. We take the date of implementation of social distancing to be the first day on which restaurants and schools were both closed statewide by executive order, as recorded in a GitHub repository maintained by researchers at the University of Washington. This definition is of course somewhat arbitrary, but given limitations of the available data, it is difficult to conceive of a richer model that would allow the effects of social distancing to phase in gradually without making similarly strong assumptions about how much each type of measure is ‘worth’ compared to the eventual statewide lockdowns that were implemented everywhere. 4. Computation We tune the constants and to obtain acceptance probabilities of approximately .2 to .4, consistent with the guidance of Roberts and Rosenthal (2001). We run for 100,000 iterations, begin adaptation after 20,000 iterations, and use 50,000 iterations of burn-in. Representative trace plots are shown in Appendix A. We also compute Gelman-Rubin statistics based on the last 50,000 iterations and five replicate chains initiated by sampling from a Gaussian centered at the maximum likelihood estimate with the bootstrap estimate of the covariance. This is done for every state for . All of the statistics are less than 1.03, which does not suggest problems with nonstationarity.5 Σ0 c0 c1 p = .01 15 15 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States 5.1. Model Fit and Projections Because the time elapsed between the promulgation of social distancing orders and the end of our training data is only about 45 days, whereas the time from infection θ 16 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States to death can be as long as 40 days, this might cause the model to erroneously infer that the trajectory had not slowed. Another possibility is that behavioral changes did not coincide with the executive orders but slowly increased since then, causing additional slowing in the death rate. Because the parameters are constant during the full time period after the executive orders have been issued, this would cause the estimated parameters to overestimate the average effect immediately after the orders were issued and underestimate it later. 17 17 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States 18 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Figure 3. Posterior mean (black dashed line), posterior 95% pointwise credible interval (gray region), raw data (gray lines), and 7-day moving average of raw data (red lines). The vertical black line indicates the last day of data used to fit the model. Note that the scale of the vertical axis differs by state. Figure 3. 5.1. Model Fit and Projections Posterior mean (black dashed line), posterior 95% pointwise credible interval (gray region), raw data (gray lines), and 7-day moving average of raw data (red lines). The vertical black line indicates the last day of data used to fit the model. Note that the scale of the vertical axis differs by state. Table 1 shows posterior means and 95% posterior credible intervals of preintervention for each state for all five values of . With the exception of Washington, where a larger value of leads to considerably smaller estimated values of , these estimates are not especially sensitive to (good news since this is the parameter about which we are most uncertain), and all fall within the range between about 2.5 and 4. That the estimates are not very sensitive to may seem surprising, since for smaller values of , the number of infected individuals at any time must be larger to produce the observed deaths. However, because our model also estimates (the time of the initial infection) and , it is possible to produce quite different time series of new infections with similar values. The data are thus indicating that changing the assumption about would imply changes in the parameters that keep nearly constant. R0 p p R0 p p p T0 γ R0 p R0 Table 1 shows posterior means and 95% posterior credible intervals of preintervention for each state for all five values of . With the exception of Washington, where a larger value of leads to considerably smaller estimated values of , these estimates are not especially sensitive to (good news since this is the parameter about which we are most uncertain), and all fall within the range between about 2.5 and 4. That the estimates are not very sensitive to may seem surprising, since for smaller values of , the number of infected individuals at any time must be larger to produce the observed deaths. However, because our model also estimates (the time of the initial infection) and , it is possible to produce quite different time series of new infections with similar values. The data are thus indicating that changing the assumption about would imply changes in the parameters that keep nearly constant. R0 p p R0 p p p T0 γ R0 p R0 Table 1. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. 5.1. Model Fit and Projections R0 CA FL NY WA .002 2.99 (1.91,3.83) 3.25 (2.59,3.77) 3.96 (3.87,4.00) 3.06 (2.37,3.39) .005 2.85 (1.45,3.79) 3.19 (2.45,3.68) 3.91 (3.70,4.00) 2.86 (2.13,3.20) Table 1. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 Table 1. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 Table 1. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses R0 19 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States .01 3.13 (1.82,3.88) 3.19 (2.32,3.68) 3.89 (3.63,4.00) 2.72 (2.05,3.06) .015 3.12 (2.06,3.83) 3.21 (2.56,3.70) 3.88 (3.65,4.00) 2.66 (1.99,2.99) .025 3.11 (1.99,3.82) 3.21 (2.49,3.69) 3.81 (3.52,3.99) 2.56 (1.94,2.88) Figure 4. Estimates of the cumulative undercount factor for each state by day. Plotted on log-10 scale. Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Figure 4. Estimates of the cumulative undercount factor for each state by day. Plotted on log-10 scale. 5.2. Undercount Estimates One quantity estimated by our model is the cumulative number of SARS-CoV-2 infections over time. Comparing these estimates with the reported number of confirmed cases by state allows us to estimate the extent by which confirmed cases of COVID-19 undercount the number of infections. We define the undercount at each time point to be our estimated number of cumulative infections as of that time point divided by the cumulative number of confirmed cases at that time. That is, the undercount is the multiplicative factor by which the recorded number of confirmed cases underestimates the true number. Figure 4 shows the undercount for each state across time for each value of , based on the posterior mean of the total number of people ever infected by day. Naturally, when is smaller, and therefore the number of deaths is a smaller proportion of the true number of infections, we estimate the undercount to be greater. Under the range of values for p p p 20 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States considered, we find that the undercount was somewhere between 5-fold (for Washington with ) and 175-fold (for New York with ) across states as of April 1. As testing availability has increased, the undercount factor has fallen to around 2.5-fold (for Washington and Florida with ) to about 45-fold (for both New York and California with ) as of April 30. Table 2 shows the undercount and associated 95% posterior credible intervals as of the last day that appears in our data, April 30, 2020. p = .025 p = .002 p = .025 p = .002 Table 2. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses. These estimated undercounts—particularly those for , , and, —are consistent with other estimates of the extent of undercounting. 5.2. Undercount Estimates The first wave of random sampling design in Indiana conducted by researchers at the University of Indiana and the Indiana State Department of Health concluded in a preliminary report that the number of positive tests undercounted the number of people ever infected by a factor of 9.6 (Menachemi et al., 2020). They also estimate the infection fatality rate at .006. We arrive at undercount factors of between 6.5 and 9.8 for the four states analyzed with and between 12.9 and 19.25 with . This places our estimates within a similar range of values as those found using a combination of serological and viral RNA testing in Indiana. New York State also recently conducted a seroprevalence study. In this study, they found that about 21.2% of N Y k Cit id t t t d iti f h i h d th di A l i thi t N Y k Cit ’ CA FL NY WA .002 43.30 (39.29,47.72) 31.92 (28.04,35.88) 44.90 (44.30,45.46) 33.77 (30.87,36.92) .005 17.60 (15.95,19.45) 12.89 (11.16,14.49) 19.25 (18.89,19.59) 13.59 (12.29,14.88) .01 8.96 (8.05,10.02) 6.47 (5.68,7.30) 9.78 (9.58,9.96) 6.86 (6.23,7.52) .015 5.99 (5.36,6.67) 4.30 (3.77,4.84) 6.55 (6.41,6.68) 4.59 (4.16,5.04) .025 3.58 (3.23,3.97) 2.59 (2.26,2.93) 3.93 (3.84,4.01) 2.77 (2.51,3.05) p = .01 p = .015 p = .025 p = .01 p = .005 Table 2. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses. CA FL NY WA .002 43.30 (39.29,47.72) 31.92 (28.04,35.88) 44.90 (44.30,45.46) 33.77 (30.87,36.92) .005 17.60 (15.95,19.45) 12.89 (11.16,14.49) 19.25 (18.89,19.59) 13.59 (12.29,14.88) .01 8.96 (8.05,10.02) 6.47 (5.68,7.30) 9.78 (9.58,9.96) 6.86 (6.23,7.52) .015 5.99 (5.36,6.67) 4.30 (3.77,4.84) 6.55 (6.41,6.68) 4.59 (4.16,5.04) .025 3.58 (3.23,3.97) 2.59 (2.26,2.93) 3.93 (3.84,4.01) 2.77 (2.51,3.05) Table 2. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses. Table 2. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses. These estimated undercounts—particularly those for , , and, —are consistent with other estimates of the extent of undercounting. The first wave of random sampling design in Indiana conducted by researchers at the University of Indiana and the Indiana State Department of Health concluded in a preliminary report that the number of positive tests undercounted the number of people ever infected by a factor of 9.6 (Menachemi et al., 2020). They also estimate the infection fatality rate at .006. We arrive at undercount factors of between 6.5 and 9.8 for the four states analyzed with and between 12.9 and 19.25 with . This places our estimates within a similar range of values as those found using a combination of serological and viral RNA testing in Indiana. p = .01 p = .015 p = .025 p = .01 p = .005 New York State also recently conducted a seroprevalence study. In this study, they found that about 21.2% of New York City residents tested positive for having had the disease. Applying this to New York City’s population of 8.4 million people, this results in an estimate of about 1.8 million infections in the New York City compared to the number of reported cases at the time of about 153,000. This implies an undercount factor of a little over 11. Compared with around 11,460 reported deaths at the time of the release of this study, this also implies a raw IFR of about .6 Given that some people who are currently infected will, unfortunately, go on to die, this likely provides a slight underestimate of . p = .006 p These kinds of estimates can also help inform discussions about herd immunity. For example, in New York as of April 30, there had been about 311,000 cases. 5.3. Effects of Executive Orders for Social Distancing Executive orders were issued and social distancing policies began taking effect in parts of the United States around March 15, and thus as of the writing of this article, enough time has now passed since the orders in at least some states that the effects will be visible in the deaths data. Recalling the time from infection to death distribution from Figure 2, changes in the dynamics of new infections should begin to be visible in death data around two weeks following the onset of the policy change, and should be mostly visible by around four weeks. This makes it now appropriate to attempt to estimate the effect of such social distancing orders on infection dynamics. In the SIR model, the number of infected individuals will grow when the rate of new infections is higher than the rate of removal and will decrease otherwise. In other words, the rates are equal when the time derivative of is zero, that is, it (5.1)     ϕβs i t t ηγ ϕβst = ηγit = 1 ≡ρ . t We thus focus on estimating the quantity (where is the last day that appears in our training data). When , the number of infected individuals is still growing, while if , it is declining and the virus is being suppressed. This quantity is sometimes called , but to avoid confusion with compartments of the SIR model, we have used unconventional notation. It is important to note that, because this quantity depends on the current state of , which is decreasing in time, it is possible for the current measures to fail to suppress the virus today yet be sufficient to suppress the virus at some later time because will have declined. ρT T ρ > T 1 ρ < T 1 Rt st st Table 3 shows estimates of the posterior mean of along with 95% posterior credible intervals. Results are reported for four states and for all five values of . It is clear that this quantity is not very sensitive to the assumption about , which is encouraging since this is the major assumption of our model. Based on these results, the current measures appear sufficient to suppress the virus in New York and Washington, and just at the boundary of being sufficient in California and Florida. Table 2. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses. In our scenario, we estimate the undercount factor p = .01 21 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States at 10 times, as of this date in New York. This would mean that about 3.1 million had been infected in New York between the start of the epidemic and April 30, which is between one sixth and one seventh of the population. This is far too small a proportion for herd immunity to be a major factor at that point. However, an analyst who assigns high probability to the case would conclude that close to 14 million people (the vast majority of the population) had been infected by April 30, and therefore that herd immunity is sufficient that almost all mitigation efforts could now be lifted and the number of infections would continue to decline. We find this latter scenario to be highly unlikely. p = .002 5.3. Effects of Executive Orders for Social Distancing It will be interesting to see how these conclusions change in the coming weeks as social distancing and other mitigation policies are relaxed. ρT p p 22 Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Table 3. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses ρT Table 3. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. ρT CA FL NY WA .002 1.06 (1.01,1.13) 1.00 (0.86,1.14) 0.44 (0.43,0.44) 0.71 (0.63,0.79) .005 1.07 (1.02,1.16) 1.01 (0.87,1.16) 0.63 (0.62,0.64) 0.73 (0.64,0.82) .01 1.10 (1.04,1.20) 1.02 (0.88,1.17) 0.68 (0.67,0.69) 0.75 (0.66,0.83) .015 1.10 (1.04,1.19) 1.02 (0.88,1.17) 0.69 (0.68,0.71) 0.75 (0.67,0.84) .025 1.10 (1.04,1.18) 1.03 (0.88,1.18) 0.70 (0.69,0.72) 0.77 (0.68,0.85) Estimated posterior mean of , with 95% posterior credible interval shown in ρT Table 3. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. ρT Our model could be sensitive to various types of misspecification, including incorrect specification of or , incorrect specification of the time point at which the parameters of the model change, and incorrect specification of the SIR model itself. Because we give results for multiple values of , this type of misspecification is less of a concern. In Appendix B, we conduct a simulation study to assess sensitivity of estimates of the quantities of interest, such as the undercount factor and , to these other types of misspecification. The results suggest that the model is fairly robust to these sources of misspecification, except in the case of estimation of when is misspecified. However, we conclude that badly misspecifying is often detectable in poor model fit. Details are provided in Appendix B. θ p T1 p R0 R0 T1 T1 Our model could be sensitive to various types of misspecification, including incorrect specification of or , incorrect specification of the time point at which the parameters of the model change, and incorrect specification of the SIR model itself. Because we give results for multiple values of , this type of misspecification is less of a concern. In Appendix B, we conduct a simulation study to assess sensitivity of estimates of the quantities of interest, such as the undercount factor and , to these other types of misspecification. 5.3. Effects of Executive Orders for Social Distancing The results suggest that the model is fairly robust to these sources of misspecification, except in the case of estimation of when is misspecified. However, we conclude that badly misspecifying is often detectable in poor model fit. Details are provided in Appendix B. θ p T1 p R0 R0 T1 T1 5.4. A Prior on p We have so far presented results for different values of . The parameter is not identifiable when the parameters of the SIR model are estimated from the data. When performing subjective Bayesian analysis for an application in which there is widespread disagreement about a non-identifiable parameter—such as in this case—it makes sense to present multiple cases and allow readers to weight the different cases according to their own priors. ‘Group’ Bayesian decision making is an especially fraught problem with no real solution, and thus when a parameter cannot be updated with data and there clearly exists widespread disagreement about the value of this parameter, it is especially important to allow analysts to impose their own prior on these parameters. In this section, we present results using our own prior on to demonstrate how one could obtain a single posterior estimate for parameters of the SIR model, averaging over their prior on . p p p p p We assign a prior on based on our own reading of the literature, media accounts, statements of public health officials, and interactions with epidemiologists and other experts. Despite this, our prior is certainly subjective, and the results we present here should not be taken to supplant the results earlier in the article. Our prior is a distribution, truncated to the interval , and discretized to support p Gamma(30, 3000) [0.002, 0.025] 23 Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances points . This prior has mean of approximately and places most of its mass between and . 0.002, 0.003, … , 0.024, 0.025 0.01 0.005 0.015 To obtain results, we run the MCMC algorithm described in section 4 for taking each value in the support, then average the samples with weights given by the prior. Results are shown in Table 4. As expected, the posterior mean for the undercount is similar to what we obtained with fixed at , but credible intervals are considerably wider. This is indeed the main difference between putting a prior on and fixing : because the undercount is sensitive to , putting a prior on results in much wider credible intervals for the undercount than with any fixed value of . Table 4. , , and the estimated undercount (95% posterior credible intervals) calculated by averaging samples over a prior on . R0 ρT p Table 4. , , and the estimated undercount (95% posterior credible intervals) calculated by averaging samples over a prior on . R0 ρT p R0 ρT Undercount CA 3.09 (1.89,3.87) 1.09 (1.03,1.19) 9.00 (6.33,13.29) FL 3.20 (2.46,3.68) 1.02 (0.88,1.17) 7.00 (4.54,9.75) NY 3.89 (3.64,4.00) 0.68 (0.65,0.70) 10.00 (7.02,14.00) WA 2.74 (2.08,3.09) 0.75 (0.66,0.83) 7.00 (4.89,10.20) Table 4. , , and the estimated undercount (95% posterior credible intervals) calculated by averaging samples over a prior on . R0 ρT p Table 4. , , and the estimated undercount (95% posterior credible intervals) calculated by averaging samples over a prior on . R0 ρT p 6. Sensitivity Analysis In this section we address sensitivity of our findings to the value we have chosen for and to the assumption that the death count data is an accurate representation of the number of COVID-19 attributable deaths. θ 5.4. A Prior on p In most cases, the results for and do not change considerably compared to any of the results with fixed since these quantities were not particularly sensitive to the assumed value of . p p .01 p p p p p R0 ρT p, p 6.1. Alternative θ One of the first major interventions outside of China to stem the spread of COVID-19 was the lockdown in Italy on March 9, 2020. Around 20 days later, the number of daily deaths in Italy showed a sustained downward trend. We adjust the used in the main text to an average time to death of 20 days consistent with Italy. We then see what effects using this might have on our results. θ θ To create a based on an average time to death of about 20 days, we induce a correlation between the time to symptom onset and the time to death for those who died. Specifically, we simulate the time from infection to symptom onset as before from a Poisson-Gamma distribution with parameters to be consistent with Lauer et al. (2020). We then simulate the time from symptom onset to death from a Poisson- θ {a, b} = {5.5, 1.1} 24 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Gamma distribution with parameters , where is the simulated time from infection to symptom onset. This induces a positive correlation such that those who had faster symptom onset also had faster time to death from symptom onset on average. This results in an alternative with average time to death of about 20.5 days and a correlation between incubation time and time from symptom onset to death of about .35. This alternative is shown in Figure 5. {a, b} = {t − 1 + t1ˉ 5.5, 1.1} t1 θ θ Figure 5. Alternative θ. Figure 5. Alternative θ. Figure 5. Alternative θ. 6.2. Excess Mortality-Inflated Death Counts Using the raw death count data assumes that deaths due to COVID-19 have been accurately recorded. Recent studies on excess mortality suggest that, in some states, there has been underreporting of COVID-19 deaths. For example, Weinberger et al. (2020) calculate excess mortality due to pneumonia and influenza (P&I) from February 9, 2020, to March 28, 2020. They note that in California during this time period, while only 101 COVID-19 deaths were reported, there were 399 excess deaths due to P&I during that same time period. If we interpret all of those deaths to be COVID-related, this implies that that only about one quarter of COVID-19 deaths were reported as such. Similar analysis for Florida and Washington showed reporting rates of about 30% and 100%, respectively. Though New York did not show underreporting when comparing only to pneumonia and influenza deaths, due to the large volume of cases there, the authors noted a reporting rate of 60% in New York City and 40% in New York State (excluding New York City) based on all-cause excess mortality. We assume a rough estimate of underreporting for New York State in its entirety is around 50%. Based on these findings, we inflate the number of observed deaths on each day by a factor of four, three, two, and one for California, Florida, New York, and Washington, respectively. By inflating the data in this way, this implicitly assumes that excess mortality during this time period is all due to COVID-19 infections. 6.2. Excess Mortality-Inflated Death Counts While many of the excess deaths during this time period may be the result of the environment caused by COVID-19 (e.g., not going to the hospital for other illnesses out of fear of contracting COVID-19, reduction in medical services 25 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States available to non COVID-19 patients, and saturation of emergency medical services), it is unlikely that all are directly attributable to infection itself. This calculation also assumes that the rate at which COVID-related deaths were not attributed to COVID-19 in official records is constant across time. As testing capacity has expanded over time and the estimates we use are based on data only through March 28, this is unlikely to be true. Because not all excess mortality is due to COVID-19 disease, these two cases (raw death counts presented as our main results and the excess mortality-inflated death counts presented here) likely bracket the true number of deaths. However, more updated estimates of P&I excess mortality do not seem to be available. Even all-cause excess mortality estimates from the CDC are lagged by a few weeks. Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in th R0 Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. Note: Rows correspond to two alternative scenarios considered: death counts adjusted using an excess mortality multiplier and alternative value of used. In both cases, . R0 CA FL NY WA multiplier 2.98 (1.73,3.74) 3.38 (2.93,3.66) 3.94 (3.81,4.00) 2.72 (2.00,3.06) alternative theta 3.26 (2.00,3.97) 3.43 (2.40,3.98) 3.58 (2.87,3.99) 2.58 (1.72,3.04) θ p = .01 6.3. Alternative Results Results from applying our model with the alternative and for excess mortality (labeled as ‘multiplier’) are given below. Each of these were run for . Table 5 gives the estimated under each of these alternative scenarios. In neither case do the estimates of substantively change under these alternative scenarios. Point estimates in the alternative scenarios fall within the posterior credible intervals of the model fit in the primary scenarios given in the main text. θ p = .01 R0 R0 Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 Note: Rows correspond to two alternative scenarios considered: death counts adjusted using an excess mortality multiplier and alternative value of used. In both cases, . θ p = .01 Table 6 gives estimates of under each of the alternative scenarios. Once again, there are no substantive changes to our estimates. It is still the case that the estimated s imply a slow rise in deaths in California, a plateau or very slow increase in Florida, and continued downward trends in New York and Washington. ρT ρT Table 6. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. ρT CA FL NY WA multiplier 1.06 (1.02,1.11) 1.07 (0.97,1.16) 0.63 (0.63,0.64) 0.75 (0.66,0.84) alternative theta 1.09 (1.05,1.14) 1.02 (0.91,1.19) 0.78 (0.77,0.80) 0.83 (0.75,0.91) Table 6. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. ρT 26 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Note: Rows correspond to two alternative scenarios considered: death counts adjusted using an excess mortality multiplier and alternative value of used. In both cases, . θ p = .01 Table 7 shows the estimated factor by which current testing undercounts the actual number of infections as estimated by our model. This is analogous to Table 2 in the main text. Unsurprisingly, we found that inflating the number of COVID-19 deaths results in higher estimates of the total infected and, consequently, a larger undercount factor (relative to results for in the main text). Using the alternative value of has minimal impact on estimates of the undercount, with three of the four point estimates calculated under the alternative falling within the posterior credible intervals obtained in the main analysis. Notably, under the alternative , New York sees a statistically significant though not substantively meaningful decrease in the undercount factor. p = .01 θ θ θ Table 7. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses for alternative scenarios: Deaths adjusted according to excess mortality multipliers or using the alternative . Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 p p p p However, early evidence suggests that accounting for under-reporting would change the death counts by at most a factor of 4, and this is likely a significant overestimate for the reasons outlined above. Since increasing the death counts with fixed has a similar effect on our analysis to decreasing with the death counts fixed, and the values of we consider in the main analysis range from 0.2% up to 2.5% (a difference of a factor of 10), the variation in results that is possible due to undercounting of deaths is already well represented by variation in in the scenarios we consider. p p p p Table 5. Estimated posterior mean of , with 95% posterior credible interval shown in parentheses. R0 Note: For both alternative scenarios, . θ CA FL NY WA multiplier 34.69 (32.93,36.79) 19.97 (18.58,21.31) 19.31 (19.07,19.56) 6.85 (6.22,7.50) alternative theta 8.51 (7.84,9.19) 6.20 (5.46,7.01) 8.87 (8.72,9.03) 6.93 (6.28,7.64) p = .01 Table 7. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses for alternative scenarios: Deaths adjusted according to excess mortality multipliers or using the alternative . θ Table 7. Estimated posterior mean of undercount, with 95% posterior credible interval shown in parentheses for alternative scenarios: Deaths adjusted according to excess mortality multipliers or using the alternative . θ Note: For both alternative scenarios, . CA FL NY WA multiplier 34.69 (32.93,36.79) 19.97 (18.58,21.31) 19.31 (19.07,19.56) 6.85 (6.22,7.50) alternative theta 8.51 (7.84,9.19) 6.20 (5.46,7.01) 8.87 (8.72,9.03) 6.93 (6.28,7.64) p = .01 In all but one of the calculations under alternative scenarios, we find that the alternative parameters do not substantively change the results. The only exception to this is the undercount factors, which—unsurprisingly— exhibit an increase when we add a multiplier to the time series to account for possible undercounting. However, early evidence suggests that accounting for under-reporting would change the death counts by at In all but one of the calculations under alternative scenarios, we find that the alternative parameters do not substantively change the results. The only exception to this is the undercount factors, which—unsurprisingly— exhibit an increase when we add a multiplier to the time series to account for possible undercounting. In all but one of the calculations under alternative scenarios, we find that the alternative parameters do not substantively change the results. The only exception to this is the undercount factors, which—unsurprisingly— exhibit an increase when we add a multiplier to the time series to account for possible undercounting. However, early evidence suggests that accounting for under-reporting would change the death counts by at most a factor of 4, and this is likely a significant overestimate for the reasons outlined above. Since increasing the death counts with fixed has a similar effect on our analysis to decreasing with the death counts fixed, and the values of we consider in the main analysis range from 0.2% up to 2.5% (a difference of a factor of 10), the variation in results that is possible due to undercounting of deaths is already well represented by variation in in the scenarios we consider. 7. Conclusion We have built a model for the transmission of SARS-CoV-2 using only information that has a reasonable chance of being measured correctly: the observed number of daily deaths, timing of containment measures, and information on the clinical progression of the disease. In contrast to models that use a wider range of information that may be less precisely measured, we believe the main strengths of our approach are that it 27 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States prioritizes simplicity, interpretability, and identifiability. Because not all parameters one might want to estimate in this setting are separately identifiable, we have carefully specified our model so that all estimated parameters are identifiable conditional on quantities for which we have high-quality auxiliary information. Our model also has a proper likelihood and is fit to data in the Bayesian paradigm, rather than relying on ad hoc calibration of model parameters to produce trajectories resembling the observed data. This allows us to formally account for uncertainty in all of our estimates by posterior credible intervals. Our model is underpinned by an SIR model of infection dynamics to link observed deaths to the underlying unobserved infections. It would not be difficult with our approach to substitute some other model in place of the SIR. In particular, any other compartmental model, such as an SEIR model could be used, or the model could be elaborated to incorporate more change points in the parameters of the compartmental model to account for fine grained policy analysis.7 We estimate that official case counts substantially undercount the number of infections. This is not a surprise. Despite recent increases in testing capabilities, our analysis suggests that testing continues to undercount the number of infections by a factor between 6 and 20 for and , the values of we consider most likely. Future work could incorporate IFRs that vary by time or other covariates. Acknowledgments We thank Alexander D’Amour for finding a misstated equation in an earlier version. We thank Amy Herring and David Dunson for comments on an early draft. 7. Conclusion R0 ρT ρT ρT 28 28 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States All of these projections are conditioned on the current policies staying in place and their effects on transmission remaining constant. Tightening or relaxing mitigation policies, or ‘quarantine fatigue’ leading to a decrease in compliance by the public, would impact the trajectory of the spread. Estimates of near one indicate that there is little room for relaxation of mitigation policies without causing an increase in the number of infections and deaths. As mitigation measures are tightened and relaxed over time, an elaboration of our model incorporating multiple change points in the parameters may be useful for future projections and evaluation of the continued efficacy of the measures. ρT Disclosure Statement This work was supported by grants to the Human Rights Data Analysis Group by the John D. and Catherine T. MacArthur Foundation and the Oak Foundation. Kristian Lum and James Johndrow acknowledge funding from National Institute of Environmental Health Sciences (NIEHS) grant 3R01ES028804-03S. 7. Conclusion p = .01 p = .005 p Seroprevalence studies done in two states in the United States result in similar conclusions with respect to undercount. Such studies have only recently become available and do not give snapshots of undercount over time. We believe that the correspondence between our estimates and serological studies that have since been done points to the utility of such a model for estimating key quantities of interest (such as the extent of undercounting), especially early in the epidemic when testing capabilities are yet built up. While the seroprevalence studies using random design are just now reporting results, our initial estimates were first posted in a preprint in late March. This suggests that approaches similar to what we’ve described here could be useful in providing indications of the undercount and the total number of infections of emerging diseases in the early days of its spread. During this time, when the number of cases is relatively low and the rate of spread is nearly exponential, accounting for the time lag between infection and death as we do here can lead to substantial differences in estimates of the total number of cases relative to naive methods, such as simply dividing the total number of deaths by the IFR. Our model also suggests wide variability in the initial transmissibility of the disease prior to intervention policies as well as wide variability in the effects of those policies. For example, we estimate that New York had the highest s at the outset of the outbreak. This is unsurprising considering New York City has so far been the epicenter of the epidemic in the United States. However, estimates of suggest that the spread of the virus in New York has slowed to the lowest rate among the states considered in this analysis. 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Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective cohort study. The Lancet, 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3 32 32 Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Appendix A. Markov Chain Monte Carlo Diagnostics MPSRF California 1.03 Florida 1.01 New York 1.00 Washington 1.00 Table A2. Multivariate Gelman-Rubin potential scale reduction factor. Appendix A. Markov Chain Monte Carlo Diagnostics Figure A1 shows representative trace plots of model parameters for for New York. Once adaptation begins, the algorithm evidently mixes quite well. A more formal assessment of convergence is given in Table A1, which shows the estimate (and upper 95% confidence interval) for the Gelman-Rubin potential scale reduction factor for each parameter, calculated using five independent chains with different starting values. Table A2 shows the multivariate potential scale reduction factor. Values of the statistics ‘near one’ indicate that nonconvergence has not been detected. p = .01 Figure A1. Markov chain Monte Carlo samples of γ − 1, η, ϕ, R0, and T0 for New York in the case where p = .01. Figure A1. Markov chain Monte Carlo samples of γ − 1, η, ϕ, R0, and T0 for New York in the case where p = .01. Table A1. Gelman-Rubin convergence diagnostic point estimate (upper 95% confidence interval) for parameters of model calculated with five independent runs of Markov Chain Monte Carlo. Table A1. Gelman-Rubin convergence diagnostic point estimate (upper 95% confidence interval) for parameters of model calculated with five independent runs of Markov Chain Monte Carlo. California Florida New York Washington Table A1. Gelman-Rubin convergence diagnostic point estimate (upper 95% confidence interval) for parameters of model calculated with five independent runs of Markov Chain Monte Carlo. California Florida New York Washington 33 33 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Table A2. Multivariate Gelman-Rubin potential scale reduction factor. T0 1.013 (1.035) 1.002 (1.003) 1.001 (1.001) 1.001 (1.002) R0 1.011 (1.028) 1.002 (1.004) 1.001 (1.001) 1.001 (1.002) 1/Gamma 1.012 (1.03) 1.003 (1.004) 1 (1.001) 1.001 (1.002) Phi 1.004 (1.008) 1.004 (1.006) 1.001 (1.002) 1.001 (1.002) Eta 1.006 (1.012) 1.012 (1.023) 1.001 (1.002) 1.005 (1.01) MPSRF California 1.03 Florida 1.01 New York 1.00 Washington 1.00 Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances T0 1.013 (1.035) 1.002 (1.003) 1.001 (1.001) 1.001 (1.002) R0 1.011 (1.028) 1.002 (1.004) 1.001 (1.001) 1.001 (1.002) 1/Gamma 1.012 (1.03) 1.003 (1.004) 1 (1.001) 1.001 (1.002) Phi 1.004 (1.008) 1.004 (1.006) 1.001 (1.002) 1.001 (1.002) Eta 1.006 (1.012) 1.012 (1.023) 1.001 (1.002) 1.005 (1.01) Table A2. Multivariate Gelman-Rubin potential scale reduction factor. Appendix B. Simulation Study We conduct a simulation study to assess sensitivity of the method to various assumptions. We analyze five simulation cases. In the first four cases, the daily new infections are obtained from the two-period susceptible- infected-recovered (SIR) model in (3.4), but we explore several ways in which other assumptions can be violated. The parameters of the SIR model are: (corresponding to February 4, since we index January 1 as time 1), , , , , and (corresponding to March 18, 2020). These parameters were selected to give a death series looking roughly like that observed in New York with . In every case, the Poisson model in (3.3) is used to generate deaths given new infections with and shown in Figure 2. We then statistically infer using our method. Since we already provide results for a range of values of , we do not include variation in here. T = 0 35 γ = 1/9 R = 0 3.8 ϕ = .3 η = 1.4 T = 1 78 p = .01 p = .01 θ p p 1. The model is properly specified. 1. The model is properly specified. 2. We use the alternative (incorrect) value of displayed in Figure 5 when statistically inferr θ 3. We assume that is one week too early (corresponding to March 11 instead of the true value of March 18) when statistically inferring. T1 4. We assume that is one week too late (corresponding to March 25 instead of the true value of March 18) when statistically inferring. T1 34 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States 5. The true new infection series is generated by a susceptible-exposed-infected-removed (SEIR) model with two time periods rather than an SIR model with two time periods, but otherwise the model is correctly specified. Appendix B. Simulation Study 35 35 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances 2 3.40 (2.30,3.98) 0.83 (0.82,0.86) 10.70 (10.51,10.90) 3 1.77 (1.61,2.14) 0.92 (0.92,0.92) 10.63 (10.44,10.81) 4 2.87 (2.63,3.33) 0.48 (0.45,0.51) 10.79 (10.54,11.06) 5 3.38 (2.45,3.98) 0.74 (0.72,0.77) 12.19 (11.85,12.54) We report estimates for , , and the proportion of the total population that has ever been infected as of the last day of the simulation in Table A3. In Cases 1-4, the true value of is 0.72 and the true value of the total proportion of the population that has ever been infected is 11.7%, while in case 5 they are 0.72 and 12.1%, respectively. Case 1 demonstrates that we recover the true parameters using our method (all values lie within the posterior credible intervals). Case 2 shows that the only result that has noticeable sensitivity to incorrect specification of is the total proportion infected. Since the true has a longer expected time to death than the used for inference in this case, it makes sense that we slightly underestimate the true proportion of the population that has been infected. Cases 3 and 4 show that estimates of , and, to a lesser extent, are sensitive to incorrect specification of the time point at which the model parameters change , but the total proportion of the population that has ever been infected is actually not very sensitive to misspecification of this parameter. Note, however, that being wrong by one week about typically has a noticeable effect on the model fit, to the extent that one would suspect a problem simply by looking at posterior summaries. This can be seen in Figure A3, which shows the observed death data and the posterior predictive point estimates and intervals for deaths for Case 4. The model fits poorly and is unable to find any set of parameters that reproduces the observed deaths. Thus while there is considerable sensitivity to misspecification of , in the cases we considered, this misspecification can be easily detected by a posterior predictive check. Appendix B. Simulation Study The SEIR model is a popular alternative to the SIR model for modeling SARS-CoV-2. We choose the parameters of the SEIR model to give a death series similar to that for the other four cases. ν Figure A2 shows the simulated data used in Cases 1–4 (left column) and Case 5 (right column). The top panels show deaths, the middle row of panels shows new infections, and the bottom row shows the state variables of the ODE model (SIR in the left column and SEIR in the right column) through a period of 121 days (corresponding to the dates January 1, 2020, through April 30, 2020). Figure A2. Simulated data for examples. Case 1 (shown in the left column) is a SIR model. Case 2 (shown in the right column) is a SEIR model. Values for the bottom panel displaying the SEIR model are displayed as a proportion of the total population and the S compartment has been omitted so that detail for the E, I, and R compartments would be visible. Figure A2. Simulated data for examples. Case 1 (shown in the left column) is a SIR model. Case 2 (shown in the right column) is a SEIR model. Values for the bottom panel displaying the SEIR model are displayed as a proportion of the total population and the S compartment has been omitted so that detail for the E, I, and R compartments would be visible. 35 Table A3. Estimated posterior mean and 95% posterior credible intervals for each simulation scenario. R0 ρT Total Infections 1 3.54 (2.82,3.98) 0.72 (0.70,0.74) 11.57 (11.23,11.91) Table A3. Estimated posterior mean and 95% posterior credible intervals for each simulation scenario. R0 ρT Total Infections 1 3.54 (2.82,3.98) 0.72 (0.70,0.74) 11.57 (11.23,11.91) Table A3. Estimated posterior mean and 95% posterior credible intervals for each simulation scenario. Table A3. Estimated posterior mean and 95% posterior credible intervals for each simulation scenario. Appendix B. Simulation Study Finally, Case 5 shows that, even when the SIR model itself is misspecified and the true generating process includes an exposed period in which people are not infectious, we are able to recover the truth with reasonable accuracy. R0 ρT ρT θ θ θ R0 ρT T1 T1 T1 Overall, the results suggest that, although some types of misspecification can lead to poor estimates of , these types of misspecification may be detectable by posterior predictive checks. Furthermore, the total proportion of the population that has ever been infected, while highly sensitive to the parameter, is reasonably robust to the types of misspecification we explore in this section. This suggests that estimates of the undercount—which will be good if and only if the estimate of the total population ever infected is good—are fairly robust to misspecification when is known. R0 p p 36 36 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Figure A3. Observed death series (red), posterior mean of deaths (dashed black line), and posterior 95% credible interval for deaths (gray region) for Case 4. Figure A3 Observed death series (red) posterior mean of deaths Figure A3. Observed death series (red), posterior mean of deaths (dashed black line), and posterior 95% credible interval for deaths (gray region) for Case 4. ©2020 James Johndrow, Patrick Ball, Maria Gargiulo, and Kristian Lum. This article is licensed under a Creative Commons Attribution (CC BY 4.0) International license, except where otherwise indicated with respect to particular material included in the article. Footnotes 1. See reports on variability in the United States in Lecher et al. (2020, April 16), Silver (2020, April 4), and Patino (2020, May 1). ↩ p y ( , p ), ( , p ), Patino (2020, May 1). ↩ 2. See, e.g., Fleshler and Goodman (2020, June 20) which notes the median age of COVID-19 cases has shifted younger. ↩ 3 It i i ibl t k l di ti ti b t th t t f t F l if th 2. See, e.g., Fleshler and Goodman (2020, June 20) which notes the median age of COVID-19 cases has shifted younger. ↩ 3. It is impossible to make a clean distinction between these two types of parameters. For example, if the rate of spread allows for the number of people requiring care to overwhelm existing health care 37 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infectio Mitigation Policie Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States infrastructures, the case fatality rate will increase, as those who require medical support to survive but cannot receive it will die. ↩ infrastructures, the case fatality rate will increase, as those who require medical support to survive but cannot receive it will die. ↩ 4. See 2010 U.S. Census data (Howden & Meyer, 2011). ↩ 5. Code for our analysis is available at https://github.com/jamesjohndrow/Covid19-modeling. ↩ 6. The study results have not yet been released, but Bonislawski (2020) provides a news media summary. ↩ 7. A GitHub repository with extensions to the current model and applications to other countries’ data can be found at https://github.com/paulo-o/covid19. This repository is still in development and contains ongoing work by two of this article’s authors, James Johndrow and Kristian Lum, as well as Paulo Orenstein [Instituto de Matemática Pura e Aplicada (IMPA)]. ↩ 7. A GitHub repository with extensions to the current model and applications to other countries’ data can be found at https://github.com/paulo-o/covid19. This repository is still in development and contains ongoing work by two of this article’s authors, James Johndrow and Kristian Lum, as well as Paulo Orenstein [Instituto de Matemática Pura e Aplicada (IMPA)]. ↩ References Altieri, N., Barter, R. 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Morbidity and Mortality Weekly Report, 69(29), 960–964. https://doi.org/10.15585/mmwr.mm6929e1 ↩ 39 Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Harvard Data Science Review • Special Issue 1: COVID-19: Unprecedented Challenges and Chances Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Estimating the Number of SARS-CoV-2 Infections and the Impact of Mitigation Policies in the United States Murray, C. J. L. (2020). Forecasting covid-19 impact on hospital bed-days, icu-days, ventilator days and deaths by us state in the next 4 months. medRxiv. https://doi.org/https://doi.org/10.1101/2020.03.27.20043752 ↩ Perkins, A., Cavany, S. M., Moore, S. M., Oidtman, R. J., Lerch, A., & Poterek, M. (2020). Estimating unobserved sars-cov-2 infections in the united states. medRxiv. Prem, K., Liu, Y., Russell, T. W., Kucharski, A. J., Eggo, R. M., Davies, N., Mathematical Modelling of Infectious Diseases COVID-19 Working Group, for C., Jit, M., & Klepac, P. (2020). The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: A modelling study. The Lancet Public Health. https://doi.org/10.1016/S2468-2667(20)30073-6 ↩ Riou, J., Hauser, A., Counotte, M. J., & Althaus, C. L. (2020). Adjusted age-specific case fatality ratio during the COVID-19 epidemic in Hubei, China, January and February 2020. medRxiv. https://doi.org/10.1101/2020.03.04.20031104 ↩ Roberts, G. O., & Rosenthal, J. S. (2001). Optimal scaling for various Metropolis-Hastings algorithms. Statistical Science, 16(4), 351–367. https://doi.org/10.1214/ss/1015346320 ↩ Russell, T. W., Hellewell, J., Jarvis, C. I., van Zandvoort, K., Abbott, S., Ratnayake, R., group, nCov working C., Eggo, R. M., & Kucharski, A. J. (2020). Estimating the infection and case fatality ratio for covid-19 using age-adjusted data from the outbreak on the diamond princess cruise ship. medRxiv. https://doi.org/10.1101/2020.03.05.20031773 ↩ Song, P. X., Wang, L., Zhou, Y., He, J., Zhu, B., Wang, F., Tang, L., & Eisenberg, M. (2020). An epidemiological forecast model and software assessing interventions on covid-19 epidemic in china. medRxiv. https://doi.org/10.1101/2020.02.29.20029421 ↩ Weinberger, D., Cohen, T., Crawford, F., Mostashari, F., Olson, D., Pitzer, V., Reich, N. G., Russi, M., Simonsen, L., Watkins, A., & Vibound, C. (2020). Estimating the early death toll of covid-19 in the united states. medRxiv. https://doi.org/10.1101/2020.04.15.20066431 ↩ Weissman, G. E., Crane-Droesch, A., Chivers, C., Luong, T., Hanish, A., Levy, M. References Z., Lubken, J., Becker, M., Draugelis, M. E., Anesi, G. L., Brennan, P. J., Christie, J. D., Hanson, C. W., Mikkelsen, M. E., & Halpern, S. D. (2020). Locally informed simulation to predict hospital capacity needs during the COVID-19 pandemic. Annals of Internal Medicine, 173(1), 21–28. https://doi.org/10.7326/M20-1260 ↩ Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., & Cao, B. (2020). Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet, 395, 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3 ↩ 40 40
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Snail Recruits Ring1B to Mediate Transcriptional Repression and Cell Migration in Pancreatic Cancer Cells
Cancer research
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804
S 1. Mutation of Ring domains of Ring1A/B proteins does not change their subcellular localization. HA-Snail, Flag-Ring1A-WT or Ring1A-MT (H66A, C69A), or Ring1B-WT or Ring1B-MT (H69A, C72A) were transiently expressed in PanC1 cells and were detected by immunofluorescence staining with Flag or HA antibodies. Confocal imaging showed either Ring1A/B-WT (green) and Snail (red), or Ring1A/B-MT (green) and Snail (red), shared similar distribution in the nucleus (orange). S 1. Mutation of Ring domains of Ring1A/B proteins does not change their subcellular localization. HA-Snail, Flag-Ring1A-WT or Ring1A-MT (H66A, C69A), or Ring1B-WT or Ring1B-MT (H69A, C72A) were transiently expressed in PanC1 cells and were detected by immunofluorescence staining with Flag or HA antibodies. Confocal imaging showed either Ring1A/B-WT (green) and Snail (red), or Ring1A/B-MT (green) and Snail (red), shared similar distribution in the nucleus (orange). S 1. Mutation of Ring domains of Ring1A/B proteins does not change their subcellular localization. HA-Snail, Flag-Ring1A-WT or Ring1A-MT (H66A, C69A), or Ring1B-WT or Ring1B-MT (H69A, C72A) were transiently expressed in PanC1 cells and were detected by immunofluorescence staining with Flag or HA antibodies. Confocal imaging showed either Ring1A/B-WT (green) and Snail (red), or Ring1A/B-MT (green) and Snail (red), shared similar distribution in the nucleus (orange). S2. qRT-PCR analysis of the known PRC1 target genes HOXC5 and HOXB4(1) and Snail target gene Cyclin D2(2) in PanC1-shLuc and PanC1-shRing1A/B cells. GAPDH was used as loading reference. Data were presented as Mean ±SD from 3 independent experiments. #1 and #2, different cell pools generated from Ring1A and Ring1B double knocking down by shRNAs; ∗ indicates statistical significance, P<0.05. Primers used for real-time PCR are as follow: Human HOXC5, forward 5-TAAGCAGAGCCCCAATATCCC-3, and reverse 5- CCAATCCGCCGTAGCAGTAC-3; Human HOXB4, forward 5-TCACGT GAGCACGGTAAAC-3, and reverse 5-CAGGTAGCGGTTGTA GTGAAA-3; Human Cyclin D2, forward 5-CTGTGTGCCACCGACTTTAAGTT-3, and reverse 5- GATGGCTGCTCCCACACTTC-3; Human Snail, forward 5-CCTCCCTGTCAGATGAGGAC- 3, and reverse 5-CCAGGCTGAGGTATTCCTTG-3; Human E-cadherin, forward 5- TGCCCAGAAAATGAAAAAGG-3, and reverse 5-GTGTATGTGGCAATGCGTTC-3. S2. qRT-PCR analysis of the known PRC1 target genes HOXC5 and HOXB4(1) and Snail target gene Cyclin D2(2) in PanC1-shLuc and PanC1-shRing1A/B cells. GAPDH was used as loading reference. Data were presented as Mean ±SD from 3 independent experiments. #1 and #2, different cell pools generated from Ring1A and Ring1B double knocking down by shRNAs; ∗ indicates statistical significance, P<0.05. Primers used for real-time PCR are as follow: Human HOXC5, forward 5-TAAGCAGAGCCCCAATATCCC-3, and reverse 5- CCAATCCGCCGTAGCAGTAC-3; Human HOXB4, forward 5-TCACGT GAGCACGGTAAAC-3, and reverse 5-CAGGTAGCGGTTGTA GTGAAA-3; Human Cyclin D2, forward 5-CTGTGTGCCACCGACTTTAAGTT-3, and reverse 5- GATGGCTGCTCCCACACTTC-3; Human Snail, forward 5-CCTCCCTGTCAGATGAGGAC- 3, and reverse 5-CCAGGCTGAGGTATTCCTTG-3; Human E-cadherin, forward 5- TGCCCAGAAAATGAAAAAGG-3, and reverse 5-GTGTATGTGGCAATGCGTTC-3. S3. Simultaneous depletion of Ring1A and Ring1B results in global decrease of H2AK119 S3. Simultaneous depletion of Ring1A and Ring1B results in global decrease of H2AK119 S3. S 1. Mutation of Ring domains of Ring1A/B proteins does not change their subcellular localization. HA-Snail, Flag-Ring1A-WT or Ring1A-MT (H66A, C69A), or Ring1B-WT or Ring1B-MT (H69A, C72A) were transiently expressed in PanC1 cells and were detected by immunofluorescence staining with Flag or HA antibodies. Confocal imaging showed either Ring1A/B-WT (green) and Snail (red), or Ring1A/B-MT (green) and Snail (red), shared similar distribution in the nucleus (orange). Simultaneous depletion of Ring1A and Ring1B results in global decrease of H2AK119 monoubiquitination, and Snail loss of repression on E-cadherin in AsPC1 cells. (A) Ring1A and Ring1B were knocked down simultaneously in AsPC1 cells by specific shRNAs via viral infection. Western blot showed Ring1A and Ring1B were depleted in AsPC1 cells. Similar to that observed in PanC1 cells, depletion of Ring1A/B resulted in global decrease of H2AK119Ub1, but no obvious change on H3K27Me3. (B) Snail was stably expressed in AsPC1-shLuc or AsPC1-shRing1A/B cells. E-cadherin was reduced when Snail was expressed in and Ring1B were knocked down simultaneously in AsPC1 cells by specific shRNAs via viral infection. Western blot showed Ring1A and Ring1B were depleted in AsPC1 cells. Similar to that observed in PanC1 cells, depletion of Ring1A/B resulted in global decrease of H2AK119Ub1, but no obvious change on H3K27Me3. (B) Snail was stably expressed in AsPC1-shLuc or AsPC1-shRing1A/B cells. E-cadherin was reduced when Snail was expressed in AsPC1-shLuc cells, but was not changed in AsPC1-shRing1A/B cells. Whole cell lysate (100µg) was loaded and β-actin was used as loading control. (C, D) qRT-PCR analysis of Snail target genes E-cadherin and Cyclin D2 in AsPC1-shLuc and AsPC1-shRing1A/B cells. GAPDH was used as loading reference. Data were presented as Mean ±SD from 3 independent experiments. #1 and #2, different cell pools generated from Ring1A and Ring1B double knocking down by shRNAs; ∗ indicates statistical significance, P<0.05. Reference 1. del Mar Lorente M, Marcos-Gutiérrez C, Pérez C, Schoorlemmer J, Ramírez A, Magin T, et al. Loss-and gain-of-function mutations show a polycomb group function for Ring1A in mice. Development. 2000;127:5093-100. 2. Vega S, Morales AV, Ocaña OH, Valdés F, Fabregat I, Nieto MA. Snail blocks the cell cycle and confers resistance to cell death. Genes & development. 2004;18:1131-43.
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English
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Genetic and Functional Characterization of Novel Brown-Like Adipocytes Around the Lamprey Brain
Frontiers in cell and developmental biology
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ORIGINAL RESEARCH published: 01 July 2021 doi: 10.3389/fcell.2021.674939 Genetic and Functional Characterization of Novel Brown-Like Adipocytes Around the Lamprey Brain XiaoLuan Xu1,2†, AnQi Ma1,2†, TieSong Li1,2†, WenXue Cui1,2, XueFeng Wang1,2, Jun Li1,2, Qingwei Li1,2 and Yue Pang1,2* 1 College of Life Sciences, Liaoning Normal University, Dalian, China, 2 Lamprey Research Center, Liaoning Normal University, Dalian, China During the process of vertebrate evolution, many thermogenic organs and mechanisms have appeared. Mammalian brown adipose tissue (BAT) generates heat through the uncoupling oxidative phosphorylation of mitochondria, acts as a natural defense against hypothermia and inhibits the development of obesity. Although the existence, cellular origin and molecular identity of BAT in humans have been well studied, the genetic and functional characteristics of BAT from lampreys remain unknown. Here, we identified and characterized a novel, naturally existing brown-like adipocytes at the lamprey brain periphery. Similar to human BAT, the lamprey brain periphery contains brown- like adipocytes that maintain the same morphology as human brown adipocytes, containing multilocular lipid droplets and high mitochondrion numbers. Furthermore, we found that brown-like adipocytes in the periphery of lamprey brains responded to thermogenic reagent treatment and cold exposure and that lamprey UCP2 promoted precursor adipocyte differentiation. Molecular mapping by RNA-sequencing showed that inflammation in brown-like adipocytes treated with LPS and 25HC was enhanced compared to controls. The results of this study provide new evidence for human BAT research and demonstrate the multilocular adipose cell functions of lampreys, including: (1) providing material energy and protecting structure, (2) generating additional heat and contributing to adaptation to low-temperature environments, and (3) resisting external pathogens. Edited by: Tobias Fromme, Technical University of Munich, Germany Reviewed by: Jasper Martin Anton De Jong, Yale University, United States Craig Porter, University of Arkansas for Medical Sciences, United States *Correspondence: Yue Pang pangyue01@163.com †These authors have contributed equally to this work Reviewed by: Jasper Martin Anton De Jong, Yale University, United States Craig Porter, University of Arkansas for Medical Sciences, United States *Correspondence: Yue Pang pangyue01@163.com †These authors have contributed equally to this work Specialty section: This article was submitted to Evolutionary Developmental Biology, a section of the journal Frontiers in Cell and Developmental Biology Keywords: brown adipocytes, lamprey, immune response, uncoupling protein 2 (UCP2), evolution Keywords: brown adipocytes, lamprey, immune response, uncoupling protein 2 (UCP2), evolution Citation: Xu X, Ma A, Li T, Cui W, Wang X, Li J, Li Q and Pang Y (2021) Genetic and Functional Characterization of Novel Brown-Like Adipocytes Around the Lamprey Brain. Front. Cell Dev. Biol. 9:674939. doi: 10.3389/fcell.2021.674939 There are large number of obesity-related diseases, including type 2 diabetes, insulin resistance, heart disease, dyslipidemia, hypertension and various cancers (Bornfeldt and Tabas, 2011; Harms and Seale, 2013). For many decades, brown adipose tissue (BAT) in mammals, as an important heat-generating tissue, has been considered an attractive target for treating metabolic disease and promoting weight loss (Vitali et al., 2012; Guénantin et al., 2017; Chan et al., 2019). July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org Brown-Like Adipocytes Around Lamprey Brain Xu et al. Xu et al. oxidative phosphorylation (Cannon and Nedergaard, 2004). Birds can regulate body temperature via the non-shivering thermogenesis of muscles (Mozo et al., 2005). Fish can maintain higher brain temperatures than the ambient temperature through the ATP-dependent Ca2+ cycle in the sarcoplasmic reticulum of heating cells around the brain (Block, 1987). Moreover, many animals use stored fat as an energy source; for example, C. elegans store lipid in their intestinal epithelial cells and Drosophila have fat bodies (Imrie and Sadler, 2010). Therefore, the identification of possible thermogenic adipocytes in lampreys was interesting. As the brain tissue of lampreys seems to play a positive role in the spawning act, we examined the morphology and development of the brain tissue and identified the characteristics of these heat- producing fat cells via histology, biochemistry, molecular biology, and transcriptome analyses. To our surprise, the morphology of the brain tissue included multivacuolar fat; this finding led us to speculate that the brain tissue shows differential thermogenic ability. Brown adipocytes in BAT contain multilocular lipid droplets and are densely packed with mitochondria, promoting energy expenditure. BAT forms prior to other types of fat depots during embryonic development. In human infants, BAT depots have also been found in interscapular regions, but BAT depots in adults regress or are absent (Heaton, 1972; Lidell et al., 2013). Previous studies have demonstrated that most brown adipocytes originate from precursor cells in embryonic mesodermal somites that can also develop into skeletal muscle cells (Seale et al., 2008; Lepper and Fan, 2010; Sanchez-Gurmaches et al., 2012). Histology Lampreys were anesthetized with 0.05% tricaine methanesulfonate (MS-222; 3-aminobenzoic acid ethyl ester, Sigma), and their brain tissues were then stripped and fixed in 10% buffered formalin and embedded in paraffin wax. The paraffin-embedded tissues were sectioned to a thickness of approximately 4 µm. Tissues were then stained with hematoxylin and eosin (HE). p p Lampreys have recently received much attention in the fields of comparative development and genomics. Lampreys belong to the jawless vertebrates and are one of the two most ancient groups of vertebrate representatives. The transition from jawless to jawed vertebrates was caused by some significant evolutionary events, including gene origination and evolution, gene duplication, and cell population and tissue structure changes. Due to its unique evolutionary status, lampreys are essential for exploring the evolution of vertebrates and the origin of different functional mechanisms (Smith et al., 2018; Guan et al., 2019). In addition, lampreys are typical migratory organisms that live in the ocean for part of the year. In autumn, they swim from the ocean into rivers and inhabit the downstream portions of rivers until May or June of the next year. The lampreys travel further upstream in the rivers and lay eggs when the water temperature rises to approximately 15◦C. Thus, we wondered how lampreys maintain an elevated body temperature while their body temperature appears to fluctuate with the temperature of the surrounding water. In mammalian BAT, fatty acids are burned to produce heat through the uncoupling of mitochondrial Citation: In rodents, the major BAT depots are located in the interscapular, axillary and cervical pad regions (Wu et al., 2013; Kajimura and Saito, 2014). In sea lampreys, males exhibit the secondary sexual characteristic of thermogenic adipose tissue, which immediately increases heat production during mating (Chung-Davidson et al., 2013). In progenitor cell populations, myogenic factor 5 (Myf5) and Pax7 expression is considered a selective marker of skeletal myoblast (Lepper and Fan, 2010; Sanchez-Gurmaches et al., 2012), and brown adipocyte precursor cells express a gene profile similar to that of muscle (Timmons et al., 2007); in addition, they possess related mitochondrial proteomes (Forner et al., 2009). Brown adipocytes in BAT are defined as cells containing multilocular lipid droplet, high mitochondrial content and the expression of brown adipocyte markers, including uncoupling protein-1 (Ucp1) (Kopecky et al., 1995; Bettini et al., 2019), cell death- inducing DNA fragmentation factor alpha-like effector A (Cidea) (Zhou et al., 2003; Toh et al., 2008), type II iodothyronine 5′- deiodinase (Dio2) (Chan et al., 2019), cytochrome c oxidase polypeptide 7A1 (Cox7a1) and cytochrome c oxidase subunit VIIIb (Cox8b) (Chan et al., 2019) as well as transcriptional regulators, including PR domain zinc finger protein 16 (PRDM16) (Forner et al., 2009), peroxisome proliferator- activated receptor-γ coactivator 1-α (Pgc-1α) (Hondares et al., 2006; Hallberg et al., 2008), and peroxisome proliferator-activated CCAAT/enlmnccr-binding protein B (C/EBPb) (Tanaka et al., 1997; Carmona et al., 2005; Karamanlidis et al., 2007) and receptor alpha (PPARα) (Tai et al., 1996; Siersbæk et al., 2012). Collection and Maintenance of Animals Collection and Maintenance of Animals Adult lamprey specimens of Lethenteron reissneri, including both males and females, were captured from the Tong jiang River of China. They were kept in a glass container at a temperature of 4◦C. Lamprey handling and all of the experimental procedures were approved by the Animal Welfare and Research Ethics Committee of the Institute of Dalian Medical University (Permit Number: SCXK2008-0002). Isolation of Brown Adipocytes From the Outside Surface of the Adult Lamprey Brain Brown adipocytes were isolated from the outside surface of the adult lamprey brain and then digested with 0.1% collagenase for 10 min. The cell suspension was passed through a 70 µM cell strainer and centrifuged at 1500 rpm for 5 min to collect the adipocytes. Since lampreys live in cold water, the cells were then cultured at 18◦C and expanded in M199 medium supplemented with 10% FBS and 1% penicillin/streptomycin. Cell samples were collected for staining, RNA extraction or immunogenic stimulation. Transmission Electron Microscopy After the tissue was isolated, it was quickly placed into pentanediol fixed solution at 4◦C to maintain the tissue cells in the original living state to the greatest extent possible. The tissue was then fixed with pentanediol for 2 h, washed with PBS several times, progressively dehydrated with gradient ethanol and acetone, and embedded in Epon 812. The sections were stained with 2% uranyl acetate (w/v) in 70% methanol (v/v) and 0.5% lead citrate. Observations and image recording of the cells were performed with a JEM-2000EX TEM. Immunohistochemical Staining Paraffin-embedded brain tissue sections were deparaffinized in xylene and hydrated with ethanol. The tissue sections were incubated with an anti-L-UCP2 polyclonal Ab at a 1/1600 dilution (0.3 µg/mL) for 3 h at room temperature. Normal mouse IgG was used as a negative control. The sections were stained with diaminobenzidine (DAB) and counterstained with hematoxylin. After dehydration, the sections were successively passed through xylene at different concentrations for 15 min and then mounted in neutral resin. Phylogenetic Analyses of the UCP Family Phylogenetic Analyses of the UCP Family All of the amino acid sequences of Lethenteron reissneri UCP family members were obtained from a three-generation sequencing library, and the corresponding sequences of other species were obtained from the Ensemble database and the NCBI database. SMART and Pfam were used to predict the functional domains of UCP family genes. MEME online software was used to analyze the conserved amino acid sequence of the UCP protein family, and 26 different motifs were identified from the results. All collected amino acid sequences of the UCP protein family from different species were input into Clustal X software, and a phylogenetic tree was then constructed in MEGA 7.0 software via the NJ method. A synteny analysis of the UCP protein family was conducted by using Genomicus online software, which can be used not only to establish genetic homology but also to provide clues about the origin of genetic mechanisms. Quantitative Real-Time PCR (Q-PCR) ( ) Brown-like adipocytes were cultured in M199 medium for 6 h and incubated with LPS (100 µg/mL), 25-hydroxycholesterol (50 µM), adrenaline (1 µM), isoprenaline (10 µM) and norepinephrine (0.5 µM) for 24 h at 18◦C. In addition, G418 was used to screen 3T3-L1 cells stably overexpressing UCP2 and control cells, and uninduced precursor adipocytes and differentiated mature adipocytes were collected. Total RNA was extracted with a MiniBEST Universal RNA Extraction kit (TAKARA, China) according to the manufacturer’s instructions, and the RNA was treated with DNase I (TaKaRa, China). Reverse transcription, Q-PCR were performed as previously described (Pei et al., 2016). The sequences of the primers and the accession numbers of the genes selected as brown-like adipocyte markers, regulators and immune molecules are provided in Supplementary Tables 1–3. Each reaction was performed in triplicate, and the data were normalized to those of L-gapdh as an internal control. Relative gene expression levels in brown-like adipocytes were calculated using the delta Ct (11Ct) method. BODIPY R⃝Lipid Probe Staining The neutral lipids of brown-like adipocytes were stained with Hoechst (Sigma) for 5 min to visualize cell nuclei and stained with 1:250 BODIPY R⃝Lipid Probes (Thermo Fisher Scientific, United States) for 40 min. Then, the cells were washed three times with PBS and analyzed on a Zeiss Axio Scope A1upright microscope (Carl Zeiss, Inc.). Oxygen Consumption (OCR) and Extracellular Acidification (ECAR) Measurements Cells were loaded into XF24 islet capture microplates (Seahorse Bioscience) before the experiment, and the optimal cell density (50000 cells/well) was determined experimentally to ensure a proportional response to the probe according to the cell number. The cells were divided into two subsets: one subset was cultured for 8 h at 4◦C for cold exposure, and the other subset was cultured for 8 h at 20◦C. To determine the absolute respiratory rate, cells were plated in non-buffered DMEM containing 25 mM Preparation of the LrUCP2 Protein and Anti-L-UCP2 Antibodies The open reading frame (ORF) of LrUCP2 was subcloned into the pCold I vector. The LrUCP2 protein was purified by a Ni-NTA His-Bind column. Four mice were used for antibody preparation. Each mouse was first injected with 100 µg of protein mixed with complete Freund’s adjuvant (CFA) (Sigma, United States) and subsequently injected with 50 µg of protein mixed with incomplete Freund’s adjuvant. After four injections at 1 week intervals, blood was drawn from the mouse, and antibody purification was conducted using Protein A (GenScript, United States). The ELISA method was used to determine the antibody titers. Briefly, the rL-UCP2 protein was diluted with a coating buffer (1:500) at 4◦C overnight, and the mouse antiserum was serially diluted; normal mouse serum (1:50000) was used as the negative control, and PBS was used as the blank control. The ELISA substrate (100 µL/well) was used for color detection, and the OD at 450 nm was detected. The final titer of the obtained antibody was determined. Oil Red O Staining Brown-like adipocytes from the lamprey brain periphery and white adipocytes from the peripheral membrane tissue of the Frontiers in Cell and Developmental Biology | www.frontiersin.org July 2021 | Volume 9 | Article 674939 2 Brown-Like Adipocytes Around Lamprey Brain Xu et al. crucian carp brain were stained with 0.3% (w/v) Oil Red O (Sigma–Aldrich, St. Louis, MO, United States) for 6 min at room temperature after being fixed with anhydrous ethanol. Cells that had been counterstained with hematoxylin for 5 min were studied using light microscopy (LSM 780, ZEISS, Germany). glucose and 1 mM pyruvate. Measurements were obtained with an Extracellular Flux Analyzer (Seahorse Bioscience, Billerica, MA, United States) to record OCR to represent mitochondrial respiration and ECAR to represent glycolysis. Determination of ATP and Free Fatty Acids (FFAs) GraphPad Prism 8 (GraphPad Software, La Jolla, CA, United States) was used for all statistical analyses. Differences between treatment groups were determined with Student’s t-test. P < 0.05 was set as the threshold for significance (∗P < 0.05, ∗∗P < 0.01). Each sample was analyzed in triplicate, and the experiment was performed three times. Bar charts were generated to show the means ± SDs of three independent experiments. The ATP and FFA concentrations of 3T3-L1 cells that overexpressed LrUCP2 with or without induction were determined by using an Enhanced ATP Assay Kit (Beyotime, Shanghai, China) and a Free fatty acid Detection Kit (Solarbio, Beijing, China), respectively. Cell Culture The 3T3-L1 cell line was purchased from the American Type Culture Collection and cultured in DMEM with 10% FBS. July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 3 Brown-Like Adipocytes Around Lamprey Brain Xu et al. package through one scaling normalized factor. Differential expression analysis of two samples was performed using the DEGseq (2010) R package. P-values were adjusted using q-values (Storey and Tibshirani, 2003). A q-value < 0.005 and a | log2 (foldchange)| > 1 were set as the thresholds for significantly differential expression. Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by using the GOseq R package-based Wallenius non-central hypergeometric distribution (Young et al., 2010), which can adjust for gene length bias in DEGs. KEGG (Kanehisa et al., 2008) is a database resource for understanding the high-level functions and utilities of biological systems, such as cells, organisms and ecosystems, from molecular-level information, especially large- scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies1. We used KOBAS (Mao et al., 2005) software to test the statistical enrichment of differentially expressed genes in KEGG pathways. For adipocytes differentiation, 3T3-L1 cells were grown to confluence, and were treated with medium containing 10% FBS, 0.5 mM isobutylmethylxanthine, 125 nM indomethacin, 1 mM dexamethasone, 20 nM insulin, and 1 nM T3. After 48 h, the cell culture medium was replaced by DMEM containing only 10% FBS, 1 nM T3, and 20 nM insulin. After 2 days, the medium was changed, and the cells were cultured with DMEM until harvest. The Origin and Morphological Characteristics of the Cells Around Lamprey Brain Tissue Lampreys have a head and a brain, which is divided into five parts (telencephalon, diencephalon, mesencephalon, cerebellum and rhombencephalon), and the overall shape of the brain is elongated (Figure 1A). Lamprey brain tissues are surrounded by a group of large cells (black line) distributed from the olfactory bulb to the cerebellum, especially in the diencephalon, mesencephalon, and cerebellum (Figures 1A,B). Hematoxylin and eosin staining (Figure 1C) revealed the existence of different types of cells around brain tissues, such as myofibroblasts and the large cells shown in Figure 1B. Spindle-shaped myofibroblasts are attached to the adjacent cartilage, and the myofibroblasts connecting the two sides of the cartilage are the large peripheral cells of the brain and myotube system. The myotube system is composed of multiple myoblasts and is characterized by multinucleation. The large cells at the brain periphery gradually become distinguishable from the myofibroblasts. There were also white adipocytes, blood vessels surrounded by multiple large cells, and pigment cells that could be clearly seen in the peripheral brain tissue. Pigment cells exhibit a protective function similar to the skull and blood–brain barrier. Some of the cells observed at the brain periphery were not of the traditional round shape but RNA-Seq Data Analysis Brown-like adipocytes were cultured in M199 medium for 6 h, then incubated with LPS (100 µg/mL) and 25-hydroxycholesterol (50 µM) for 12 h and 24 h. 25HC can induce the production of IL-8 and a variety of cytokines and cause a proinflammatory response (Sottero et al., 2007; Gold et al., 2012). It was used to simulate a proinflammatory environment to test whether lamprey brown-like adipocytes have an effect on this. RNA- seq libraries were generated using the NEBNext R⃝UltraTM RNA Library Prep Kit for Illumina R⃝(NEB, United States) following the manufacturer’s recommendations, and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot- HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on the Illumina HiSeq platform, and paired-end reads were generated. Raw data were first processed with in-house Perl scripts. In this step, clean data were obtained by removing reads containing adapters or poly-N sequences and low-quality reads from the raw data. All downstream analyses were based on clean data with high quality. Transcriptome assembly was accomplished using Trinity (Grabherr et al., 2011) with min_kmer_cov set to 2 by default and all other parameters set to the defaults. The accession number for the RNA-seq sequencing data is PRJNA733594. Confocal Microscopy for the Localization of LrUCP2 Firstly, 3T3-L1 cells were cultured overnight in DMEM containing 10% FBS. Then, the cells were transfected with pEGFP-N1 and pEGFP-N1-ucp2 by using Lipofectamine 3,000 (Life Technologies, Thermo Fisher Scientific, Waltham, MA, United States) in 8-well chamber slides. At 30 h after transfection, confocal microscopy was used to detect the localization of lamprey UCP2 in 3T3-L1 cells. 1http://www.genome.jp/kegg/ Transcriptome Analyses Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by the edgeR program July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 4 Brown-Like Adipocytes Around Lamprey Brain Xu et al. FIGURE 1 | The structure of the lamprey brain and multilocular adipocytes (Lethenteron reissneri). (A) Coronal section view of the adult lamprey brain. Scale bars, 200 µm. (B) The morphology of multilocular adipocytes and the location in the olfactory bulb. di, diencephalon; mes, mesencephalon; met, metencephalon; ob, olfactory bulb; cer, cerebrum. Scale bars, 20 µm or 50 µm. (C) Morphological observation of the origin and differentiation of multilocular adipocytes. x, myofibroblasts; y, myofibroblasts; z, multilocular adipocytes; {, myotube; |, white adipocytes; }, blood vessel; ~, pigment cells. The images on the right are partial magnifications of the image on the left. (D) The black arrow shows that multilocular adipocytes can extend into brain tissue (left pane). The interaction of multilocular adipocytes with the brain (right pane). FIGURE 1 | The structure of the lamprey brain and multilocular adipocytes (Lethenteron reissneri). (A) Coronal section view of the adult lamprey brain. Scale bars, 200 µm. (B) The morphology of multilocular adipocytes and the location in the olfactory bulb. di, diencephalon; mes, mesencephalon; met, metencephalon; ob, olfactory bulb; cer, cerebrum. Scale bars, 20 µm or 50 µm. (C) Morphological observation of the origin and differentiation of multilocular adipocytes. x, myofibroblasts; y, myofibroblasts; z, multilocular adipocytes; {, myotube; |, white adipocytes; }, blood vessel; ~, pigment cells. The images on the right are partial magnifications of the image on the left. (D) The black arrow shows that multilocular adipocytes can extend into brain tissue (left pane). The interaction of multilocular adipocytes with the brain (right pane). lampreys, we conducted RNA-seq analysis of the multilocular adipocytes and annotated all genes based on the first chromosomal-level assembly of the Reissner lamprey genome (PRJNA558325). Many homologs of thermogenesis and lipid metabolism regulators found in human brown adipocytes were identified in lampreys, as shown in Table 1. The mRNA expression of these genes was detected in different lamprey tissues. Our data demonstrated that Acbp was highly expressed in all tissues, while Scd1, Fads2, Fabp1, Fabp3, Acadl, Acadm, Plin and Slc25a20 were highly expressed in the gill, kidney, muscle and supraneural body (Figure 3A). Transcriptome Analyses Interestingly, the expression of Ucp1, which is considered to be related to thermogenesis in mammals, was very low in all tissues of lampreys. We also detected the expression of BAT metabolism and thermogenic regulators, such as Scd1, Fabp1, Fabp3, Acsl, Acadm, Acadl, Pgc-1α, Plin, Cpt1, Cpt2 and Ucp1, in lamprey multilocular adipose cells. The results showed that the mRNAs of Scd1, Fabp1, Fabp3, Acsl3, Acadm, Acadl, Pgc-1α, Plin and Cpt1 were expressed in the multilocular adipose cells, while Cpt1 and Ucp1 showed extremely low expression, and the mRNA expression of Ucp2 was higher than that of Ucp1 (Figure 3B). rather were fibrous (Figure 1D). Some cells in the brain can also extend to the peripheral tissue of the brain, and can communicate with each other, rather than existing independently. The morphological characteristics of the large cells were observed by live cell imaging microscopy and confocal fluorescence microscopy. The results demonstrated that the morphology of the cells was round or oval and that they were approximately 30–50 µm in diameter; the cytoplasm contained multiple dispersed lipid droplets, and the round nucleus was located in the cell center (Figures 2A,B). When cells were stained with Oil Red O and lipid probes, the results were consistent with those described above (Figures 2C,D). In addition, a large number of mitochondria were distributed in the inner membrane of cells according to either mitochondrial staining combined with confocal fluorescence microscopy or transmission electron microscopy (Figures 2E,F). In summary, we referred to the large cells as multilocular adipocytes. Identification of the Molecular Features and Functional Phenotypes of Brown-Like Adipocytes in Multilocular Adipocytes Because the multilocular adipose cells showed some morphological and molecular characteristics of BAT, we suspected that these cells might be thermogenic and exhibit a function related to energy metabolism. To further characterize To further identify gene signatures and characterize the thermogenic potential of the cells surrounding the brain in July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 5 Brown-Like Adipocytes Around Lamprey Brain Xu et al. FIGURE 2 | Morphological characteristics of brown adipocytes surrounding the brain tissue of lampreys. (A) Time-lapse images of brown adipocytes were acquired every 10 min for 24 h. (B) The brown adipocytes were incubated in medium containing 0.5 µg CellMaskTM orange plasma membrane stain for 3 min and then stained with Hoechst. (C) Oil Red O was used to examine the morphology of brown adipocytes and white adipocytes. (D) Brown adipocytes were stained with lipid probes prior to staining with Hoechst. (E) The brown adipocytes were incubated in medium containing 30 nM MitoTracker Red. Merged images of cells double-stained with Hoechst are shown. (F) Mitochondria with dense cristae and larger lipid droplets in brown adipocytes under transmission electron microscopy (left pane). A higher magnification image is shown in the right pane. FIGURE 2 | Morphological characteristics of brown adipocytes surrounding the brain tissue of lampreys. (A) Time-lapse images of brown adipocytes were acquired every 10 min for 24 h. (B) The brown adipocytes were incubated in medium containing 0.5 µg CellMaskTM orange plasma membrane stain for 3 min and then stained with Hoechst. (C) Oil Red O was used to examine the morphology of brown adipocytes and white adipocytes. (D) Brown adipocytes were stained with lipid probes prior to staining with Hoechst. (E) The brown adipocytes were incubated in medium containing 30 nM MitoTracker Red. Merged images of cells double-stained with Hoechst are shown. (F) Mitochondria with dense cristae and larger lipid droplets in brown adipocytes under transmission electron microscopy (left pane). A higher magnification image is shown in the right pane. energy production route from aerobic to glycolytic metabolism. In conclusion, we preliminarily considered the multilocular adipocytes in the periphery of the lamprey brain to be brown- like adipocytes. the thermogenesis potential of multilocular adipose cells, the cells were treated with adrenaline, isoprenaline and noradrenaline, which are thermogenesis-inducing agents in mammalian BAT. Identification of the Molecular Features and Functional Phenotypes of Brown-Like Adipocytes in Multilocular Adipocytes We compared the gene expression levels of these thermogenic and lipid metabolism regulators in multilocular adipose cells before or after stimulation. The expression of these important regulators was significantly higher in multilocular adipose cells treated with adrenaline than in control cells treated with PBS (Figure 3C). However, there was a little change in the expression of these genes when multilocular adipose cells were treated with isoprenaline and noradrenaline (Figure 3C). In addition, we found that Ucp1 did not respond to stimulation; however, the expression of Ucp2 was highly upregulated after treatment with adrenaline. Molecular Evolution of the UCP Gene Family, a Characteristic Marker of Brown Adipocytes UCP1 is an important marker molecule of brown adipocytes. By searching the Reissner lamprey genome database, we identified three UCP gene families. Based on structural domain, motif and syntenic gene analyses, three UCP genes were identified as orthologous genes of mammalian UCP1, UCP2 and UCP4 (Supplementary Figure 1). The phylogenetic analysis showed that the UCP paralogs of Reissner lamprey can be grouped into two major clades: one encompassing the LrUCP1 and LrUCP2 paralogs and another comprising the LrUCP4 paralog. The results also showed that LrUCP1 appears to be an ancestral molecule of vertebrate UCP1, UCP2, and UCP3, whereas UCP2 and UCP4 show high homology with other vertebrate homologs (Figure 4A). From the above results, we deduced the evolutionary history of the UCP gene family (Figure 4B). The origins of the UCP molecule can be traced back to protists. The analyses suggest that UCPs were acquired through three rounds of gene duplication, in which the first duplication gave rise to the ancestral UCP1-UCP3, UCP4 and UCP5 genes. The second duplication gave rise to the ancestral UCP1 and UCP2/UCP3 The Seahorse XF Extracellular Flux Analyzer provides real- time measurements of mitochondrial respiration and glycolysis in cultured cells, reported as OCR and ECAR values, respectively. Bioenergetic assays of multilocular adipocytes showed an altered mitochondrial function at 4◦C relative to 20◦C. The basal OCR- and ECAR-induced maximal OCR of multilocular adipose cells showed an approximately 50% increase at 4◦C compared to that at 20◦C (Figure 3D). The multilocular adipose cells treated at 4◦C showed increases in both OCR and ECAR relative to those in the control at 20◦C. The stressed OCR (%) at 4◦C was higher than that in the control, but the difference was not significantly greater than that for the stressed ECAR (%) (Figure 3E). This finding indicated that treatment at 4◦C preferentially changed the July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 6 Brown-Like Adipocytes Around Lamprey Brain Xu et al. TABLE 1 | Identification of the molecule relative to thermogenesis and lipid metabolism in lamprey. Gene symbol Description ORF (bp) Amino acids (aa) Function References SCD1 Stearoyl-CoA desaturase 1 1140 379 It plays a pivotal role in the synthesis of fatty acids. Young et al. (2010) FADS2 Fatty acid desaturase-2 1143 380 It plays a very important role in the biosynthesis of polyunsaturated fatty acids. Kanehisa et al. Molecular Evolution of the UCP Gene Family, a Characteristic Marker of Brown Adipocytes (2008) ACBP Acyl coenzyme A binding protein 264 87 It can bind, store and transport long chain lipophyl CoA with high specificity and affinity. Mao et al. (2005) FABP1 Fatty acid-binding protein 1 396 131 It regulates fatty acid oxidation, lipid metabolism such as triglyceride synthesis and phospholipid synthesis. Shu et al. (1999) FABP3 Fatty acid-binding protein 3 405 134 It mainly binds free fatty acids and other hydrophobic ligands in cells and transports them to organelles such as peroxidase mitochondria and nucleus. Gesta et al. (2007) LPL Lipoprotein lipase 1467 488 It can catalyze the hydrolysis of triglyceride to glycerol and free fatty acid. Rodeheffer et al. (2008) ACSL Long-chain fatty acyl CoA synthetases 1413 470 It catalyzes the synthesis of substrate fatty acyl coenzyme A from fatty acids and coenzyme A. Ohno et al. (2012) FATP1 Fatty acid transport protein 1 1425 474 It is an important protein for the transport of long chain fatty acids. Kajimura et al. (2009) CPT1 Carnitine palmitoyltransferase 1 2076 691 It is a key enzyme for carnitine-dependent transport through the mitochondrial inner membrane Mendes et al. (2020) CPT2 Carnitine palmitoyltransferase 2 2091 696 It can oxidize long-chain fatty acids in the mitochondria. Blondin et al. (2020) ACADL Acyl-CoA dehydrogenase long chain 1683 560 It is a family of mitochondrial flavin enzymes involved in the metabolism of fatty acids and branched amino acids. Zhao et al. (2020) ACADM Acyl-CoA dehydrogenase medium chain 1353 450 It can catalyze the initial steps of mitochondrial fatty acid-oxidation pathway. Kim et al. (2006) UCP1 Uncoupling protein 1 951 316 This gene is expressed only in brown adipose tissue, a specialized tissue which functions to produce heat. Ricquier (2017) UCP2 Uncoupling protein 2 957 318 It is thought to play a role in non-shivering thermogenesis, obesity and diabetes. Li et al. (2019) PGC-1α PPARγ coactivator 1 Alpha 2244 747 The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. Cheng et al. (2018) ATF2 Cyclic AMP-dependent transcription factor 1593 530 It is critical for induction of thermogenic genes by cAMP in BAT. Yoon et al. (2018) CREB CAMP responsive element binding protein 690 229 An important transcription factor regulating adipocyte differentiation. Berdeaux and Hutchins (2019 ATGL Adipose triglyceride lipase 2259 752 It can catalyze the first step in the hydrolysis of triglycerides in adipose tissue. Sathyanarayan et al. Molecular Evolution of the UCP Gene Family, a Characteristic Marker of Brown Adipocytes (2017) PLIN Perilipin 1494 497 The protein encoded by this gene coats lipid storage droplets in adipocytes, thereby protecting them until they can be broken down by hormone-sensitive lipase. Hayward et al. (2017) SLC25A20 Solute carrier family 25 member 20 903 300 This protein mediates the transport of acylcarnitines into mitochondrial matrix for their oxidation by the mitochondrial fatty acid-oxidation pathway. Iacobazzi et al. (2004) TABLE 1 | Identification of the molecule relative to thermogenesis and lipid metabolism in lamprey. genes, and the third round of duplication, which gave rise to UCP2 and UCP3, occurred early in invertebrate evolution. Subsequent to these duplications, different UCP genes were lost in different lineages. LrUCP3 and LrUCP5 were lost after the duplication event that occurred after lampreys differentiated from other vertebrates. genes, and the third round of duplication, which gave rise to UCP2 and UCP3, occurred early in invertebrate evolution. Subsequent to these duplications, different UCP genes were lost in different lineages. LrUCP3 and LrUCP5 were lost after the duplication event that occurred after lampreys differentiated from other vertebrates. In addition, an expression profiling analysis of the lamprey UCP gene family was conducted. By comparing the expression of the three genes in lamprey tissues, it was demonstrated that UCP2 was more widely and highly expressed in different tissues than UCP1 and UCP4 (Figure 4C). Considering these findings together with the above analysis and the practical results, we July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 7 Brown-Like Adipocytes Around Lamprey Brain Xu et al. FIGURE 3 | Identification of lamprey brown adipocytes through molecular and functional analysis. (A) Expression profiles of brown adipocyte-enriched markers and key transcription factors in lamprey tissues obtained by real-time PCR. Gapdh expression was used as an internal control. The expression profiles of marker genes are shown in a heat map. Blue and red indicate low and high expression levels. (B) The mRNA expression of selected genes enriched in lamprey brown adipocytes. (C) The lamprey brown adipocytes were treated with adrenaline (1 µM), isoprenaline (10 µM) and norepinephrine (0.5 µM) for 24 h at 18◦C. Expression analysis of enriched markers and key transcription factors was performed using real-time PCR. All of the data are presented as the means ± SDs based on three independent cDNA samples with three replicates per sample. Molecular Evolution of the UCP Gene Family, a Characteristic Marker of Brown Adipocytes (D) Metabolic profile of the stimulatory effect of temperature on oxidative phosphorylation and glycolysis. (E) The stressed OCRs and ECARs of glycolysis and oxidative phosphorylation. Each bar represents the mean value from three determinations with the standard deviation (SD). FIGURE 3 | Identification of lamprey brown adipocytes through molecular and functional analysis. (A) Expression profiles of brown adipocyte-enriched markers and key transcription factors in lamprey tissues obtained by real-time PCR. Gapdh expression was used as an internal control. The expression profiles of marker genes are shown in a heat map. Blue and red indicate low and high expression levels. (B) The mRNA expression of selected genes enriched in lamprey brown adipocytes. (C) The lamprey brown adipocytes were treated with adrenaline (1 µM), isoprenaline (10 µM) and norepinephrine (0.5 µM) for 24 h at 18◦C. Expression analysis of enriched markers and key transcription factors was performed using real-time PCR. All of the data are presented as the means ± SDs based on three independent cDNA samples with three replicates per sample. (D) Metabolic profile of the stimulatory effect of temperature on oxidative phosphorylation and glycolysis. (E) The stressed OCRs and ECARs of glycolysis and oxidative phosphorylation. Each bar represents the mean value from three determinations with the standard deviation (SD). conclude that UCP2 is likely to be a molecule that plays a major role in the Reissner lamprey. A prokaryotic expression vector of LrUCP2 was subsequently constructed, and the LrUCP2 recombinant protein was purified to prepare a mouse antibody (Supplementary Figure 2). Immunohistochemistry was used to detect the expression of UCP2 in brown-like adipocytes, and it was found that UCP2 was widely and highly expressed in these cells and showed an intracellular dotted distribution (Figure 4D). was increased compared to those in the control (Figures 5B,C). The mRNA expression levels of mitochondrial proteins and brown adipocyte marker molecules did not change; however, the mRNA levels of Fabp4 were upregulated (Figures 5D–F). When the 3T3-L1 cells overexpressing LrUCP2 were differentiated, both the intracellular ATP and FFA contents were decreased compared to those in the control (Figures 5G,H), and the mRNA expression levels of mitochondrial proteins, adipocyte differentiation and brown adipocyte marker molecules were all increased (Figures 5I–K). These results suggest that LrUCP2 has different functions in 3T3-L1 cells and differentiated 3T3-L1 cells. The Effect of Lamprey UCP2 on Differentiation Into Brown Adipocytes and Decreases in Intracellular ATP and FFA Contents To further describe the important role of UCP2 in brown- like adipocytes at the periphery of the lamprey brain, mouse 3T3-L1 were used, and LrUCP2 was inserted into the pEGFP- N1 eukaryotic expression vector. The results obtained by confocal laser imaging showed that LrUCP2 was located on the mitochondria of 3T3-L1 cells (Figure 5A). To demonstrate the function of UCP2 more accurately, G418 was used to screen the cell lines with stable UCP2 expression (Supplementary Figure 3). When LrUCP2 was overexpressed in 3T3-L1 cells, the intracellular ATP content was decreased, and the FFA content Molecular Evolution of the UCP Gene Family, a Characteristic Marker of Brown Adipocytes The overexpression of LrUCP2 can upregulate the expression of Fabp4 and increase the intracellular FFA content in 3T3- L1 cells, which may promote the decomposition of lipids and the transport of fatty acids. In contrast, the overexpression of LrUCP2 in differentiated 3T3-L1 cells may accelerate browning. The Global Transcriptome of Brown-Like Adipocytes Reveals the Role of the Immune Response A previous study demonstrated that lampreys exhibit a blood– brain barrier, similar to other vertebrates, and an endothelial blood–brain barrier to macromolecules. However, the five brain July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 8 Brown-Like Adipocytes Around Lamprey Brain Xu et al. FIGURE 4 | Phylogenetic analysis and expression profiling of UCPs in lampreys. (A) Phylogenetic tree of the UCP family based on the NJ method. The numbers on interior branches indicate the bootstrap values derived from 1000 replications. All the amino acid sequence data used are from the Ensemble database and NCBI database. Hs, Homo sapiens; Mm, Mus musculus; Gg, Gallus gallus; Ls, Lonchura striata; Ac, Anolis carolinensis; Vk, Varanus komodoensis; Ca, Chelonoidis abingdonii; Xt, Xenopus tropicalis; Dr, Danio rerio; Lo, Lepisosteus oculatus; Eb, Eptatretus burgeri; Lr, Lethenteron reissneri; Bb, Branchiostoma belcheri; Dm, Drosophila melanogaster; Cv, Crassostrea virginica; Ml, Macrostomum lignano; Sm, Symbiodinium microadriaticum. (B) Evolutionary scenario of the UCP gene in vertebrates. The major evolutionary events are highlighted. The \ symbol indicates genes that have been lost. (C) Expression of UCPs in different tissues of Reissner lampreys. (D) Immunohistochemistry of LrUCP2 in brown adipocytes in lamprey brains. FIGURE 4 | Phylogenetic analysis and expression profiling of UCPs in lampreys. (A) Phylogenetic tree of the UCP family based on the NJ method. The numbers on interior branches indicate the bootstrap values derived from 1000 replications. All the amino acid sequence data used are from the Ensemble database and NCBI database. Hs, Homo sapiens; Mm, Mus musculus; Gg, Gallus gallus; Ls, Lonchura striata; Ac, Anolis carolinensis; Vk, Varanus komodoensis; Ca, Chelonoidis abingdonii; Xt, Xenopus tropicalis; Dr, Danio rerio; Lo, Lepisosteus oculatus; Eb, Eptatretus burgeri; Lr, Lethenteron reissneri; Bb, Branchiostoma belcheri; Dm, Drosophila melanogaster; Cv, Crassostrea virginica; Ml, Macrostomum lignano; Sm, Symbiodinium microadriaticum. (B) Evolutionary scenario of the UCP gene in vertebrates. The major evolutionary events are highlighted. The \ symbol indicates genes that have been lost. (C) Expression of UCPs in different tissues of Reissner lampreys. (D) Immunohistochemistry of LrUCP2 in brown adipocytes in lamprey brains. regions of lampreys, surrounded by a layer of brown-like adipocytes, are exposed in the brain cavity, and it is unclear whether the layer of brown-like adipocytes is involved in the immune response against pathogens. The Global Transcriptome of Brown-Like Adipocytes Reveals the Role of the Immune Response Among these pathways, “signal transduction” (1,515; 13.4%), “endocrine system” (855; 7.6%) and “immune system” (676; 6.0%) were the most prominent pathways (Figure 6B). The differential expression data revealed many gene expression differences between brown-like adipocytes subjected to LPS/25HC treatment and those not receiving LPS/25HC- treatment, showing a more than 2-fold difference in mRNA transcript levels (Figure 6C). Thus, these data demonstrated the upregulation of energy expenditure pathways and repression of inflammation in normal brown adipocytes relative to those subjected to LPS and 25HC treatment. The expression levels of immune molecules were further analyzed via real-time PCR The Global Transcriptome of Brown-Like Adipocytes Reveals the Role of the Immune Response To characterize the immune response of brown adipocytes from a molecular perspective, we performed paired-end RNA-seq analysis of poly(A)-selected RNAs from brown-like adipocytes responding to LPS and 25HC treatments. We firstly calculated all possible pairwise correlations among the four samples by using the expression levels of annotated protein-coding genes to quantitatively reveal the overall transcriptome proximity of normal brown-like fat cells to that of the treatment group. All unigenes were assigned to three GO term categories: biological processes, cellular components, and molecular functions (Figure 6A). According to the KEGG classification of all unigenes, 11,324 genes were mapped to 35 different pathways. Among these pathways, “signal transduction” (1,515; 13.4%), “endocrine system” (855; 7.6%) and “immune system” (676; 6.0%) were the most prominent pathways (Figure 6B). The differential expression data revealed many gene expression differences between brown-like adipocytes subjected to LPS/25HC treatment and those not receiving LPS/25HC- treatment, showing a more than 2-fold difference in mRNA transcript levels (Figure 6C). Thus, these data demonstrated the upregulation of energy expenditure pathways and repression of inflammation in normal brown adipocytes relative to those subjected to LPS and 25HC treatment. The expression levels of immune molecules were further analyzed via real-time PCR using total RNA obtained from LPS/25HC-treated or untreated brown-like adipocytes (Figure 6D and Supplementary Table 1). The real-time PCR results were consistent with those of the transcription analysis. Taken together, the brown-like adipocytes are not only a distinct fat depot but also function as immune cells with a role in immune defense. regions of lampreys, surrounded by a layer of brown-like adipocytes, are exposed in the brain cavity, and it is unclear whether the layer of brown-like adipocytes is involved in the immune response against pathogens. To characterize the immune response of brown adipocytes from a molecular perspective, we performed paired-end RNA-seq analysis of poly(A)-selected RNAs from brown-like adipocytes responding to LPS and 25HC treatments. We firstly calculated all possible pairwise correlations among the four samples by using the expression levels of annotated protein-coding genes to quantitatively reveal the overall transcriptome proximity of normal brown-like fat cells to that of the treatment group. All unigenes were assigned to three GO term categories: biological processes, cellular components, and molecular functions (Figure 6A). According to the KEGG classification of all unigenes, 11,324 genes were mapped to 35 different pathways. DISCUSSION Jawless vertebrates are the most primitive vertebrates on earth and appeared 520 million years ago, as early as the Cambrian period. In 1999, a paper in Nature reported that fossils of Myllokunmingia and Halou:Chthys were found among the early Cambrian Chengjiang Fauna in China (Shu et al., 1999). These two fish have spindle-shaped bodies, W-shaped sarcomeres, and relatively complex bony skulls, gill arches, pericardial cavities, and fin bars. These characteristics are similar to those of current lamprey larvae, which represent the origin of the vertebrates. Jawless vertebrates are the most primitive vertebrates on earth and appeared 520 million years ago, as early as the Cambrian period. In 1999, a paper in Nature reported that fossils of Myllokunmingia and Halou:Chthys were found among the early Cambrian Chengjiang Fauna in China (Shu et al., 1999). These two fish have spindle-shaped bodies, W-shaped sarcomeres, and relatively complex bony skulls, gill arches, pericardial cavities, and fin bars. These characteristics are similar to those of current lamprey larvae, which represent the origin of the vertebrates. Although ostracoderm fossils have been found as far back as the Middle Ordovician and even the late Cambrian, the most promising vertebrates had not fully developed at that time, and the whole Ordovician ocean was still the realm of invertebrates. At the end of the Ordovician period, due to the influence of the great ice age of the Hirnantian, vertebrates suffered mass extinction, and vast ecosystems emerged in the ancient oceans. The ostracoderms that survived the great ice age gave rise to Frontiers in Cell and Developmental Biology | www.frontiersin.org July 2021 | Volume 9 | Article 674939 9 Brown-Like Adipocytes Around Lamprey Brain Xu et al. FIGURE 5 | Localization and functional identification of lamprey UCP2 in 3T3L1 cells. (A) The localization of lamprey UCP2 in 3T3L1 cells was observed by confocal microscopy at 30 h after UCP2 overexpression in 3T3L1 cells. (B,C) ATP content and FFA content of 3T3L1 cells overexpressing UCP2. (D–F) mRNA levels of mitochondrial genes (D), general adipocyte markers (E), and brown-selective genes (F) after overexpression of UCP2 in 3T3L1 cells (n = 3). (G,H) ATP content and FFA content of mature brown adipocytes overexpressing UCP2. (I–K) mRNA levels of mitochondrial genes (I), general adipocyte markers (J), and brown-selective genes (K) in mature brown adipocytes overexpressing UCP2 (n = 3). DISCUSSION All expression data are presented as the mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001. FIGURE 5 | Localization and functional identification of lamprey UCP2 in 3T3L1 cells. (A) The localization of lamprey UCP2 in 3T3L1 cells was observed by confocal microscopy at 30 h after UCP2 overexpression in 3T3L1 cells. (B,C) ATP content and FFA content of 3T3L1 cells overexpressing UCP2. (D–F) mRNA levels of mitochondrial genes (D), general adipocyte markers (E), and brown-selective genes (F) after overexpression of UCP2 in 3T3L1 cells (n = 3). (G,H) ATP content and FFA content of mature brown adipocytes overexpressing UCP2. (I–K) mRNA levels of mitochondrial genes (I), general adipocyte markers (J), and brown-selective genes (K) in mature brown adipocytes overexpressing UCP2 (n = 3). All expression data are presented as the mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001. radiant development during the Silurian-Devonian period. The agnathans passed through the late Silurian and Early Devonian and began to decline in the Middle Devonian. Finally, nearly all of the agnathan fishes disappeared because of the late Devonian extinction, with the exception of lampreys and hagfish. Thus, the question of why lampreys have survived the long evolutionary process arises. The reason is closely related to their unique way of life and genetic characteristics. In this study, we identified a type of tissue surrounding the lamprey brain that is composed of a series of brown-like adipocytes, and the function of these cells in lampreys may provide some clues to answer the above question. precursor cells into brown adipocytes, induces myofibroblast differentiation into brown adipocytes (Kajimura et al., 2009). The multilocular adipocytes that we found at the periphery of the brain become distinguishable from the myofibroblasts; these brown-like adipocytes may differentiate from myofibroblasts, but further experimental investigation is required. Lamprey adipose tissue contains a range of transcription factors and important regulators similar to those of mammals, such as Pgc-1α and Ucp1. The thermogenesis of brown- like adipocytes is related to the regulation of epinephrine in lampreys. β–Adrenergic activators stimulate beige and brown adipocyte development in mammals (brown and beige fat). In addition, Ucp1 shows almost no change after stimulation and is poorly expressed in various tissues, whereas Ucp2 shows high expression and a thermogenic response, suggesting that Ucp2 is likely to be the molecule that has more important functions in lampreys. Frontiers in Cell and Developmental Biology | www.frontiersin.org DISCUSSION (C) Global transcriptome landscape of lamprey brown adipocytes treated with PBS, DMSO, LPS (100 µg/mL) and 25HC (50 µM). The processing time was 12 h or 24 h. Heatmap of clustered correlations among the six groups. (D) Heatmap of immune molecule expression levels, which were determined via Q-PCR in lamprey brown adipocytes after stimulation with PBS, DMSO, LPS (100 µg/mL) and 25HC (50 µM) at 12 h and 24 h. Blue and red represent low and high expression levels, and the color scales correspond to the expression levels of the genes. highly expressed in peripheral multilocular adipocytes of the lamprey brain. Thus, we consider the brown-like adipocytes found in adult lampreys to be a unique type of primitive thermogenic adipose tissue. Interestingly, we found that the lamprey β-adrenergic receptor shows the highest similarity to β1 adrenergic receptors in humans and mice, however, the molecules that receive thermogenesis signals in humans and mice are β2 and β3 adrenergic receptors (Blondin et al., 2020). This may explain why these brown-like adipocytes in lampreys respond very strongly only to adrenaline. preferentially changed the energy production route from aerobic to glycolytic metabolism to produce heat to maintain basal metabolism. According to our results, we propose that LrUCP2 is involved in regulating brown-like adipocyte differentiation. The expression of brown adipocyte markers, mitochondrial proteins and adipocyte differentiation markers was upregulated in differentiated 3T3-L1 cells which overexpressing UCP2. Our results indicate that LrUCP2 overexpression can induce positive feedback regulation of mouse UCP1 and its upstream regulatory factors in 3T3-L1 cells, and the precise regulatory mechanism needs further experimental verification. Brown adipose tissue in mammals burns fatty acids and generates heat by uncoupling oxidative phosphorylation from ATP production in mitochondria. However, birds produce heat through their muscles and regulate their body temperature. Several species of fish maintain brain temperatures that are higher than the surrounding environmental temperature through ATP-dependent Ca2+ cycling in the sarcoplasmic reticulum of "heating cells" around the brain. The present study showed that the brown-like adipocytes around the lamprey brain contain “heating cells” similar to those of other fish. As shown in Figures 3D,E, the treatment of multilocular adipose cells at 4◦C increased both ECAR level and OCR compared to those in the control at 20◦C, and the 4◦C treatment Furthermore, our transcriptome results shed light on the potential immune activity of lamprey multilocular fat cells that may affect metabolic events in these cells. DISCUSSION Studies have shown that mammalian orthologs display an accelerated evolutionary rate relative to non-mammalian Ucp1 orthologs and other mammalian paralogs, and the thermogenic function of Ucp1 in placental mammals seems to result from such neofunctionalization (Mendes et al., 2020). The immunohistochemical results showed that UCP2 was In mammals, there are two types of brown adipocytes: classic brown adipocytes in rodents, which appear in scapular tissues, and brown-like adipocytes or brite adipocytes, identified in WAT in specific situations. The former cell type is formed by the differentiation of brown precursor adipocytes, while the latter may originate from stem cells that are derived from adipose tissue or are directly transformed from white adipocytes (Gesta et al., 2007; Rodeheffer et al., 2008; Seale et al., 2008; Ohno et al., 2012). Classic brown adipocytes arise from Myf5-positive myofibroblast precursors, and the coexpression of C/EBPβ and PRDM16, which controls the differentiation of July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 10 Xu et al. Xu et al. Brown-Like Adipocytes Around Lamprey Brain FIGURE 6 | Transcriptome analysis of brown adipose cells at the periphery of the lamprey brain. (A) GO enrichment map of all the annotated unigenes, which were divided into three categories. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) classifications of non-redundant unigenes. A, cellular processes; B, environmental information processing; C, genetic information processing; D, metabolism; E, organismal systems. (C) Global transcriptome landscape of lamprey brown adipocytes treated with PBS, DMSO, LPS (100 µg/mL) and 25HC (50 µM). The processing time was 12 h or 24 h. Heatmap of clustered correlations among the six groups. (D) Heatmap of immune molecule expression levels, which were determined via Q-PCR in lamprey brown adipocytes after stimulation with PBS, DMSO, LPS (100 µg/mL) and 25HC (50 µM) at 12 h and 24 h. Blue and red represent low and high expression levels, and the color scales correspond to the expression levels of the genes. FIGURE 6 | Transcriptome analysis of brown adipose cells at the periphery of the lamprey brain. (A) GO enrichment map of all the annotated unigenes, which were divided into three categories. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) classifications of non-redundant unigenes. A, cellular processes; B, environmental information processing; C, genetic information processing; D, metabolism; E, organismal systems. Frontiers in Cell and Developmental Biology | www.frontiersin.org July 2021 | Volume 9 | Article 674939 SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcell.2021. 674939/full#supplementary-material Supplementary Figure 1 | The evolutionary analysis of UCPs in lamprey. (A) The domains of UCPs from different species. The Mito_carr (mitochondrial carrier protein) domains are shown with orange boxes based on identification by Pfam. (B) The MEME motifs and sequence alignment of the UCP family. A total of 26 motifs are shown in different colored squares. (C) The red boxes in the sequence alignment indicate the three energy transfer protein signatures. (D) Conservation of genes neighboring UCP1, UCP2, and UCP4. The orthologous genes were similarly color-coded, and arrows or arrowheads in opposite directions indicate genes located on opposite strands. DATA AVAILABILITY STATEMENT The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI, PRJNA733594. Supplementary Figure 2 | Preparation of the recombinant UCP2 protein and polyclonal antibody. (A) Analysis of LrUCP2 expression via SDS-PAGE. M, low molecular-weight protein marker. The LrUCP2 protein concentration is 0.4 mg/mL. (B) Antibody titer of anti-LrUCP2 antibodies. (C) Western blot of BAT in the peripheral of brain and the rL-UCP2 protein in lampreys. FUNDING This work was funded by Chinese National Natural Science Foundation grants (nos. 31772884 and 32070518), the project of Department of Ocean and Fisheries of Liaoning Province (no. 201805), the Program of Science and Technology of Liaoning Province (no. 2019-MS-218), and the Science and Technology Innovation Fund Research Project (no. 2018J12SN079). This work was funded by Chinese National Natural Science Foundation grants (nos. 31772884 and 32070518), the project of Department of Ocean and Fisheries of Liaoning Province (no. 201805), the Program of Science and Technology of Liaoning Province (no. 2019-MS-218), and the Science and Technology Innovation Fund Research Project (no. 2018J12SN079). In conclusion, we identified brown-like adipocytes around the lamprey brain. These cells may provide nutrients and energy sources supporting metabolic activity in the brain and protect the brain from outside pathogen infection. The identification of brown-like adipocytes in the lamprey brain has improved our understanding of the mechanism of thermogenesis in mammals and the unique characteristics of lampreys. Further investigations of the significance and specificity of this kind of cell with thermogenic potential in lampreys and the related regulatory pathways are an important future goal. ETHICS STATEMENT Supplementary Figure 3 | Screening for cell lines with stable UCP2 expression. Cells with stable expression of UCP2 and its control were obtained after Supplementary Figure 3 | Screening for cell lines with stable UCP2 expression. Cells with stable expression of UCP2 and its control were obtained after The animal study was reviewed and approved by Animal Welfare and Research Ethics Committee of the Institute of DISCUSSION Some DEGs related to immune pathways were identified in lamprey adipocytes after LPS and 25HC treatment. According to the DEG annotation information, we found upregulation of proinflammatory factors that play a role in resisting external stimuli, while the expression of some molecules associated with lipid metabolism was downregulated. There may be a complex regulatory network between the inflammatory response and metabolic function in adipose cells. July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 11 Brown-Like Adipocytes Around Lamprey Brain Xu et al. Xu et al. Based on the above results, we considered the cells surrounding the lamprey brain not only be equivalent to the brown adipocytes of higher species but also to exhibit unique functional characteristics. The brown-like adipose tissue that cocoons the lamprey brain protects the structure of its five parts, and these cells may provide material energy for adaptation to long fasting periods during the lifecycle. These brown-like adipocytes can consume energy and generate additional heat to maintain a sufficient temperature for lampreys to complete their lifecycle in benthic and cold water environments and to ensure normal physiological function and developmental processes. Chung- Davidson also revealed a secondary sexual characteristic of male sea lamprey to be thermogenic adipose tissue that instantly increases heat production during sexual encounters. This tissue is located in front of the anterior dorsal fin of mature males and presents as a swollen dorsal ridge, called rope tissue, but is not BAT (Chung-Davidson et al., 2013). In addition, our results showed that the brown-like adipose tissue around the brain may function similarly to the blood–brain barrier of higher vertebrates and protect against pathogen invasion. 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The adipose organ of obesity-prone C57BL/6J mice is composed of mixed white and brown adipocytes. J. Lipid Res. 53, 619–629. doi: 10.1194/jlr. M018846 July 2021 | Volume 9 | Article 674939 Frontiers in Cell and Developmental Biology | www.frontiersin.org 14
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A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel <i>Limnoperna fortunei</i>
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fortunei Marcela Uliano-Silva1,2,3,∗, Francesco Dondero4, Thomas Dan Otto5,6, Igor Costa7, Nicholas Costa Barroso Lima7,8, Juliana Alves Americo1, Camila Junqueira Mazzoni2,3, Francisco Prosdocimi7 and Mauro de Freitas Rebelo1,∗ 1Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil, 2Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany, 3Berlin Center for Genomics in Biodiversity Research, Berlin, Germany, 4Department of Science and Technological Innovation (DiSIT), Universit`a del Piemonte Orientale Amedeo Avogadro, Vercelli-Novara-Alessandria, Italy, 5Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK, 6Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK, 7Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil and 8Bioinformatics Laboratory (LabInfo) of the National Laboratory for Scientific Computing, Petr´opolis, Rio de Janeiro, Brazil Vercelli-Novara-Alessandria, Italy, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK, 6Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK, 7Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil and 8Bioinformatics Laboratory (LabInfo) of the National Laboratory for Scientific Computing, Petr´opolis, Rio de Janeiro, Brazil ∗Correspondence address: Marcela Uliano-Silva, Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany. Tel: +49 30 83859956; E-mail: marcela.uliano@gmail.com; Mauro de Freitas Rebelo, Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; E-mail: mrebelo@biof.ufrj.br GigaScience, 7, 2018, 1–10 C⃝The Author(s) 2017. Published by Oxford University Press. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei Genome sequencing in short Illumina and long PacBio reads Limnoperna fortunei mussels were collected from the Jacui River, Porto Alegre, Rio Grande do Sul, Brazil (29◦59′29.3′′S 51◦16′24.0′′W). Voucher specimens were housed at the zoolog- ical collection (specimen number: 19 643) of the Biology Insti- tute at the Universidade Federal do Rio de Janeiro, Brazil. For the genome assembly, a total of 3 individuals were sampled for DNA extraction from gills and to produce the 3 types of DNA libraries used in this study. DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) to prepare libraries for Illu- mina Nextera paired-end reads, with ∼180-bp and ∼500-bp in- sert sizes, (ii) Illumina Nextera mate-paired reads with insert sizes ranging from 3 to 15 Kb, and (iii) Pacific Biosciences long reads (Table 1). Illumina libraries were sequenced, respectively, in a HiScanSQ or HiSeq 1500 machine, and Pacific Biosciences reads were produced with the P4C6 chemistry and sequenced in 10-SMRT Cells. All Illumina reads were submitted to qual- ity analysis with FastQC (FastQC, RRID:SCR 014583) followed by trimming with Trimmomatic (Trimmomatic, RRID:SCR 011848) [15]. Pacific Biosciences adaptor-free subread sequences were used as input data for the genome assembly. A recent review has shown that, before arriving in South America, L. fortunei was already an invader in China. Originally from the Pearl River Basin, the golden mussel has traveled 1500 km into the Yang Tse and Yellow River basins, being limited further north only by the extreme natural barriers of Northern China [5]. Today, L. fortunei is found in the Paraguaizinho River, located only 150 km from the Teles-Pires River that belongs to the Alto Tapaj´os River Basin and is the first to directly connect with the Amazon River Basin [6]. Due to its fast dispersion rates, it is very likely that L. fortunei will reach the Amazon River Basin in the near future. The reason why some freshwater bivalves, such as L. fortunei, Dreissena polymorpha, and Corbicula fluminea, are aggressive in- vaders is not fully understood. These bivalves present charac- teristics such as (i) tolerance to a wide range of environmental variables, (ii) short life span, (iii) early sexual maturation, and (iv) high reproductive rates that allow them to reach densities as high as 150 000 ind.m−2 over a year [7, 8] that may explain the aggressive behavior. Keywords: Amazon; binding domain; bivalves; genomics; TLR; transposon Keywords: Amazon; binding domain; bivalves; genomics; TLR; transposon Genome sequencing in short Illumina and long PacBio reads On the other hand, these traits are not ex- clusive to invasive freshwater bivalves and do not explain how they outcompete native species and disperse so widely. For transcriptome sequencing, RNA was sampled from 4 tissues (gills, adductor muscle, digestive gland, and foot) of 3 different golden mussel specimens. RNA was extracted using the NEXTflex Rapid Directional RNA-Seq Kit (Bio Scientifics, TX, USA) and 12 barcodes from NEXTflex Barcodes compatible with Illumina NexSeq Machine. Resulting reads (Supplementary Table S1) were submitted to FastQC quality analysis and trimmed with Trimmomatic for all NEXTflex adaptors and bar- codes. A total of 3 sets of de novo assembled transcriptomes were generated using Trinity (Trinity, RRID:SCR 013048) (Table 2); 1 set for each specimen was a pool of the 4 tissue samples to avoid as- sembly bias due to intraspecific polymorphism [16]. To the best of our knowledge, there are no reports of strate- gies successful at controlling the expansion of mussel invasion in industrial facilities. Bivalves can sense chemicals in the wa- ter and close their valves as a defensive response [9], making them tolerant to a wide range of chemical substances, including strong oxidants like chlorine [10]. Microencapsulated chemicals have shown better results in controlling mussel populations in closed environments [10, 11], but it is unlikely they would work in the wild. Currently, there is no effective and efficient approach to control the invasion by L. fortunei. Data Description Brazil [14]. In this campaign, we were able to raise around USD$20 000.00 at the same time as we promoted scientific ed- ucation and awareness in Brazil. The golden mussel Limnoperna fortunei is an Asian bivalve that ar- rived in the southern part of South America about 25 years ago [1]. Research suggests that L. fortunei was introduced in South America through ballast water of ships coming from Hong Kong or Korea [2]. It was found for the first time in the estuary of the La Plata River in 1991 [1]. Since then, it has moved ∼5000 km, invading upstream continental waters and reaching northern parts of the continent [3], leaving behind a track of great eco- nomic impact and environmental degradation [4]. The latest in- festation was reported in 2016 in the S˜ao Francisco River, one of the main rivers in the northeast of Brazil, with a 2700-km riverbed that provides water to more than 14 million people. At Paulo Afonso, one of the main hydroelectric power plants in the S˜ao Francisco River, maintenance due to clogging of pipelines and corrosion caused by the golden mussel is estimated to cost U$700 000 per year (personal communication, Mizael Gusm˜a, Chief Maintenance Engineer for Centrais Hidrel´etricas do S˜ao Francisco [CHESF]). Here we present the first complete genome dataset for the invasive bivalve Limnoperna fortunei, assembled from short and long DNA reads and using a hybrid and hierarchical assembly strategy. This high-quality reference genome represents a sub- stantial resource for further studies of genetics and evolution of mussels, as well as for the development of new tools for plague control. 2 Uliano-Silva et al. genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control. genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control. Abstract Background: For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions: We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei’s Received: 13 July 2017; Revised: 5 November 2017; Accepted: 11 December 2017 C⃝The Author(s) 2017. Published by Oxford University Press. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 1 1 2 Uliano-Silva et al. Genome assembly using a hybrid and hierarchical strategy The genome sequence is one of the most relevant and in- formative descriptions of species biology. The genetic substrate of invasive populations, upon which natural selection operates, can be of primary importance to understanding and controlling a biological invader [12, 13]. Jellyfish software (Jellyfish, RRID:SCR 005491) [17] was used to count and determine the distribution frequency of lengths 25 and 31 kmers (Fig. 1) for the Illumina DNA paired-end and mate- paired reads (Table 1). The genome size was estimated to be 1.6 Gb by using the 25-kmer distribution plot as total kmer number and then subtracting erroneous reads (starting kmer counts from ×12 coverage) to further divide by the homozygous We have partially funded the golden mussel genome sequencing through a pioneer crowdfunding initiative in Limnoperna fortunei hybrid genome 3 Table 1: DNA reads produced for L. fortunei genome assembly Library technology Raw data Trimmed data∗ Reads insert size Pairs Number of reads Number of bases Number of reads Number of bases Illumina Nextera Paired-end – 180 bp R1 209 542 721 21 060 365 702 209 036 571 21 001 101 404 R2 209 542 721 21 049 308 698 209 036 571 20 991 650 008 Paired-end – 500 bp R1 153 948 902 15 472 966 961 153 482 290 15 423 123 500 R2 153 948 902 15 462 883 157 153 482 290 15 414 813 589 Mate-paired 3 – 12 Kb R1 178 392 944 18 017 687 344 58 157 933 5 822 572 152 R2 178 392 944 18 017 687 344 58 157 933 5 811 310 412 Pacific Biosciences P4C – 10/SMTRC Subreads 1 663 730 11 171 487 485 ∗Trimmomatic parameters for Illumina reads—ILLUMINACLIP: NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:2 LEADING:10 TRAILING:10 CROP:101 HEADCROP:0 MINLEN:80. Table 1: DNA reads produced for L. fortunei genome assembly Table 2: Trinity assembled transcripts used in the assembly and annotation of L. fortunei genome Number of reads Number of Number of Average GC Sample Pooled tissues prior assembly trinity transcripts trinity genes contig length % Mussel 1 Gills, mantle, digestive gland, foot 406 589 144 433 197 303 172 854 34 Mussel 2 Gills, mantle, digestive gland, foot 376 577 660 435 054 298 117 824 34 Mussel 3 Gills, mantle, digestive gland, foot 334 316 116 499 392 351 649 844 34 Figure 1: Kmer distribution of Limnoperna fortunei Illumina DNA reads (Table 1). Genome assembly using a hybrid and hierarchical strategy the resulting contigs were assembled into scaffolds using Pacific Biosciences long subreads data and the PacBio- correction-free assembly algorithm DBG2OLC [24] with pa- rameters LD1 0 k 17 KmerCovTh 10 MinOverlap 20 AdaptiveTh 0.01. Finally, (iii) resulting scaffolds were submitted to 6 iter- ative runs of the program L RNA Scaffolder [25], which uses exon distance information from de novo assembled transcripts (Table 2) to fill gaps and connect scaffolds whenever appropri- ate. At the end, (iv) the final genome scaffolds were corrected for Illumina and Pacific Biosciences sequencing errors with the software PILON [26]: All DNA and RNA short Illumina reads were re-aligned back to the genome with BWA aligner (BWA, RRID:SCR 010910) [27], and resulting SAM files were BAM-converted, sorted, and indexed with the SAMTOOLs package (SAMTOOLS, RRID:SCR 002105) [28]. Pilon [26] identifies INDELS and mismatches by coverage of reads and yields a final corrected genome draft. Pilon was run with parameters –diploid –duplicates. Figure 1: Kmer distribution of Limnoperna fortunei Illumina DNA reads (Table 1). coverage-peak depth (×45 coverage), as performed by Li et al. (2010) [18]. A double-peak kmer distribution was used as evi- dence of genome diploidy (Fig. 1) and high heterozygosity. The rate of heterozygosity was estimated to be 2.3%, and it was cal- culated as described by Vij et al. (2016) [19], using as input data the 17-kmer distribution plot for reads from 1 unique specimen. coverage-peak depth (×45 coverage), as performed by Li et al. (2010) [18]. A double-peak kmer distribution was used as evi- dence of genome diploidy (Fig. 1) and high heterozygosity. The rate of heterozygosity was estimated to be 2.3%, and it was cal- culated as described by Vij et al. (2016) [19], using as input data the 17-kmer distribution plot for reads from 1 unique specimen. Initially, we attempted to assemble the golden mus- sel genome using only short Illumina reads of different insert sizes (paired-end and mate-paired) (Table 1) using traditional de novo assembly software such as ALLPATHS (ALLPATHS-LG, RRID:SCR 010742) [20], SOAPdenovo (SOAP- denovo, RRID:SCR 010752) [21], and MaSuRCA (MaSuRCA, RRID:SCR 010691) [22]. All these attempts resulted in very fragmented genome drafts, with an N50 no higher than 5 Kb and a total of 4 million scaffolds. Genome assembly using a hybrid and hierarchical strategy To reduce fragmentation, we further sequenced additional long reads (10 PacBio SMTR Cells) (Table 1) and performed a hybrid and hierarchical de novo assembly, described below and depicted in Fig. 2. The final genome was assembled in 20 548 scaffolds, with an N50 of 312 Kb and a total assembly length of 1.6 Gb (Table 3). The golden mussel genome presents 81% of all Benchmark- ing Universal Single Copy Orthologs (BUSCO version 3.3 analysis with Metazoa database; BUSCO, RRID:SCR 015008) (Table 4) and, compared with the mollusk genomes currently available [29–36], it represents one of the best assemblies of molluscan genomes so far also in terms of scaffold N50 and contiguity (Table 5). Initially, we attempted to assemble the golden mus- sel genome using only short Illumina reads of different insert sizes (paired-end and mate-paired) (Table 1) using traditional de novo assembly software such as ALLPATHS (ALLPATHS-LG, RRID:SCR 010742) [20], SOAPdenovo (SOAP- denovo, RRID:SCR 010752) [21], and MaSuRCA (MaSuRCA, RRID:SCR 010691) [22]. All these attempts resulted in very fragmented genome drafts, with an N50 no higher than 5 Kb and a total of 4 million scaffolds. To reduce fragmentation, we further sequenced additional long reads (10 PacBio SMTR Cells) (Table 1) and performed a hybrid and hierarchical de novo assembly, described below and depicted in Fig. 2. One main challenges of assembling bivalve genomes lies in the high heterozygosity and amount of repetitive elements these organisms present: (i) the mussels L. fortunei and Modiolus philippinarum and the oyster Crassostrea gigas genomes were es- timated to have heterozygosity rates of 2.3%, 2.02%, and 1.95%, respectively, which are substantially higher than other animal genomes [30], and (ii) repetitive elements correspond to at least 30% of the genomes of all studied bivalves so far (Table 3) [29–32, 34–36]. Also, retroelements might be active in some species such as L. fortunei (refer to the “Retroelements” section of this pa- per) and C. gigas [30], allowing genome rearrangements that may hinder genome assembly. One exception seems to be the deep- sea mussel B. platifrons, which has lower heterozygosity rates First, (i) trimmed paired-end and mate-paired DNA Illumina reads (Table 1) were assembled into contigs using the software Sparse Assembler [23] with parameters LD 0 NodeCovTh 1 EdgeCovTh 0 k 31 g 15 PathCovTh 100 GS 1 800 000 000. Next, (ii) 4 Uliano-Silva et al. Uliano-Silva et al. Genome assembly using a hybrid and hierarchical strategy erarchical assembly strategy employed for the golden mussel genome assembly. Trimmed Illumina reads were assembled to the level of co embler algorithm (Step 1). Then, Illumina contigs and PacBio reads were used to build scaffolds with the DBG2OLC assembler, which anc rroneous PacBio subreads, correcting them and building longer scaffolds (Step 2), followed by transcriptome joining scaffolds using L RNA sc affolds were corrected by re-aligning all Illumina DNA and RNA-seq reads back to them and calling consensus with Pilon software (Step 4). tics software used in each step. Red blocks indicate PacBio errors, which are represented by insertions and/or deletions, found in approxim eads. Figure 2: Hierarchical assembly strategy employed for the golden mussel genome assembly. Trimmed Illumina reads were assembled to the level of contigs with the Sparse Assembler algorithm (Step 1). Then, Illumina contigs and PacBio reads were used to build scaffolds with the DBG2OLC assembler, which anchors Illumina contigs to erroneous PacBio subreads, correcting them and building longer scaffolds (Step 2), followed by transcriptome joining scaffolds using L RNA scaffolder (Step 3). Final scaffolds were corrected by re-aligning all Illumina DNA and RNA-seq reads back to them and calling consensus with Pilon software (Step 4). In bold is the bioinformatics software used in each step. Red blocks indicate PacBio errors, which are represented by insertions and/or deletions, found in approximately 12% of PacBio subreads. Genome assembly using a hybrid and hierarchical strategy Limnoperna fortunei hybrid genome 5 Haliotis Lottia Aplysia Ruditapes Patinopecten Crassostrea Mytillus Bathymodiolus Modiolus Limnoperna discus hannai gigantea californica philippinarum yessoensis gigas Pinctadafucata galloprovincialis platifrons philippinarum fortunei Estimated genome size 1.65 Gb 359.5 Mb 1.8 Gb 1.37 Gb 1.43 Gb 545 Mb 1.15 Gb 1.6 Gb 1.64 Gb 2.38 Gb 1.6 Gb Number of scaffolds 80 032 4475 8766 223 851 82 731 11 969 7997 1746 447 65 664 74 575 20 548 Total size of scaffolds 1 865 475 499 359 512 207 715 791 924 2 561 070 351 987 685 017 558 601 156 915 721 316 1 599 211 957 1 659 280 971 2 629 649 654 1 673 125 894 Longest scaffold 2 207 537 9 386 848 1 784 514 572 939 7 498 238 1 964 558 5 897 787 67 529 2 790 175 715 382 2 720 304 Shortest scaffold 854 1000 5001 500 200 100 1807 100 292 205 558 Number of scaffolds >1 K nt (%) 79 923 (99.9) 4471 (99.9) 8766 (100) 138 771 (61.9) 16 004 (19.3) 5788 (48.4) 7997 (100) 393 685 (22.5) 38 704 (58.9) 44 921 (60.2) 20 547 (100) Number of scaffolds >1 M nt (%) 67 (0.1) 98 (2.2) 27 (0.3) 0 (0.0) 248 (0.3) 60 (0.5) 27 (0.3) 0 (0.0) 164 (0.2) 0 (0) 95 (0.5) Mean scaffold size 23 309 80 338 81 655 11 441 11 939 46 671 114 508 916 25 269 35 262 81 425 Median scaffold size 1697 3622 13 763 1327 362 824 14 683 258 1284 13 722 22 134 N50 scaffold length 200 099 1 870 055 264 327 48 447 803 631 401 319 345 846 2651 343 373 100 161 312 020 Sequencing coverage ×322 ×8.87 ×11 ×39.7 ×297 ×155 ×234 ×32 ×319 ×209.5 ×60 Sequencing Technology Illumina + PacBio Sanger Sanger Illumina Illumina Illumina Illumina + BACs Illumina Illumina Illumina Illumina + PacBio Table 3: Assembly statistics for Limnoperna fortunei’s genome Parameter Value Estimated genome size by kmer analysis, Gb 1.6 Total size of assembled genome, Gb 1.673 Number of scaffolds 20 548 Number of contigs 61 093 Scaffold N50, Kb 312 Maximum scaffold length, Mb 2.72 Percentage of genome in scaffolds >50 Kb 82.55 Masked percentage of total genome 33 Mapping percentage of Illumina reads back to scaffolds 91 Table 3: Assembly statistics for Limnoperna fortunei’s genome Table 4: Summary statistics of BUSCO analysis for L. Genome assembly using a hybrid and hierarchical strategy fortunei genome run for Metazoans Categories Number of genes Percentage Total BUSCO groups searched 978 – Complete BUSCOs 801 81.9 Complete and single-copy BUSCOs 769 78.62 Complete and duplicated BUSCOs 32 3.27 Fragmented BUSCOs 72 7.36 Missing BUSCOs 105 10.73 Table 4: Summary statistics of BUSCO analysis for L. fortunei genome run for Metazoans compared with other bivalves [32]. Sun et al. [32] suggested that it might be due to recurrent population bottlenecks that hap- pened after events of population extinction and recolonization in the extreme environment [32]. Nevertheless, most of the bi- valve genome projects relying only on short Illumina reads are likely to present fragmented initial drafts [29, 31]. PacBio long reads allowed us to increase the N50 to 32 Kb and to reduce the number of scaffolds from millions to 61 102, using the DBG2OLC [24] assembler. Finally, interactive runs of L RNA scaffolder [25] using the transcriptomes (Table 2) rendered the final result of N50 312 Kb in 20 548 scaffolds. It is important to note that as- sembly statistics can perform better for genomes assembled with reads generated with DNA extracted from 1 unique individ- ual. This, however, was not possible for L. fortunei’s genome due to the high amount of high-quality DNA necessary to produce Illumina mate-pairs and PacBio long reads. In this study, the challenge of assembling the high polymorphic regions between haplotypes was enhanced by the difficulties of assembling reads that originated from highly polymorphic regions across indi- viduals. However, the golden mussel assembly presented here shows that the use of Illumina contigs, low coverage of PacBio long reads, and transcriptome and Illumina re-mapping for final correction (Fig. 2) represent an option for cost-efficient assem- bly of highly heterozygous genomes of nonmodel species such as bivalves. Around 10% of repetitive elements are transposons More than 30 000 sequences were identified by gene prediction and automated annotation analyzed. A total of 6337 ortholog groups are shared among the 5 bivalve species. To annotate the golden mussel genome, we sequenced a num- ber of transcriptomes (Table S1), de novo assembled (Table 2) and aligned these transcriptomes to the genome scaffolds, and cre- ated gene models with the PASA pipeline [37]. These models were used to train and run the ab initio gene predictor AUGUS- TUS (Augustus: Gene Prediction, RRID:SCR 008417) (Supplemen- tary Fig. S1) [38]. The complete gene models yielded by PASA [43] were BLASTed (e-value 1e-20) against the Uniprot database (UniProt, RRID:SCR 002380), and those with 90% or more of their sequences showing in the BLAST hit alignment were consid- ered for further analysis. Next, all the necessary filters to run an AUGUSTUS [44] personalized training were performed: (i) only gene models with more than 3 exons were maintained, (ii) sequences with 90% or more overlap were withdrawn and only the longest sequences were retained, and (iii) only gene models free of repeat regions, as indicated by BLASTN similar- ity searches with de novo library of repeats, were maintained. These curated data yielded a final set of 1721 gene models on which AUGUSTUS [36] was trained in order to predict genes in the genome using the default AUGUSTUS [44] parameters. Once the gene models were predicted, a final step was performed by using the PASA pipeline [43] once again in the update mode (parameters -c -A -g -t). This final step compared the 55 638 gene models predicted by AUGUSTUS [44] with the 40 780 ini- tial transcript-based gene-structure models from PASA [43] to generate the final set of 60 717 gene models for L. fortunei. Of those, 58% had transcriptional evidence based on RNA Illumina reads (Table S2) re-mapping, a rate that was expected as our RNA-Seq libraries were constructed for only 4 tissues of adult golden mussel specimens without any environmental stress in- duction (Table 2). Therefore, these libraries lack transcripts for developmental stages for some other cell types (i.e., hemocytes) and stress-inducible genes. Finally, 67% of the gene models were annotated by homology searches against Uniprot or NCBI NR (Table 6). Of all the orthologs found for the total 10 species, 44 groups are composed of single-copy orthologs containing 1 represen- tative protein sequence of each species. More than 30 000 sequences were identified by gene prediction and automated annotation These sequences were used to reconstruct a phylogeny: the single-copy ortholog se- quences were concatenated and aligned with CLUSTALW [46], with a resulting alignment 30 755 sites in length (Fig. 3B). ProtTest 3.4.2 [47] was used to estimate the best-fitting substitu- tion model, which was VT+G+I+F [48]. With this alignment and model, we reconstructed the phylogeny using PhyML [49] and 100 bootstrap repetition; the resulting tree is shown in Fig. 3B. Protein domain analysis shows expansion of binding domain in L. fortunei Protein domain analysis shows expansion of binding domain in L. fortunei We performed a quantitative comparison of protein domains predicted from whole-genome projects of 10 molluscan species. The complete protein sets of M. galloprovincialis, M. philippinarum, B. platifrons, Ruditapes philippinarum, Patinopecten yessoensis, C. gi- gas, Pinctada fucata, Lottia gigantean, and Haliotis discus hannai (Supplementary Table S3) were submitted to domain annota- tion using HMMER against the Pfam-A database (e-value 1e-05). Protein expansions in L. fortunei were rendered using the nor- malized Pfam count value (average) obtained from the other 9 mollusks, according to a model based on the Poisson cumula- tive distribution. Bonferroni correction (P ≤0.05) was applied for false discovery, and absolute frequencies of Pfam-assigned do- mains were initially normalized by the total count number of Pfam-assigned domains found in L. fortunei to compensate for discrepancies in genome size and annotation bias. For L. fortunei, the annotation against Pfam-A classified 40 127 domains in 24 513 gene models, of which 83 and 67 were expanded or contracted, respectively, in comparison with the other mollusks (Fig. 4A; Supplementary Table S4 and S5). The 83 overrepresented domains were further analyzed for functional enrichment using domain-centric Gene Ontology (Fig. 4B). The analysis shows a prominent expansion of binding domains in L. fortunei, such as Thrombospondin (TSP 1), Colla- gen, Immunoglobulins (Ig, I-set, Izumo-Ig Ig 3), and Ankyrins (Ank 2, Ank 3, and Ank 4). These repeats have a variety of binding properties and are involved in cell-cell, protein-protein, and receptor-ligand interactions driving the evolutionary im- provement of complex tissues and the immune defense system in metazoans [50–54]. An evolutionary pressure toward the development of a diversified innate immune system is also suggested by the high amount of leucine rich repeats (LRR) and Toll/interleukin-1 receptor homology domains (TIR). Death, an- other over-represented Pfam, is also part of TLR signaling, being present in several docking proteins such as Myd88, Irak4, and Around 10% of repetitive elements are transposons Initial masking of L. fortunei genome was done using the Re- peatMasker program (RepeatMasker, RRID:SCR 012954) [37] with the parameter -species bivalves and masked 3.4% of the total genome. This content was much lower than the masked por- tion of other molluscan genomes, 34% in C. gigas [30] and 36% in M. galloprovincialis [29], suggesting that the fast evolution of interspersed elements limits the use of repeat libraries from di- vergent taxa [38]. Thus, we generated a de novo repeat library for L. fortunei using the program RepeatModeler (RepeatModeler, RRID:SCR 015027) [39] and its integrated tools RECON [40], TRF 6 Uliano-Silva et al. Table 6: Summary of gene annotation against various databases for L. fortunei whole-genome-predicted genes [41], and RepeatScout [42]. This de novo repeat library was the input to RepeatMasker, together with the first masked genome draft of L. fortunei, and resulted in a final masking of 33.4% of the genome. Even though more than 90% of the repeats were not classified by RepeatMasker (Supplementary Table S2), 8.85% of the repeats were classified as LINEs, Class I transposable ele- ments. In addition, large numbers of reverse-transcriptases (824 counts, Pfam RVT 1 PF00078), transposases (177 counts, Pfam HTH Tnp Tc3 2 PF01498), integrases (501 counts, Pfam Retrovi- ral integrase core domain PF00665), and other related elements were detected; more than 98% of these had detectable tran- scripts. Total number of genes 60 717 Total number of exons 220 058 Total number of proteins 60 717 Average protein size, aa 304 Number of protein BLAST hits∗with Uniprot 26 198 Number of protein BLAST hits∗with NR NCBI (no hits with Uniprot) 14 810 Number of protein HMMER hits∗with Pfam.A 24 513 Number with proteins with KO assigned by KEGG 8387 Number of proteins with BLAST hits∗with EggNOG 36 868 ∗All considered hits had a minimum e-value of 1e-05. More than 30 000 sequences were identified by gene prediction and automated annotation Protein clustering indicates evolutionary proximity among mollusk species Gene family relationships were assigned using reciprocal best BLAST and OrthoMCL software (version 1.4) [45] between L. fortunei proteins and the total protein set predicted for 9 other mollusks: the mussels M. galloprovincialis, M. philippinarum, and B. platifrons, the clam Ruditapes philippinarum, the scallop Patinopecten yessoensis, the pacific oyster C. gigas, the pearl oyster Pinctada fucata (genome version from Du et al. [36]), and the gas- tropods Lottia gigantea and Haliotis discus hannai (see Supplemen- tary Table S3 for detailed information on the comparative data). Figure 3A presents orthologs relationships for 5 of the bivalves Limnoperna fortunei hybrid genome 7 Figure 3: (A) Gene family assigned with OrthoMCL for the total set of proteins predicted from 5 mussel genome projects. Outside the Venn diagram, the species name represented, and below it is the number of proteins/number of clustered proteins/number of clusters. (B) Phylogeny of the concatenated dataset using 44 single-cop orthologs extracted from 10 molluscan genomes. The VT model was estimated to be the best-fitting substitution model with ProtTest 3.4.2. We reconstructed th phylogeny using PhyML and 100 bootstrap repetition. Figure 3: (A) Gene family assigned with OrthoMCL for the total set of proteins predicted from 5 mussel genome projects. Outside the Venn diagram, the species name is represented, and below it is the number of proteins/number of clustered proteins/number of clusters. (B) Phylogeny of the concatenated dataset using 44 single-copy orthologs extracted from 10 molluscan genomes. The VT model was estimated to be the best-fitting substitution model with ProtTest 3.4.2. We reconstructed the phylogeny using PhyML and 100 bootstrap repetition. Pelle [55]. Interestingly, BLAST analysis of L. fortunei gene models against Uniprot identified 2 types of TLRs whose prototypical architecture of N-terminal extracellular LRR motifs including either a single or multiple cysteine cluster domain, a C-terminal TIR domain spaced by a single transmembrane-spanning do- main [56], could be correctly identified using the Simple Modular Architecture Research Tool (SMART) [57]. Indeed, we confirmed 141 sequences with similarity to single cysteine clusters TLRs (scc) typical of vertebrates and 29 sequence hits with the multiple cysteine cluster TLRs (mcc) typical of Drosophila [56]. Phylogenetic analysis of all sequences (using PhyML [49], model JTT) (Supplementary Fig. S2) shows evidence for TLRs clade separation in L. fortunei; the scc TLRs exhibit a higher degree of amino acid changes, higher molecular evolution, and diversifi- cation than the mcc TLRs. Availability of supporting data Limnoperna fortunei’s genome and transcriptome data are available in the Sequence Read Archive (SRA) as Bio- Project PRJNA330677 and under the accession numbers SRR5188384, SRR5195098, SRR518800, SRR5195097, SRR5188315, SRR5181514. This Whole Genome Shotgun Project has been deposited in the DDBJ/ENA/GenBank under accession number NFUK00000000. The version described in this paper is version NFUK01000000. Supporting data, also including annotations and BUSCO results, are available via the GigaScience repository, GigaDB [60]. Protein clustering indicates evolutionary proximity among mollusk species Overall, the expansion of these gene families might suggest an improved resistance to infections. It is, however, equally curious that other immune-related gene families such as Fribinogen C and C1q seem to be contracted (Supplementary Table S5). This feature may depend on the evolution-driven, yet random fate of the L. fortunei genome, a consequence of different specific duplicate genes in other species. Also, other protein families involved in toxin metabolism, especially glutathione-based processes and sulfotransferases, are clearly contracted (Table S5). were funded through a crowdfunding initiative in Brazil. This genome contains valuable information for further evolutionary studies of bivalves and metazoa in general. Additionally, our team will further search for the presence of proteins of biotech- nology interest such as the adhesive proteins produced by the foot gland that we have described elsewhere [58] or genes related to the reproductive system that have been shown to be very ef- fective for invertebrate plague control [59]. The golden mussel genome and the predicted proteins are available for download in the GigaScience repository, and the scientific community is welcome to further curate the gene predictions. As the golden mussel advances towards the Amazon River Basin, the information provided in this study may be used to help develop biotechnological strategies that may control the ex- pansion of this organism in both industrial facilities and open environment. Final considerations Here we have described the first version of the golden mus- sel complete genome and its automated gene prediction, which re 4: Gene family representation analysis in the L. fortunei genome. (A) Pfam hierarchical clustering, heatmap. Features were selected according to a model ba he Poisson cumulative distribution of each Pfam count in the golden mussel genome vs the normalized average values found in the other 9 molluscan genom ferroni correction, P ≤0.05). Transposable elements were included in the analysis. Colors depict the log2 ratio between Pfam counts found in each single geno the corresponding mean values. The hierarchical clustering used the average dot product for the data matrix and complete linkage for branching. Abbreviatio athymodioulus platifrons; Cg: Crassostrea gigas; Hd: Haliotus discus hannai; Lf: L. fortunei; Lg: Lottia gigantean; Mg: Mytilus galloprovincialis; Mp: Modioulus philippinar nctada fucata; Py: Patinopecten yessoensis; Rp: Ruditapes philippinarum. (B) Gene Ontology analysis of expanded gene families, semantic scatter plot. Shown er representatives after redundancy reduction in a 2-dimensional space applying multidimensional scaling to a matrix of semantic similarities of GO ter r indicates the GO enrichment level (legend in upper left-hand corner); size indicates the relative frequency of each term in the UNIPROT database (larger bubb sent less specific processes). Figure 4: Gene family representation analysis in the L. fortunei genome. (A) Pfam hierarchical clustering, heatmap. Features were selected according to a model based on the Poisson cumulative distribution of each Pfam count in the golden mussel genome vs the normalized average values found in the other 9 molluscan genomes (Bonferroni correction, P ≤0.05). Transposable elements were included in the analysis. Colors depict the log2 ratio between Pfam counts found in each single genome and the corresponding mean values. The hierarchical clustering used the average dot product for the data matrix and complete linkage for branching. Abbreviations: Bp: Bathymodioulus platifrons; Cg: Crassostrea gigas; Hd: Haliotus discus hannai; Lf: L. fortunei; Lg: Lottia gigantean; Mg: Mytilus galloprovincialis; Mp: Modioulus philippinarum; Pf: Pinctada fucata; Py: Patinopecten yessoensis; Rp: Ruditapes philippinarum. (B) Gene Ontology analysis of expanded gene families, semantic scatter plot. Shown are cluster representatives after redundancy reduction in a 2-dimensional space applying multidimensional scaling to a matrix of semantic similarities of GO terms. Color indicates the GO enrichment level (legend in upper left-hand corner); size indicates the relative frequency of each term in the UNIPROT database (larger bubbles represent less specific processes). Figure 4: Gene family representation analysis in the L. fortunei genome. (A) Pfam hierarchical clustering, heatmap. Features were selected according to a model based on the Poisson cumulative distribution of each Pfam count in the golden mussel genome vs the normalized average values found in the other 9 molluscan genomes (Bonferroni correction, P ≤0.05). Transposable elements were included in the analysis. Colors depict the log2 ratio between Pfam counts found in each single genome and the corresponding mean values. The hierarchical clustering used the average dot product for the data matrix and complete linkage for branching. Abbreviations: Bp: Bathymodioulus platifrons; Cg: Crassostrea gigas; Hd: Haliotus discus hannai; Lf: L. fortunei; Lg: Lottia gigantean; Mg: Mytilus galloprovincialis; Mp: Modioulus philippinarum; Pf: Pinctada fucata; Py: Patinopecten yessoensis; Rp: Ruditapes philippinarum. (B) Gene Ontology analysis of expanded gene families, semantic scatter plot. Shown are cluster representatives after redundancy reduction in a 2-dimensional space applying multidimensional scaling to a matrix of semantic similarities of GO terms. Color indicates the GO enrichment level (legend in upper left-hand corner); size indicates the relative frequency of each term in the UNIPROT database (larger bubbles represent less specific processes). References Supplementary Table S3. Details of the online availability of the data used for ortholog assignment and protein domain ex- pansion analysis. Supplementary Table S3. Details of the online availability of the data used for ortholog assignment and protein domain ex- pansion analysis. 1. Pastorino G, Darrigran G, Maris MS et al. Limnoperna fortunei (Dunker, 1857) (Mytilidae), nuevo bivalvo inva- sor em ´aguas Del Rio de la plata. Neotropica 1993;39: 101–2. Supplementary Table S4. Expanded protein families in the L. fortunei genome. Supplementary Table S5. Contracted protein families in the L. fortunei genome. Supplementary Table S5. Contracted protein families in the L. fortunei genome. 2. Darrigran G. Potential impact of filter-feeding invaders on temperate inland freshwater environments. Biol Invasions 2002;4(1/2):145–56. Supplementary Table S6. Fantasy names given to L. fortunei genes and proteins from the backers that supported us through crowdfunding (www.catarse.me/genoma). 3. Uliano-Silva M, Fernandes F da C, Holanda IBB et al. Inva- sive species as a threat to biodiversity: the golden mussel Limnoperna fortunei approaching the Amazon River basin. In: Alodi S, ed. Exploring Themes on Aquatic Toxicology. Re- search Signpost, India; 2013. 3. Uliano-Silva M, Fernandes F da C, Holanda IBB et al. Inva- sive species as a threat to biodiversity: the golden mussel Limnoperna fortunei approaching the Amazon River basin. In: Alodi S, ed. Exploring Themes on Aquatic Toxicology. Re- search Signpost, India; 2013. Supplementary Figure 1. Steps performed for the prediction and annotation of the L. fortunei genome. Supplementary Figure 1. Steps performed for the prediction and annotation of the L. fortunei genome. Supplementary Figure 2. Phylogenetic tree of Toll-like (TLRs) receptors found in the L. fortunei genome. Supplementary Figure 2. Phylogenetic tree of Toll-like (TLRs) receptors found in the L. fortunei genome. 4. Boltovskoy D, Correa N. Ecosystem impacts of the invasive bivalve Limnoperna fortunei (golden mussel) in South America. Hydrobiologia 2015;746(1):81–95. 4. Boltovskoy D, Correa N. Ecosystem impacts of the invasive bivalve Limnoperna fortunei (golden mussel) in South America. Hydrobiologia 2015;746(1):81–95. Abbreviations 5. Xu M. Distribution and spread of Limnoperna fortunei in China. In: Boltovskoy D, ed. Limnoperna fortunei. Cham, Switzer- land: Springer International Publishing; 2015:313–20. 5. Xu M. Distribution and spread of Limnoperna fortunei in China. In: Boltovskoy D, ed. Limnoperna fortunei. Cham, Switzer- land: Springer International Publishing; 2015:313–20. BUSCO: Benchmarking Universal Single-Copy Orthologs; KEGG: Kyoto Encyclopedia of Genes and Genomes; SRA: Sequence Read Archive. 6. Oliveira M, Hamilton S, Jacobi C. Forecasting the expansion of the invasive golden mussel Limnoperna fortunei in Brazil- ian and North American rivers based on its occurrence in the Paraguay River and Pantanal wetland of Brazil. Aquat In- vasions 2010;5(1):59–73. Additional files Additional files to the genes and proteins that we found in the genome to thank the backers for their support. The name list is available in Supplementary Table S6. Supplementary Table S1. RNA raw reads sequenced for 3 L. for- tunei specimens, 4 tissues each. Supplementary Table S1. RNA raw reads sequenced for 3 L. for- tunei specimens, 4 tissues each. Supplementary Table S2. RepeatMasker classification of re- peats predicted in the L. fortunei genome. Funding 10. Calazans SHC, Americo JA, Fernandes F da C et al. Assess- ment of toxicity of dissolved and microencapsulated bio- cides for control of the Golden Mussel Limnoperna fortunei. Mar Environ Res 2013 91:104–8. This work was supported by the Brazilian Government agen- cies CAPES (PVE 71/2013), FAPERJ APQ1 (2014), and FAPERJ/DFG (39/2014). Also, this work was funded through crowdfunding with the support of 346 people (www.catarse.me/genoma). 11. Aldridge DC, Elliott P, Moggridge GD. Microencapsulated biobullets for the control of biofouling zebra mussels. Env- iron Sci Technol 2006;40(3):975–9. Author contributions 12. Cox GW. Alien species and evolution: the evolutionary ecol- ogy of exotic plants, animals, microbes, and interacting na- tive species. Washington DC: Island Press; 2004:377. Conceived and designed the experiments: M.R., M.U., T.O., C.M., F.D. Performed the experiments: M.U., J.A. Analyzed the data: M.U., T.O., C.M., F.D., F.P., N.C., I.C., M.R. Contributed reagents/materials/analysis tools: M.R., F.P., C.M. Wrote the pa- per: M.U., F.D., M.R. All authors read and approved the final manuscript. 13. Hall MR, Kocot KM, Baughman KW et al. The crown-of- thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature 2017;544(7649):231–4. 14. www.catarse.me/genoma. 15. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trim- mer for Illumina sequence data. Bioinformatics 2014;1;170. Competing interests The authors declare that they have no competing interests. 9. Claudi R, Mackie GL. Practical manual for zebra mussel moni- toring and control. Boca Raton, FL: Lewis Publishers; 1994:227 Final considerations Figure 4: Gene family representation analysis in the L. fortunei genome. (A) Pfam hierarchical clustering, heatmap. Features were selected according to a model based on the Poisson cumulative distribution of each Pfam count in the golden mussel genome vs the normalized average values found in the other 9 molluscan genomes (Bonferroni correction, P ≤0.05). Transposable elements were included in the analysis. Colors depict the log2 ratio between Pfam counts found in each single genome and the corresponding mean values. The hierarchical clustering used the average dot product for the data matrix and complete linkage for branching. Abbreviations: Bp: Bathymodioulus platifrons; Cg: Crassostrea gigas; Hd: Haliotus discus hannai; Lf: L. fortunei; Lg: Lottia gigantean; Mg: Mytilus galloprovincialis; Mp: Modioulus philippinarum; Pf: Pinctada fucata; Py: Patinopecten yessoensis; Rp: Ruditapes philippinarum. (B) Gene Ontology analysis of expanded gene families, semantic scatter plot. Shown are cluster representatives after redundancy reduction in a 2-dimensional space applying multidimensional scaling to a matrix of semantic similarities of GO terms. Color indicates the GO enrichment level (legend in upper left-hand corner); size indicates the relative frequency of each term in the UNIPROT database (larger bubbles represent less specific processes). Ethics approval Limnoperna fortunei specimens used for DNA extraction and sequencing were collected in the Jacu´ı River (29◦59′29.3′′S 51◦16′24.0′′W), southern Brazil. This bivalve is an exotic species in Brazil and is not characterized as an endangered or protected species. 7. Karatayev AY, Boltovskoy D, Padilla DK, Burlakova LE. The in- vasive bivalves Dreissena polymorpha and Limnoperna fortunei: parallels, contrasts, potential spread and invasion impacts. J Shellfish Res 2007;26(1):205–13. 8. Orensanz JM (Lobo), Schwindt E, Pastorino G et al. No longer the pristine confines of the world ocean: a survey of exotic marine species in the Southwestern Atlantic. Biol Invasions 2002;4(1/2):115–43. Competing interests Acknowledgements 16. Trapnell C, Roberts A, Goff L et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012;7(3):562–78. 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Child anthropometry data quality from Demographic and Health Surveys, Multiple Indicator Cluster Surveys, and National Nutrition Surveys in the West Central Africa region: are we comparing apples and oranges?
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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 Permanent link http://nrs.harvard.edu/urn-3:HUL.InstRepos:33732170 Published Version doi:10.1080/16549716.2017.1328185 Published Version doi:10.1080/16549716.2017.1328185 Citation Corsi, Daniel J., Jessica M. Perkins, and S. V. Subramanian. 2017. “Child Anthropometry Data Quality from Demographic and Health Surveys, Multiple Indicator Cluster Surveys, and National Nutrition Surveys in the West Central Africa Region: Are We Comparing Apples and Oranges?” Global Health Action 10 (1) (January): 1328185. doi:10.1080/16549716.2017.1328185. ARTICLE HISTORY ARTICLE HISTORY Background: There has been limited work comparing survey characteristics and assessing the quality of child anthropometric data from population-based surveys. Received 16 February 2017 Accepted 18 April 2017 Received 16 February 2017 Accepted 18 April 2017 q y p p p y Objective: To investigate survey characteristics and indicators of quality of anthropometric data in children aged 0–59 months from 23 countries in the West Central Africa region. Objective: To investigate survey characteristics and indicators of quality of anthropometric data in children aged 0–59 months from 23 countries in the West Central Africa region. Methods: Using established methodologies and criteria to examine child age, sex, height, and weight, we conducted a comprehensive assessment and scoring of the quality of anthropometric data collected in 100 national surveys. RESPONSIBLE EDITOR Stig Wall, Umeå University, Sweden RESPONSIBLE EDITOR Stig Wall, Umeå University, Sweden Methods: Using established methodologies and criteria to examine child age, sex, height, and weight, we conducted a comprehensive assessment and scoring of the quality of anthropometric data collected in 100 national surveys. KEYWORDS Undernutrition; child health; data quality; anthropometry; DHS; MICS; NNS; height; weight p y Results: The Multiple Indicator Cluster Surveys (MICS) and Demographic and Health Surveys (DHS) collected data from a greater number of younger children than older children while the opposite was found for the National Nutrition Surveys (NNS). Missing or implausible height/ weight data proportions were 12% and 8% in MICS and DHS compared to 3% in NNS. Average data quality scores were 14 in NNS, 33 in DHS, and 41 in MICS. Conclusions: Although our metric of data quality suggests that data from the NNS appear more consistent and robust, it is equally important to consider its disadvantages related to access and lack of broader socioeconomic information. In comparison, the DHS and MICS are publicly-accessable for research and provide socioeconomic context essential for assessing and addressing the burden of undernutrition within and between countries. The strengths and weaknesses of data from these three sources should be carefully considered when seeking to determine the burden of child undernutrition and its variation within countries. CONTACT S. V. Subramanian svsubram@hsph.harvard.edu Harvard School of Public Health, Boston, MA 02115-6096, USA Supplemental data for this article can be accessed here. © 2017 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. Child anthropometry data quality from Demographic and Health Surveys, Multiple Indicator Cluster Surveys, and National Nutrition Surveys in the West Central Africa region: are we comparing apples and oranges? Daniel J. Corsia,b, Jessica M. Perkinsb,c and S. V. Subramanianb,d aOMNI Research Group, Ottawa Hospital Research Institute, Ottawa, ON, Canada; bCenter for Population & Development Studies, Harvard School of Public Health, Cambridge, MA, USA; cMGH Global Health, Massachusetts General Hospital, Boston, MA, USA; dDepartment of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA g dDepartment of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Heal 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 GLOBAL HEALTH ACTION, 2017 VOL. 10, 1328185 https://doi.org/10.1080/16549716.2017.1328185 GLOBAL HEALTH ACTION, 2017 VOL. 10, 1328185 https://doi.org/10.1080/16549716.2017.1328185 ORIGINAL ARTICLE Background Oral or writ- ten informed consent for the survey was obtained from respondents by interviewers. This analysis was reviewed by the Harvard School of Public Health Institutional Review Board and was considered exempt from full review because the study was based on a de-identified and anonymous data-set available for secondary analyses. DHS are large, standardized, household surveys pro- duced by the Demographic and Health Surveys Program [14]. The targeted sample is based on nationally repre- sentative sampling plans. The surveys emphasize data collection on standardized measures of fertility and child mortality, and indicators of access to maternal and child health interventions, illness, treatment, and nutritional status [1]. These surveys also collect an exten- sive set of standardized socioeconomic indicators and other such information. These data-sets are fully open- access. Based on DHS measurement protocols, all chil- dren of selected mothers who are of appropriate age based on the three- or five-year reference window are potentially eligible for measurement. In some surveys, one-third, one-half, or two-thirds subsamples of children are selected for anthropometric measurements. In addi- tion, in the more recent DHS surveys, all children of appropriate age in selected households are eligible for measurement regardless of whether their mother parti- cipated in the women’s questionnaire. There were 304,858 children eligible for measurements across the individual DHS included in this study (mean n across surveys = 7001 and SD = 4194). Age and sex were assessed by self-reports, and completion of reproductive calendars during household visits (used to determine age at first pregnancy and duration between pregnancies). Standard protocols in DHS instructed field investigators to weigh each child using a solar-powered digital scale (Seca 878) with a precision of ±100 g. Standing height was measured for children older than two years and lying length obtained in children less than two years old using an adjustable measuring board which is theoretically local nodal organizations and agencies to collect data with technical support and financial assistance from the United States Agency for International Development (USAID; DHS), UNICEF (MICS and NNS), and other national and international sources. Supplemental Table 1 indicates the specific countries included in this study. The data collection procedures were approved by the relevant institutional review board in each country. Oral or writ- ten informed consent for the survey was obtained from respondents by interviewers. Background There were 304,858 children eligible for measurements across the individual DHS included in this study (mean n across surveys = 7001 and SD = 4194). Age and sex were assessed by self-reports, and completion of reproductive calendars during household visits (used to determine age at first pregnancy and duration between pregnancies). Standard protocols in DHS instructed field investigators to weigh each child using a solar-powered digital scale (Seca 878) with a precision of ±100 g. Standing height was measured for children older than two years and lying length obtained in children less than two years old using an adjustable measuring board which is theoretically accurate to 1 millimeter [15]. In some early (phase 2–3) DHS, the age of eligibility ended at 35 months (n = 7 among the surveys included here). The use of a standard overall data quality score facilitates comparisons of anthropometric data quality across surveys and survey sources. Preliminary analyses suggest that prevalence estimates of child wasting (low weight-for-height) in DHS/MICS may be biased by 3–5% at a national level due to variation in criteria for excluding implausible values for height and/or weight [13]. The current study assesses multiple characteristics of three survey sources (DHS, NNS, and MICS) and the quality of anthropometric data produced through sur- veys conducted between 1990 and 2012 in the UNICEF- designated West Central Africa region. This region is the only one where the three survey programs currently operate. Three data quality issues were assessed: (1) incorrect measurement of child age (which is important for determining whether a child is stunted or under- weight), (2) incorrect measurement of height, and (3) incorrect measurement of weight. Background This analysis was reviewed by the Harvard School of Public Health Institutional Review Board and was considered exempt from full review because the study was based on a de-identified and anonymous data-set available for secondary analyses. studies serve to give fieldworkers an opportunity to self- correct and, if necessary, allow data to be adjusted post- collection based on trends among individual fieldwor- kers. The World Health Organization (WHO) has com- piled a database of expected anthropometric measurements that can serve as a standardization tool for analysis [2]. Several individual papers also present standardization corrections for analysis given expected error ranges [6]. The Emergency Nutrition Assessment (ENA) and Standardized Monitoring and Assessment of Relief and Transitions (SMART) provide a basic, integrated survey method for assessing nutritional status in emergency and surveillance situations [10]. Methodologies used in SMART and built into the ENA software package, which can be used in the field, incorporate a quality assessment for nutrition data focusing on several issues: terminal digit preference, prevalence of implausible or missing values for anthropometric and demographic data (especially for age), and implausible age and sex ratios (which may indicate a non-representative sample) [2,10–12]. A composite quality score based on these parameters can indicate overall data quality as well as specific issues around missing data, heaping/rounding of values, and implausible age or sex distributions and can be disseminated to researchers [2]. and anonymous data set available for secondary analyses. DHS are large, standardized, household surveys pro- duced by the Demographic and Health Surveys Program [14]. The targeted sample is based on nationally repre- sentative sampling plans. The surveys emphasize data collection on standardized measures of fertility and child mortality, and indicators of access to maternal and child health interventions, illness, treatment, and nutritional status [1]. These surveys also collect an exten- sive set of standardized socioeconomic indicators and other such information. These data-sets are fully open- access. Based on DHS measurement protocols, all chil- dren of selected mothers who are of appropriate age based on the three- or five-year reference window are potentially eligible for measurement. In some surveys, one-third, one-half, or two-thirds subsamples of children are selected for anthropometric measurements. In addi- tion, in the more recent DHS surveys, all children of appropriate age in selected households are eligible for measurement regardless of whether their mother parti- cipated in the women’s questionnaire. Background on-site digital data input or in-field checks [4]. Second, fieldworker variation has the potential to dramatically affect the output of analyses using the recorded data although this source of data error may be less apparent than error due to variation in instrument use [5]. Moreover, fieldworkers tend to have a subtle directional bias in their measurements, which may go unnoticed without undertaking specialized analyses (for example digit preference) and can often be exacerbated when there are multiple fieldworkers collecting data [6,7]. Finally, the study population may not be representative of the base population being studied [8]. Population-based surveys such as the Demographic and Health Surveys (DHS), National Nutrition Surveys (NNS), and Multiple Indicator Cluster Surveys (MICS) are important sources of information on child health and nutritional status in low-income countries [1,2]. Anthropometric measurement in large-scale surveys is a complex and difficult undertaking. Inaccuracies and other deficiencies in the quality of the anthropometric data collected by these surveys arise frequently and may have important implications for understanding the burden of malnutrition at the population level in low-income settings. Potential threats to high data quality may occur across various research stages, from survey and questionnaire devel- opment, to training, fieldwork, and data entry, to data cleaning and analysis. First, variability inherently exists in the precision and validity of anthropometric mea- surement tools (e.g. measuring tapes/boards, scales, calipers) [3]. In addition, errors may arise when using measurement instruments including when reading and recording measurements. These can be identified using Measures to address data error and low data quality vary. Some studies may alter data recording protocols throughout the collection phase. Alternatively, research- ers may test for evidence of systematic differences in data trends basedon recordingpractices after data collection is finished [4]. Previous studies have implemented repeat- ability and test–retest measures to look at both measure- ment performance within fieldworkers on separate occasions and measurement comparison between differ- ent fieldworkers on the same subject [9]. Such reliability D. J. CORSI ET AL. 2 local nodal organizations and agencies to collect data with technical support and financial assistance from the United States Agency for International Development (USAID; DHS), UNICEF (MICS and NNS), and other national and international sources. Supplemental Table 1 indicates the specific countries included in this study. The data collection procedures were approved by the relevant institutional review board in each country. Data quality indicators domain. The survey employs a two-stage cluster design and households are randomly selected without replace- ment from a listing of households within primary sample units (PSU). Children eligible for measurement are aged 0–59 months with some surveys restricted to 0-36 months. There were 232,124 children eligible for mea- surements in the MICS included in this study (mean n across surveys = 6775 and SD = 4439). Age and sex were assessed by self-reports and confirmed during field inter- views. Similar to DHS, MICS used Seca digital scales to measure weight and standing/lying height/length was obtained via Shorr measuring boards. Child age ratios were calculated across survey popu- lations. The age ratio was defined as the number of children aged 6–29 months over the number of chil- dren aged 30–59 months. (Age ratios were not calcu- lated for some DHS as the age of eligibility ended at 35 months.) If the sample has good coverage of all ages in the 6–59 month range, then the ratio should be close to 1.0. However, some variability may arise due to age recording error, lack of knowledge of the child’s birthday, and/or demographic changes and changes in mortality rates over time. In addition, information on the age distribution of children cover- ing 0–59 months (in six-month intervals) was also calculated to examine departures from the expected distribution for under-five populations. The statistics for age ratios are based on original data quality score reports (according to SMART methods). It should be noted that there has been some disagreement in the literature about what the ideal age ratio should show given differences in the month intervals between 6–29 and 30–59 and changes in fertility and other variations which may arise. Therefore, formal statis- tical tests of these intervals were not conducted. NNS are rapid surveys conducted on a by-country basis (typically every two years, annually or bi-annually) and are not part of a standardized data collection pro- gram. They focus on assessing child and maternal nutri- tion indicators using SMART methodology, crude under-five mortality rates, and selected interventions (e.g. vitamin A supplementation and measles vaccina- tion). As the NNS are not standardized across countries, they typically collect less extensive data on socioeco- nomic status and other characteristics. The information included may vary from country to country. Data quality indicators Special permission is required from country governments to obtain access to these data, which were provided to the study authors via UNICEF West and Central Africa Regional Office (WCARO). Children aged less than 5 years are selected from a random/systematic sample of households without replacement within clusters. Many NNS do not have children aged 0–5 months in their samples, which are restricted to ≥6 months of age. There were 189,029 children eligible for measurements in the NNS included in this study (mean n across sur- veys = 8290 and SD = 5291). Age and sex were assessed by self-reports and verified by interviewers during house- hold visits. The NNS height and weight protocol was similar to that of DHS and MICS, and used Seca 878 digital scales to measure weight and Shorr measuring boards (or equivalent locally made boards) to measure length (in children < 2 years or < 87 cm)/standing height. Child sex ratios were calculated, defined as the number of males to females in a population. In the- ory, this ratio should be 1.0. True ratios may deviate somewhat from this ideal, and some variability may arise due to sampling variation or recording error. We created three categories of children according to the presence and validity of their height and weight data. The first category represents children who were targeted for measurement, but who could not be located for measurement or their mothers refused measurement. We refer to these children as having ‘missing’ data. The second category represents children with standardized anthropometric z-scores (based on age, sex, height, and weight) that were biologically implausible, which was defined as values that were five standard deviations above or below (for weight- for-height – WHZ), six standard deviations above or below (for height-for-age – HAZ), and five standard deviations above or six standard deviations below (for weight-for-age – WAZ) the mean (i.e. greater than or less than WHO 2006 defined norms) [19,20]. Children who had both height and weight data that were neither missing nor implausible were considered to have ‘valid’ anthropometric data. It is anticipated that these indi- cators of missing and implausible data will be lower in the NNS due to field use of laptops and ENA software that provides daily feedback to interviewers regarding missing and implausible values. Data sources A total of 100 surveys providing information on anthro- pometric measures (i.e. child age, sex, height – or length if under 2 years, and weight) in children aged 0–59 months were available from 23 countries in the United Nations Children’s Fund (UNICEF)-designated West Central Africa region. There were 45 DHS covering 19 countries, 27 NNS covering 13 countries, and 28 MICS covering 16 countries. Each of the survey programs partners with MICS are large, standardized, multi-topic household surveys produced by UNICEF [16]. They tend to focus on reproductive health, maternal and child health inter- ventions, child nutritional status, and early childhood development, and use similar methodology and mea- surement protocols to DHS. MICS also collect a standar- dized set of socioeconomic characteristics of individuals and households. Data-sets can be accessed in the public GLOBAL HEALTH ACTION GLOBAL HEALTH ACTION 3 Data quality indicators As the p-values from a chi-square test of departure from a uniform distribution are generally very small when large sample sizes are used, such as in this study, the absolute values of DPSs were the present focus. The DPS varies between 0 and 100. Scores are low in instances of high agreement with the ideal of nonprefer- ence of the terminal digits, whereas scores rise as devia- tions from a uniform distribution across the terminal digits 0 through 9 increase. Scores above 20 are indicative of a statistically significant preference detected for the terminal digit. We calculated the percentage of surveys within a survey source that had a DPS above 20 for height and weight, separately. Finally, a total data quality score was created using the aforementioned indicators according with weight- ing applied following the SMART criteria, which is one method available to review and assess anthropo- metric data quality [10–12]. The score represents a weighted combination of the level of missing and/or implausible data, overall sex ratio, overall age ratio, digit preference score for weight, digit preference score for height, standard deviation of WHZ, skew- ness of WHS, and kurtosis of WHZ. Weights and points for each measure were used to calculate a total data quality score with a maximum possible score of 90. Lower scores indicate higher- quality data. Analyses We examined the number of children in each of the age categories against the expected values from a chi- squared distribution. A graphical assessment was also performed on the DHS data-set using all children irrespective of survivor status to examine the distri- bution of ages of children within sampled house- holds. In the other surveys, information on deceased children was not available. The main analyses pro- vided summary statistics (across surveys, but within survey source) using the various data quality indica- tors described previously (e.g. average and distribu- tion of age and sex ratios, prevalence of valid, missing, and implausible data, and spread of DPSs, anthropometric z-scores, and data quality scores). Supplementary analyses provided similar information at the individual survey level, which is the national level for a given year. Using age, sex, height, and weight data, and the WHO Child Growth Standards [21], we transformed the height and weight data into standardized z-scores representing HAZ, WAZ, and WHZ. For each survey, we calculated the mean and standard deviation as well as estimates of skewness and kurtosis for HAZ, WAZ, and WHZ for children. Skewness is a measure of dis- tribution symmetry or asymmetry. In general, a positive value for skewness indicates that the probability density function for a particular variable is longer and/or fatter on the right side; negative values indicate a distribution is longer and/or fatter on the left side. Kurtosis is an indication of peakedness and/or tail weight of a distri- bution. A perfectly symmetrical normal distribution would have a skewness of 0 and kurtosis of 3. These indicators were derived from an existing score card for nutrition data quality that we used as a basis for com- parison. Although the distributions of z-scores may have a certain level of skew in situations with high prevalence of undernutrition (and this phenomenon has been observed among adults across countries of similar socioeconomic conditions), data quality issues may be observed if certain distributions are dramati- cally skewed beyond what would be expected. Data quality indicators This study also used information from six waves of the National Health and Nutrition Examination Survey (NHANES) as a comparison data-set. The chosen NHANES represents a stratified, multistage probability sample of the civilian, non-institutionalized US popula- tion from 2003–2010 [17,18]. There were 8890 eligible children aged 0–59 months in NHANES (mean n across surveys = 1482 and SD = 127). Age and sex were assessed by self-reports and verified by field interviewers. NHANES protocol instructed trained health technicians to collect data on weight to the nearest 0.1 kilogram, and stature, length, and circumference measurements to the nearest millimeter. NHANES includes two measure- ments. A third measurement is also triggered if there is observed deviation between the first two measurements that is beyond an acceptable range [2]. We chose to assess terminal digit preference as an indicator of interviewer performance because demo- graphic methods have been developed that are able to parse random vs. non-random recoding of digits as an D. J. CORSI ET AL. D. J. CORSI ET AL. 4 indication of data quality and interviewer performance. Thus, we calculated terminal digit preference scores (DPSs) for height and weight data using methods pro- posed by SMART and the WHO Monica blood pressure study, which involves a chi-square test of homogeneity of DPS [10,12]. As the p-values from a chi-square test of departure from a uniform distribution are generally very small when large sample sizes are used, such as in this study, the absolute values of DPSs were the present focus. The DPS varies between 0 and 100. Scores are low in instances of high agreement with the ideal of nonprefer- ence of the terminal digits, whereas scores rise as devia- tions from a uniform distribution across the terminal digits 0 through 9 increase. Scores above 20 are indicative of a statistically significant preference detected for the terminal digit. We calculated the percentage of surveys within a survey source that had a DPS above 20 for height and weight, separately. indication of data quality and interviewer performance. Thus, we calculated terminal digit preference scores (DPSs) for height and weight data using methods pro- posed by SMART and the WHO Monica blood pressure study, which involves a chi-square test of homogeneity of DPS [10,12]. include children older than 39 months. DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. Age ratio was defined as the number of children aged 6–29 months over the number of children aged 30–59 months. Sex ratio was defined as the number of males to females in a population. Results Table 1 presents the mean age and sex ratios across the surveys from each survey source. The range of age ratios in MICS varied from 0.69 in Chad in 2010 to 1.11 in Gambia in 2005. The range of age ratios in the DHS varied from 0.82 in both Burkina Faso in 1993 Table 1. Summary statistics for age and sex ratios from children aged 0–59 months across MICS, DHS, and NNS surveys in West Central African countries and NHANES in the US. Age ratio Sex ratio Mean ratio across surveys Surveys with ratio < 0.95 Surveys with ratio > 1.05 Mean ratio across surveys Surveys with ratio < 0.95 Surveys with ratio > 1.05 N of surveys Mean SD Range n (and %) N (and %) Mean SD Range n (and %) n (and %) MICS 28 0.90 0.10 0.69 to 1.11 20 (71%) 2 (7%) 1.01 0.03 0.93 to 1.06 1 (4%) 2 (7%) DHS 38a 0.93 0.07 0.82 to 1.15 25 (67%) 2 (5%) 1.03 0.03 0.94 to 1.11 1 (2%) 11 (24%) NNS 26b 1.01 0.08 0.84 to 1.13 4 (15%) 8 (31%) 1.04 0.03 0.99 to 1.13 0 (0%) 6 (22%) NHANES 6 1.3 0.10 1.2 to 1.4 0 (0%) 6 (100%) 1.08 0.06 1.02 to 1.18 0 (0%) 2 (33%) Notes: a7 out of 45 DHS did not include children older than 35 months so the age ratio was not calculated for these surveys. b1 out of 27 surveys did not include children older than 39 months. DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. Age ratio was defined as the number of children aged 6–29 months over the number of children aged 30–59 months. Sex ratio was defined as the number of males to females in a population. for age and sex ratios from children aged 0–59 months across MICS, DHS, and NNS surveys in West d NHANES in the US Table 1. Summary statistics for age and sex ratios from children aged 0–59 months across MICS, DHS, and Central African countries and NHANES in the US. c ude c d e o de t a 39 o t s. DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. Results Percentage with valid data Percentage with implausible data Percentage with missing data Percentage with implausible or missing data Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range MICS 87.6% 8.0 %-points 68.5% to 96.3% 4.5% 3.2 %- points 0.4% to 12.1% 7.9% 5.7 %-points 0.6% to 21.5% 12.4% 8.0 %-points 3.7% to 31.5% DHS 92.0% 4.6 %-points 76.3% to 95.6% 4.1% 3.2 %-points 2.1% to 23.7% 3.0% 2.2 %-points 0.6% to 8.7% 8.0% 4.6 %-points 2.1% to 23.7% NNS 96.8% 3.2 %-points 88.3% to 100% 0.5% 0.8 %-points 0% to 4.1% 2.7% 3.2 %-points 0% to 11.1% 3.2% 3.2 %-points 0% to 11.7% NHANES 92.9% 6.9 %-points 78.9% to 96.1% 0.4% 0.2 %-points 0.2% to 0.6% 6.7% 7.0 %-points 3.3% to 20.9% 7.1% 6.9 %-points 3.9% to 21.1% Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There was a total of 232,124 eligible children across 28 MICS (mean n across surveys = 6775 and SD = 4439); a total of 304,858 eligible children across 45 DHS (mean n across surveys = 7001 and SD = 4194); a total of 189,029 eligible children across 27 NNS (mean n across surveys = 8290 and SD = 5291); and a total of 8890 eligible children across 6 waves of NHANES (mean n across surveys = 1482 and SD = 127). and Cameroon in 1991 to 1.15 in Sierra Leone in 2008. The NNS age ratios varied from 0.84 in Cameroon in 2011 to 1.13 in Mauritania in 2009. Each survey source had several surveys where the age ratio differed from 1.0 though the direction of the ratio differed. The average age ratio for MICS and DHS was less than 1.0 with more than half of the surveys from each source exhibiting an age ratio of less than 0.95, indicating that fewer younger children (6–29 months) were measured as compared to chil- dren aged 35–59 months. The opposite was true for the NNS where 30% of surveys exhibited ratios greater than 1.05. The age ratio in NHANES was 1.27, indicating greater numbers of younger children surveyed. Plots of the age distributions are provided in Supplemental Figure 1. Results Percentage with valid data Percentage with implausible data Percentage with missing data Percentage with implausible or missing data Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range MICS 87.6% 8.0 %-points 68.5% to 96.3% 4.5% 3.2 %- points 0.4% to 12.1% 7.9% 5.7 %-points 0.6% to 21.5% 12.4% 8.0 %-points 3.7% to 31.5% DHS 92.0% 4.6 %-points 76.3% to 95.6% 4.1% 3.2 %-points 2.1% to 23.7% 3.0% 2.2 %-points 0.6% to 8.7% 8.0% 4.6 %-points 2.1% to 23.7% NNS 96.8% 3.2 %-points 88.3% to 100% 0.5% 0.8 %-points 0% to 4.1% 2.7% 3.2 %-points 0% to 11.1% 3.2% 3.2 %-points 0% to 11.7% NHANES 92.9% 6.9 %-points 78.9% to 96.1% 0.4% 0.2 %-points 0.2% to 0.6% 6.7% 7.0 %-points 3.3% to 20.9% 7.1% 6.9 %-points 3.9% to 21.1% Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There was a total of 232,124 eligible children across 28 MICS (mean n across surveys = 6775 and SD = 4439); a total of 304,858 eligible children across 45 DHS (mean n across surveys = 7001 and SD = 4194); a total of 189,029 eligible children across 27 NNS (mean n across surveys = 8290 and SD = 5291); and a total of 8890 eligible children across 6 waves of NHANES (mean n across surveys = 1482 and SD = 127) Table 2. The percentage of children (aged 0–59 months) with valid, missing, or implausible height and weight data across surveys within the MICS, DHS, and NNS programs in West and Central African countries, and the NHANES program in the US. Results Age ratio was defined as the number of children aged 6–29 months over the number of children aged 30–59 months. Sex ratio was defined as the number of males to females in a population. GLOBAL HEALTH ACTION 5 2. The percentage of children (aged 0–59 months) with valid, missing, or implausible height and weight data across surveys within the MICS, DHS, and NNS programs in West and Central countries, and the NHANES program in the US. Percentage with valid data Percentage with implausible data Percentage with missing data Percentage with implausible or missing data Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range Mean across surveys SD Range 87.6% 8.0 %-points 68.5% to 96.3% 4.5% 3.2 %- points 0.4% to 12.1% 7.9% 5.7 %-points 0.6% to 21.5% 12.4% 8.0 %-points 3.7% to 31.5% 92.0% 4.6 %-points 76.3% to 95.6% 4.1% 3.2 %-points 2.1% to 23.7% 3.0% 2.2 %-points 0.6% to 8.7% 8.0% 4.6 %-points 2.1% to 23.7% 96.8% 3.2 %-points 88.3% to 100% 0.5% 0.8 %-points 0% to 4.1% 2.7% 3.2 %-points 0% to 11.1% 3.2% 3.2 %-points 0% to 11.7% S 92.9% 6.9 %-points 78.9% to 96.1% 0.4% 0.2 %-points 0.2% to 0.6% 6.7% 7.0 %-points 3.3% to 20.9% 7.1% 6.9 %-points 3.9% to 21.1% HS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There was a total of 232,124 eligible children 28 MICS (mean n across surveys = 6775 and SD = 4439); a total of 304,858 eligible children across 45 DHS (mean n across surveys = 7001 and SD = 4194); a total of 189,029 eligible children across 27 NNS (mean n across s = 8290 and SD = 5291); and a total of 8890 eligible children across 6 waves of NHANES (mean n across surveys = 1482 and SD = 127). Table 2. The percentage of children (aged 0–59 months) with valid, missing, or implausible height and weight data across surveys within the MICS, DHS, and NNS programs in West and Central African countries, and the NHANES program in the US. Results Summary statistics for terminal digit preference score (DPS) for height and weight data from children aged 0–59 months in MICS, DHS, and NNS surveys in West and Central African countries, and from the NHANES program in the US. Mean height DPS across surveys Surveys with mean height DPS above 20 Mean weight DPS across surveys Surveys with mean weight DPS above 20 Mean SD Range n and % Mean SD Range n and % MICS 31.6 23.6 4.2 to 92.4 17 (61%) 9.8 15.4 1.2 to 71.2 4 (14%) DHS 20.6 14.8 6.7 to 91.8 20 (44%) 5.4 12.1 20.7 to 80.3 3 (7%) NNS 5.9 4.2 2.0 to 19.7 0 (0%) 1.7 0.7 0.6 to 3.2 0 (0%) NHANES 2.6 1.1 1.6 to 4.0 0 (0%) 2.9 0.5 2.1 to 3.5 0 (0%) Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There were 28 MICS covering 16 countries, 45 DHS covering 19 countries, and 27 NNS covering 13 countries. Scores above 20 are indicative of a statistically significant preference detected for the terminal digit. Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There were 28 MICS covering 16 countries, 45 DHS covering 19 countries, and 27 NNS covering 13 countries. Scores above 20 are indicative of a statistically significant preference detected for the terminal digit. Table 4. Summary statistics across surveys within the MICS, DHS, and NNS survey programs, separately, for the average height- for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) z-scores (based on the WHO 2006 reference standard across surveys) from children aged 0–59 months in West Central African countries, and from US children in the NHANES program. Table 4. Summary statistics across surveys within the MICS, DHS, and NNS survey programs, separately, for the average height- for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) z-scores (based on the WHO 2006 reference standard across surveys) from children aged 0–59 months in West Central African countries, and from US children in the NHANES program. Table 4. Results Summary statistics across surveys within the MICS, DHS, and NNS survey programs, separately, for the average height for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) z-scores (based on the WHO 2006 reference standard across surveys) from children aged 0–59 months in West Central African countries, and from US children in the NHANES program. Mean of mean z-scores across surveys Standard deviation of mean z-scores across surveys HAZ WAZ WHZ HAZ WAZ WHZ MICS −1.46 −1.06 −0.26 0.21 0.25 0.34 DHS −1.40 −1.08 −0.35 0.24 0.33 0.33 NNS −1.35 −1.14 −0.54 0.22 0.18 0.26 NHANES 0.06 0.44 0.57 0.05 0.04 0.04 Mean standard deviation of z-scores across surveys Standard deviation of mean standard deviation of z-scores across surveys HAZ WAZ WHZ HAZ WAZ WHZ MICS 1.82 1.40 1.45 0.24 0.16 0.22 DHS 1.80 1.39 1.44 0.20 0.14 0.19 NNS 1.36 1.13 1.11 0.13 0.10 0.06 NHANES 1.12 1.07 1.06 0.04 0.03 0.03 Mean z-score skewness across surveys Standard deviation of z-score skewness across surveys HAZ WAZ WHZ HAZ WAZ WHZ MICS 0.39 −0.04 −0.07 0.13 0.10 0.09 DHS 0.37 −0.01 −0.03 0.13 0.14 0.14 NNS 0.23 −0.11 −0.04 0.16 0.14 0.12 NHANES 0.08 0.11 0.25 0.03 0.03 0.08 Mean z-score kurtosis across surveys Mean standard deviation of z-score kurtosis across surveys HAZ WAZ WHZ HAZ WAZ WHZ MICS 3.78 3.79 3.68 0.34 0.38 0.33 DHS 3.79 3.80 3.83 0.36 0.37 0.40 NNS 3.93 3.64 3.69 0.57 0.39 0.32 NHANES 3.85 3.85 3.71 0.52 0.31 0.18 Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. There were 28 MICS covering 16 countries, 45 DHS covering 19 countries, and 27 NNS covering 13 countries. Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANE and Nutrition Examination Survey. There were 28 MICS covering 16 countries, 45 DHS covering 19 countries, and 27 NNS coveri hic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health tion Survey. There were 28 MICS covering 16 countries, 45 DHS covering 19 countries, and 27 NNS covering 13 countries. Means and standard deviations (SDs) of the mean z-score, SD, skewness, and kurtosis for HAZ, WAZ, and WHZ are presented across surveys by survey source (Table 4). Results The average SDs of the mean HAZ, WAZ, and WHZ scores across the NNS surveys were lower than the mean SDs for these indicators across surveys in the DHS and MICS and closer to the means for NHANES of 1.12 (HAZ), 1.07 (WAZ), and 1.06 (WHZ). The average skewness for HAZ across surveys within each source was positive while the average skew- ness was slightly negative for WAZ and WHZ across survey sources. Supplemental Tables 11–13 present the mean z-score and SD for the HAZ, WAZ, and WHZ indicators for each survey within each survey source. Skewness and kurtosis statistics are also provided. Table 5. Summary statistics of mean data quality scores (lower = worse) for anthropometric data from children aged 0–59 months across MICS, DHS, and NNS surveys in West Central African countries, and NHANES in the US. Mean data quality score across surveys Surveys with a data quality score of less than 10 Surveys with a data quality score from 10–19 Mean SD Range n (%) n (%) MICS 40.9 13.5 18 to 61 0 (0%) 1 (4%) DHS 33.0 12.7 11 to 70 0 (0%) 4 (9%) NNS 14.0 8.0 4 to 35 9 (33%) 14 (52%) NHANES 24.3 7.5 16 to 38 0 (0%) 1 (17%) Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. Lower scores indicate higher quality of data. The potential range of scores is from 0 to 90. Notes: DHS = Demographic and Health Surveys; MICS = Multiple Indicator Cluster Surveys; NNS = National Nutrition Surveys; NHANES = National Health and Nutrition Examination Survey. Lower scores indicate higher quality of data. The potential range of scores is from 0 to 90. in 2011. The average data quality score in the NNS was 14.0, with a range from a low score of 4 in Mauritania in July 2011 to a score of 35 in Cameroon in 2011. One third of the NNS had a data quality score below 10 (n = 9), with 14/27 (52%) falling between scores of 10 and 19. For comparison, the average data quality score in Information on the overall data quality scores is pre- sented in Table 5. Results In several surveys, there was clear evidence of age heaping around or just after 12, 24, and 36 months of age. The sex ratio among the MICS varied from 0.93 in Sao Tome et Principe in 2000 to 1.06 in Niger in 2000. The sex ratios among the DHS ranged from 0.94 in Senegal in 1992 to 1.11 in Guinea in 1999. Finally, the sex ratios varied from 0.99 in Sierra Leone in 2010 to 1.13 in Mauritania in 2008 in the NNS. Among the NHANES, the sex ratios varied from 1.02 to 1.18. Age and sex ratios for each individual survey within each survey source are presented in Supplemental Tables 2–4. Table 2 presents basic statistics about the percentages of children with valid, missing, and implausible height and weight data across the surveys conducted by each survey source. The average percentage of children with valid data was 88% in MICS, 92% in DHS, 97% in NNS, and 93% in NHANES. The presence of valid data varied from 69% to 96% in the MICS, from 76% to 96% in the DHS, and from 88% to 100% in the NNS. Out of 28 MICS surveys, 46% of the surveys had 10% or more missing or implausible anthropometric data (among children who were targeted for measurement). Likewise, 20% of the DHS had 10% or more missing or implausible data. The NNS only had 2 out of 28 surveys with 10% or more missing or implausible data. The percentages of children who fall into these categories in each survey within each source are presented in Supplemental Tables 5–7. Summary statistics regarding terminal DPSs for height and weight data are presented in Table 3. The average height DPS was 5.9 in NNS, 20.6 in DHS, and 31.6 in MICS while the average weight DPS was 1.7 in NNS, 5.4 in DHS, and 9.8 in MICS. In comparison, the DPSs for height and weight in NHANES were 2.6 and 2.9, respectively. None of the NNS surveys had height DPSs above 20 whereas 44% and 61% of surveys in DHS and MICS, respectively, had height DPSs above 20. Similarly, 7% and 14% of surveys in DHS and MICS, respectively, had weight DPSs above 20 while no NNS surveys did. Information on the DPSs within each sur- vey is presented in Supplemental Tables 8–10. D. J. CORSI ET AL. D. J. CORSI ET AL. 6 Table 3. Discussion This study presents a comprehensive assessment of the quality of child anthropometric data in 100 surveys conducted in the West Central Africa region. The most salient findings suggest that (1) there is an unequal distribution in the age of children being recorded and measured, (2) there is a substantial amount of missing or implausible anthropometric data across surveys in the DHS and MICS, (3) there is definite evidence of terminal digit preference for height data, and (4) anthropometric data quality was highly variable both between and within survey sources and over time, on average. Finally, although the data quality score is a useful starting point for comparison across multiple surveys, issues remain with some of the score components. First, the score gives relatively large weight to missing and/or implausible values. If that component of the data quality score is removed, then the NNS has an overall mean score of 10.1 across surveys (versus 33.0), the DHS has a mean score of 22.6 (versus 33) across surveys, and the MICS has a mean score of 27.1 (versus 40.9) across surveys. Second, there is lack of consensus around the ‘true’ population parameter for the age ratio given that a comparison is being made between groups spanning an unequal num- ber of months (6–29 months versus 30–59 months). Age ratios may be sensitive within countries to demographic changes from changing fertility rates and rates of infant and child mortality. In addition, many NNS surveys do not cover children in the range of 0–5 months (ages which may be more difficult to assess). It is not clear if this ratio should be 1.0 or some other value and if the true value may vary between countries and over time. Although derivation of the data quality score is subjective as different weight values are applied to each parameter making up the overall score are not empirically derived, the data quality score is based on key parameters which literature has shownto be important forthe assessmentof anthropometric data quality. Further work is needed to explore the measurement properties of this score along with its performance across nutrition data-sets of various types and sample sizes. Critically, the statistics for data quality assessment are still in their infancy. More work is needed to improve the ability to assess and determine the presence of poor data quality given complexities and differences across survey platforms. Results The MICS had a mean data quality score of 40.9 with a range from 18 in Central African Republic in 2010 to 61 in Central African Republic in 2000. The average data quality score across the DHS was 33, with a range from 11 in Congo in 2012 to 70 in Benin 7 GLOBAL HEALTH ACTION 7 nearly all accepted height values) covers 600 unique values compared to 170 unique values across the interval of 3.0–19.9 kg for weight. Separately, although there was sizeable variation in the distribution of the anthropo- metric z-scores, in particular as indicated by the SD of WHZ, it is not clear what the ideal parameters may be and whether the variability may decrease as the nutri- tional status of children in the population improves. Moreover, many of the NNS were conducted from 2010 and onward, whereas some of the DHS and MICS surveys are much older. It is likely that nutritional improvements were made during the time gap. For example, the mean WHZ for Ghana was −0.56 in 1993. That score improved to −0.31 by 2008, although the SD remained relatively stable, decreasing from 1.422 to 1.416. NHANES was 24.3 with a range from 16 to 38, and 4/45 (9%) falling in the 10–19 range. Supplemental Tables 14–16 present equivalent data by regions within coun- tries for each of the surveys within each of the three survey sources. Appendices A–L present all of the major analyses at the sub-national region (domain) level within countries. Discussion The variation in age ratios and age distribution as well as in levels of missing and implausible data may be due to variation in child eligibility, interviewer training across the surveys, and data collection protocols. In addition, the prevalence of missing and implausible data may be lower in the NNS because the NNS is a narrow-topic survey and teams are dedicated to anthropometric indi- cators. Moreover, the NNS use specialized software to collect and flag data while interviewers are in the field, which could then permit implausible values to be flagged and corrected. It has been suggested, however, that this process itself may generate data which are ‘in range’ but of poor quality if data are modified on the fly in order to satisfy software range checks without remeasurement of the child. In the multi-topic surveys (DHS, MICS), the level of missing data among anthropometric variables exceeded that of other types of variables (e.g. socioeco- nomic status), illustrating the increased complexity in gathering such data [7]. Critically, the NNS does not record a complete household listing of all members in all surveys. In the DHS and MICS, all children are recorded, making it possible to view who is measured and who is not measured. In the NNS, however, there is no household roster . Information on children who were not part of the measurement sample is not captured. Therefore, it is not clear if the complete denominator of eligible children for whom anthropometric data could have been collected was recorded. Although efforts are made to revisit households to ensure complete follow-up of those children, the omission of any children with missing anthropometric data from the NNS data-set may artificially lower the proportion of missing data. I d i l di i f f d d There are several limitations to this study. First, it was not possible to assess the impact of non-normality and age misclassification on the prevalence of stunting, underweight, and wasting. Future research should con- sider conducting a simulation analysis where different values for mean, SD, skewness, and kurtosis are used to simulate the prevalence of stunting, underweight, and wasting under different data quality assumptions. This Increased terminal digit preference for recorded heights is likely related to the larger number of possible values for height. The interval of 50 to 110 cm (including D. J. CORSI ET AL. D. J. CORSI ET AL. Discussion 8 exercise would help determine the extent to which inac- curacies in each parameter (e.g. skewness) result in the greatest change in the estimates of undernutrition. Doing so would inform future iterations of the data quality score where the weight values can be adjusted to repre- sent the most important parameters. For instance, our preliminary simulation work conducted with a sample of DHS and MICS data-sets to induce heaping/digit pre- ference in age distributions found that inaccuracies in age could result in a 4.5% over-estimation in the preva- lence of stunting and a 4.2% overestimation in the pre- valence of underweight, while inaccuracies in weight at the level of 0.1 kg could result in a 2% over-estimation of prevalence of underweight or wasting. Second, further work is needed to ensure that robust data quality scores can be derived at lower levels of aggregation despite large variations in sample sizes. Third, although we did not explicitly model variation across interviewers, we addressed this by examining terminal digit preference as one proxy for interviewer-caused variation. In addi- tion, our supplemental analyses by sub-national regions within countries are implicitly related to interviewer performance because field teams are assigned to specific clusters and regions within countries during fieldwork. The literature suggests that interviewer variation is pre- sent in many DHS, particularly for anthropometric data [7,22]. Future analyses could incorporate this issue into the overall data quality score. Examination of sub- national estimates may also identify regions with poor data quality which may need to be excluded from certain analyses or prevalence calculations. changing, and making it a moving target. Thus, contin- uous training in, and monitoring of, data collection are needed to ensure the highest possible quality of anthro- pometric data given these inherent challenges. Despite these limitations, this study has several strengths. First, we included 100 surveys for data assess- ment and provided a detailed explanation of how data were collected by the associated survey program, obtained by the authors, and analysed. Second, we con- ducted many sub-national analyses and applied data quality scores to all available regions within countries. These analyses will enable researchers using these data to be aware of potential data quality issues at the national and regional levels. Third, we combined sev- eral methods from leading contributors in the fields of data quality and anthropometric assessment to create a balanced and comprehensive data quality score. Discussion The score itself is not a panacea but can be a starting point for comparisons between surveys and to further empha- size the need for continued monitoring, training, and improvements in anthropometric data collection in field surveys in low-income settings. Our recommendations for improvement in data qual- ity include continuous fieldworker training and monitor- ing, streamlining and monitoring of data processing, use of high-quality measurement equipment designed for survey settings, and overall simplification of data collec- tion processes to reduce both interviewer and respondent burden [7,22]. Another suggestion is to reduce the num- ber of values recorded for height, by measuring to the nearest fifth or half of a centimeter, without substantially impacting data quality [7]. In addition, range checks and calculation of z-scores could be implemented during fieldwork and before leaving a particular village by team supervisors who could monitor the need for child reas- sessment. Such procedures would allow for early identi- fication of problematic data, thus helping data collection teams revisit households where problems exist. Finally, implementing SMART/ENA methods to review data quality during the collection process and during analyses might help to improve both collection and interpretation of anthropometric data in resource-limited settings. Finally, this study did not attempt to make direct comparisons between survey programs as many metho- dological and sampling differences exist between them, which may indirectly impact the quality of the nutrition data. Moreover, survey performance may be related to implementing agency, funding, or a country's political situation, which would not be uniform across a survey program. For example, anthropometric data for Benin 2011 (DHS) was identified as low quality in the final DHS survey report [23]. Indeed, this particular sur- vey was one of the worst-performing surveys according to our metrics, suggesting that surveys with similar qual- ity scores (> 70) should be flagged prior to analyses. Regional estimates, however, may be valid if data quality scores are improved at the sub-national level. In addition, countries such as Congo, Cameroon, Togo, and Central Africa Republic seem to have some consistency in lower overall quality scores regardless of program, perhaps due to instability or other challenges in operating a large survey program within the country. Moreover, for coun- tries with multiple surveys, there were no patterns over time in data quality scores. Instead, data quality varied from year to year. Discussion Such variability may be due to the difficulty inherent in collecting anthropometric measure- ments, that the data quality assessment itself is not per- fect, or that nutritional status in the population may be Author contributions DJC and SVS designed and planned the study. DJC acquired the data, conducted analyses, and wrote the manuscript. JMP contributed substantially to manuscript writing and revisions. All authors participated in interpre- tation of data and critical revisions of the manuscript, and approve the final accepted version. [8] Farkas L. Accuracy of anthropometric measurements: past, present, and future. Cleft Palate Craniofac J. 1996;33:10–22. [9] Stomfai S, Ahrens W, Bammann K, et al. Intra- and inter-observer reliability in anthropometric measure- ments in children. Int J Obes. 2011;35:S45–S51. [10] Standardized Monitoring & Assessment of Relief & Transitions (SMART). Measuring mortality, nutritional status, and food security in crisis situations: SMART methodology. 2006. Available from: http://www.nutrisur vey.de/ena2011/SMART_Methodology_08-07-2006.pdf Ethics and consent Oral or written informed consent for the interview or survey was obtained from respondents by interviewers. This analysis was reviewed by the Harvard School of Public Health Institutional Review Board and was consid- ered exempt from full review because the study was based on a de-identified and anonymous data-set available for secondary analyses. [12] Cassard F, Johnston R. Nigeria DHS 2008 anthropo- metric data quality report. Dakar: UNICEF WCARO; 2010. [13] Crowe S, Seal A, Grijalva-Eternod C, et al. Effect of nutrition survey ‘cleaning criteria’ on estimates of malnutrition prevalence and disease burden: second- ary data analysis. PeerJ. 2014;2:e380. [14] The DHS Program. Demographic and Health Surveys 2017. Rockville (MD): ICF International; 2017. Available from: www.dhsprogram.com. Disclosure statement No potential conflict of interest was reported by the authors. [11] Golden M, Grellety Y Population nutritional status during famine. 2002. Available from: http://wwwnutri surveyde/ena2011/Golden_Population_nutritional_sta tus_during_famile_surveywhzdispdf Conclusions Thus, when identifying a data-set and survey source from which to obtain child anthropometric data, users should weigh which survey characteristics are relevant for their work, including whether data are publicly available, the extent of standardized socioeconomic and other information collected, the population sample, and the data quality. Overall, this study suggests that errors in anthropometric measures are both common- place and difficult to isolate. Thus, assessment of data quality before, during, and after data collection is needed. References [1] Corsi DJ, Neuman M, Finlay JE, et al. Demographic and health surveys: a profile. Int J Epidemiol. 2012;41:1602–1613. [2] USAID. Anthropometric data in population-based surveys, meeting report, July 14–15, 2015. Washington, DC: FHI 360/FANTA; 2016. g [3] Schmidt PK, Carter JE. Static and dynamic differences among five types of skinfold calipers. Hum Biol. 1990;62:369–388. [4] Gordon CC, Bradtmiller B. Interobserver error in a large scale anthropometric survey. Am J Hum Biol. 1992;4:253–263. [5] Pelletier DL, Low J, Msukwa L. Sources of measure- ment variation in child anthropometry in the Malawi maternal and child nutrition study. Am J Hum Biol. 1991;3:227–237. Paper context The measurement of anthropometric (height and weight) data in young children is routinely done in large popula- tion surveys to assess and monitor undernutrition in low- resource settings. Important differences often arise in the results of these surveys within countries, across survey agencies, and over time. Recent efforts have been made to develop quality standards and assessments of anthropo- metric data in these contexts. This study describes and compares survey characteristics and indicators of quality in 100 surveys from 23 countries in West Central Africa. Acknowledgments We acknowledge the helpful comments, suggestions, and expertise given by Robert Johnston and Roland Kupka and participants of a technical meeting on anthropometric data in population-based surveys (Washington, DC, July 2015). [6] Ulijaszek SJ, Lourie JA. Anthropometry in health assessment: the importance of measurement error. Coll Antropol. 1997;21:429–438. [7] Pullum TW. An assessment of the quality of data on health and nutrition in the DHS surveys, 1993-2003. Calverton, MD: Macro International Inc.;2008. (Methodological reports no 6). Conclusions These survey programs provide key information on the nutritional status of young children across countries. Stunting and underweight indicators are commonly used in comparative analyses and in the assessment of progress toward international development goals. Therefore, a reasonable concern is that their anthropo- metric data be of the highest possible quality. In addi- tion, pairing socioeconomic information with anthropometric data is also critically important to show inequality in outcomes and understand which sub-populations are most affected by the burden of child malnutrition [24–31]. Moreover, comparing the GLOBAL HEALTH ACTION 9 GLOBAL HEALTH ACTION 9 9 distribution of malnutrition between countries requires that surveys in each country collect the same data. At present, however, it is not possible to examine nutri- tional status along many socioeconomic factors or other dimensions in many of the NNS, although stratification by region is possible in all survey sources. Further, comparison of anthropometric data between countries according to non-anthropometric information is not possible when using NNS. In contexts where chronic nutritional deprivation is a key burden, the benefits and richness of MICS and DHS outweigh any perceived weakness in terms of greater variability in data quality. Thus, when identifying a data-set and survey source from which to obtain child anthropometric data, users should weigh which survey characteristics are relevant for their work, including whether data are publicly available, the extent of standardized socioeconomic and other information collected, the population sample, and the data quality. Overall, this study suggests that errors in anthropometric measures are both common- place and difficult to isolate. Thus, assessment of data quality before, during, and after data collection is needed. distribution of malnutrition between countries requires that surveys in each country collect the same data. At present, however, it is not possible to examine nutri- tional status along many socioeconomic factors or other dimensions in many of the NNS, although stratification by region is possible in all survey sources. Further, comparison of anthropometric data between countries according to non-anthropometric information is not possible when using NNS. In contexts where chronic nutritional deprivation is a key burden, the benefits and richness of MICS and DHS outweigh any perceived weakness in terms of greater variability in data quality. Funding information Funding was received from UNICEF/West Central Africa Region as part of a commissioned report on anthropo- metric data quality. [15] Macro ORC. Demographic and health survey inter- viewer’s manual. Calverton, MD: MEASURE DHS Basic Documentation No. 2; 2006. 10 D. J. CORSI ET AL. 10 D. J. CORSI ET AL. 10 evidence from 80 countries, from 1990 to today. Intl J Epidemiol. 2014;43:1328–1335. [16] UNICEF. New York: United Nations Children's Fund; 2016. Available from: https://www.unicef.org/statis tics/index_24302.html. [25] Subramanyam MA, Kawachi I, Berkman LF, et al. Socioeconomic inequalities in childhood undernutri- tion in India: analyzing trends between 1992 and 2005. Plos One. 2010;5:e11392. [17] McDowell MA, Fryar CD, Ogden CL Anthropometric reference data for children and adults: United States, 1988-1994. Vital and health statistics Series 11, Data from the national health survey; 2009. p. 1–68 [26] Barros FC, Victora CG, Scherpbier R, et al. Socioeconomic inequities in the health and nutrition of children in low/middle income countries. Rev Saude Publica. 2010;44:1–16. [18] CDC. About NHANES. Atlanta, GA: National Center for Health Statistics; 2015. [19] Mei Z, Grummer-Strawn LM. Standard deviation of anthropometric Z-scores as a data quality assessment tool using the 2006 WHO growth standards: a cross country analysis. Bull World Health Organ. 2007;85:441–448. [27] Van de Poel E, Hosseinpoor AR, Speybroeck N, et al. Socioeconomic inequality in malnutrition in devel- oping countries. Bull World Health Organ. 2008;86:282–291. [28] Kien VD, Lee H-Y, Nam Y-S, et al. Trends in socio- economic inequalities in child malnutrition in Vietnam: findings from the multiple indicator cluster surveys, 2000–2011. Glob Health Action. 2016;9. DOI:10.3402/gha.v9.29263 [20] WHO. Physical status: the use and interpretation of anthropometry. Vol. 854. Report of a WHO Expert Committee. World Health Organization technical report series; 1995. p. 1–452 [21] World Health Organization. WHO child growth stan- dards: length/height-for-age, weight-for-age, weight- for-length, weight-for-height and body mass index- for-age: methods and development. Geneva: World Health Organization; 2006. g [29] Novignon J, Aboagye E, Agyemang OS, et al. Socioeconomic-related inequalities in child malnu- trition: evidence from the Ghana multiple indicator cluster survey. Health Econ Rev. 2015;5:1–11. y [30] Abalo K, Agbodji AE, Batana YM. Nutritional health inequalities among children in Togo. Afr Dev Rev. 2014;26:584–596. g [22] Assaf S, Kothari MT, Pullum TW. An assessment of the quality of DHS anthropometric data, 2005-2014. DHS methodological reports. Rockville, MD: ICF International; 2015. [31] Corsi DJ, Mejía-Guevara I, Subramanian SV. Funding information Risk factors for chronic undernutrition among children in India: estimating relative importance, population attributable risk and fractions. Soc Sci Med. 2016 May;157:165–185. [23] The DHS Program. Demographic and health surveys. Rockville, MD: ICF; 2017. [24] Bredenkamp C, Buisman LR, Van de Poel E. Persistent inequalities in child undernutrition:
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Consolidation behavior of various types of slurry tailings co-disposed with waste rock inclusions: a numerical study
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Consolidation behavior of various types of slurry tailings co-disposed with waste rock inclusions: a numerical study Ngoc Dung Nguyen  Polytechnique Montréal Thomas Pabst  (  t.pabst@polymtl.ca ) Polytechnique Montréal Thomas Pabst  (  t.pabst@polymtl.ca ) Polytechnique Montréal Research Article Posted Date: August 25th, 2022 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Version of Record: A version of this preprint was published at Environmental Earth Sciences on January 16th, 2023. See the published version at https://doi.org/10.1007/s12665-023-10750-4. Page 1/25 Page 1/25 Page 1/25 Abstract The co-disposition of mine tailings and waste rock in tailings storage facilities (TSFs) could contribute to increase the consolidation rate and decrease long-term settlement of tailings. Non-linear change of tailings properties during the filling process and interaction between tailings and waste rock inclusion (WRI) are critical to mechanical analysis but can, however, be complicated to simulate. The question of net volume gains or losses of tailings was also raised. In this study, fully coupled analysis which considered continuous variation of hydraulic conductivity and stiffness of tailings were performed to assess the evolution of consolidation of various tailing types in the presence of WRI. Effects of volume ratio of tailings over WRI on the net volume was investigated. Finally, effect of several practical aspects such as filling rates, and instantaneous filling assumption were considered. Results indicated that WRI could increase by 3.3 times the rate of consolidation of tailings. The zone of influence of WRI on tailings consolidation varied for each tailings. Using updated properties showed significant differences compared to models with constant values. The application of WRI can reduce volume available for the storage of tailings and net volumetric change due to settlement of the tailings with or without WRI could be estimated explicitly. Equations predicting evolution of net volume with the changes in the volume ratio of tailings and WRI were accordingly proposed. WRI effects was more pronounced with the increase of the filling rate. Finally, instantaneous filling assumption had little effect on the simulated rate of consolidation. 1. Introduction A balance should also be found between maximizing the quantities of tailings deposited and ensuring a good performance of WRI by reducing the distance between them. WRI design optimization, thus, requires to consider net volume gains or losses due to the addition of waste rocks within the tailings and thus volume available for the storage of tailings afterwards (L.Bolduc and Aubertin 2014; Saleh- Mbemba and Aubertin 2021b). Several factors can pose uncertainties to the efficiency of this technique including the filling rate and hydro-mechanical properties of tailings and waste rocks (L.Bolduc and Aubertin 2014). Finally, comparative research on the behaviors of different types of tailings applying co- disposal technique can accordingly contribute further to the application of this technique to management operations of various types of tailings and somewhat improve optimization of co-disposal technique as a function of tailings properties. Critical concerns when studying consolidation of tailings with WRI include capturing properly the evolution of tailings consolidation characteristics and the acceleration of dissipation of excess PWP in tailings. A balance should also be found between maximizing the quantities of tailings deposited and ensuring a good performance of WRI by reducing the distance between them. WRI design optimization, thus, requires to consider net volume gains or losses due to the addition of waste rocks within the tailings and thus volume available for the storage of tailings afterwards (L.Bolduc and Aubertin 2014; Saleh- Mbemba and Aubertin 2021b). Several factors can pose uncertainties to the efficiency of this technique including the filling rate and hydro-mechanical properties of tailings and waste rocks (L.Bolduc and Aubertin 2014). Finally, comparative research on the behaviors of different types of tailings applying co- disposal technique can accordingly contribute further to the application of this technique to management operations of various types of tailings and somewhat improve optimization of co-disposal technique as a function of tailings properties. The objective of this paper was, therefore, to evaluate numerically the effect of WRI on various types of tailings sequentially filled in a simplified TSF and considering the evolution of consolidation properties. Potential differences of models with constant and updated properties when applying WRI were subsequently investigated. Effects of volume ratio between tailings and WRI on the volume gains or losses of tailings in the impoundment were studied. Influences of the filling rate on the consolidation rate of tailings were examined. 1. Introduction Finally, influences of the assumption of instantaneous filling in simulations (i.e., no consolidation of tailings occurs during the filling process) compared to the progressive filling scheme in practice (i.e., consolidation occurs during the filling process) was studied. Limitations of the models were also discussed in this study. 1. Introduction Tailings generated from mining activities are typically deposited hydraulically (i.e., as a slurry) in tailings storage facilities. Consolidation of mine tailings can take a very long time because of their initially high- water content and their relatively low hydraulic conductivity (Vick 1990; Blight 2010). Progressive deposition of slurry tailings in TSFs might lead to the build-up of excess porewater pressure (PWP) that has been linked to various geotechnical instabilities issues, including failure of tailings impoundments and static/dynamic liquefaction of tailings (Azam and Li 2010; Morgenstern et al. 2016; Robertson et al. 2019). A novel approach of tailings and waste rocks co-disposal was developed for surface tailings storage facilities that could contribute to accelerate tailings consolidation. In this method, waste rocks are placed as linear inclusions within the tailings and raised at the same time (Fig. 1). This technique can contribute to accelerate the dissipation rate of excess PWP generated during the continuous accretion of tailings (and thus speed up the consolidation of tailings) by promoting horizontal movement of pore water (L.Bolduc and Aubertin 2014). WRI can also provide other advantages such as reducing the size of waste rock piles (i.e., WRI could contribute to completely remove the necessity to build a waste rock piles for underground mines) (Aubertin 2013, 2018; Saleh-Mbemba and Aubertin 2021a). Strength and stiffness of tailings can consequently be improved more quickly. The increase in the consolidation rate and magnitude of tailings in the presence of WRI were experimentally evaluated using physical laboratory tests (Saleh-Mbemba and Aubertin 2021a, b), while consolidation behavior of tailings in the vicinity of WRIs was also numerically investigated at the large scale (Jaouhar et al. 2013; L.Bolduc and Aubertin Page 2/25 Page 2/25 2014; Boudrias 2018). WRIs can also help to provide mechanical reinforcement to the tailings impoundment enhancing both static and dynamic stability of the retaining structures (PépinNicolas et al. 2012; Ferdosi et al. 2015). Effect of WRI configuration was evaluated by changing various values of width of the inclusions and center-to-center spacing between these inclusions (Ferdosi et al. 2015). In general, results indicated that downstream slope deformation tended to decrease with the increase of the number of inclusions and to increase with the increase of spacing between inclusions (Ferdosi et al. 2015). Critical concerns when studying consolidation of tailings with WRI include capturing properly the evolution of tailings consolidation characteristics and the acceleration of dissipation of excess PWP in tailings. 2 Methodology Many multi-dimensional codes have been developed to investigate the settlement of slurry tailings under sequential filling (Liu and Znidarčić 1991; Fredlund et al. 2015) and the explicit finite volume code Flac3D (Itasca Int., 2021) is one of the most frequently used to simulate multi-dimensional and non-linear consolidation of tailings materials. For example, Shahsavari and Grabinsky (2015) used Flac3D to investigate the effect of non-zero boundary condition on the consolidation of the cemented paste backfill layers, while Zhou et al (2019) simulated mine tailings consolidation in an impoundment with the presence of wick drain systems. In this study, a series of simulations were performed using Flac3D to model tailings placed sequentially in a simplified TSF with WRI. Common practice for TSFs design Page 3/25 Page 3/25 Page 3/25 usually considers 1-D geometries (Fredlund et al. 2015). 1-D models are fast and particularly suited for cases where impoundments have small depths compared to the width and the length of the retaining structures. In these cases, the fluid flow direction and the consolidation are essentially vertically oriented (Priestley 2011; Fredlund et al. 2015). However, such assumption may be not applicable when highly permeable regions and horizontal drainage systems (such as WRIs or wick drains) are installed in TSFs. In these cases, 2-D or 3-D analysis are required to capture the principal effect of lateral flow and strain (Coffin 2010; Fredlund et al. 2015). 2.1 Conceptual models A 100 × 5 m section was modelled to simulate the consolidation of tailings in the TSF and the effect of the WRI (Fig. 2). The dimensions of the model were chosen to reduce the mesh size and computation time, yet remaining representative of field conditions. This width of the TSF was assumed to be far enough from the dams so they would not affect simulated settlements. The influences of the volume ratio between tailings and WRI on the calculated results were also investigated. The simulated WRI represented a simple central inclusion whose crest width was around 12 m. WRI geometry was simplified as parallelepiped instead of the typical successive trapezes usually constructed on real mine sites. This assumption has shown no influence on the results but reduces numerical instabilities (L.Bolduc and Aubertin 2014). Saturated tailings were filled into the TSF in successive 10 layers over a period of 10 years. Each layer was 3 m thick for a total height of 30 m. Tailings deposition was assumed instantaneous (i.e., a new 3 m thick layer was added every year at once and left to consolidate before a new layer was added one year later). Four types of tailings were modelled in this study (see below). WRI was raised sequentialy at the same rate as tailings (similarly to field conditions). Displacements at the bottom of the TSF were fixed in all directions, and an impervious bottom was considered. Side boundaries of the models were allowed to move vertically only and also considered impervious (i.e., axis of symmetry). Zero PWP was assiged at the surface of the model to simulate groundwater table and to allow upward movement of water in the tailings. The deposition of a new layer of tailings induced the generation of excess PWP, followed by the dissipation of PWP (towards the surface and the WRI) and the consolidation of the materials. A parametric analysis was also conducted to evaluate the impact of filling rate and effect of the filling scheme. 2.2 Material properties Four different tailings were considered in this study: 2 types of gold mine tailings (tailings A and B), uranium mine tailings (tailings C) and bauxite mine tailings (tailings D). Tailings properties (i.e., unit weight, relative density, friction angle, and relations of void ratio – effective stress and hydraulic conductivity – void ratio) of tailings A were obtained from experiments by authors, while those for other mine tailings were obtained from literature (Somogyi 1976; Bhuiyan et al. 2015; Lévesque 2019). Unit Page 4/25 weight was highest for tailings A (e.g., around 19.7 kN/m3), while that for tailings B, C, D was around 18.7, 13.0 and 17.5 kN/m3 respectively. Specific gravity of those materials was 2.61, 2.82, 2.70 and 3.27 respectively (the relative high value of tailings D was attributed to the presence of iron). These corresponded to dry density of 1.55, 1.39, 0.46 and 0.98 respectively (Das 2010), which indicated high initial void ratios of uranium and bauxite tailings relative to those of gold tailings. Friction angles were assigned as 37°, 36°, 30° and 39° for those tailings respectively. All four tailings were cohesionless as mine tailings usually are (Blight 2010). The relations between void ratio and effective stress, hydraulic conductivity and void ratio, and Young’s modulus and effective stress were derived from column test for tailings A, B and C. There were some differences in terms of dimensions of samples and load applied in the tests for tailings C: the dimension of the columns used was around 10 x 10 cm, and tailings were underwent incremental loads (from 1 to 8 kPa) while those for tests on tailings A and B might reach around 300 kPa (Bhuiyan et al. 2015; Lévesque 2019; Nguyen and Pabst 2020). Details on how to derive these relations from compression column tests can be seen in Essayad and Aubertin (2021) and Lévesque (2019). Those relations were obtained from conventional consolidation tests in conjunction with hydraulic conductivity measurements for tailings D (Somogyi 1976). weight was highest for tailings A (e.g., around 19.7 kN/m3), while that for tailings B, C, D was around 18.7, 13.0 and 17.5 kN/m3 respectively. Specific gravity of those materials was 2.61, 2.82, 2.70 and 3.27 respectively (the relative high value of tailings D was attributed to the presence of iron). 2.2 Material properties These corresponded to dry density of 1.55, 1.39, 0.46 and 0.98 respectively (Das 2010), which indicated high initial void ratios of uranium and bauxite tailings relative to those of gold tailings. Friction angles were assigned as 37°, 36°, 30° and 39° for those tailings respectively. All four tailings were cohesionless as mine tailings usually are (Blight 2010). The relations between void ratio and effective stress, hydraulic conductivity and void ratio, and Young’s modulus and effective stress were derived from column test for tailings A, B and C. There were some differences in terms of dimensions of samples and load applied in the tests for tailings C: the dimension of the columns used was around 10 x 10 cm, and tailings were underwent incremental loads (from 1 to 8 kPa) while those for tests on tailings A and B might reach around 300 kPa (Bhuiyan et al. 2015; Lévesque 2019; Nguyen and Pabst 2020). Details on how to derive these relations from compression column tests can be seen in Essayad and Aubertin (2021) and Lévesque (2019). Those relations were obtained from conventional consolidation tests in conjunction with hydraulic conductivity measurements for tailings D (Somogyi 1976). The same waste rocks were considered for WRI in all models. WRI were assigned a simple linear elastic constitutive model with a high Young’s modulus to represent the very high stiffness of the material (i.e., E The same waste rocks were considered for WRI in all models. WRI were assigned a simple linear elastic constitutive model with a high Young’s modulus to represent the very high stiffness of the material (i.e., E  = 500 MPa) and a Poisson’s ratio of 0.277 (L.Bolduc and Aubertin 2014). WRIs were assigned a hydraulic conductivity of 3 x 10− 6 m/s (around 20 times higher than that of tailings) to facilitate the horizontal drainage of water in tailings. In practice, hydraulic conductivity of WRI might be greater but a smaller value was chosen to reduce computational time. This is because the presence of the two materials with contrastive permeabilities in the model can significantly increase the computational time of the model (Itasca 2021). Page 5/25 Page 5/25 Table 1 Properties and constitutive relations of various types of tailings used in the simulations. Properties A B C D   (Nguyen and Pabst 2020) (Lévesque 2019) (Bhuiyan et al. 2.2 Material properties 2015) (Somogyi 1976) Unit weight (kN/m3) 19.7 18.7 13.0 17.5 Specific gravity 2.62 2.82 2.70 3.27 Dry density (103kg/m3) 1.55 1.39 0.46 1.13 Friction angle (degree) 37 36 30 39 Cohesion (kPa) 0 0 0 0 Poisson’s ratio 0.28 0.28 0.33 0.27 e-σ' relation 2.31 k-e relation E-σ' relation 0.81σ′−0.06 1.01σ′−0.06 3.94σ′−0.10 σ′−0.10 1.2x10−6e4.6 2.0x10−7e3.7 1.2x10−9e4 6x10−10e5.3 85.6σ′0.74 35.0σ′0.91 4.0σ′1.9 15.9σ′0.94 Table 1 2.3 Constitutive models and update of tailings properties 2.3 Constitutive models and update of tailings properties Tailings properties vary with time as their void ratio decreases and the assumptions of constant properties might not be representative of actual and non-linear behaviours of slurry materials (Schiffman 1982; Townsend and McVay 1990; Morris 2002). Several studies have shown discrepancies between tailings consolidation simulated with assumption of constant properties and field observations. For instance, simulated consolidation rates were around 3 times faster than observation in the case of gold tailings disposed in pit (McDonald and Lane 2010). Various mathematical functions representing the relations effective stress - void ratio and void ratio - hydraulic conductivity for slurry tailings have been proposed. These include power function (Somogyi 1980), extended power function (Liu and Znidarčić 1991), logarithmic function (Bartholomeeusen et al. 2002), Weibull function and modified Kozeny– Carman equation (Mbonimpa et al. 2002; Chapuis and Aubertin 2003). Among these, the power function is often used for its simplicity and good representativity (Priestley 2011; Agapito and Bareither 2018), and was chosen in the present study to represent variation of tailings hydraulic conductivity with void ratio (Table 1). From hydraulic conductivity relations (Table 1), tailings A and B exhibited a reduction of around 2.5 times after the first 3 loading before continuing to decrease slightly for the next loading steps (Lévesque 2019; Nguyen and Pabst 2020), while those for tailings C and D decreased by around 3 and 4 Page 6/25 Page 6/25 times (Somogyi 1976; Bhuiyan et al. 2015). Young’s modulus of those tailings remained relatively small at low level of loads and non-linearly increased with the increased of applied loads, and values of tailings A and B were usually somewhat double that of tailings D (Table 1). times (Somogyi 1976; Bhuiyan et al. 2015). Young’s modulus of those tailings remained relatively small at low level of loads and non-linearly increased with the increased of applied loads, and values of tailings A and B were usually somewhat double that of tailings D (Table 1). Linear elastic-perfectly plastic Mohr-Coulomb model was used to simulate tailings. The non-linear relations between e-σ', k-e and Young’s modulus and effective stress of the four types of tailings followed an approach applied in Flac3D to modify these properties and were based on relations from Table 1. 2.3 Constitutive models and update of tailings properties During the analysis, the value of void ratio was updated at every iteration based on the value of effective stress, and this new value of void ratio was then used to conduct an automatic update of hydraulic conductivity and stiffness in FLAC3D. The validity and precision of continuous update of tailings properties in Flac was presented by Zhou et al. (2019). This approach was compared with simulations using a constant saturated hydraulic conductivity. 3.1 Effect of WRI on the dissipation of excess PWP The decrease in the effect of WRI on the consolidation rate Page 7/25 Page 7/25 Page 7/25 with the increase of the distance for tailings B, C, and D were also demonstrated for points at 6 m and 29 m after the placement of the 5th layer (Fig. 4b, 4c, 4d). Accordingly, the radius of influence of the WRI was estimated as the location where time t90 for the cases with and without WRIs were less than 5% different. For example, the radius of influence for tailings A was around 54 m when the tailings thickness was 30 m, 44 m for the thickness of 24 m and 34 m for the thickness of 18 m. The ratio between WRI’s radius of influence and the thickness of tailings could be then estimated for each type of tailings (e.g., equal around 1,8 for the tailings A) (Fig. 5). This ratio for tailings B and C were around 1.8 and 2.6 at the end of the filling process (i.e., the 10th layer) respectively (Fig. 5). The WRI’s zone of influence for tailings D could not be estimated from t90 values as excess PWP did not fully dissipate, and this value was thus estimated as the distance where the differences of U between models with and without WRI were smaller than 5%. The radius of influence in that case was around 3.4 times the thickness of tailings (Fig. 5). The radius of influence was different for each type of tailings, but they all exhibited a similar trend, that is a rapid and strong decrease after the filling of the first four layers before becoming relatively stable (Fig. 5). The ratio between WRI’s radius of influence and the thickness of tailings after the placement of the 2nd layer was around 4 for tailings A and B, 8 and 10 for tailings C and D, respectively, before decreasing to somewhat stable values when the tailings thickness was higher than 12 m (i.e., after the placement of the 4th layer) (Fig. 5). The decrease of the radius of influence during the deposition of the first few layers can be attributed to the decrease of the hydraulic conductivity of the tailings under the applied loading and the decrease of void ratio under tailings settlement. 3.1 Effect of WRI on the dissipation of excess PWP Simulation results indicated that WRI significantly contributed to the horizontal dissipation of PWP and therefore to the acceleration of consolidation. For example, the PWP iso-contours immediately after the addition of the 7th layer for tailings A (i.e., t = 7 years) were curved close the WRI, indicating a higher dissipation rate of PWP (Fig. 3). In other words, the dissipation of PWP close to the WRI could occur both vertically (to the surface of the TSF) and horizontally (to the WRI). Also, PWP always reached hydrostatic equilibrium at the end of each consolidation period (even for the cases without inclusions), therefore suggesting that no excess PWP remained before adding new tailings layers. Similar trends were observed for tailings B and C. The presence of WRI also contributed to accelerate tailings consolidations of tailings D, but excess PWP did not completely dissipate during the considered period and their effect was more limited compared to those for other tailings. For example, maximum degree of consolidation, U, after the addition of the 4th layer was around 93% at 2 m from the WRI, while that reached only around 80% at 6 m from the WRI and excess PWP thus cannot fully dissipate. Such limited effect can be attributed to the relatively low hydraulic conductivity of these tailings (Newson et al. 2006; Matt 2015; Zhang et al. 2021). Results therefore indicated that WRI effectiveness is strongly affected by the tailings’ hydraulic conductivity and that WRI for clay-like tailings might be significant in terms of improvement of the overall strength of the impoundment (Ferdosi et al. 2015) rather than improvement of consolidation rate of tailings. Simulations results showed that the effect of WRI on consolidation decreased rapidly with the distance from WRI (Fig. 4). For example, after the deposition of the 5th layer the degree of consolidation (at the base of the TSF, i.e., z = 0 m) for tailings A reached 95% in 13 days at 2 m from the inclusion, 34 days 14 m from the inclusion and 43 days 29 m from the inclusion (value for the case without inclusion was 45 days) (Fig. 4a). Consequently, the rate of dissipation of excess PWP was increased by over three times, but only in the direct vicinity of the inclusion. 3.1 Effect of WRI on the dissipation of excess PWP These decreases in hydraulic conductivity of tailings can lead to the change in the hydraulic gradient and therefore possibly in the radius of influence (Hansbo et al. 1981; Indraratna et al. 2012; Han 2015; Saleh-Mbemba and Aubertin 2021b). Several endeavors with models of different constant permeabilities of tailings were performed to check the influences of hydraulic gradient on the radius of influence of WRI. Results, however, showed a limited effect of the hydraulic gradient on the WRI’s radius of influence. Similar trend was also observed by Bolduc and Aubertin (2014). Simulations also indicated using updated hydraulic conductivity values (changing with void ratio during consolidation) or constant values had a strong influence on the results. For example, the time required to reach 90% consolidation (or t90) for tailings A 65 m from the inclusion after the placement of the 10th layer was 130 days for model with updated properties, 41 days with ksat = 3.5 x 10− 7 m/s, and 162 days with ksat = 1.0 x 10− 7 m/s (Fig. 6). Using updated properties, however, requires to measure hydraulic conductivity in the laboratory for various void ratios to fit a descriptive models (Bhuiyan et al. 2015), and to input the hydraulic conductivity functions in the code, which is not always convenient. In practice, using a constant value ksat = 1.3 x 10− 7 m/s yielded somewhat similar results in terms of consolidation rate which corresponded to a void ratio of 0.62 (Fig. 6). The equivalent hydraulic conductivity for tailings B and C was 1.2 x 10− 7 and 1.1 x 10− 7 m/s, corresponding to the void ratio of 0.87 and 3.09 respectively. 3.2 Tailings settlement Page 8/25 Page 8/25 Settlements occured as pore pressures dissipated and varied depending on tailings properties, time and distance to the WRI. For example, the total settlement of the tailings body at the end of the placement process (t = 10 years) for tailings A was around 1.67 m, around 1.65, 0.5 and 1.94 m for tailings B, C and D, repsectively. The increase in displacements of layer 1 reduced with the increase of tailings thickness, which indicated that the stiffness of the materials increaed under staged filling. For example, Settlements occured as pore pressures dissipated and varied depending on tailings properties, time and distance to the WRI. For example, the total settlement of the tailings body at the end of the placement process (t = 10 years) for tailings A was around 1.67 m, around 1.65, 0.5 and 1.94 m for tailings B, C and D, repsectively. The increase in displacements of layer 1 reduced with the increase of tailings thickness, which indicated that the stiffness of the materials increaed under staged filling. For example, displacements in layer 1 for tailings A one year after the filling of the 3rd layer increased by around 47% but only 5% after the placement of the 10th layer (Fig. 7). Similar trends were observed for the other tailings with the increase of displacement after the filling of the last layer was generally less than 5%. Models thus represented very well the change in the stiffness of the materials. Settlement of tailings tended to be smaller closer to the WRI, which was attributed to the different in the strength and stiffness of WRI and the tailings as loads from tailings were partially transformed to the WRI. This depends on the modulus ratio of the WRI and surrounding tailings(van Eekelen et al. 2013; Han 2015) and the interface elements used in the models (Li and Aubertin 2009). The volume change of tailings due to the presence of WRI can then be estimated based on the settlement evolution of tailings. 4.1 Volume change of tailings with the presence of WRI The amount of volumetric compression of the tailings body resulting from settlement of tailings (i.e., equal to the average settlement of the tailings body times the area of the TSF, which was automatically calculated using a Fish function). Simulated results indicated that volume change always increased with time as more tailings were disposed (Fig. 8a). For example, volume change after the placement of the 2nd layer for tailings A without WRI was around 62 m3 and increased to around 132 m3 after the placement of the 10th layer. The changes in the slope of the curves also indicated a slower rate of volume change as tailings height increased (Fig. 8a). Tailings C had the smallest volume change (around only 40 m3) among simulated tailings, which was explained by the smallest settlement of this type of tailings (session 3.2). The presence of WRI can increase the consolidation rate of tailings, but they also occupy some space in the TSF. In practice, results have shown that most of the simulated tailings were fully consolidated after around 6 months. Using WRI therefore did not have a significant influence on the volume gain, but rather contributed to decrease the space available for tailings deposition. In other words, the volume of tailings that could be deposited in the TSF with the presence of WRI was always smaller than the case without WRI for all types of tailings (Fig. 8a). For example, the volume change of tailings A without WRI after the placement of the 10th layer was around 132 m3/per 5 linear meter, i.e., around 14% more than that of model with WRI (113 m3/ per 5 linear meter) (Fig. 8a). The differences of volume change (DV) between models with and without WRI was estimated as: Page 9/25 ∗100 (Vt −Vw) Vt Page 9/25 Where Vt: the volume change of model with tailings only (m3); Vw: the volume change of model with WRI (m3) (m3) DV tended to become relatively constant after the deposition of the first fifth layers (Fig. 8b). For instance, DV of tailings A decreased from 25% after the placement of the 2nd layer to 16% after the filling of the 5th layer, while that of tailings C exhibited a reduction of nearly 17% (Fig. 8b). DV for tailings C and D tended to be greater than those of tailings A and B. 4.1 Volume change of tailings with the presence of WRI For example, DV for gold tailings after the filling of the last layers were around 15%, while that for tailings C were somewhat higher, at around 20% (Fig. 8b). These differences could be explained by the difference in the stiffness evolution during compression of other types of tailings. The additional height of the TSF required to dispose the same amount of tailings with WRI presence as without WRI can be accordingly estimated. This height can be estimated as the sum of volume occupied by WRI and total differences of volume change of tailings body between models with and without WRI divided by the area of the TSF (Table 2). These heights were around 2.22, 2.17, 2.06 and 2.45 m for tailings A, B, C and D, respectively. In other words, the increase of thickness of the TSF was less than 8% total thickness of tailings (Table 2). This was very meaningful for practitioners to briefly calculate the additional height of TSFs required when applying co-disposal technique (at least at the primary design stage). Table 2 Additional height required because of the presence of WRI in the TSF for various types of tailings   Volume occupied by WRI (m3) Total volume loss* (m3) TSF area (m2) Additional height (m) Tailings A 900 143 470 2.22 Tailings B 900 119 470 2.17 Tailings C 900 69 470 2.06 Tailings D 900 251 470 2.45 * Equal total differences of volume change resulting from tailings settlement between models with and without WRI Table 2 * Equal total differences of volume change resulting from tailings settlem and without WRI * Equal total differences of volume change resulting from tailings settlement between models with and without WRI Ratio between volume of tailings and WRI disposed in this study was around 15.7. In practice, this ratio could widely change depending on the practical considerations of each mine sites. For example, this could depend on the primary goal of mine waste management of each mine site. Some might prioritize the volume of WRI that can be disposed to eliminate the need for the construction of waste rock piles. Coarse waste rocks might, indeed, contain sulfide minerals that can oxidize and generate acid mine Page 10/25 Page 10/25 drainage, and the placement of waste rock as inclusions inside the TSF could therefore efficiently contribute to prevent potential AMD generation (Jahanbakhshzadeh et al. 2019; Bussière and Guittonny 2020). 4.1 Volume change of tailings with the presence of WRI The volumes of tailings and waste rock produced by mining activities can also vary widely in practice depending on the ore body characteristic and production technique (Blight 2010). The ratio of tailings and waste rocks volume was thus changed by changing the width of WRI in the model (i.e., from 6 m to 10, 12, 18 and 24 m corresponding to the volume ratio of 15.7, 9.0, 7.3, 4.6 and 3.2, respectively) to estimate the volume loss as a function of the quantity of waste rocks used in the TSF as inclusions. In general, the more volume of WRI placed in the pit, the less space dedicated for tailings that can be stored in the TSF (Fig. 9). For example, the DV values of tailings A for model with WRI width of 24 m was around 30 % which was nearly 2 times higher than that of model with WRI width o 6 m. The same trend was recorded for tailings B and C (Fig. 9). The trend of tailings A and B was somewhat similar to each other, while DV for tailings C seemed to be higher than those of tailings A and B. Accordingly, equations presenting the evolution of DV with the changes in the volume ratio of tailings and WRI were derived as: (R2 = 0.97) for tailings A, for tailings B (R2 = 0.99) and (R2 = 0.980) for uranium tailings. These results can, thus, provide practitioners with a brief estimation (at least for the primary design stage) the potential volume of tailings that might be loss due to the presence of WRI for various volume ratios. y = 49.6x−0.48 y = 55.6x−0.58 y = 56.8x−0.39 4.2 Effect of the filling rate TSF depth and deposition rates vary with mine size, production rate and type of operations (surface or underground) (Blight 2010; MEND 2015). Filling rate for TSF at Malartic mine is, for example, around 3 m per year (Boudrias 2018), and between 2 m and 14 m per year at Rabbit Lake mine (MEND 2015). Additional simulations corresponding to 6 and 9 m/year filling rate were therefore carried out for tailings A to evaluate effects of tailings thickness on the evolution of tailings consolidation with the presence of WRI. Filling rate seemed to have a negligible effect on the volume change between the cases with and without WRI, which remained around 14% at the end of the filling process for all models regardless of layer thickness (Fig. 10a). TSF depth and deposition rates vary with mine size, production rate and type of operations (surface or underground) (Blight 2010; MEND 2015). Filling rate for TSF at Malartic mine is, for example, around 3 m per year (Boudrias 2018), and between 2 m and 14 m per year at Rabbit Lake mine (MEND 2015). Additional simulations corresponding to 6 and 9 m/year filling rate were therefore carried out for tailings A ratio Rt90, i.e., the ratio of t90 between models with and without WRI, was introduced to represent the effect of filling rate on the consolidation rate of tailings (Fig. 10b). The effect of WRI on the consolidation rate was increased for greater filling rates, which indicated that the use of WRI would be more beneficial with higher filling rate in practice. Rt90 at 10 m from the WRI after the deposition of the 6th layer was 1.45, 1.70 and 1.83 for the 3-m, 6-m and 9-m thick models respectively (Fig. 10b). The ratio also increased with the number of tailings layers. This ratio was, for example, around 1.46 and 1.54 for the 6-m thick model after the placement of the 2nd and 4th layer (Fig. 10b). Models with 3 m/year but with different filling scheme instead of an instantaneously adding (i.e., layer of 1.5 m per 6 months and layer of 1 m per 4 months, respectively) were performed for tailings A to evaluate the potential effect of the assumption of instantaneous filling scheme on the rate of consolidation of tailings. 5 Discussion WRI can contribute to accelerate the rate of consolidation of tailing but also reduces the volume available for tailings storage at the same time. The geometry of the TSF in this study and the configuration of the WRIs were simplified, and the results can be applied for the relatively simple geometry TSFs. This paper only dealt with one row of inclusion, while there might be several orthogonal inclusions (not only parallel inclusions) installed for the typical design of WRIs in TSFs (Aubertin et al. 2016). Other simulations on the more complex geometries of the TSFs and various permeable conditions (i.e., only central WRI was considered in this study) can be further performed to evaluate their influences on the evolution of tailings consolidation. The models carried out with various type of tailings highlighted the importance of the constitutive relations describing the changes in the consolidation properties of tailings, which are unique for each type of tailings. For example, the relations for the tailings C were derived from large strain consolidation tests with pressure up to 8 kPa (Bhuiyan et al. 2015). In practice, the loads resulting from the filling of tailings might be significantly higher, and the change in the hydraulic conductivity and stiffness of tailings might become less non-linear when the applied loadings increase. Tests covering the actual range of pressures that are expected in the field are therefore recommended to improve the accuracy of constitutive relations. Models with several values of constant Young’s modulus of tailings were performed for tailings A to test the effect of stiffness differences on the influence of WRI on the settlement of tailings materials. In general, the higher the stiffness of tailings, the smaller zone of influence of WRI on tailings settlement. Also, tailings settlement simulated close to the WRI may be affected by the interface element used in this numerical study. The interface elements introduced in the simulations might not necessarily represent the real contact between WRI and tailings in practice. It is recommended that stiffness and frictions angles of the contact interface between these two materials should be estimated to improve the precision of the calculation. Despite these boundary effects, general behaviour are expected to remain similar (Li and Aubertin 2009; Yang 2016). Finally, field-scale investigations would be required to validate or calibrate the numerical results and the upscaling of the approach in this study. 4.2 Effect of the filling rate Simulated results indicated that the effect of instantaneous filling on the rate of consolidation of Page 11/25 Page 11/25 tailings was insignificant. It took essentially the same amount of time with such filling intervals to dissipate 90% of excess PWP. The same trend was also observed by Boudrias (2018). 6 Conclusion An investigation on the effect of a drainage system composed of WRI on the consolidation behaviors of several types of tailings in a simple TSF were numerically performed using Flac3D. Simulations were conducted considering continuously updating properties of tailings under sequential filling. Several Page 12/25 practical considerations related to the operational aspects that could have effect on the settlement of tailings were also evaluated. Results including excess PWP dissipation rate and magnitude of consolidation were compared, bringing the following conclusions: practical considerations related to the operational aspects that could have effect on the settlement of tailings were also evaluated. Results including excess PWP dissipation rate and magnitude of consolidation were compared, bringing the following conclusions: WRI had a significant effect on the acceleration of PWP dissipation and thus on tailings consolidation rate. The effect of WRI depended on the distance and the thickness of the tailings. PWP always reached the hydrostatic value at the end of each filling stage for tailings A, B and C, while excess PWP in tailings D were not fully dissipated after one year because of their relatively low hydraulic conductivity. Significant differences (up to 3 times) were observed when using a model with updated properties or with constant properties. Equivalent constant values of hydraulic conductivity were derived for these types of tailings, which can bring about an acceptable tolerance of t90 compared to the model with updated properties, reducing the computational efforts and the necessity of laboratory tests on non- linear evolution of tailings’ properties. The zone of influence of WRI was different for each type of tailings, decreasing significantly during the filling of the first few layers before remaining relatively constant after the thickness of tailings reached 12 m. The zone of influence was usually a function of the thickness of the tailings, around 1.8 times tailings thickness for tailings A and B, 2.6 for tailings C and 3.4 for tailings D respectively. Settlement of tailings C was smallest, while largest value was observed for the tailings D. Changes in the tailings settlement was less pronounced after the placement of few last layers which demonstrated very well the increases in the stiffness of the materials during consolidation process. The zone of influence of WRI was different for each type of tailings, decreasing significantly during the filling of the first few layers before remaining relatively constant after the thickness of tailings reached 12 m. 6 Conclusion The zone of influence was usually a function of the thickness of the tailings, around 1 8 times tailings thickness for tailings A and B 2 6 for tailings C and 3 4 for tailings D respectively The volume change due to settlement of tailings of model with only tailings was always greater than that of model with WRI for all types of tailing. In other words, the use of WRI decreased the volume available for the storage of tailings in the TSF, despite the acceleration of their consolidation. Additional height required when applying WRI was less than 8% of total thickness of tailings. DV for tailings A, B and D after the filling of the last layers were around 15%, while that for tailings C was around 20%. The volume change due to settlement of tailings of model with only tailings was always greater than that of model with WRI for all types of tailing. In other words, the use of WRI decreased the volume available for the storage of tailings in the TSF, despite the acceleration of their consolidation. Additional height required when applying WRI was less than 8% of total thickness of tailings DV for Additional height required when applying WRI was less than 8% of total thickness of tailings. DV for tailings A, B and D after the filling of the last layers were around 15%, while that for tailings C was around 20%. Space available for tailings to be stored in the TSF was lower with the increase of volume of WRI placed in the TSF, and formulations estimating evolution of DV with the changes in the volume ratio of tailings and WRI were proposed. Increase of the filling rate led to a more pronounced influence of WRI on the consolidation rate of tailings but had a negligible effect on the DV values. 3D effects because of complex drainage paths and permeable conditions are being investigated in an on- going project in the group. 3D effects because of complex drainage paths and permeable conditions are being investigated in an on- going project in the group. Declarations 7 ACKNOWLEDGEMENTS 7 ACKNOWLEDGEMENTS 7 ACKNOWLEDGEMENTS Page 13/25 Page 13/25 The authors are thankful to the financial support from Fonds de recherche du Québec—Nature et Technologies (FRQNT) and partners of Research Institute on Mines and the Environment (RIME UQAT - Polytechnique; http://rime-irme.ca/en). The authors also gratefully acknowledge Dr. Huy Tran, Dr. Kazim and Itasca technical support team for their valuable support and comments to improve the code in this study. References 1. Agapito LA, Bareither CA (2018) Application of a one-dimensional large-strain consolidation model to a full-scale tailings storage facility. Minerals Engineering 119:38–48. https://doi.org/https://doi.org/10.1016/j.mineng.2018.01.013 2. Aubertin M (2013) Waste rock disposal to improve the geotechnical and geochemical stability of piles. In: 23rd World Mining Congress. Montreal, Canada 3. Aubertin M (2018) Waste rock inclusions in tailings impoundment: analysis (and design) based on the Canadian Malartic Mine. In: Mines and the environment. Rouyn Noranda 4. Aubertin M, Bussière B, Pabst T, et al (2016) Review of reclamation techniques for acid generating mine wastes upon closure of disposal sites. In: Geo-Chicago 2016 5. 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Saleh-Mbemba F, Aubertin M (2021a) Physical Model Testing and Analysis of Hard Rock Tailings Consolidation Considering the Effect of a Drainage Inclusion. Geotechnical and Geological Engineering 39:2777–2798. https://doi.org/10.1007/s10706-020-01656-0 40. Saleh-Mbemba F, Aubertin M (2021b) Physical and numerical modelling of drainage and consolidation of tailings near a vertical waste rock inclusion. 0:1–14. https://doi.org/10.1139/cgj- 2020-0372 40. Saleh-Mbemba F, Aubertin M (2021b) Physical and numerical modelling of drainage and consolidation of tailings near a vertical waste rock inclusion. 0:1–14. https://doi.org/10.1139/cgj- 2020-0372 41. Schiffman RL (1982) The consolidation of soft marine sediments. Geo-Marine Letters 2:199–203. https://doi.org/10.1007/bf02462763 41. Schiffman RL (1982) The consolidation of soft marine sediments. Geo-Marine Letters 2:199–203. https://doi.org/10.1007/bf02462763 42. 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Vick SG (1990) Planning, Design and Analysis of Tailings Dams. BiTech Publishers Ltd, Vancouver, BC 48. Yang P (2016) Investigation of the geomechanical behavior of mine backfill and its interaction with rock walls and barricades 48. Yang P (2016) Investigation of the geomechanical behavior of mine backfill and its interaction with rock walls and barricades 49. Zhang J, Yao Z, Wang K, et al (2021) Sustainable utilization of bauxite residue (Red Mud) as a road material in pavements: A critical review. Construction and Building Materials 270:121419. https://doi.org/https://doi.org/10.1016/j.conbuildmat.2020.121419 Page 16/25 Page 16/25 50. Zhou, Amodio A, Boylan N (2019) Informed mine closure by multi-dimensional modelling of tailings deposition and consolidation. Mine Closure 2019 50. Zhou, Amodio A, Boylan N (2019) Informed mine closure by multi-dimensional modelling of tailings deposition and consolidation. Mine Closure 2019 Figures Figure 1 Conceptual configuration of a simple WRIs system in a tailings impoundment with (a) only tailings an water can only move upward and (b) tailings co-disposed with WRI and water can move either verticall or horizontally due to the presence of WRI, reducing the length of the drainage pathway (modified after James (2009)). Figures g Figure 1 Conceptual configuration of a simple WRIs system in a tailings impoundment with (a) only tailings and water can only move upward and (b) tailings co-disposed with WRI and water can move either vertically or horizontally due to the presence of WRI, reducing the length of the drainage pathway (modified after James (2009)). Page 17/25 Figure 2 Conceptual model with sequential filling of tailings (94 m wide) in 10 layers and the inclusion of granular waste rocks (6m wide) (dash lines represented the interfaces between taillings layers). Figure 2 Conceptual model with sequential filling of tailings (94 m wide) in 10 layers and the inclusion of granular waste rocks (6m wide) (dash lines represented the interfaces between taillings layers). References Figure 3 Evolution of PWP right after the placement of the 7th layer for tailings A (the vertical dashed line indicates the boundary between WRI and taillings, and the horizontal dahsed line shows tailings layers). Figure 3 Evolution of PWP right after the placement of the 7th layer for tailings A (the vertical dashed line indicates the boundary between WRI and taillings, and the horizontal dahsed line shows tailings layers). Evolution of PWP right after the placement of the 7th layer for tailings A (the vertical dashed line indicates the boundary between WRI and taillings, and the horizontal dahsed line shows tailings layers). Page 18/25 Page 18/25 Figure 4 Degree of consolidation U (%) at various locations at the base of TSF after the deposition of the 5th layer for (a) tailings A, (b) tailings B, (c) tailings C and (d) tailings D. Figure 4 Figure 4 Degree of consolidation U (%) at various locations at the base of TSF after the deposition of the 5th layer for (a) tailings A, (b) tailings B, (c) tailings C and (d) tailings D. Page 19/25 Page 19/25 Figure 5 Ratio of radius of influence of WRI over the tailings thickness for various types of tailings. The influence radius was different for each type of tailings and varied during the filling process: it exhibited a significant decrease after the placement of the first few layers before tending to a relatively constant value after the thickness reached around 12 m. Figure 5 Ratio of radius of influence of WRI over the tailings thickness for various types of tailings. The influence radius was different for each type of tailings and varied during the filling process: it exhibited a significant decrease after the placement of the first few layers before tending to a relatively constant value after the thickness reached around 12 m. Page 20/25 Figure 6 Comparison of t90 at the base of the TSF (tailings A) after the placement of the 10th layer as a function of the horizontal distance from the WRI and for various estimations of the hydraulic conductivity. A value of 1.3 x 10-7 m/s generated somewhat similar results to those obtained with the model using updated hydraulic conductivity, while a value of 3.5 x 10-7 m/s could yield results 3 times lower than those for model with updated hydraulic conductivity. Figure 6 Figure 6 Comparison of t90 at the base of the TSF (tailings A) after the placement of the 10th layer as a function of the horizontal distance from the WRI and for various estimations of the hydraulic conductivity. A value of 1.3 x 10-7 m/s generated somewhat similar results to those obtained with the model using updated hydraulic conductivity, while a value of 3.5 x 10-7 m/s could yield results 3 times lower than those for model with updated hydraulic conductivity. Comparison of t90 at the base of the TSF (tailings A) after the placement of the 10th layer as a function of the horizontal distance from the WRI and for various estimations of the hydraulic conductivity. A value of 1.3 x 10-7 m/s generated somewhat similar results to those obtained with the model using updated hydraulic conductivity, while a value of 3.5 x 10-7 m/s could yield results 3 times lower than those for model with updated hydraulic conductivity. Page 21/25 Page 21/25 Page 21/25 Figure 7 Figure 7 Displacements of the first layer 1 year after the addition of the 2nd, 3rd, 9th and 10th layer (noted as L2, L3, L9 and L10) for 4 types of tailings. Displacements of the first layer 1 year after the addition of the 2nd, 3rd, 9th and 10th layer (noted as L2, L3, L9 and L10) for 4 types of tailings. Page 22/25 Figure 8 (a) Evolutions of average volume changes as a function of time resulting from tailings s models with and without WRI for tailings A and (b) differences of volume change (expres Figure 8 (a) Evolutions of average volume changes as a function of time resulting from tailings settlement for models with and without WRI for tailings A and (b) differences of volume change (expressed in percentage) between models with and without WRI for various types of tailings. Figure 8 (a) Evolutions of average volume changes as a function of time resulting from tailings settlement for models with and without WRI for tailings A and (b) differences of volume change (expressed in percentage) between models with and without WRI for various types of tailings. Figure 8 Figure 8 (a) Evolutions of average volume changes as a function of time resulting from tailings settlement for models with and without WRI for tailings A and (b) differences of volume change (expressed in percentage) between models with and without WRI for various types of tailings. Page 23/25 Page 23/25 Page 23/25 Figure 9 Evolution of DV with the ratio of volume of tailings and WRI in the TSF. Calculations assumed that the displacement at the boundary interface is zero and the width of the tailings part was large enough to reduce the effect of TSF sides. Figure 9 Evolution of DV with the ratio of volume of tailings and WRI in the TSF. Calculations assumed that the displacement at the boundary interface is zero and the width of the tailings part was large enough to reduce the effect of TSF sides. Page 24/25 Figure 10 Figure 10 Page 24/25 (a) DV values for models with various filling rates and (b) Rt90 values for the point located at 10 m from WRI at the TSF base after the placement of the 2nd, 4th and 6th layer for models of 3-m, 6-m and 9-m thick layers for tailings A. Page 25/25
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Rabex-5 Protein Regulates Dendritic Localization of Small GTPase Rab17 and Neurite Morphogenesis in Hippocampal Neurons
Journal of biological chemistry/˜The œJournal of biological chemistry
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Rabex-5 Protein Regulates Dendritic Localization of Small GTPase Rab17 and Neurite Morphogenesis in Hippocampal Neurons* 12, and in revised form, February 14, 2013 Published, JBC Papers in Press,February 19, 2013, DOI 10.1074/jbc.M112.427591 Received for publication,October 12, 2012, and in revised form, February 14, 2013 Published, JBC Papers in P Yasunori Mori, Takahide Matsui1, and Mitsunori Fukuda2 Yasunori Mori, Takahide Matsui1, and Mitsunori Fukuda2 Yasunori Mori, Takahide Matsui1, and Mitsunori Fukuda2 From the Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578, Japan Background: Small GTPase Rab17 regulates dendritic morphogenesis of hippocampal neurons, but its activation mecha- nism is completely unknown. p y Results: Expression of Rabex-5 in mouse hippocampal neurons promoted dendritic localization of Rab17, and Rabex-5 knock- down resulted in inhibition of neurite morphogenesis. Conclusion: Rabex-5 regulates neurite morphogenesis by activating Rab5 and Rab17. Significance: Our findings revealed a crucial role of Rabex-5 and its targets in neuronal development. Conclusion: Rabex-5 regulates neurite morphogenesis by activating Rab5 and Rab17. Significance: Our findings revealed a crucial role of Rabex-5 and its targets in neuronal development. Small GTPase Rab17 has recently been shown to regulate den- dritic morphogenesis of mouse hippocampal neurons; however, the exact molecular mechanism of Rab17-mediated dendrito- genesis remained to be determined, because no guanine nucle- otide exchange factor (GEF) for Rab17 had been identified. In this study we screened for the Rab17-GEF by performing yeast two-hybrid assays with a GDP-locked Rab17 mutant as bait and found that Rabex-5 and ALS2, both of which were originally described as Rab5-GEFs, interact with Rab17. We also found that expression of Rabex-5, but not of ALS2, promotes translo- cation of Rab17 from the cell body to the dendrites of developing mouse hippocampal neurons. The shRNA-mediated knock- down of Rabex-5 or its known downstream target Rab5 in hip- pocampal neurons inhibited morphogenesis of both axons and dendrites, whereas knockdown of Rab17 affected dendrite mor- phogenesis alone. Based on these findings, we propose that Rabex-5 regulates neurite morphogenesis of hippocampal neu- rons by activating at least two downstream targets, Rab5, which is localized in both axons and dendrites, and Rab17, which is localized in dendrites alone. mote the release of GDP from Rab and binding of GTP to Rab (3), and the activated Rabs are then inactivated by GTPase- activating proteins (GAPs) or spontaneously inactivated by their intrinsic GTPase activity, either of which terminates the cycle (3, 4). * This work was supported in part by grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, and Technology (MEXT) of Japan (to Y. M. and M. F.) and by a grant from the Daiichi-Sankyo Founda- tion of Life Science (to M. F.). 1 Supported by the Japan Society for the Promotion of Science (JSPS). 2 To whom correspondence should be addressed. Fax: 81-22-795-7733; E-mail: nori@m.tohoku.ac.jp. 3 The abbreviations used are: GEF, guanine nucleotide exchange factor; aa, amino acid residues; ALS, amyotrophic lateral sclerosis; CA/CN, constitu- tive active/negative; DENN, differentially expressed in normal and neo- plastic cells; DIV, days in vitro; EGFP, enhanced GFP; SR, shRNA-resistant; VPS9, vacuolar protein sorting 9. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 288, NO. 14, pp. 9835–9847, April 5, 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. 14, pp. 9835–9847, April 5, 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. 14, pp. 9835–9847, April 5, 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. 14, pp. 9835–9847, April 5, 2013 © 2013 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. EXPERIMENTAL PROCEDURES Antibodies—The following antibodies used in this study were obtained commercially: anti-c-Myc (9E10) mouse monoclonal antibody (Santa Cruz Biotechnology, Santa Cruz, CA), anti- actin mouse monoclonal antibody (ABM, Richmond, Canada), anti-neurofilament-H mouse monoclonal antibody (American Research Products, Belmont, MA), anti-MAP2 chick polyclonal antibody (Millipore Corp., Billerica, MA), anti-GFP rabbit poly- clonal antibody (MBL, Nagoya, Japan), horseradish peroxidase (HRP)-conjugated anti-FLAG tag (M2) mouse monoclonal antibody and M2-conjugated agarose beads (Sigma), HRP-con- jugated anti-T7 tag antibody (Novagen, Darmstadt, Germany), and Alexa-Fluor 488/594/633-conjugated anti-mouse/rabbit/ chick IgG goat antibody (Invitrogen). Anti-Rab17 rabbit poly- clonal antibody and anti-GFP guinea pig polyclonal antibody were prepared as described previously (21). Anti-Rabex-5 rab- bit polyclonal antibody was raised against glutathione S-trans- ferase (GST)-Rabex5-C (amino acid residues (aa) 208–491) and affinity purified by exposure to antigen-bound Affi-Gel 10 beads (Bio-Rad) as described previously (24). pEGFP-C1-Rabex-5SR (an shRNA-resistant Rabex-5 mu- tant) and pEGFP-C1-Rabex-5SR-D313A were produced by using the same method as described previously (21) and the following mutagenic oligonucleotides (substituted nucleotides are shown in italics): Rabex-5-SR-5 primer, 5-CGGGATTG- CCAAGGAGGTACAGGATATAGTAGAAAAATACCCAC- TGGAG-3, and Rabex-5-SR-3 primer, 5-CTCCAGTGG- GTATTTTTCTACTATATCCTGTACCTCCTTGGCAATC- CCG-3. pEF-FLAG-Rab17, pEF-Myc-Rab17, pEF-Myc- Rab17-Q77L, pEGFP-C1-Rab17, pEGFP-C1-Rab17-Q77L, pmCherry-C1-Rab17, and pSilencer-EGFP-Rab17 were pre- pared as described previously (21). pEF-FLAG-Rab5A, pEF- FLAG-Rab5B, pEF-FLAG-Rab5C, and pEF-FLAG-Rab21 were also prepared as described previously (29, 30). The cDNAs of Rab5A, Rab17, and Rab21 were subcloned into the pMyc vector (31). pmStrawberry-C1 was also prepared as described previ- ously (32). ( ) p y ( ) Plasmid Construction—cDNAs encoding the human DENN domain-containing proteins, mouse VPS9 domain-containing proteins, and mouse Sec2 domain-containing proteins were amplified from Marathon-Ready adult human or mouse brain and/or testis cDNA (Clontech-Takara Bio Inc., Shiga, Japan) by performing PCR with the following specific oligonucleotides as described previously (25): DENN/MADD/Rab3-GEP (aa 1–570), DENND1A (aa 1–380), DENND1B (aa 5–410), DENND1C (aa 1–424), DENND2A (aa 551–1009), DENND2B (aa 669–1237), DENND2C (aa 392–881), DENN2D (aa 1–471), DENND3 (aa 24–435), DENND4A (aa 139–660), DENND4B (aa 99–650), DENND4C (aa 1–420), DENND5A (aa 1–599), DENND5B (aa 18–600), DENND6A (aa 1–605), DENND6B (aa 1–585), Sbf1/MTMR5 (aa 1–467), Sbf2/ MTMR13 (aa 1–585), Varp (aa 1–450), Rabex-5 (aa 208–491), Gapex-5 (aa 1281–1437), Rin1 (aa 446–763), Rin2 (aa 593– 858), Rin3 (aa 713–980), ALS2 (aa 1485–1651), ALS2-cl (aa 764–947), RINL (aa 314–563), Rabin3 (aa 1–428), and GRAB (aa 1–384). The sequences of the oligonucleotides used are available from the authors on request. Rabex-5 Activates Rab17 in Hippocampal Neurons priate restriction enzymes and then subcloned into the pGAD-C1 vector (26). pGBD-C1 vector harboring constitutive negative (CN or GDP-fixed) or constitutive active (CA, GTP- fixed) mutants of Rab1–43 lacking the C-terminal geranylgera- nylation site was prepared as described previously (27). cDNAs encoding mouse Rabex-5 (aa 1–491), Rabex-5-C (aa 208–491), ALS2 (aa 1–1651), and ALS2-C (aa 1485–1651) were similarly produced by conventional PCR techniques (see Fig. 1D). A Rabex-5 mutant carrying an Asp-to-Ala mutation at amino acid positions 313 (D313A) and an ALS2 mutant (D1593A) were prepared by using conventional PCR techniques and mutagenic oligonucleotides as described previously (28) (see Fig. 1D). The cDNA of each of the Rabex-5 (or ALS2) constructs was sub- cloned into the pGAD-C1 vector, pEF-T7 vector (25), pEF-Myc vector (21), pEGFP-C1 vector (Clontech-Takara Bio Inc.), and/or pGEX-4T-3 vector (GE Healthcare). The pSilencer- EGFP vector (21) or pSilencer 2.1-U6 neo (Ambion, Austin, TX) encoding a mouse Rabex-5-shRNA (short hairpin RNA) (19-base target site 5-GTTCAAGACATTGTTGAGA-3), Rab5A-shRNA (19-base target site 5-GCACAGTCCTATG- CAGATG-3), Rab5B/C-shRNA (19-base target site 5-GTTT- GAGATCTGGGACACA-3), Rab21-shRNA (19-base target site 5-TTTACTACCGAGATTCGAA-3), and ALS2-shRNA (21-base target site 5-GAACTCTTGCAAGATTTGTCA-3) was constructed as described previously (21). dendrite-specific Rab protein, unraveling the activation mech- anism of Rab17 is crucial to a better understanding the molec- ular mechanism of dendrite outgrowth and branching. In this study we screened for Rab17-GEFs by using a GDP-locked Rab17 mutant as bait and identified Rabex-5 (22) and ALS2 (amyotrophic lateral sclerosis 2) (23), both of which were orig- inally described as Rab5-GEFs, as putative Rab17-GEFs. We found that Rabex-5, but not ALS2, is required for stage-depen- dent movement of Rab17 protein from the cell body to the dendrites of mouse hippocampal neurons. We also showed that knockdown of Rabex-5 inhibited morphogenesis of both axons and dendrites in developing neurons. We discuss the possible functions of Rabex-5 in neurite morphogenesis of hippocampal neurons based on our findings. Rabex-5 Protein Regulates Dendritic Localization of Small GTPase Rab17 and Neurite Morphogenesis in Hippocampal Neurons* Therefore, the identification and character- ization of these Rab regulators, especially of GEFs, is crucial to understanding the spatiotemporal regulation of Rab GTPase activation. A variety of putative Rab-GEFs have been identified during the past decade, and they have largely been classified into four groups based on the similarities between their putative Rab- GEF domains or their structures (3), i.e. DENN (differentially expressed in normal and neoplastic cells) domains (5), Sec2 domains (6, 7), VPS9 (vacuolar protein sorting 9) domains (8), and multimeric GEFs, including a TRAPP complex (9), Hps1- Hps4 (10), and Mon1-Ccz1 (11). The DENN domain-contain- ing proteins constitute the largest group of these putative Rab- GEFs, and the in vitro targets of most of them have recently been identified. For example, DENN/MADD/Rab3-GEP exhib- its GEF activity toward Rab3 and Rab27 (12, 13), DENND1/ connecdenn/RME-4 toward Rab35 (14, 15), DENND2 toward Rab9 (16), and DENND4 toward Rab10 (16, 17). One of the other three groups, the VPS9 domain-containing proteins, acti- vate Rab5/Ypt51p subfamily GTPases (8, 18), whereas the Sec2 domain-containing proteins, Sec2p and Rabin8, activate Sec4p and Rab8, respectively (6, 7). Despite the increasing numbers of Rab-GEFs that have been identified, specific GEFs for about half of the mammalian Rabs remain unknown. Rab-type small GTPases are conserved membrane traffick- ing proteins in all eukaryotes, and they mediate various steps in membrane trafficking, including vesicle budding, vesicle move- ment, vesicle docking to specific membranes, and vesicle fusion (1, 2). Rabs function as a molecular switch by cycling between two nucleotide-bound states, a GDP-bound inactive state and a GTP-bound active state. In general, Rabs are activated by spe- cific guanine nucleotide exchange factors (GEFs),3 which pro- Rab17 is one of the Rab isoforms whose specific and physio- logical GEFs have not been identified. Rab17 was originally described as an epithelial cell-specific Rab that regulates polar- ized trafficking (19, 20), but the results of our previous study indicated that Rab17 is also expressed in mouse brain and that it regulates dendrite morphogenesis and postsynaptic develop- ment of hippocampal neurons (21). Because Rab17 is the only JOURNAL OF BIOLOGICAL CHEMISTRY 9835 9835 APRIL 5, 2013•VOLUME 288•NUMBER 14 EXPERIMENTAL PROCEDURES The positions of the molecular mass markers (in kilodaltons) are shown on the left. D, shown is a schematic represen- tationoftheRabex-5constructsandALS2constructsusedinthisstudy.Rabex-5(aa1–491)containsazincfingerdomain(ZnF),VPS9domain,andcoiled-coiled domain (CC). Rabex-5-C (aa 208–491) contains the VPS9 domain and CC domain. ALS2 (aa 1–1651) contains a RCC1 domain, DH domain, PH domain, MORN motifs I and II, and VPS9 domain (see Ref. 38). ALS2-C (aa 1485–1651) contains only the VPS9 domain. GEF activity-deficient VPS9 mutants, Rabex-5-D313A and ALS2-D1593A, are shown. FIGURE 1. Identification of Rabex-5 and ALS2 as putative Rab17-GEFs. A, screening of Rab-GEFs by yeast two-hybrid assays with the GDP-locked CN form of Rab17 as bait is shown. Yeast cells containing pGBD plasmid expressing Rab17(CN) and pGAD-C1 plasmid expressing each of the DENN, VPS9, or Sec2 domain-containing proteins were streaked on SC-LW (top panels) and SC-AHLW (selection medium; bottom panels) and incubated at 30 °C for 1 day and for 1 week,respectively.Notethatonlytwoofthe29putativeRab-GEFstested,Rabex-5(lane20)andALS2(lane25),boundRab17(CN).BandC,Rabex-5(B)andALS2 (C) interact with Rab17 in the presence of 1 mM GDP. The T7-tagged VPS9 domain of Rabex-5 (Rabex-5-C) or VPS9 domain of ALS2 (ALS2-C) and FLAG-tagged Rab17 were co-expressed in COS-7 cells, and they were analyzed for associations by coimmunoprecipitation assays with anti-FLAG tag antibody-conjugated agarose beads. Input means 1⁄80 volume of the reaction mixture used for immunoprecipitation (top panels). Immunoprecipitated (IP) FLAG-Rab17 (bottom panels) and coimmunoprecipitated T7-Rabex-5-C or T7-ALS2-C (middle panels) were detected with HRP-conjugated anti-FLAG tag antibody and HRP-conju- gated anti-T7 tag antibody, respectively. The positions of the molecular mass markers (in kilodaltons) are shown on the left. D, shown is a schematic represen- tationoftheRabex-5constructsandALS2constructsusedinthisstudy.Rabex-5(aa1–491)containsazincfingerdomain(ZnF),VPS9domain,andcoiled-coiled domain (CC). Rabex-5-C (aa 208–491) contains the VPS9 domain and CC domain. ALS2 (aa 1–1651) contains a RCC1 domain, DH domain, PH domain, MORN motifs I and II, and VPS9 domain (see Ref. 38). ALS2-C (aa 1485–1651) contains only the VPS9 domain. GEF activity-deficient VPS9 mutants, Rabex-5-D313A and ALS2-D1593A, are shown. FIGURE 1. Identification of Rabex-5 and ALS2 as putative Rab17-GEFs. A, screening of Ra dishes (35-mm dish, MatTek Corp., Ashland, MA) coated with poly-L-lysine hydrobromide (Nacalai Tesque, Kyoto, Japan). The cells were maintained in MEM containing B27 supple- ments, 1% fetal bovine serum, and 0.5 mM glutamine (Invitro- gen). Plasmid DNAs were transfected into neurons at 2–4 days in vitro (DIV) by using Lipofectamine 2000 (Invitrogen) accord- ing to the manufacturer’s instructions. 6-well plate. EXPERIMENTAL PROCEDURES GEF activity-deficient VPS9 mutants, Rabex-5-D313A and A are shown Rabex 5 Activates Rab17 in Hippocampal Neurons FIGURE 1. Identification of Rabex-5 and ALS2 as putative Rab17-GEFs. A, screening of Rab-GEFs by yeast two-hybrid assays with the GDP-loc of Rab17 as bait is shown. Yeast cells containing pGBD plasmid expressing Rab17(CN) and pGAD-C1 plasmid expressing each of the DENN, V domain-containing proteins were streaked on SC-LW (top panels) and SC-AHLW (selection medium; bottom panels) and incubated at 30 °C for 1 week,respectively.Notethatonlytwoofthe29putativeRab-GEFstested,Rabex-5(lane20)andALS2(lane25),boundRab17(CN).BandC,Rabex-5 (C) interact with Rab17 in the presence of 1 mM GDP. The T7-tagged VPS9 domain of Rabex-5 (Rabex-5-C) or VPS9 domain of ALS2 (ALS2-C) and F Rab17 were co-expressed in COS-7 cells, and they were analyzed for associations by coimmunoprecipitation assays with anti-FLAG tag antibody agarose beads. Input means 1⁄80 volume of the reaction mixture used for immunoprecipitation (top panels). Immunoprecipitated (IP) FLAG-Ra panels) and coimmunoprecipitated T7-Rabex-5-C or T7-ALS2-C (middle panels) were detected with HRP-conjugated anti-FLAG tag antibody an gated anti-T7 tag antibody, respectively. The positions of the molecular mass markers (in kilodaltons) are shown on the left. D, shown is a schema tationoftheRabex-5constructsandALS2constructsusedinthisstudy.Rabex-5(aa1–491)containsazincfingerdomain(ZnF),VPS9domain,and domain (CC). Rabex-5-C (aa 208–491) contains the VPS9 domain and CC domain. ALS2 (aa 1–1651) contains a RCC1 domain, DH domain, PH do motifs I and II, and VPS9 domain (see Ref. 38). ALS2-C (aa 1485–1651) contains only the VPS9 domain. GEF activity-deficient VPS9 mutants, Rabex- ALS2-D1593A, are shown. FIGURE 1. Identification of Rabex-5 and ALS2 as putative Rab17-GEFs. A, screening of Rab-GEFs by yeast two-hybrid assays with the GDP-locked CN form of Rab17 as bait is shown. Yeast cells containing pGBD plasmid expressing Rab17(CN) and pGAD-C1 plasmid expressing each of the DENN, VPS9, or Sec2 domain-containing proteins were streaked on SC-LW (top panels) and SC-AHLW (selection medium; bottom panels) and incubated at 30 °C for 1 day and for 1 week,respectively.Notethatonlytwoofthe29putativeRab-GEFstested,Rabex-5(lane20)andALS2(lane25),boundRab17(CN).BandC,Rabex-5(B)andALS2 (C) interact with Rab17 in the presence of 1 mM GDP. The T7-tagged VPS9 domain of Rabex-5 (Rabex-5-C) or VPS9 domain of ALS2 (ALS2-C) and FLAG-tagged Rab17 were co-expressed in COS-7 cells, and they were analyzed for associations by coimmunoprecipitation assays with anti-FLAG tag antibody-conjugated agarose beads. Input means 1⁄80 volume of the reaction mixture used for immunoprecipitation (top panels). Immunoprecipitated (IP) FLAG-Rab17 (bottom panels) and coimmunoprecipitated T7-Rabex-5-C or T7-ALS2-C (middle panels) were detected with HRP-conjugated anti-FLAG tag antibody and HRP-conju- gated anti-T7 tag antibody, respectively. EXPERIMENTAL PROCEDURES Purified PCR products were directly inserted into the pGEM-T Easy vector (Promega, Madison, WI) and verified with an automated sequencer. The cDNAs were excised from the pGEM-T Easy vector with appro- Yeast Two-hybrid Assays—The yeast strain, medium, culture conditions, and transformation protocol used are described in James et al. (26). The materials used for the two-hybrid assay in this study were: yeast strain pJ69-4A, a synthetic complete medium lacking leucine and tryptophan (SC-LW medium: 0.67% yeast nitrogen base without amino acids, 2% glucose, 2% Bacto agar, 0.02% adenine, 0.01% uracil, 0.01% histidine, 0.015% lysine, and 0.01% methionine), and a synthetic complete medium lacking adenine, histidine, leucine, and tryptophan (SC-AHLW) as the selection medium. Hippocampal Neuron Culture and Transfection—Mouse hippocampal neuronal cultures were prepared essentially as described previously (33). In brief, hippocampi were dissected from embryonic day 16.5 mice and dissociated with 0.25% tryp- sin (Invitrogen). The cells were plated at a density of 3–6  104 cells/ml onto coverglasses in a 6-well plate or glass-bottom VOLUME 288•NUMBER 14•APRIL 5, 2013 9836 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 14•APRIL 5, 2013 Rabex-5 Activates Rab17 in Hippocampal Neurons entification of Rabex-5 and ALS2 as putative Rab17-GEFs. A, screening of Rab-GEFs by yeast two-hybrid assays with the GDP-locked CN form bait is shown. Yeast cells containing pGBD plasmid expressing Rab17(CN) and pGAD-C1 plasmid expressing each of the DENN, VPS9, or Sec2 aining proteins were streaked on SC-LW (top panels) and SC-AHLW (selection medium; bottom panels) and incubated at 30 °C for 1 day and for 1 tively.Notethatonlytwoofthe29putativeRab-GEFstested,Rabex-5(lane20)andALS2(lane25),boundRab17(CN).BandC,Rabex-5(B)andALS2 with Rab17 in the presence of 1 mM GDP. The T7-tagged VPS9 domain of Rabex-5 (Rabex-5-C) or VPS9 domain of ALS2 (ALS2-C) and FLAG-tagged co-expressed in COS-7 cells, and they were analyzed for associations by coimmunoprecipitation assays with anti-FLAG tag antibody-conjugated ds. Input means 1⁄80 volume of the reaction mixture used for immunoprecipitation (top panels). Immunoprecipitated (IP) FLAG-Rab17 (bottom coimmunoprecipitated T7-Rabex-5-C or T7-ALS2-C (middle panels) were detected with HRP-conjugated anti-FLAG tag antibody and HRP-conju- 7 tag antibody, respectively. The positions of the molecular mass markers (in kilodaltons) are shown on the left. D, shown is a schematic represen- Rabex-5constructsandALS2constructsusedinthisstudy.Rabex-5(aa1–491)containsazincfingerdomain(ZnF),VPS9domain,andcoiled-coiled Rabex-5-C (aa 208–491) contains the VPS9 domain and CC domain. ALS2 (aa 1–1651) contains a RCC1 domain, DH domain, PH domain, MORN , and VPS9 domain (see Ref. 38). ALS2-C (aa 1485–1651) contains only the VPS9 domain. EXPERIMENTAL PROCEDURES Plasmid DNAs were transfected into COS-7 cells and Neuro2A cells by using Lipofectamine Plus (Invitrogen) and Lipofectamine 2000, respectively, each according to the manufacturer’s instructions. Immunocytochemistry—Neurons were fixed for 10 min at room temperature with 4% paraformaldehyde (Wako Pure Chemicals Industries) and 4% sucrose in 0.1 M sodium phos- phate buffer. After permeabilizing the cells with 0.1% Triton X-100 for 1 min, they were blocked with the blocking buffer (10% fetal bovine serum in phosphate-buffered saline) for 1 h. The cells were then immunostained for 1 h with anti-MAP2 chick antibody (1/1000 dilution), anti-neurofilament-H mouse Other Cell Cultures and Transfections—COS-7 cells and Neuro2A cells were cultured in Dulbecco’s modified Eagle’s medium (Wako Pure Chemical Industries, Osaka, Japan) sup- plemented with 10% fetal bovine serum, 50 units/ml penicillin, and 50 units/ml streptomycin. The cells were plated onto a APRIL 5, 2013•VOLUME 288•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 9837 APRIL 5, 2013•VOLUME 288•NUMBER 14 Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 Activates Rab17 in Hippocampal Neurons FIGURE 2. The constitutive active mutant of Rab17 preferentially localized in the dendrites of hippocampal neurons. A and B, shown are typical images of Rab17-expressing neurons and Rab17-Q77L-expressing neurons. At 4 DIV hippocampal neurons were transfected with vectors encoding EGFP and Myc- tagged Rab17 (A) or Myc-tagged Rab17-Q77L (B), and at 7 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green),Myc(black),andMAP2(adendritemarker;red).Thearrowsandarrowheadspointtoaxonsanddendrites,respectively.Thebottomthreepanels(a–c)are magnifiedviewsoftheboxedareasinthetoprightpanels.Bars,10m.C,shownisquantificationoftheproportionsofMyc-Rab17(n20)andMyc-Rab17-Q77L (n  20) in the dendrites shown in A and B. The proportion (%) of dendrite-localized Myc-Rab17 was calculated by dividing the dendrite-specific Myc-Rab17 fluorescence intensity by the total Myc-Rab17 fluorescence intensity. Note that active Rab17 was preferentially localized in the dendrites. **, p  0.0025. Rabex 5 Activates Rab17 in Hippocampal Neurons FIGURE 2. The constitutive active mutant of Rab17 preferentially localized in the dendrites of hippocampal neurons. A and B, shown are typical images of Rab17-expressing neurons and Rab17-Q77L-expressing neurons. At 4 DIV hippocampal neurons were transfected with vectors encoding EGFP and Myc- tagged Rab17 (A) or Myc-tagged Rab17-Q77L (B), and at 7 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green),Myc(black),andMAP2(adendritemarker;red).Thearrowsandarrowheadspointtoaxonsanddendrites,respectively.Thebottomthreepanels(a–c)are magnifiedviewsoftheboxedareasinthetoprightpanels.Bars,10m.C,shownisquantificationoftheproportionsofMyc-Rab17(n20)andMyc-Rab17-Q77L (n  20) in the dendrites shown in A and B. The proportion (%) of dendrite-localized Myc-Rab17 was calculated by dividing the dendrite-specific Myc-Rab17 fluorescence intensity by the total Myc-Rab17 fluorescence intensity. Note that active Rab17 was preferentially localized in the dendrites. **, p  0.0025. EXPERIMENTAL PROCEDURES immunostaining of the morphometric marker GFP. Dendrites and axons were identified based on the presence of a dendrite- specific marker (MAP2) and an axon-specific marker (neuro- filament-H or Tau), respectively. Total dendrite length, total dendrite branch tip numbers, total axon length, and total axon branch tip numbers were determined manually by using the NeuronJ (Version 1.1.0) (34) plug-in to the ImageJ software program. antibody (1/500 dilution), anti-Tau mouse antibody (1/100 dilution), anti-Myc mouse antibody (1/500 dilution), anti- Rab17 rabbit antibody (1/500 dilution), anti-GFP rabbit anti- body (1/1000 dilution), and/or anti-GFP guinea pig antibody (1/1000 dilution), after which they were incubated for 1 h at room temperature with Alexa-Fluor 488/594/633-labeled sec- ondary IgG (1/5000 dilution). The cells were examined for fluorescence with a confocal laser-scanning microscope (Fluo- view 1000, Olympus, Tokyo, Japan), and the images were pro- cessed with Adobe Photoshop software (CS4). Fluorescent intensity was quantified with ImageJ software (Version 1.42q; National Institutes of Health). Statistical Analyses—The results shown in Figs. 2C, 3F, 4D, 5 (F and I), 6 (B–F, H, and J), 7(C and D), and 8 (E–H) are pre- sented as the means and S.E. Values were compared by means of Student’s unpaired t test. A p value of 0.05 was considered statistically significant. All statistical analyses were performed on data from three independent experiments, and the data from a representative experiment are shown here. Quantification of Rab Proteins Translocated into the Axon or Dendrites of Hippocampal Neurons—To quantify the signals of each Rab protein in the entire neuron (cell body, dendrites, and axon) or just the axon region or dendrite region, image thresh- olds were set to exclude pixels that did not fall over the cell body, the axon, or the dendrites, and after subtracting the back- ground intensity values from each image before quantification, the integrated fluorescence intensity of Rab proteins in the entire neuron or just the axon (or dendrite) region was obtained. The proportion (%) of each Rab protein in the axon (or the dendrites) was calculated by dividing the fluorescence intensity of the axon (or dendrite) region by the fluorescence intensity of the entire neuron (i.e. total fluorescence intensity). RESULTS Rabex-5 Activates Rab17 in Hippocampal Neurons IGURE 3 Th VPS9 d i f R b 5 b t t f ALS2 t d t l ti f bi t R b17 t th d d it f hi l FIGURE 3. The VPS9 domain of Rabex-5, but not of ALS2, promoted translocation of recombinant Rab17 to the dendrites of hippocampal neurons. A–E, shown are typical images of mCherry-Rab17 in Rabex-5-C-coexpressing or EGFP-ALCS-2-C-coexpressing neurons. At 4 DIV hippocampal neurons were transfected with vectors encoding mCherry-tagged Rab17 and EGFP (A), EGFP-Rabex-5-C (B), EGFP-Rabex-5-C-D313A (C), EGFP-ALS2-C (D), or EGFP-ALS2-C- D1593A (E), and at 7 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (a dendrite marker; red). The arrows and arrowheads point to axons and dendrites, respectively. The bottom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. F, shown is quantification of the proportion of mCherry-Rab17 in the dendrites in the presence of EGFP (n  20), EGFP-Rabex-5-C (n  20), EGFP-Rabex-5-C-D313A (n  10), EGFP-ALS2-C (n  10), or EGFP-ALS2-C-D1593A (n  10) shown in A–E. The proportion (%) of dendrite-localized mCherry-Rab17 was calculated by dividing the dendrite-specific mCherry-Rab17 fluorescence intensity by the total mCherry- Rab17 fluorescence intensity. Note that EGFP-Rabex-5-C, but not ALS2-C, promoted translocation of mCherry-Rab17 from the cell body to the dendrites. **, p  0.0025. The VPS9 Domain of Rabex-5, but Not of ALS2, Activates Rab17 in Hippocampal Neurons—We next investigated whether these candidate proteins actually act as a Rab17 acti- vator in cultured mouse hippocampal neurons. We focused on the stage-dependent difference in Rab17 localization in hip- pocampal neurons as a means of monitoring activation of Rab17. We previously showed that Rab17 was detected only in the cell body at an early stage (3 DIV, 6.0  1.7% of Rab17; 7 DIV, 6.4  2.3% of Rab17 in the dendrites) but that some of the Rab17 had translocated from the cell body to the dendrites at a later stage (11 DIV, 11.6  1.2% of Rab17 in the dendrites) (21). domains (Rabin3 and GRAB) by yeast two-hybrid assays and succeeded in identifying two candidates, Rabex-5 and ALS2 (Fig. 1, A, lanes 20 and 25, and D), as Rab17-GEFs. RESULTS Screening for Rab17-GEFs by Yeast Two-hybrid Assays with a GDP-locked Rab17 Mutant as Bait—To identify a Rab17-GEF molecule(s) that functions in neurons, we focused on previous reports showing that Rab-GEFs often physically interact with their substrate GDP-Rabs, e.g. DENND1/RME-4 interacts with Rab35 (14), ALS2 with Rab5 (23), Rin1 with Rab5 (35), Varp with Rab21 (36), and Rabin8 with Rab8 (7). We, therefore, per- formed yeast two-hybrid assays to test for possible interactions between putative GEF domains and a GDP-locked, constitutive negative (CN) form of Rab17 (Rab17-T33N). As shown in Fig. 1A, we screened 18 DENN domains (DENN, DENND1A–C, DENND2A–D, DENND3, DENND4A–C, DENND5A–B, DENND6A–B, and Sbf1–2), 9 VPS9 domains (Varp, Rabex-5, Gapex-5, Rin1–3, ALS2, ALS-cl, and RINL), and 2 Sec2 Morphometric Analyses of the Neurites of Hippocampal Neurons—Neurites were morphometrically analyzed as de- scribed previously with slight modifications (21). Hippocampal neurons were fixed and then subjected to immunocytochemis- try with antibodies against GFP, MAP2, and neurofilament-H (or Tau). All quantitative analyses were carried out based on 9838 VOLUME 288•NUMBER 14•APRIL 5, 2013 9838 JOURNAL OF BIOLOGICAL CHEMISTRY Rabex-5 Activates Rab17 in Hippocampal Neurons he VPS9 domain of Rabex-5, but not of ALS2, promoted translocation of recombinant Rab17 to the dendrites of hippocampal neurons. are typical images of mCherry-Rab17 in Rabex-5-C-coexpressing or EGFP-ALCS-2-C-coexpressing neurons. At 4 DIV hippocampal neurons were with vectors encoding mCherry-tagged Rab17 and EGFP (A), EGFP-Rabex-5-C (B), EGFP-Rabex-5-C-D313A (C), EGFP-ALS2-C (D), or EGFP-ALS2-C- and at 7 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (a rker; red). The arrows and arrowheads point to axons and dendrites, respectively. The bottom three panels (a–c) are magnified views of the boxed top right panels. Bars, 10 m. F, shown is quantification of the proportion of mCherry-Rab17 in the dendrites in the presence of EGFP (n  abex-5-C (n  20), EGFP-Rabex-5-C-D313A (n  10), EGFP-ALS2-C (n  10), or EGFP-ALS2-C-D1593A (n  10) shown in A–E. The proportion rite-localized mCherry-Rab17 was calculated by dividing the dendrite-specific mCherry-Rab17 fluorescence intensity by the total mCherry- escence intensity. Note that EGFP-Rabex-5-C, but not ALS2-C, promoted translocation of mCherry-Rab17 from the cell body to the dendrites. 25. Rabex-5 Activates Rab17 in Hippocampal Neurons FIGURE 4. Rabex-5 promotes translocation of endogenous Rab17 to the dendrites of hippocampal neurons. A–C, shown are typical images of endogenous Rab17 protein in Rabex-5-expressing or EGFP-Rabex-5-D313A- expressing neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding EGFP (A), EGFP-Rabex-5 (B), or EGFP-Rabex-5-D313A (C), and at 12 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (red). The arrows and arrowheads point to axons and dendrites, respectively. The bot- tom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. D, shown is quantification of the proportion of endogenous Rab17 protein in the dendrites in the presence of EGFP (n  20), EGFP-Rabex-5 (n  20), or EGFP-Rabex-5-D313A (n  12) shown in A–C. The proportion (%) of Rab17 in the dendrites was calculated by dividing the den- drite-specific Rab17 fluorescence intensity by the total Rab17 fluorescence intensity. Note that EGFP-Rabex-5, but not its GEF activity-deficient mutant (D313A), promoted translocation of Rab17 from the cell body to the den- drites. *, p  0.025. We hypothesized that the differences in the localization of Rab17 during neuronal development are attributable to the dif- ference in ratio of GTP-Rab17 to GDP-Rab17. If activation of Rab17, i.e. an increase in GTP-Rab17, is required for Rab17 to translocate to dendrites, a constitutive active form of Rab17 (Rab17-Q77L) should be preferentially localized in the den- drites rather than in the cell body. As expected, at 7 DIV the wild-type Rab17 was found to be mainly localized in the cell body, and only a small portion of Rab17 was detected in the dendrites (31.3  1.9% of Myc-Rab17 was in the dendrites, and this value was higher than the proportion of endogenous Rab17 in the dendrites described above; the discrepancy may be caused by the lower expression level of endogenous Rab17 and by the low quality of our anti-Rab17 antibody, which does not sufficiently detect the low level expression of endogenous Rab17 protein in the dendrites) (Fig. 2A and C). By contrast, a large proportion of the Rab17-Q77L was localized in the den- drites (65.9  1.6% of Rab17-Q77L was in the dendrites) (Fig. 2, B and C). Rabex-5 Activates Rab17 in Hippocampal Neurons Interestingly, however, a small proportion of the Myc- Rab17-Q77L signals was also detected in the axon, in contrast to the lack of wild-type Myc-Rab17 signals in the axon (Fig. 2, A and B, panels b, left). These results strongly supported our hypothesis that Rab17 is translocated from the cell body to the dendrites in a GTP-dependent manner. FIGURE 4. Rabex-5 promotes translocation of endogenous Rab17 to the dendrites of hippocampal neurons. A–C, shown are typical images of endogenous Rab17 protein in Rabex-5-expressing or EGFP-Rabex-5-D313A- expressing neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding EGFP (A), EGFP-Rabex-5 (B), or EGFP-Rabex-5-D313A (C), and at 12 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (red). The arrows and arrowheads point to axons and dendrites, respectively. The bot- tom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. D, shown is quantification of the proportion of endogenous Rab17 protein in the dendrites in the presence of EGFP (n  20), EGFP-Rabex-5 (n  20), or EGFP-Rabex-5-D313A (n  12) shown in A–C. The proportion (%) of Rab17 in the dendrites was calculated by dividing the den- d f b fl b h l b fl If Rabex-5 and ALS2 actually have the ability to activate Rab17 in neurons, forced overexpression of their GEF domains, i.e. enhanced GFP (EGFP)-tagged Rabex-5-C and ALS-2-C, in hippocampal neurons should promote translocation of Rab17 from the cell body to the dendrites. As expected, at 7 DIV the proportion of dendrite-localized Rab17 was significantly higher in the EGFP-Rabex-5-C-expressing neurons than it was in the control neurons (52.3  2.9% of mCherry-Rab17 in the den- drites of the Rabex-5-C-expressing neurons versus 30.0  1.9% of mCherry-Rab17 in the dendrites of control neurons) (Fig. 3, A, B, and F). Interestingly, some mCherry-Rab17 signals were also detected in the axon of Rabex-5-C-expressing cells (Fig. 3B, panel b, left), the same as in the Rab17-Q77L-expressing cells (Fig. 2B, panel b, left). This Rabex-5-C-dependent translocation of Rab17 to dendrites must have been caused by the GEF activ- ity of the VPS9 domain of Rabex-5, because a GEF activity- deficient mutant of Rabex-5-C-D313A (18) had no effect on the Rab17 distribution (21.8  2.5% of mCherry-Rab17 in the den- drites of Rabex-5-C-D313A-expressing neurons) (Fig. 3, C and F). RESULTS It should be noted that Rabex-5 has recently been reported to exhibit Rab17-GEF activity in vitro (16), thereby validating our screen- ing procedure. The interaction between GDP-Rab17 and the VPS9 domain of Rabex-5 (Rabex-5-C) or ALS2 (ALS2-C) was confirmed by co-immunoprecipitation assays in COS-7 cells (Fig. 1, B and C). We, therefore, selected Rabex-5 and ALS2 for subsequent analysis as candidates for the Rab17-GEF(s) in mouse hippocampal neurons. APRIL 5, 2013•VOLUME 288•NUMBER 14 APRIL 5, 2013•VOLUME 288•NUMBER 14 9839 JOURNAL OF BIOLOGICAL CHEMISTRY 9839 Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 Activates Rab17 in Hippocampal Neurons I, shown is quantification of the proportion of Rab17 in the dendrites of control-shRNA-transfected neurons (n  20) and Rabex-5-shRNA- transfected neurons (n  20) shown in G and H. The proportion (%) of Rab17 in the dendrites was calculated by dividing the dendrite-specific Rab17 fluorescence intensity by the total Rab17 fluorescence intensity. Note that translocation of Rab17 to the dendrites was significantly reduced after knockdown of Rabex-5. **, p  0.0025. FIGURE 5. Rabex-5 is required for the dendritic localization of Rab17 in hippocampal neurons. A, Rabex-5 is expressed in primary mouse hippocampal neuron cultures. Lysates of mouse hippocampal neurons at 3, 7, 11, 14, 21, or 28 DIV were analyzed by immunoblotting with anti-Rabex-5 antibody (upper panel) and anti-actin antibody (lower panel). The asterisks indicate nonspecific bands. B and C, knockdown efficiency of Rabex-5-shRNA is shown. B, Neuro2A cells were transfected with a vector encoding control-shRNA (lanes 1, 3, 5, and 7) or Rabex-5-shRNA (lanes 2, 4, 6, and 8) together with pEGFP-C1-Rabex-5 (lanes 1 and 2), pEGFP-C1-Rabex-5SR (lanes 3 and 4), pEGFP-C1-Rabex-5-D313A (lanes 5 and 6), or pEGFP-C1-Rabex-5-D313ASR (lanes 7 and 8). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-GFP antibody (upper panel) and anti-actin antibody (lower panel). C, Neuro2A cells were transfected with a vector encoding control-shRNA (lane 1) or Rabex-5-shRNA (lane 2). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-Rabex-5 antibody (upper panel) and anti-actin antibody (lower panel). The asterisk indicates nonspecific bands. Note that the levelofexpressionofendogenousRabex-5inNeuro2AcellswasreducedinthepresenceofRabex-5-shRNA.D,shownisacomparisonoftheproteinexpression level of EGFP-Rabex-5SR and endogenous Rabex-5 in Neuro2A cells. Neuro2A cells were transfected with pEGFP-C1-Rabex-5SR (lane 2) or nothing (lane 1). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-Rabex-5 antibody. The positions of the molecular mass markers (in kilodaltons) are shown on the left. Note that the expression level of EGFP-Rabex-5SR is approximately 5 times higher than that of endogenous Rabex-5 in Neuro2A cells. E and F, shown are typical images of EGFP-Rabex-5-expressing neurons in the presence and absence of Rabex-5-shRNA. At 3 DIV hippocampal neurons were transfected with a vector encoding control-shRNA or Rabex-5-shRNA together with EGFP-Rabex-5 and mStrawberry, and at 5 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green). Bar, 10 m. Rabex-5 Activates Rab17 in Hippocampal Neurons By contrast, neither the wild-type ALS-2-C nor a GEF activ- ity-deficient mutant of ALS-2-C-D1593A altered the Rab17 distribution (Fig. 3, D–F). These results indicated that the VPS9 domain of Rabex-5, but not of ALS2, has the ability to activate Rab17 in hippocampal neurons. FIGURE 4. Rabex-5 promotes translocation of endogenous Rab17 to the dendrites of hippocampal neurons. A–C, shown are typical images of endogenous Rab17 protein in Rabex-5-expressing or EGFP-Rabex-5-D313A- expressing neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding EGFP (A), EGFP-Rabex-5 (B), or EGFP-Rabex-5-D313A (C), and at 12 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (red). The arrows and arrowheads point to axons and dendrites, respectively. The bot- tom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. D, shown is quantification of the proportion of endogenous Rab17 protein in the dendrites in the presence of EGFP (n  20), EGFP-Rabex-5 (n  20), or EGFP-Rabex-5-D313A (n  12) shown in A–C. The proportion (%) of Rab17 in the dendrites was calculated by dividing the den- drite-specific Rab17 fluorescence intensity by the total Rab17 fluorescence intensity. Note that EGFP-Rabex-5, but not its GEF activity-deficient mutant (D313A), promoted translocation of Rab17 from the cell body to the den- drites. *, p  0.025. To further confirm that endogenous Rab17 protein is also activated by Rabex-5, we overexpressed full-length Rabex-5 in hippocampal neurons and evaluated its effect on the subcellular localization of endogenous Rab17 protein by immunocyto- chemistry with the anti-Rab17-specific antibody. The results showed that at 12 DIV the proportion of endogenous Rab17 protein localized in the dendrites was 11.8  1.9% in the control EGFP-expressing cells (Fig. 4, A and D) and significantly higher (21.8  2.5%) in the Rabex-5-expressing neurons (Fig. 4, B and D). Interestingly, in contrast to the mCherry-Rab17- and EGFP-Rabex-5-C-expressing cells (Fig. 3B, panel b, left), no endogenous Rab17 signals were observed in the axon of EGFP- Rabex-5-expressing cells (Fig. 4B, panel b, left). 9840 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 14•APRIL 5, 2013 Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 Activates Rab17 in Hippocampal Neurons -5 is required for the dendritic localization of Rab17 in hippocampal neurons. A, Rabex-5 is expressed in primary mouse hippocampal Lysates of mouse hippocampal neurons at 3, 7, 11, 14, 21, or 28 DIV were analyzed by immunoblotting with anti-Rabex-5 antibody (upper ctin antibody (lower panel). The asterisks indicate nonspecific bands. B and C, knockdown efficiency of Rabex-5-shRNA is shown. B, Neuro2A ected with a vector encoding control-shRNA (lanes 1, 3, 5, and 7) or Rabex-5-shRNA (lanes 2, 4, 6, and 8) together with pEGFP-C1-Rabex-5 (lanes -C1-Rabex-5SR (lanes 3 and 4), pEGFP-C1-Rabex-5-D313A (lanes 5 and 6), or pEGFP-C1-Rabex-5-D313ASR (lanes 7 and 8). Two days after cells were lysed and subjected to immunoblot analysis with anti-GFP antibody (upper panel) and anti-actin antibody (lower panel). C, Neuro2A ected with a vector encoding control-shRNA (lane 1) or Rabex-5-shRNA (lane 2). Two days after transfection the cells were lysed and subjected nalysis with anti-Rabex-5 antibody (upper panel) and anti-actin antibody (lower panel). The asterisk indicates nonspecific bands. Note that the nofendogenousRabex-5inNeuro2AcellswasreducedinthepresenceofRabex-5-shRNA.D,shownisacomparisonoftheproteinexpression bex-5SR and endogenous Rabex-5 in Neuro2A cells. Neuro2A cells were transfected with pEGFP-C1-Rabex-5SR (lane 2) or nothing (lane 1). Two ection the cells were lysed and subjected to immunoblot analysis with anti-Rabex-5 antibody. The positions of the molecular mass markers (in shown on the left. Note that the expression level of EGFP-Rabex-5SR is approximately 5 times higher than that of endogenous Rabex-5 in and F, shown are typical images of EGFP-Rabex-5-expressing neurons in the presence and absence of Rabex-5-shRNA. At 3 DIV hippocampal nsfected with a vector encoding control-shRNA or Rabex-5-shRNA together with EGFP-Rabex-5 and mStrawberry, and at 5 DIV the neurons ubjected to immunocytochemistry with antibodies against GFP (green). Bar, 10 m. F, shown is quantification of the EGFP-Rabex-5 of the ansfected neurons (n  20) or Rabex-5-shRNA-transfected neurons (n  20) shown in E. a.u., arbitrary units. G and H, shown are typical images Rabex-5-shRNA-transfected neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding control-shRNA (G) or Rabex-5- t 14 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (blue). FIGURE 5. Rabex-5 is required for the dendritic localization of Rab17 in hippocampal neurons. A, Rabex-5 is expressed in primary mouse hippocampal neuron cultures. Rabex-5 Activates Rab17 in Hippocampal Neurons Lysates of mouse hippocampal neurons at 3, 7, 11, 14, 21, or 28 DIV were analyzed by immunoblotting with anti-Rabex-5 antibody (upper panel) and anti-actin antibody (lower panel). The asterisks indicate nonspecific bands. B and C, knockdown efficiency of Rabex-5-shRNA is shown. B, Neuro2A cells were transfected with a vector encoding control-shRNA (lanes 1, 3, 5, and 7) or Rabex-5-shRNA (lanes 2, 4, 6, and 8) together with pEGFP-C1-Rabex-5 (lanes 1 and 2), pEGFP-C1-Rabex-5SR (lanes 3 and 4), pEGFP-C1-Rabex-5-D313A (lanes 5 and 6), or pEGFP-C1-Rabex-5-D313ASR (lanes 7 and 8). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-GFP antibody (upper panel) and anti-actin antibody (lower panel). C, Neuro2A cells were transfected with a vector encoding control-shRNA (lane 1) or Rabex-5-shRNA (lane 2). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-Rabex-5 antibody (upper panel) and anti-actin antibody (lower panel). The asterisk indicates nonspecific bands. Note that the levelofexpressionofendogenousRabex-5inNeuro2AcellswasreducedinthepresenceofRabex-5-shRNA.D,shownisacomparisonoftheproteinexpression level of EGFP-Rabex-5SR and endogenous Rabex-5 in Neuro2A cells. Neuro2A cells were transfected with pEGFP-C1-Rabex-5SR (lane 2) or nothing (lane 1). Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-Rabex-5 antibody. The positions of the molecular mass markers (in kilodaltons) are shown on the left. Note that the expression level of EGFP-Rabex-5SR is approximately 5 times higher than that of endogenous Rabex-5 in Neuro2A cells. E and F, shown are typical images of EGFP-Rabex-5-expressing neurons in the presence and absence of Rabex-5-shRNA. At 3 DIV hippocampal neurons were transfected with a vector encoding control-shRNA or Rabex-5-shRNA together with EGFP-Rabex-5 and mStrawberry, and at 5 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green). Bar, 10 m. F, shown is quantification of the EGFP-Rabex-5 of the control-shRNA-transfected neurons (n  20) or Rabex-5-shRNA-transfected neurons (n  20) shown in E. a.u., arbitrary units. G and H, shown are typical images of Rab17 in the Rabex-5-shRNA-transfected neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding control-shRNA (G) or Rabex-5- shRNA (H), and at 14 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (blue). The arrows and arrowheads point to axons and dendrites, respectively. The bottom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. Rabex-5 Activates Rab17 in Hippocampal Neurons F, shown is quantification of the EGFP-Rabex-5 of the control-shRNA-transfected neurons (n  20) or Rabex-5-shRNA-transfected neurons (n  20) shown in E. a.u., arbitrary units. G and H, shown are typical images of Rab17 in the Rabex-5-shRNA-transfected neurons. At 4 DIV hippocampal neurons were transfected with a vector encoding control-shRNA (G) or Rabex-5- shRNA (H), and at 14 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green), Rab17 (black), and MAP2 (blue). The arrows and arrowheads point to axons and dendrites, respectively. The bottom three panels (a–c) are magnified views of the boxed areas in the top right panels. Bars, 10 m. I, shown is quantification of the proportion of Rab17 in the dendrites of control-shRNA-transfected neurons (n  20) and Rabex-5-shRNA- transfected neurons (n  20) shown in G and H. The proportion (%) of Rab17 in the dendrites was calculated by dividing the dendrite-specific Rab17 fluorescence intensity by the total Rab17 fluorescence intensity. Note that translocation of Rab17 to the dendrites was significantly reduced after knockdown of Rabex-5. **, p  0.0025. APRIL 5, 2013•VOLUME 288•NUMBER 14 APRIL 5, 2013•VOLUME 288•NUMBER 14 9841 JOURNAL OF BIOLOGICAL CHEMISTRY APRIL 5, 2013•VOLUME 288•NUMBER 14 Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 Activates Rab17 in Hippocampal Neurons morphogenesis. To pursue this possibility, we performed yeast two-hybrid assays with a panel of 60 different CA (GTP-locked) and CN (GDP-locked) Rabs to identify additional target Rabs of Rabex-5 (36). The results of the Rab-family-wide analysis showed that Rabex-5 specifically interacted with the CN forms of Rab5A/B/C, Rab17, and Rab21 (Fig. 7A), which was consist- ent with the known GEF activity of Rabex-5 in vitro (16, 18). In addition, the D313A mutation of Rabex-5 completely abro- gated the binding of Rabex-5 to Rab5A, Rab17, and Rab21 in yeast two-hybrid assays (Fig. 7B). Next, we investigated whether Rabex-5 also regulates the localization of Rab5 and Rab21, in addition to the localization of Rab17, in hippocampal neurons. The results showed that Rabex-5 knockdown resulted in a marked reduction in the proportions of Myc-tagged Rab5A, Rab17, and Rab21 that had been translocated to the dendrites (Myc-Rab5A, 34.7  5.2% reduction; Myc-Rab17, 57.6  4.6% reduction; Myc-Rab21, 49.8  5.1% reduction in comparison with the control) (Fig. 7C) and to the axon (Myc-Rab5A, 55.5  8.8% reduction; Myc-Rab21, 84.2  1.6% reduction in compar- ison with the control) (Fig. 7D). These results indicated that Rabex-5 also functions as an upstream regulator of Rab5 and Rab21. Rabex-5 Regulates Dendrite and Axon Morphogenesis of Hip- pocampal Neurons—Because we previously showed that Rab17 specifically regulates dendrite morphogenesis of hippocampal neurons, we proceeded to investigate the involvement of Rabex-5 in neurite morphogenesis of hippocampal neurons. In contrast to the knockdown of Rab17, however, Rabex-5 knock- down resulted in a marked reduction in the total dendrite length, total axon length, and number of axon branches (to 72.3  8.3, 61.8  5.7, and 76.9  7.7%, respectively, of the control), but it had no effect on the number of dendrite branches (Fig. 6, A–E). These effects could not have been caused by an off-target effect of shRNA, because the reduction in the total dendrite length in Rabex-5 knockdown neurons (to 69.0  5.7% of the control) was completely rescued by re-ex- pression of shRNA-resistant Rabex-5SR (Fig. 5, B and D) (to 129.5  10.1% of the control neurons) but not of a GEF activity- deficient Rabex-5SR-D313A mutant (Fig. 6F). Moreover, we found that the reduction in total dendrite length of the Rabex-5 knockdown neurons was partially rescued by co-expression of Rab17-Q77L, i.e. forced activation of Rab17 (to 89.0  5.9% of the control) (Fig. Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 Is Required for Translocation of Rab17 to the Den- drites of Hippocampal Neurons—To determine whether endogenous Rabex-5 protein also regulates the dendritic localization of Rab17 in hippocampal neurons, we evaluated the impact of knockdown of endogenous Rabex-5. First, we investigated whether Rabex-5 is actually expressed in cul- tured mouse hippocampal neurons by immunoblotting with a specific antibody against Rabex-5. As shown in Fig. 5A, endogenous Rabex-5 protein was easily detected in cultured hippocampal neurons, and the level of Rabex-5 protein seemed to peak at 7–14 DIV. We then knocked down Rabex-5 with a specific shRNA, Rabex-5-shRNA (Fig. 5, B and C), which dramatically decreased the protein expression level of EGFP-Rabex-5 (77.2  3.0% reduction in compari- son with the control) in hippocampal neurons (Fig. 5, E and F). We found that Rabex-5 knockdown resulted in a marked reduction in the proportion of Rab17 that had been translo- cated to the dendrites of the hippocampal neurons at 14 DIV (22.9  1.9% of endogenous Rab17 in the dendrites of the control neurons versus 15.3  2.2% of endogenous Rab17 in the dendrites of the Rabex-5 knockdown neurons) (Fig. 5, G–I). These results enabled us to conclude that Rabex-5 is required for the translocation of Rab17 to the dendrites of hippocampal neurons. NAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 9842 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 14•APRIL 5, 2013 9842 VOLUME 288•NUMBER 14•APRIL 5, 2013 Rabex-5 Activates Rab17 in Hippocampal Neurons 6F), indicating that Rabex-5 contributes to Rab17-mediated dendrite outgrowth. Because knockdown of Rabex-5 did not affect the number of dendrite branches, we next investigated the possible involve- ment of ALS2, another GDP-Rab17-binding protein (Fig. 1), in dendrite branching by knocking down its expression with a spe- cific shRNA (Fig. 6, G–I). Although the ALS2-shRNA we pre- pared dramatically decreased the protein expression level of EGFP-ALS2 in the hippocampal neurons (80.7  1.5% reduc- tion in comparison with the control) (Fig. 6H), neither knock- down of ALS2 alone nor double knockdown of Rabex-5 and ALS2 affected the number of dendrite branches of hippocampal neurons (Fig. 6J). The same results were obtained with two independently prepared ALS2-shRNAs (data not shown). Based on these findings, ALS2 is unlikely to regulate Rab17- mediated dendrite branching. Rab5 and Rab17 Regulate Neurite Morphogenesis of Hip- pocampal Neurons Differently—Last, we investigated the in- volvement of Rab5A/B/C and Rab21, other putative downstream targets of Rabex-5, in neurite morphogenesis of hippocampal neurons by using specific shRNAs (Fig. 8, A–D). Consistent with our previous finding (21), knockdown of Rab17 resulted in a marked reduction in both total dendrite length and the num- ber of dendrite branches (to 39.7  4.4 and 47.4  3.1%, respec- tively, of the control) (Fig. 8, E and F), but total axon length and the number of axon branches were unaffected (Fig. 8, G and H). By contrast, knockdown of all three Rab5 isoforms (Rab5A/ B/C) resulted in a marked reduction in total dendrite length, the number of dendrite branches, total axon length, and the num- ber of axon branches (to 53.7  7.0, 49.7  5.2, 41.8  5.0, and 64.3  6.0%, respectively, of the control) (Fig. 8, E–H). Interest- ingly, however, knockdown of Rab21 did not reduce total neu- rite length or the total number of neurite branches (Fig. 8, E–H). The same results were obtained when we used another site of Rab21-shRNA (data not shown). These results indicated that Rab5 and Rab17, but not Rab21, are likely to function as down- Rabex-5 Is Also Required for the Neuritic Localization of Rab5 and Rab21 in Hippocampal Neurons—Different contributions of Rabex-5 and Rab17 to neurite morphogenesis (i.e. Rabex-5 to dendrite outgrowth and axon morphogenesis and Rab17 to dendrite morphogenesis) suggests that Rabex-5 activates other Rab family proteins besides Rab17 during the course of neurite FIGURE 6. FIGURE 6. Rabex-5 regulates axon and dendrite morphogenesis in hippocampal neurons. A, shown are typical images of Rabex-5 knockdown neurons. At 4DIVhippocampalneuronsweretransfectedwithavectorencodingEGFPandcontrol-shRNA(upperpanels)orRabex-5-shRNA(lowerpanels),andat11DIVthe neurons were fixed and subjected to immunocytochemistry with antibodies against GFP, neurofilament-H (an axon marker; red), and MAP2 (blue). The arrows and arrowheads point to axons and dendrites, respectively. Bar, 50 m. B–E, shown is quantification of the total dendrite length (B), total dendrite branching tipnumbers(C),totalaxonlength(D),andtotalaxonbranchingtipnumbers(E)ofthecontrolneurons(n20),andRabex-5knockdownneurons(n20).Note that the total dendrite length, total axon length, and total axon branching tip numbers of the Rabex-5 knockdown neurons were significantly lower than in the control cells. **, p  0.0025. F, shown is quantification of the total dendrite length of the control neurons (n  32), Rabex-5 knockdown neurons (n  35), EGFP-Rabex-5SR-expressing Rabex-5 knockdown neurons (n  32), EGFP-Rabex-5-D313ASR-expressing Rabex-5 knockdown neurons (n  34), and EGFP- Rab17-Q77L-expressing Rabex-5 knockdown neurons (n  35). Note that the reduction in total dendrite length of the Rabex-5 knockdown neurons was rescued by re-expression of Rabex-5SR or by expression of Rab17-Q77L. **, p  0.0025; *, p  0.025. G, shown are typical images of EGFP-ALS2-expressing neurons in the presence and absence of ALS2-shRNA. At 3 DIV hippocampal neurons were transfected with a vector encoding control-shRNA or ALS2-shRNA together with EGFP-ALS2 and mStrawberry, and at 5 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green). Bar, 10 m. H, shown is quantification of the EGFP-ALS2 of control-shRNA-transfected neurons (n  20) and Rabex-5-shRNA-transfected neurons (n  20) shown in G. a.u., arbitrary units. I, COS7 cells were transfected with a vector encoding EGFP-ALS2 together with control-shRNA or ALS2-shRNA. Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-GFP antibody (upper panel) and anti-actin antibody (lower panel). The positions of the molecular mass markers (in kilodaltons) are shown on the left. J, shown is quantification of the total dendrite branching tip numbers of the control neurons (n  20), ALS2 knockdown neurons (n  20), Rabex-5 knockdown neurons (n  20), and Rabex-5 and ALS2 double-knockdown neurons (n  20). Note that the total dendrite branching tip numbers of neither the ALS2 knockdown neurons nor the Rabex-5 and ALS2 double-knockdown neurons were altered in comparison with the control neurons. DISCUSSION We previously showed that Rab17 regulates dendrite mor- phogenesis and postsynaptic development of hippocampal neurons (21). However, the spatiotemporal regulation of Rab17 activation remained completely unknown, because no Rab17- GEF that functions in hippocampal neurons had been identi- fied. In the present study we succeeded in identifying Rabex-5 and ALS2 as candidate Rab17-GEFs by means of yeast two- hybrid assays (Fig. 1A). Several lines of evidence indicated that Rabex-5, but not ALS2, is likely to function as a Rab17-GEF in mouse hippocampal neurons: (i) overexpression of the GEF domain of Rabex-5, but not of ALS2, in hippocampal neurons promoted the dendritic localization of Rab17 (Figs. 3 and 4), (ii) knockdown of endogenous Rabex-5, but not of ALS2, in hip- pocampal neurons decreased the dendritic localization of Rab17 (Fig. 5, H and I), (iii) the total dendrite length of Rabex-5 knockdown neurons was partially restored by forced activation of Rab17, i.e. expression of Rab17-Q77L (Fig. 6F). Based on our findings together with the previous report that Rabex-5 exhib- ited Rab17-GEF activity in vitro (16), we concluded that Rabex-5 is an upstream activator of Rab17 in mouse hippocam- pal neurons. FIGURE7.Rabex-5promotestranslocationofRab5andRab21totheaxon and dendrites of hippocampal neurons. A, shown is Rab binding specificity of Rabex-5 as revealed by yeast two-hybrid panels. Yeast cells containing pGBD plasmid expressing CA or CN mutants of Rab (positions indicated in the left panels) and pGAD plasmid expressing Rabex-5-C protein were streaked on SC-AHLW and incubated at 30 °C for 1 week. Positive patches are boxed. Note the specific interactions between Rabex-5-C and the CN (GDP-fixed) form of Rab5A, Rab5B, Rab5C, Rab17, and Rab21. B, yeast cells containing 9844 JOURNAL OF BIOLOGICAL CHEMISTRY However, Rabex-5 cannot be the sole Rab17-GEF in hip- pocampal neurons because the phenotypes of Rabex-5 knock- down neurons and Rab17 knockdown neurons differed with respect to dendrite branching (Figs. 6C and 8F), although both exhibited reduced total dendrite length (Figs. 6B and 8E). We speculate that Rab17 is differently activated by two GEFs, i.e. by Rabex-5 and by an as yet unidentified GEF, in the following manner; activation of Rab17 by Rabex-5 specifically regulates dendrite outgrowth, whereas activation of Rab17 by the as yet unidentified GEF promotes dendrite branching. One plausible candidate for the unidentified GEF is ALS2, which also binds the GDP-locked Rab17 (Fig. 1). However, the GEF domain of ALS2 was unable to promote dendritic localization of Rab17 in hippocampal neurons (Fig. pGBD plasmid expressing GDP-locked CN forms of Rab5A, Rab17, and Rab21 and pGAD plasmid expressing the VPS9 domain of Rabex-5 or of Rabex-5- D313A were streaked on an SC-LW plate (upper panels) or SC-AHLW plate (lower panels) and incubated at 30 °C. Note that the GEF activity-deficient Rabex5-D313A mutant completely abrogated the interaction with Rab5A, Rab17, and Rab21. C and D, shown is quantification of the proportions of Myc-Rab5A, Myc-Rab17, and Myc-Rab21 in the dendrites (C) and axon (D) of control shRNA-transfected neurons (n  20) and Rabex-5-shRNA-transfected neurons (n  20). At 4 DIV hippocampal neurons were transfected with a vector encoding control shRNA or Rabex-5-shRNA together with Myc-Rab5A, Myc-Rab17, or Myc-Rab21, and at 11 DIV the neurons were fixed and sub- jected to immunocytochemistry with antibodies against GFP, Myc, and MAP2. The proportions (%) of Myc-Rab5A, Myc-Rab17, and Myc-Rab21 in the axonanddendriteswerecalculatedbydividingtheaxon-ordendrite-specific Myc-RabsfluorescenceintensitybythetotalMyc-Rabsfluorescenceintensity. Note that translocation of Myc-Rab5A and Myc-Rab21 to the axon and den- drites was significantly reduced after knockdown of Rabex-5. **, p  0.0025. Rabex-5 Activates Rab17 in Hippocampal Neurons Rabex-5 regulates axon and dendrite morphogenesis in hippocampal neurons. A, shown are typical images of Rabex-5 knockdown neurons. At 4DIVhippocampalneuronsweretransfectedwithavectorencodingEGFPandcontrol-shRNA(upperpanels)orRabex-5-shRNA(lowerpanels),andat11DIVthe neurons were fixed and subjected to immunocytochemistry with antibodies against GFP, neurofilament-H (an axon marker; red), and MAP2 (blue). The arrows and arrowheads point to axons and dendrites, respectively. Bar, 50 m. B–E, shown is quantification of the total dendrite length (B), total dendrite branching tipnumbers(C),totalaxonlength(D),andtotalaxonbranchingtipnumbers(E)ofthecontrolneurons(n20),andRabex-5knockdownneurons(n20).Note that the total dendrite length, total axon length, and total axon branching tip numbers of the Rabex-5 knockdown neurons were significantly lower than in the control cells. **, p  0.0025. F, shown is quantification of the total dendrite length of the control neurons (n  32), Rabex-5 knockdown neurons (n  35), EGFP-Rabex-5SR-expressing Rabex-5 knockdown neurons (n  32), EGFP-Rabex-5-D313ASR-expressing Rabex-5 knockdown neurons (n  34), and EGFP- Rab17-Q77L-expressing Rabex-5 knockdown neurons (n  35). Note that the reduction in total dendrite length of the Rabex-5 knockdown neurons was rescued by re-expression of Rabex-5SR or by expression of Rab17-Q77L. **, p  0.0025; *, p  0.025. G, shown are typical images of EGFP-ALS2-expressing neurons in the presence and absence of ALS2-shRNA. At 3 DIV hippocampal neurons were transfected with a vector encoding control-shRNA or ALS2-shRNA together with EGFP-ALS2 and mStrawberry, and at 5 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP (green). Bar, 10 m. H, shown is quantification of the EGFP-ALS2 of control-shRNA-transfected neurons (n  20) and Rabex-5-shRNA-transfected neurons (n  20) shown in G. a.u., arbitrary units. I, COS7 cells were transfected with a vector encoding EGFP-ALS2 together with control-shRNA or ALS2-shRNA. Two days after transfection the cells were lysed and subjected to immunoblot analysis with anti-GFP antibody (upper panel) and anti-actin antibody (lower panel). The positions of the molecular mass markers (in kilodaltons) are shown on the left. J, shown is quantification of the total dendrite branching tip numbers of the control neurons (n  20), ALS2 knockdown neurons (n  20), Rabex-5 knockdown neurons (n  20), and Rabex-5 and ALS2 double-knockdown neurons (n  20). Note that the total dendrite branching tip numbers of neither the ALS2 knockdown neurons nor the Rabex-5 and ALS2 double-knockdown neurons were altered in comparison with the control neurons. Rabex-5 Activates Rab17 in Hippocampal Neurons APRIL 5, 2013•VOLUME 288•NUMBER 14 9843 JOURNAL OF BIOLOGICAL CHEMISTRY APRIL 5, 2013•VOLUME 288•NUMBER 14 Rabex-5 Activates Rab17 in Hippocampal Neurons stream targets of Rabex-5 during neurite morphogenesis of hip- pocampal neurons. pGBD plasmid expressing GDP-locked CN forms of Rab5A, Rab17, and Rab21 and pGAD plasmid expressing the VPS9 domain of Rabex-5 or of Rabex-5- D313A were streaked on an SC-LW plate (upper panels) or SC-AHLW plate (lower panels) and incubated at 30 °C. Note that the GEF activity-deficient Rabex5-D313A mutant completely abrogated the interaction with Rab5A, Rab17, and Rab21. C and D, shown is quantification of the proportions of Myc-Rab5A, Myc-Rab17, and Myc-Rab21 in the dendrites (C) and axon (D) of control shRNA-transfected neurons (n  20) and Rabex-5-shRNA-transfected neurons (n  20). At 4 DIV hippocampal neurons were transfected with a vector encoding control shRNA or Rabex-5-shRNA together with Myc-Rab5A, Myc-Rab17, or Myc-Rab21, and at 11 DIV the neurons were fixed and sub- jected to immunocytochemistry with antibodies against GFP, Myc, and MAP2. The proportions (%) of Myc-Rab5A, Myc-Rab17, and Myc-Rab21 in the axonanddendriteswerecalculatedbydividingtheaxon-ordendrite-specific Myc-RabsfluorescenceintensitybythetotalMyc-Rabsfluorescenceintensity. Note that translocation of Myc-Rab5A and Myc-Rab21 to the axon and den- drites was significantly reduced after knockdown of Rabex-5. **, p  0.0025. DISCUSSION Note that the dendrite length and branching tip numbers of the Rab17 knockdown neurons were significantly lower than in the control cells, whereas the length and branching tip numbers of both the axon and dendrites of the Rab5A/B/C knockdown neurons were significantly lower than in the control cells. **, p  0.0025; *, p  0.025. Rabex 5 Activates Rab17 in Hippocampal Neurons FIGURE 8. Rab5 and Rab17, but not Rab21, are required for the control of neurite morphogenesis of hippocampal neurons. A–D, COS7 cells were transfected with a vector encoding FLAG-Rab5A together with control-shRNA or Rab5A-shRNA (A), FLAG-Rab5B/C together with control-shRNA or Rab5B/C- shRNA (B and C), or FLAG-Rab21 together with control-shRNA or Rab21-shRNA (D). Two days after transfection the cells were lysed and subjected to immuno- blot analysis with anti-FLAG tag antibody (upper panels) and anti-actin antibody (lower panels). The positions of the molecular mass markers (in kilodaltons) are shown on the left. The knockdown efficiency of each shRNA was also evaluated by expressing EGFP-Rab in hippocampal neurons (Rab5A-shRNA, 46.5  17.7% reduction of EGFP-Rab5A; Rab5B/C-shRNA, 69.0  9.5% reduction of EGFP-Rab5B and 84.4  2.7% reduction of EGFP-Rab5C; Rab17-shRNA, 78.8  7.8% reduction of EGFP-Rab17; Rab21-shRNA, 91.2  2.1% reduction of EGFP-Rab21 in comparison with the control shRNA). E–H, shown is quantification of the total dendrite length (E), total dendrite branching tip numbers (F), total axon length (G), and total axon branching tip numbers (H) of the control neurons (n  21), Rab17 knockdown neurons (n  20), Rab5A/B/C knockdown neurons (n  21), and Rab21-knockdown neurons (n  21). At 4 DIV hippocampal neurons were transfected with a vector encoding EGFP and control-shRNA, Rab17-shRNA, Rab5A-shRNA/Rab5B/C-shRNA, or Rab21-shRNA, and at 11 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP, neurofilament-H, and MAP2. Note that the dendrite length and branching tip numbers of the Rab17 knockdown neurons were significantly lower than in the control cells, whereas the length and branching tip numbers of both the axon and dendrites of the Rab5A/B/C knockdown neurons were significantly lower than in the control cells. **, p  0.0025; *, p  0.025. ent study (Figs. 6, D and E, and 8, G and H) indicated that Rab5 is the most likely target of Rabex-5 during axon morphogenesis of hippocampal neurons. DISCUSSION 3, D and E), and knockdown of ALS2 alone (or double knockdown of ALS2 and Rabex-5) in hippocampal neurons had no effect on the number of their dendrite branches (Fig. 6J), indicating that ALS2 is not involved in the dendrite branching step in hippocampal neurons. Although ALS2 does not contribute to dendrite outgrowth or FIGURE7.Rabex-5promotestranslocationofRab5andRab21totheaxon and dendrites of hippocampal neurons. A, shown is Rab binding specificity of Rabex-5 as revealed by yeast two-hybrid panels. Yeast cells containing pGBD plasmid expressing CA or CN mutants of Rab (positions indicated in the left panels) and pGAD plasmid expressing Rabex-5-C protein were streaked on SC-AHLW and incubated at 30 °C for 1 week. Positive patches are boxed. Note the specific interactions between Rabex-5-C and the CN (GDP-fixed) form of Rab5A, Rab5B, Rab5C, Rab17, and Rab21. B, yeast cells containing 9844 9844 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 14•APRIL 5, 2013 VOLUME 288•NUMBER 14•APRIL 5, 2013 Rabex-5 Activates Rab17 in Hippocampal Neurons FIGURE 8. Rab5 and Rab17, but not Rab21, are required for the control of neurite morphogenesis of hippocampal neurons. A–D, COS7 cells were transfected with a vector encoding FLAG-Rab5A together with control-shRNA or Rab5A-shRNA (A), FLAG-Rab5B/C together with control-shRNA or Rab5B/C- shRNA (B and C), or FLAG-Rab21 together with control-shRNA or Rab21-shRNA (D). Two days after transfection the cells were lysed and subjected to immuno- blot analysis with anti-FLAG tag antibody (upper panels) and anti-actin antibody (lower panels). The positions of the molecular mass markers (in kilodaltons) are shown on the left. The knockdown efficiency of each shRNA was also evaluated by expressing EGFP-Rab in hippocampal neurons (Rab5A-shRNA, 46.5  17.7% reduction of EGFP-Rab5A; Rab5B/C-shRNA, 69.0  9.5% reduction of EGFP-Rab5B and 84.4  2.7% reduction of EGFP-Rab5C; Rab17-shRNA, 78.8  7.8% reduction of EGFP-Rab17; Rab21-shRNA, 91.2  2.1% reduction of EGFP-Rab21 in comparison with the control shRNA). E–H, shown is quantification of the total dendrite length (E), total dendrite branching tip numbers (F), total axon length (G), and total axon branching tip numbers (H) of the control neurons (n  21), Rab17 knockdown neurons (n  20), Rab5A/B/C knockdown neurons (n  21), and Rab21-knockdown neurons (n  21). At 4 DIV hippocampal neurons were transfected with a vector encoding EGFP and control-shRNA, Rab17-shRNA, Rab5A-shRNA/Rab5B/C-shRNA, or Rab21-shRNA, and at 11 DIV the neurons were fixed and subjected to immunocytochemistry with antibodies against GFP, neurofilament-H, and MAP2. 4 Y. Mori and M. Fukuda, unpublished observations. REFERENCES 1. Fukuda, M. (2008) Regulation of secretory vesicle traffic by Rab small GTPases. Cell. Mol. Life Sci. 65, 2801–2813 23. Otomo, A., Hadano, S., Okada, T., Mizumura, H., Kunita, R., Nishijima, H., Showguchi-Miyata, J., Yanagisawa, Y., Kohiki, E., Suga, E., Yasuda, M., Osuga, H., Nishimoto, T., Narumiya, S., and Ikeda, J.-E. 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Cell 118, 607–617 In summary, we demonstrated that Rabex-5 functions as a Rab17-GEF that regulates Rab17 localization. We also showed that Rabex-5 and Rab5 are required for both axon morphogen- esis and dendrite morphogenesis. Based on our findings, we propose that Rabex-5 activates at least two distinct Rabs, Rab5 and Rab17, and that the activated Rabs cooperatively mediate dendritic morphogenesis of hippocampal neurons. 19. Hunziker, W., and Peters, P. J. (1998) Rab17 localizes to recycling endo- somes and regulates receptor-mediated transcytosis in epithelial cells. J. Biol. Chem. 273, 15734–15741 20. Zacchi, P., Stenmark, H., Parton, R. G., Orioli, D., Lim, F., Giner, A., Mell- man, I., Zerial, M., and Murphy, C. (1998) Rab17 regulates membrane trafficking through apical recycling endosomes in polarized epithelial cells. J. Cell Biol. 140, 1039–1053 21. Mori, Y., Matsui, T., Furutani, Y., Yoshihara, Y., and Fukuda, M. (2012) Small GTPase Rab17 regulates dendritic morphogenesis and postsynaptic development of hippocampal neurons. J. Biol. Chem. 287, 8963–8973 22. Horiuchi, H., Lippé, R., McBride, H. M., Rubino, M., Woodman, P., Sten- mark, H., Rybin, V., Wilm, M., Ashman, K., Mann, M., and Zerial, M. (1997) A novel Rab5 GDP/GTP exchange factor complexed to Rabaptin-5 links nucleotide exchange to effector recruitment and function. Cell 90, 1149–1159 Acknowledgments—We thank Megumi Aizawa for technical assist- ance and members of the Fukuda Laboratory for valuable discussions. DISCUSSION However, activation of Rab5 (and also Rab17) at the dendrite branching step is unlikely to be mediated by Rabex-5, because Rabex-5 is not involved in dendrite branching (Fig. 6C). Another type of Rab5-GEF, e.g. Rin (35), or Gapex-5/RME-6 (42) may be involved in this process. branching, it is still possible that ALS2 activates Rab17 at the spine, because Rab17 is required for postsynaptic development (21), and ALS2 has been reported to localize at the spine (37). At any rate, further extensive studies are necessary to determine whether ALS2 possesses in vitro Rab17-GEF activity and func- tions as a Rab17-GEF in hippocampal neurons. Because ALS2 was originally identified from ALS patients and hereditary spas- tic paraplegia (HPS) motor neuron disease patients (38–40), it will also be interesting to investigate the relationship between Rab17 and these diseases in motor neurons in the future. Although involvement of two other target Rabs, Rab21 and Rab22, in neurite outgrowth of PC12 cells has been reported (41, 43), knockdown of neither Rab21 nor Rab22A/B with spe- cific shRNAs had virtually any effect on neurite morphogenesis under our experimental conditions (Fig. 8, E–H).4 The lack of effect of our Rab21-shRNA is unlikely to be caused by insuffi- cient knockdown of Rab21, because the same shRNA strongly inhibited forskolin-induced dendrite formation of melano- cytes (44). In contrast to our finding, however, it has been Our findings also indicated that Rab17 is not the sole target of Rabex-5, because defects in axon morphogenesis were ob- served in Rabex-5 knockdown neurons alone (Figs. 6, D and E, and 8, G and H). 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Ataxin-3, The Spinocerebellar Ataxia Type 3 Neurodegenerative Disorder Protein, Affects Mast Cell Functions
Frontiers in immunology
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ORIGINAL RESEARCH published: 26 April 2022 doi: 10.3389/fimmu.2022.870966 Edited by: Frans J. Van Overveld, University College Roosevelt, Netherlands Reviewed by: Claudia Gonzalez-Espinosa, Centro de Investigacio´ n y de Estudios Avanzados del Instituto Polite´ cnico Nacional, Mexico Jiro Kitaura, J t d U i it J Reviewed by: Claudia Gonzalez-Espinosa, Centro de Investigacio´ n y de Estudios Avanzados del Instituto Polite´ cnico Nacional, Mexico Jiro Kitaura, *Correspondence: Jeannette Hübener-Schmid Jeannette.Huebener@med.uni- tuebingen.de Axel Lorentz lorentz@uni-hohenheim.de Specialty section: This article was submitted to Inflammation, a section of the journal Frontiers in Immunology Specialty section: This article was submitted to Inflammation, a section of the journal Frontiers in Immunology Received: 07 February 2022 Accepted: 23 March 2022 Published: 26 April 2022 Ataxin-3, The Spinocerebellar Ataxia Type 3 Neurodegenerative Disorder Protein, Affects Mast Cell Functions Anna S. Sowa 1, Eva Haas 2, Jeannette Hübener-Schmid 2* and Axel Lorentz 1* 1 Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany, 2 Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany 1 Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany, 2 Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease, is a progressive neurodegenerative disorder characterized by loss of neuronal matter due to the expansion of the CAG repeat in the ATXN3/MJD1 gene and subsequent ataxin-3 protein. Although the underlying pathogenic protein expansion has been known for more than 20 years, the complexity of its effects is still under exploration. The ataxin-3 protein in its expanded form is known to aggregate and disrupt cellular processes in neuronal tissue but the role of the protein on populations of immune cells is unknown. Recently, mast cells have emerged as potential key players in neuroinflammation and neurodegeneration. Here, we examined the mast cell-related effects of ataxin-3 expansion in the brain tissues of 304Q ataxin-3 knock-in mice and SCA3 patients. We also established cultures of mast cells from the 304Q knock-in mice and examined the effects of 304Q ataxin-3 knock-in on the immune responses of these cells and on markers involved in mast cell growth, development and function. Specifically, our results point to a role for expanded ataxin-3 in suppression of mast cell marker CD117/c-Kit, pro-inflammatory cytokine TNF-a and NF- kB inhibitor IkBa along with an increased expression of the granulocyte-attracting chemokine CXCL1. These results are the beginning of a more holistic understanding of ataxin-3 and could point to the development of novel therapeutic targets which act on inflammation to mitigate symptoms of SCA3. INTRODUCTION Received: 07 February 2022 Accepted: 23 March 2022 Published: 26 April 2022 Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), belongs to the group of neurodegenerative disorders known as polyglutamine (polyQ) disease associated with a polyQ expansion in the protein expressed by the corresponding causative gene (1). In SCA3, the polyQ-expanded protein is known as ataxin-3 and patients carry an expansion between 61 and 87 repeats on the affected allele resulting in the observed phenotype characterized by a disturbance of movement coordination (cerebellar ataxia), bulbar, pyramidal and extrapyramidal signs, and a possible occurrence of peripheral neuropathy or ophthalmoplegia (2). Currently, there is no cure or no therapy mitigating disease progression available for SCA3. Keywords: ataxin-3, MJD, SCA3, mast cell, cytokine, neurodegeneration, inflammation Generation of 304Q Ataxin-3 Knock-In Mice This study was carried out in strict accordance with the recommendations presented in the Guide for Care and Use of Laboratory Animals of the University of Tübingen, Germany. The protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Tübingen, Germany. Ataxin-3 knock-in C57Bl/6 mice with 304Q were generated using zinc finger technologies and providing a donor vector with (CAACAGCAG)48 as described (4). One out of three founders integrated up to 304 CAGs into the ataxin-3 gene. 304Q ataxin-3 knock-in mice used in the current study were either heterozygous or homozygous. Mouse housing and genotyping were described earlier (4). For qRT-PCR 3 mice per genotype at the age of 2 and 12 months and western blot analyses 4 mice per genotype were analyzed at the age of 3 and 12 months. Mast cells are important players in the immune system and exert their effects via expression and release of mediators involved in physiological functions of the body including innate and adaptive immune response, tissue healing, angiogenesis, and normal neuronal growth (5). The best-known activation of mast cells occurs during type I allergic reactions through crosslinking of immunoglobulin (Ig) E bound FcϵRI receptors by antigens. Degranulation occurs a few seconds after crosslinking and results in release of granules stored mediators attracting leukocytes such as eosinophils, neutrophils, or Th2 lymphocytes and increasing permeability of the blood vessels to allow immune cell passage (5, 6). In addition to the FcϵRI, mast cells express a variety of receptors such as other Fc receptors, receptors for chemokines and cytokines, or receptors for pathogen associated molecular patterns such as Toll-like receptors, all involved in mast cell activation and immune response (5, 6). In the last decade, mast cells have gained traction in their role in neurodegeneration. They are incredibly potent and considered the first responders able to initiate and magnify immune responses in the brain partly due to their capacity to access neuronal tissue and to affect the blood brain barrier (7). Although mast cells are important immune cells, their role in SCA3 remains to be discovered. It is still unclear if mast cells could play a pathogenic role as mediators of ataxin- 3 activity. Histological Analysis of Tissue Mast Cells Formalin-fixed tissue samples were embedded in paraffin. After deparaffinization and rehydration, 5 µM thick sections were stained with toluidine blue (Carl Roth, Karlsruhe, Germany) for visualization of mast cells. Generation of 304Q Ataxin-3 Knock-In Mice Mast cells were counted at 200- 400x magnification. Microscopic analysis was performed using AxioVision software (Carl Zeiss Microscopy, Jena, Germany). Abbreviations: ATXN3, ataxin-3 gene/protein; BMMC, bone marrow-derived mast cells; CD117, proto-oncogene c-KIT; ERK, extracellular signal-regulated kinases; LPS, lipopolysaccharide; NF-kB, nuclear factor kappa B; PMA, Phorbol- 12-myristat-13-acetat; SCA3, spinocerebellar ataxia type 3; MJD, Machado Joseph Disease; TNF-a, tumor necrosis factor alpha; IL, interleukin; DNP, 2,4- dinitrophenyl; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; CXCL, C- X-C motif chemokine ligand; WT, wild type. Citation: Sowa AS, Haas E, Hübener-Schmid J and Lorentz A (2022) Ataxin-3, The Spinocerebellar Ataxia Type 3 Neurodegenerative Disorder Protein, Affects Mast Cell Functions. Front. Immunol. 13:870966. doi: 10.3389/fimmu.2022.870966 April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org Ataxin-3 Affects Mast Cell Functions Sowa et al. Although in the 20 years since the discovery of the ataxin-3 protein large strides have been made to understand the cellular dysfunction underlying the disease such as, mitochondrial and autophagic disturbances, as well as the protein cleavage and aggregation (3), the full mechanisms behind neuronal death are still unknown. The newly developed 304Q ataxin-3 knock-in mouse model is an important promising tool to further reveal the pathologic effects of ataxin-3 expansion (4). These knock-in mice express 304Q instead of the 6Q normally present in either one or both of the murine ataxin-3 alleles. With twelve months of age these heterozygous and homozygous mice show a significant weight reduction compared to wild type (WT) mice. Despite a very mild motor phenotype, they already show massive SDS- insoluble ataxin-3 and ubiquitin-positive aggregates throughout the brain supporting a strong positive correlation between the polyQ expansion and a toxic function of ataxin-3 related to neurons (4). suppression of mast cell marker CD117/c-Kit, pro-inflammatory cytokine TNF-a and NF-kB inhibitor IkBa along with an increased expression of the granulocyte-attracting chemokine CXCL1. This is the first report to describe an immune cell phenotype for SCA3 and a mast cell-specific phenotype for neurodegenerative conditions. Western Blot Analysis Western blot analysis of BMMC was performed as described previously (11) and murine brain lysates as described in Haas et al. (4). Shortly, frozen brain tissue was homogenized in TES buffer (4% Tris Base pH 7.5, 0.1 mM EDTA, 100 mM Na2Cl) containing protease inhibitor complete EDTA-free protease inhibitor cocktail (Roche). Afterwards, TNES (TES-buffer plus 10% Igepal CA-630) was added in a relation of 1:10 and homogenates incubated on ice for 30 min. Homogenates were centrifuged at 13.200 g for 25 min at 4°C and to supernatants glycerol to a final concentration of 10% were added. For Western blot analyses, 4x LDS sample buffer (1 M Tris basepH8.5,2mMEDTA,8%LDS,40%glycerol,0.025%phenolred) and 100 mM 1,4-dithiothreitol (MerckMillipore) was added to 30 µg of protein lysates and heat-denatured at 70°C for 10 min. Protein samples were separated electrophoretically using 8% Bis-Tris gel and MOPS (50 mM MOPS, 50 mM Trisbase pH 7.3, 3.5 mM SDS, 1 mM EDTA) electrophoresis buffer. Proteins were transferred on 0.2 um nitrocellulose membrane (GE Healthcare) using a Bicine/Bis-Tris transfer buffer (25 mM Bicine, 25 mM Bis-Tris pH 7.2, 1 mM EDTA, 15% methanol). After membrane blocking with 5% skimmed milk powder (Sigma-Aldrich), membranes were incubated with the respective primary antibody at 4°C overnight. For visualization of proteins of brain lysates, membranes were incubated with fluorescence tagged secondary antibodies (IRdye 800CW goat anti- mouse IgG (H+L), LI-COR or IRdye 800CW goat anti-rabbit IgG (H +L) LI-COR) for 1.5 hours at room temperature and fluorescence signal detection was performed on the LI-COR ODYSSEY FC (LI- COR). Visualization of proteins of BMMC was performed by the secondary antibodies anti-mouse IgG or anti-rabbit IgG HRP-linked (Cell Signaling Technology®) and Super Signal® West Dura Extended Duration Substrate (Thermo Fisher Scientific, Waltham, MA). The obtained signals were measured by bioimaging analyzer (Alpha Innotech Corporation, San Leandro, CA). The membranes were stripped and used for a second or third staining. Membranes were probed with phospho-ERK (MAPK)-1/2 (12D4) mouse mAb, IkBa(44D4)rabbit mAb, CD117(D13A2)rabbitmAb(allfromCell Signaling Technology®, Frankfurt, Germany), TNF alpha (EPR19147) rabbit mAb (from Abcam), b-Actin (AC-15) mouse mAb (Sigma Aldrich), GAPDH (D-6) mouse mAb (from SantaCruz Biotechnology, Dallas, TX). b-Actin or GAPDH labeling was used as loading control for normalization. RNA Preparation and Real-Time RT-PCR For analysis of BMMC, total RNA was prepared by using EXTRACTME RNA isolation kit (7Bioscience, Hartheim, Germany). Generation and Culture of Bone Marrow- Derived Mast Cells (BMMC) G, mouse Cxcl1: 5’ TAG GGT GAG GAC ATG TGT G/5’ GCC CTA CCA ACT AGA CAC AA, mouse Sdha: 5’ GCA GCA CAG GGA GGT ATC A/5’ CTC AAC CAC AGA GGC AGG A, mouse Pdh: 5’ GTA GAG GAC ACG GGC AAG AT/5’ TGA AAA CGC CTC TTC AGC A, mouse mActb: 5’ CCA CAC CCG CCA CCA GTT CG/5’ TAC AGC CCG GGG AGC ATC GT, mouse Tbp: 5’ TCT ATT TTG GAA GAG CAA CAA AGA C/5’ GAG GCT GCT GCA GTT GCT A G, mouse Cxcl1: 5’ TAG GGT GAG GAC ATG TGT G/5’ GCC CTA CCA ACT AGA CAC AA, mouse Sdha: 5’ GCA GCA CAG GGA GGT ATC A/5’ CTC AAC CAC AGA GGC AGG A, mouse Pdh: 5’ GTA GAG GAC ACG GGC AAG AT/5’ TGA AAA CGC CTC TTC AGC A, mouse mActb: 5’ CCA CAC CCG CCA CCA GTT CG/5’ TAC AGC CCG GGG AGC ATC GT, mouse Tbp: 5’ TCT ATT TTG GAA GAG CAA CAA AGA C/5’ GAG GCT GCT GCA GTT GCT A Treatment and Analyses of BMMC To detect release of b-hexosaminidase, BMMC were loaded with 2,4-dinitrophenyl (DNP)-specific IgE for 90 min and stimulated with 0.1 µg/ml DNP (Thermo Fisher Scientific), for 90 min. To analyze phosphorylation status of signaling molecules, BMMC were stimulated with DNP/IgE or with 1 µM phorbol ester PMA and 1 µM ionomycin (In vivoGen, San Diego, USA) for 10 min or with 1 mg/ml lipopolysaccharide (LPS) from Escherichia coli 0111:B4 (Sigma-Aldrich, Munich, Germany) for 30 min. To analyze cytokine expression and release, BMMC were stimulated for 90 min or for 6 h and culture supernatants were tested by ELISA (R&D systems, MN) in accordance with the manufacturer’s instructions. Degranulation of BMMC was quantified by determining the amount of released b-hexosaminidase in the supernatant by color enzyme assay (9). The percent degranulation of mast cells was estimated by the following formula: (b-hexosaminidase activity in the supernatant fraction/total b-hexosaminidase activity in the cellular and supernatant fraction) ×100. Generation and Culture of Bone Marrow- Derived Mast Cells (BMMC) Bone marrow cells were collected from femurs of homozygous (304Q/304Q) and heterozygous (WT/304Q) 12 month old 304Q ataxin-3 knock-in and wild type (WT/WT) mice and cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum, penicillin/ streptomycin (Biochrom, Berlin, Germany), plus 30 ng/mL mouse IL-3 (PeproTech, Hamburg, Germany). Cells were cultured in 6 well plates, incubated at 37°C in a humidified incubator under 5% (v/v) CO2. Starting after 3 days, half of the medium was changed once a week every week. In addition, starting after 3 weeks, medium was changed completely once a week every week by transferring the non-adherent cells in fresh medium into a new plate. After culture for 9 weeks, cells were used for functional assays. For each genotype, several lines were generated. Maturity and purity of the BMMC were examined on cytospins stained with May-Grünwald/Giemsa (Carl Roth). We did not detect differences in the staining of pure BMMC from The role of ataxin-3 in cell autonomous inflammatory pathways is only beginning to be examined (8). Therefore, we analyzed the effects of ataxin-3 expansion in the brain tissues of the 304Q ataxin-3 knock-in mice and the cerebellar post-mortem brain tissue of SCA3 patients on markers involved in mast cell growth, development and function. For these studies, we also established cultures of mast cells from the 304Q ataxin-3 knock- in mice. Our results point to a role for expanded ataxin-3 in April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 2 Ataxin-3 Affects Mast Cell Functions Sowa et al. 304Q/304Q mice compared to BMMC from WT/WT mice (not shown). 304Q/304Q mice compared to BMMC from WT/WT mice (not shown). Western Blot Analysis Real-time RT-PCR was performed using SsoFastTM EVAGreen Supermix (Bio Rad Laboratories, Munich, Germany) and as described (10). To analyze data, a relative quantification method was performed by using the housekeeping gene of glyceraldehyde 3-phosphate dehydrogenase (Gapdh) or b-actin as a reference for expression of the target gene. The CFX Manager 2.1 software of BioRad Laboratories was used. For analysis of human and murine brain tissue, total RNA was prepared using AllPrep DNA/RNA/ microRNA Universal Kit (Qiagen, Hilden, Germany) as described earlier (4). 500 ng purified RNA was transcribed into cDNA using QuantiTect Reverse Transcription Kit (Qiagen) Real-time RT-PCR was performed using SYBR Green PCR Master Mix (Qiagen) as described. qRT-PCR was run on the LightCycler 480 II (Roche, Mannheim, Germany). Relative gene expression quantification was performed by normalization to the housekeeping genes Sdha, Pdh, mActb and Tbp using LightCycler 480 SW 1.5.1 software (Roche). Specific sense/anti-sense primers: human ACTB: 5’ AAA GAC CTG TAC GCC AAC AC/5’ CTC AGG AGG AGC AAT GAT CT, human CD117: 5’ GCC CAA TAT AAA AGG CAA AT/5’ AGT GCA AAT GGT TAC TTC CA, human IL-3RA: 5’ CCT CCT TTG GCT CAC GCT G/5’ GCC CAC TCG GAC GGT GTA G, human TNF: 5’ CAG ATA GAT GGG CTC ATA CCA GGG/5’ GCC CTC TGG CCC AGG CAG TCA G, human CXCL8: 5’ CTG AGA GTG ATT GAG AGT GG/5’ ACA ACC CTC TGC ACC CAG TT, mouse Gapdh: 5’ TGT TCC TAC CCC CAA TGT GT/5’ AGA GTG GGA GTT GCT GTT GA, mouse Cd117: 5’ CTG GTG GTT CAG AGT TCC ATA GAC/5’ TCA ACG ACC TTC CCG AAG G, mouse Il-3ra chain: 5’ TGG AGG AAG TCG CTG CTC TA/5’ CGT CAC CTC GCA GTC TTC AA, mouse Tnf: 5’ GGA GGC AAC AAG GTA GAG/5’ TGT CCA TTC CTG AGT TCT 304Q Ataxin-3 Modulates Cytokine Release by BMMC BMMC from 12-month-old 304Q ataxin-3 knock-in mice were stimulated with either IgE/DNP or ionomycin/PMA for 90 min and the release of pre-stored b-hexosaminidase as marker of degranulation was measured (Figure 3D). In both cases the stimulated BMMC demonstrated robust degranulation; however, there was no difference between the responses of BMMC from 304Q ataxin-3 knock-in mice compared to WT/WT mice demonstrating that the expanded 304Q ataxin-3 did not influence the capacity of BMMC to degranulate (Figure 3D). In order to demonstrate the relevance of our findings in the SCA3 mouse model to human disease, we tested the expression of IL3RA, TNF and CXCL8 in the post-mortem brain tissues of human SCA3 patients. Noteworthy, we found a tendency towards an increased expression of CXCL8 associated with a significantly decreased expression of CD117 compared to controls consistent with our observations in 304Q ataxin-3 knock-in mice (Figure 1E). To confirm the findings for gene expression on protein level, we analyzed the expression of CD117 and TNF-a in brain tissues by Western blot. A significant down-regulation of both CD117 and TNF-a was detected in the 12-month-old 304Q/304Q and WT/304Q mice compared to WT/WT mice (Figure 2). We have not established mast cell staining in the available brain tissues, but we have stained mast cells in intestinal tissues. There was a trend towards lower mast cell numbers in duodenal and jejunal tissues of 304Q/304Q ataxin-3 knock-in mice compared to WT controls (Supplementary Figure S1). To analyze the release of de novo synthesized cytokines, BMMC from 12-month-old 304Q ataxin-3 knock-in mice were stimulated with either IgE/DNP, ionomycin/PMA, or LPS for 6 h. The amount of released TNF-a protein measured by ELISA showed a strong decrease upon ionomycin/PMA stimulation inBMMC from304Q/ 304Q mice compared to WT/WT mice (Figure 3F) in agreement with the gene expression data. The release of CXCL1 also correlated to the measured mRNA levels, with a strong increase in CXCL1 levels in BMMC from 304Q/304Q mice (Figure 3G). 304Q Ataxin-3 Modulates Activation of NF-kB Signaling Pathway in BMMC Further, we aimed to analyze the signaling pathways altered in BMMC from 304Q ataxin-3 knock-in 3 mice compared to BMMC from WT/WT mice to observe which proteins could be responsible for the transcriptional changes in cytokine production. We analyzed two main signaling pathways Brain Tissues of 304Q Ataxin-3 Knock-In Mice and Post-Mortem SCA3 Patients Show an Effect of Expanded Ataxin-3 on the Expression of Mast Cell Markers and Inflammatory Cytokines In ordertoelucidate theeffectsof polyglutamineexpansion of ataxin- 3onmastcellswechosetoanalyzethemRNAexpressionlevelsofthe mast cell markers CD117/c-Kit and IL-3 receptor a-chain (IL-3Ra) using 304Q ataxin-3 knock-in mice. The 304Q ataxin-3 knock-in mouse model represents the human patient phenotype on a neuropathological, behavioral, and transcriptomic levels in a more complete manner than any existing SCA3 mouse. CD117 is a mast/ stem cell receptor for growth factor SCF important in the mast cell development and function, while IL-3R is a potent receptor involved inthestimulationofmastcellgrowthinresponsetoIL-3producedby activatedTcells(12).Therewasbothasignificantdown-regulationof Cd117 expression and a significant up-regulation of mKc/Cxcl1 expression in the brains of 12-month-old 304Q/304Q and WT/ 304Q mice compared to WT/WT mice (Figures 1B, D). Also, the brains of 304Q ataxin-3 knock-in mice were tested for expression of the cytokine gene Tnf and the chemokine mKc/Cxcl1. Tnf is well known to participate in an acute inflammation and mKc/Cxcl1 (homologue to human IL-8/CXCL8) is involved in pro- inflammatory chemotaxis of mast cells. The Cxcl1 expression was reliably increased, but no changes in the levels of Tnf expression were detected in 304Q ataxin-3 knock-in mice relative to WT/WT mice. ThehousekeepinggenesSdha,Pdh,mActb,andTbpwerenotaffected (Figures 1A, C). Expression levels of Cd117, Tnf and Cxcl1 mRNA were determined before and after stimulation of BMMC with IgE/2,4- dinitrophenyl (DNP), ionomycin/phorbol-12-myristat-acetate (PMA) or lipopolysaccharide (LPS). The Cd117 expression was strongly reduced in BMMC from homozygous and, to a lesser extent, heterozygous 304Q ataxin-3 knock-in mice compared to cells from WT/WT mice (Figure 3A). This finding could be confirmed on protein level by Western blot, which showed a significantly lower expression of CD117 in BMMC from 304Q/ 304Q ataxin-3 knock-in compared to cells from WT/WT mice (Figure 3E). Tnf expression in response to ionomycin/PMA stimulation was substantially reduced in cells from 304Q/304Q and WT/304Q micecompared to WT/WT controls (Figure 3B).In contrast, a marked increase of mRNA expression for the proinflammatory chemokine gene Cxcl1 was detected in BMMC from 304Q/304Q mice relative to WT/WT mice in response to LPS stimulation (Figure 3C).These observations are inaccordancewith our findings in mouse and human SCA3 brain tissues. RESULTS ataxin-3 knock-in the presence of IL-3 for 6 weeks resulted in 71 ± 9.5% mature BMMC compared to 91 ± 1.3 and 97 ± 2% from WT/WT or WT/304Q mice, respectively. Pure BMMC were found in all cases following 9 weeks of culture. Recovery was 406 ± 159% of BMMC from WT/WT mice compared to 234 ± 33% and 225 ± 82% of BMMC from WT/304Q or 304Q/304Q ataxin-3 knock-in mice. No differences concerning size and degree of granulation were observed between mature BMMC derived from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. Statistics Data expressed as mean ± SEM. Unpaired t-test was used to analyze differences between two groups. Two-way analysis of variance was used to analyze differences between genotypes and stimulation conditions with Bonferroni multiple comparisons. A value of p < 0.05 was considered to be statistically significant. April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 3 Ataxin-3 Affects Mast Cell Functions Sowa et al. 304Q Ataxin-3 Modulates Activation of NF-kB Signaling Pathway in BMMC Further, we aimed to analyze the signaling pathways altered in BMMC from 304Q ataxin-3 knock-in 3 mice compared to BMMC from WT/WT mice to observe which proteins could be responsible for the transcriptional changes in cytokine production. We analyzed two main signaling pathways Next, we aimed to analyze the effect of ataxin-3 directly in mast cells. Thus, we generated cultures of BMMC from the 12-month- old WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. Interestingly, culturing bone marrow cells from 304Q/304Q April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org Sowa et al. Ataxin-3 Affects Mast Cell Functions A B D E C FIGURE 1 | Expression of Il-3ra, Cd117, Tnf, and Cxcl1/mKc as well as the housekeeping genes Sdha, Pdh, mActb and Tbp mRNA in brain tissue from 2-month- old (A, B) and from 12-month-old (C, D) WT/WT, WT/304Q, and 304Q/304Q ataxin-3 knock-in mice. Unpaired t test shows statistically significant differences, n = 3, Values are mean ± SEM, *p < 0.05, **p < 0.01. Expression of CD117, IL-3RA, TNF, and CXCL8 mRNA in cerebellar brain tissue of SCA3 patients normalized using b-actin (E). Total RNA was extracted, reverse-transcribed and analyzed by quantitative real-time PCR, n = 4-6. Values are mean ± SEM, p values were calculated by unpaired t-test, *p < 0.05. A C A C B D B D D E E E FIGURE 1 | Expression of Il-3ra, Cd117, Tnf, and Cxcl1/mKc as well as the housekeeping genes Sdha, Pdh, mActb and Tbp mRNA in brain tissue from 2-month- old (A, B) and from 12-month-old (C, D) WT/WT, WT/304Q, and 304Q/304Q ataxin-3 knock-in mice. Unpaired t test shows statistically significant differences, n = 3, Values are mean ± SEM, *p < 0.05, **p < 0.01. Expression of CD117, IL-3RA, TNF, and CXCL8 mRNA in cerebellar brain tissue of SCA3 patients normalized using b-actin (E). Total RNA was extracted, reverse-transcribed and analyzed by quantitative real-time PCR, n = 4-6. Values are mean ± SEM, p values were calculated by unpaired t-test, *p < 0.05. involved in mast cell cytokine expression, the MAPK pathway ERK1/2 and the NF-kB pathway. and the immune system (13). Since the discovery of the polyQ- expanded ataxin-3 in patients with SCA3 (1) it was reported that this protein causes a complex pattern of gene expression changes in transgenic SCA3 cell lines and human SCA3 pontine neurons (14). 304Q Ataxin-3 Modulates Activation of NF-kB Signaling Pathway in BMMC Various molecular mechanisms have been proposed to explain the toxic function of polyQ expansion, including dysregulation of transcription, impairment of the ubiquitin– proteasome system, mitochondrial dysfunction, dysregulation of intracellular Ca2+ homeostasis, impairment of axonal transport and genotoxic stress (15). These single-cause hypotheses are not entirely satisfactory and, taken together, indicate that the disease pathogenesis might not be exclusive to one particular structure or dysfunction. Therefore, further We did not observe significant differences in phosphorylation of ERK1/2 (Figure 4A). However, we found a significant increase of the NF-kB inhibitor IkBa in BMMC from homozygous 304Q/ Q304 ataxin-3 knock-in mice (Figure 4B). The increase of IkBa could be responsible for a decreased expression of TNF-a as a consequence of a decreased NF-kB activity. DISCUSSION Ataxin-3, a causative protein of SCA3, is ubiquitously expressed throughout different organs, tissues and cells, including the brain April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 5 Ataxin-3 Affects Mast Cell Functions Sowa et al. A B FIGURE 2 | CD117 and TNF-a are down-regulated in cerebellar brain tissue of 304Q/304Q ataxin-3 knock-in mice. Protein levels of CD117 (A) and TNF-a (B) in relation to b-actin in brain tissue from 3-month-old and from 12-month-old WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. Unpaired t test shows statistically significant differences, n = 4. Values are mean ± SEM, *p < 0.05, ***p < 0.001. A B B FIGURE 2 | CD117 and TNF-a are down-regulated in cerebellar brain tissue of 304Q/304Q ataxin-3 knock-in mice. Protein levels of CD117 (A) and TNF-a (B) in relation to b-actin in brain tissue from 3-month-old and from 12-month-old WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. Unpaired t test shows statistically significant differences, n = 4. Values are mean ± SEM, *p < 0.05, ***p < 0.001. studies are required to evaluate the implications of a polyQ expansion in SCA3 toxicity. and heterozygous 304Q ataxin-3 knock-in mice. In agreement with the brain data, expression levels of CD117 in BMMC from 304Q ataxin-3 knock-in mice were reduced compared to cells from WT/WT mice in stimulated and unstimulated cells. We conclude that mast cells are negatively regulated by the expanded ataxin-3. Analyses of post-mortem brain samples from the SCA3 patients corroborate this conclusion. Mast cells were recently implicated as agents of neurodegeneration in several disease (16). Mast cells are potent activators and regulators of the peripheral immune system with access to neuronal tissue. They are able to affect the blood-brain barrier and thus could be involved in CNS pathology. Mast cells are involved in a multitude of conditions including cancer, allergy, psoriasis, multiple sclerosis, Parkinson’s disease, stroke, autism, migraines, sleep disorders, stress and inflammation (17). Brain mast cells are crucial mediators of sleep and fundamental neurobehavior which are all involved in ataxia and similar neurodegenerative disorders (18). p Consistently, we found that maturation of BMMC from 304Q/304Q ataxin-3 knock-in mice takes longer than from homozygous WT and heterozygous 304Q ataxin-3 knock-in mice. However, these findings need to be confirmed in future studies by more quantitative techniques such as flow cytometry or transmission electron microscopy. Frontiers in Immunology | www.frontiersin.org DISCUSSION FIGURE 3 | Expression of Cd117 and Tnf is down-regulated and expression of Cxcl1 is upregulated in BMMC from 304Q/304Q ataxin-3 knock-in mice. Cd117 (A), Tnf (B), and Cxcl1 (C) mRNA levels were determined following stimulation of BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice with IgE/DNP, ionomycin/PMA or LPS for 90 min. Release of b-hexosaminidase (b-Hex) (D) as a marker of degranulation was measured following stimulation with IgE/DNP or ionomycin/ PMA. Protein levels of CD117 in relation to GAPDH were measured in BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice (E). Release of cytokines TNF-a (F) and CXCL1 (G) in supernatants of BMMC from 304Q ataxin-3 knock-in mice were measured following stimulation with IgE/DNP, ionomycin/PMA or LPS for 6h Unpaired t test (E) and two-way ANOVA (A–D, F, G) show statistically significant differences, n = 3-5. Values are mean ± SEM, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. The best-known activation of mast cells occurs during type-I allergic reactions through crosslinking of IgE bound to FcϵRI receptors by antigens (6). However, no effect of 304Q ataxin-3 on degranulation was found in our experiments with BMMC judging by the amounts of released b-hexosaminidase following stimulation with IgE/DNP or ionomycin/PMA. We conclude that the mast cell signaling involved in degranulation is not targeted by the expanded ataxin-3. including cell proliferation, gene activation or cell death (22). The intracellular signaling pathways induced by this cytokine in SCA3 along with the role of ataxin-3 are only beginning to be examined (8). In contrast to CD117 and TNF-a, the mRNA and protein levels of CXCL1 were found stimulated by the expanded ataxin-3 both in the brains and BMMC. Mast cells, like macrophages, have the capacity to newly synthesize CXCL1, making detectable amounts within 1 hour of LPS treatment (23). CXCL1 is a mouse homologue to human IL-8/CXCL8 involved in a number of pro- inflammatory activities, including the chemotaxis of neutrophils to the site of injury thereby aggravating the ongoing inflammatory response. CXCL1 is also shown to display a neuroprotective function (24). Future work will reveal the specific role for the mast cell-released CXCL1 stimulation in response to expanded ataxin-3 in the mechanism of SCA3. DISCUSSION Furthermore, the cell recovery/proliferation of pure mature BMMC from 304Q/304Q ataxin-3 knock-in mice was lower compared to BMMC from WT controls. Interestingly, expression of mutant huntingtin, the disease protein in Huntington´s disease (HD), was also shown to affect maturation of BMMC (20). This finding combined with our observation suggests a significant impairment in mast cells maturation in polyQ-associated neurodegenerative conditions such as SCA3 and HD. In this study we evaluated the hypothesis of mast cell contribution to SCA3. For this purpose, we tested the mRNA and protein expression levels of the inflammatory mast cell marker CD117/c-Kit and IL-3Ra in the brains of normal and 304Q ataxin-3 knock-in mice. CD117/c-Kit signaling network plays an important role in several cell functions including proliferation, survival, apoptosis, motility, adhesion and angiogenesis (19). We found that the expression of CD117, but not of IL-3Ra, was reduced in comparison with healthy controls. In order to analyze the effect of expanded ataxin-3 directly in mast cells we established the BMMC cultures from homozygous In general, mast cells exert their effects via expression and release of mediators involved in physiological functions of the body through the intracellular activation of tyrosine kinases (5). April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 6 Sowa et al. Ataxin-3 Affects Mast Cell Functions A B D E F G C FIGURE 3 | Expression of Cd117 and Tnf is down-regulated and expression of Cxcl1 is upregulated in BMMC from 304Q/304Q ataxin-3 knock-in mice. Cd117 (A), Tnf (B), and Cxcl1 (C) mRNA levels were determined following stimulation of BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice with IgE/DNP, ionomycin/PMA or LPS for 90 min. Release of b-hexosaminidase (b-Hex) (D) as a marker of degranulation was measured following stimulation with IgE/DNP or ionomycin/ PMA. Protein levels of CD117 in relation to GAPDH were measured in BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice (E). Release of cytokines TNF-a (F) and CXCL1 (G) in supernatants of BMMC from 304Q ataxin-3 knock-in mice were measured following stimulation with IgE/DNP, ionomycin/PMA or LPS for 6h Unpaired t test (E) and two-way ANOVA (A–D, F, G) show statistically significant differences, n = 3-5. Values are mean ± SEM, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. Frontiers in Immunology | www.frontiersin.org DISCUSSION g g y Along with the reduced expression of CD117, we detected a suppressive effect of expanded ataxin-3 on the mRNA and protein expression of the proinflammatory TNF-a both in the cerebellar brain regions and supernatants of ionomycin/PMA- stimulated BMMC. TNF-a expression in response to FcϵRI cross-linking was low compared to ionomycin/PMA stimulation. This may be due to different time courses and the strength of the ionomycin/PMA stimulation which skips receptor-mediated signals and directly induces PKC phosphorylation and calcium concentration elevation, respectively (21). TNF-a is a pleiotropic cytokine. Activation of signaling by TNF-a initiates a variety of potential outcomes, The modulation of transcription of TNF-a and CXCL1 in BMMC expressing the expanded 304Q ataxin-3 compared to the healthy controls prompted us to test if this process involves NF- kB which is a protein complex that controls transcription, April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 7 Ataxin-3 Affects Mast Cell Functions Sowa et al. A B FIGURE 4 | ERK1/2 and NF-kB signaling in BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. (A) BMMC from WT/WT, WT/304Q, and 304Q/ 304Q ataxin-3 knock-in mice stimulated or unstimulated with IgE/DNP, ionomycin/PMA or LPS for 10 min. Supernatants of BMMC cultures were analyzed by Western blot for ERK1/2 phosphorylation (A) and IkBa (B) relative to GAPDH. Representative pictures and densitometric analyses as integrated density values (IDV) are shown. Unpaired t test shows statistically significant differences, n = 3. Values are mean ± SEM, *p < 0.05. B FIGURE 4 | ERK1/2 and NF-kB signaling in BMMC from WT/WT, WT/304Q, or 304Q/304Q ataxin-3 knock-in mice. (A) BMMC from WT/WT, WT/304Q, and 304Q/ 304Q ataxin-3 knock-in mice stimulated or unstimulated with IgE/DNP, ionomycin/PMA or LPS for 10 min. Supernatants of BMMC cultures were analyzed by Western blot for ERK1/2 phosphorylation (A) and IkBa (B) relative to GAPDH. Representative pictures and densitometric analyses as integrated density values (IDV) are shown. Unpaired t test shows statistically significant differences, n = 3. Values are mean ± SEM, *p < 0.05. ataxin-3 could be via the U-box E3 ligase CHIP, which has been identified as a direct interaction partner of ataxin-3. Thereby, ataxin-3 and CHIP interact and regulate each other’s activity (28). On the other side, CHIP was shown to promote the activation of NF-kB signaling (30). DISCUSSION Additionally, an siRNA- based drug screen in mammalian cells expressing expanded ataxin-3 identified 15 genes which are related to TNF/NF-kB and ERK1/2 pathways and concluded that expanded ataxin-3 can be regulated by these pro-inflammatory and cell death/survival pathways (31). Moreover, ataxin-3 may be involved in deubiquitination of several signaling molecules and it is hard to predict how expanded ataxin-3 may affect certain modifications and thus the behavior or fate of such proteins. cytokine/chemokine production and cell survival. NF-kB is found in almost all animal cell types and is involved in cellular responses to diverse stimuli. Canonically, TNF-a is one of the major inducers of NF-kB activity (25) which in turn is expected to activate expression of CXCL1 (26). Therefore, the reduced expression of TNF-a in the BMMC from 304Q ataxin-3 knock- in mice is consistent with the increased expression of the NF-kB inhibitor, IkBa, but not with the increased expression of CXCL1 we observed. Moreover, CXCL1 binding to its receptors CXCR1/ 2 is supposed to activate the downstream extracellular signal- regulated kinases 1 and 2 (ERK1/2) (27). However, we did not observe significant differences in phosphorylation of ERK1/2. This conundrum points out to the profound interference of the polyQ-expanded ataxin-3 with the normal transcriptional and signaling responses of mast cells. The exploration of alternative pathways is warranted to clarify this point further. Recently, expression of mutant huntingtin (mHtt) was shown to affect toll-like receptor 4 (TLR-4) intracellular trafficking and cytokine production in BMMC (20). Similar to our findings in BMMC with the expanded ataxin-3, expression of TNF-a was reduced while the release of b-hexosaminidase was not affected in mHtt-expressing BMMC. Besides NF-kB several transcription factors such as AP-1, SP1, ETS-1, ELK-1, and NFAT have been found to be involved in TNF-a mRNA production (32). Pérez- Rodrı́guez et al. report that the ERK-ELK-c-Fos signaling axis, but not NF-kB, participate in TNF-a gene transcription in BMMCs in response to LPS stimulation via TLR-4. We found the highest induction of TNF-a in response to stimulation with ionomycin/PMA, which is known to cause PKC activation and Ataxin-3 is a deubiquitylating enzyme that removes and disassembles ubiquitin chains from specific substrates (28). NF-kB signaling consists of a series of positive and negative regulatory elements. Inducing stimuli trigger IKK activation leading to phosphorylation, ubiquitination, and degradation of IkB proteins, resulting in release of NF-kB, its nuclear translocation and ultimately induction of NF-kB target genes (29). Frontiers in Immunology | www.frontiersin.org ACKNOWLEDGMENTS We would like to thank Yvonne Soltow, Chrisovalantou Huridou and Teresa Braun for excellent technical assistance. We would also like to thank Serguei Popov for his assistance with this manuscript. We also acknowledge support by the Open Access Publishing Fund of the University of Tübingen. ETHICS STATEMENT The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu.2022. 870966/full#supplementary-material The studies involving human participants were reviewed and approved by Ethics Committee Tübingen. The patients/ REFERENCES 9. Schwartz LB, Austen KF, Wasserman SI. 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DISCUSSION However, a direct interaction of NF-kB pathway and the deubiquitinase ataxin-3 has not yet been shown. A possible pathway that activates NF-kB signaling in context of expanded April 2022 | Volume 13 | Article 870966 Frontiers in Immunology | www.frontiersin.org 8 Ataxin-3 Affects Mast Cell Functions Sowa et al. an increase in intracellular calcium (21). Consistently, we found a strong activation of the downstream signaling molecules ERK1/ 2 in response to ionomycin/PMA stimulation. Thus, TNF-a expression in response to ionomycin/PMA also appears to depend on ERK1/2-related transcription factors such as ELK-1. However, different from the findings in BMMC expressing mutant huntingtin, we observed no significant differences in the phosphorylation of ERK1/2 in BMMC with expanded ataxin- 3 compared to wild type BMMC. Further investigations are needed to identify all signaling molecules involved and all effects of ataxin-3 in mast cells. participants provided their written informed consent to participate in this study. The animal study was reviewed and approved by Institutional Animal Care and Use Committee (IACUC) of the University of Tübingen. AUTHOR CONTRIBUTIONS AS and AL contributed to conception and design of the study. AS, EH, JH-S, and AL performed experiments and data analyses. AS wrote the first draft of the manuscript. All authors contributed to manuscript revision, read, and approved the submitted version. AS and AL contributed to conception and design of the study. AS, EH, JH-S, and AL performed experiments and data analyses. AS wrote the first draft of the manuscript. All authors contributed to manuscript revision, read, and approved the submitted version. 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Mast Cell and Macrophage Chemokines CXCL1/CXCL2 Control the Early Stage of Neutrophil Recruitment During Tissue Inflammation. Blood (2013) 121:4930–37. doi: 10.1182/blood-2013-02-486217 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. 24. Omari KM, Lutz SE, Santambrogio L, Lira SA, Raine CS. Neuroprotection and Remyelination After Autoimmune Demyelination in Mice That Inducibly Overexpress CXCL1. Am J Pathol (2009) 174:164–76. doi: 10.2353/ ajpath.2009.080350 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. 25. Hayden MS, Ghosh S. 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Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments
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Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments Olof Leimar1*, Sasha R. X. Dall2, Peter Hammerstein3, John M. McNamara4 1 Department of Zoology, Stockholm University, Stockholm, Sweden, 2 Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom, 3 Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany, 4 School of Mathematics, University of Bristol, Bristol, United Kingdom * olof.leimar@zoologi.su.se a1111 OPEN ACCESS OPEN ACCESS Citation: Leimar O, Dall SRX, Hammerstein P, McNamara JM (2016) Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments. PLoS Comput Biol 12(6): e1005006. doi:10.1371/journal.pcbi.1005006 Editor: Samuel Alizon, CNRS, FRANCE Received: February 3, 2016 Accepted: May 27, 2016 Published: June 24, 2016 Copyright: © 2016 Leimar 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. OPEN ACCESS Citation: Leimar O, Dall SRX, Hammerstein P, McNamara JM (2016) Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments. PLoS Comput Biol 12(6): e1005006. doi:10.1371/journal.pcbi.1005006 Editor: Samuel Alizon, CNRS, FRANCE Received: February 3, 2016 Accepted: May 27, 2016 Published: June 24, 2016 Copyright: © 2016 Leimar 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. OPEN ACCESS Citation: Leimar O, Dall SRX, Hammerstein P, McNamara JM (2016) Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments. PLoS Comput Biol 12(6): e1005006. doi:10.1371/journal.pcbi.1005006 Editor: Samuel Alizon, CNRS, FRANCE Received: February 3, 2016 Accepted: May 27, 2016 Published: June 24, 2016 Copyright: © 2016 Leimar 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. Copyright: © 2016 Leimar 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. Data Availability Statement: This study is a theoretical work and does not contain original empirical data. The C++ computer programs used in the study are available at http://www.zoologi.su.se/ research/leimar/SoftwarePCB2016.zip and can also be obtained by request from the corresponding author. RESEARCH ARTICLE Abstract There are many situations where relatives interact while at the same time there is genetic polymorphism in traits influencing survival and reproduction. Examples include cheater- cooperator polymorphism and polymorphic microbial pathogens. Environmental heteroge- neity, favoring different traits in nearby habitats, with dispersal between them, is one general reason to expect polymorphism. Currently, there is no formal framework of social evolution that encompasses genetic polymorphism. We develop such a framework, thus integrating theories of social evolution into the evolutionary ecology of heterogeneous environments. We allow for adaptively maintained genetic polymorphism by applying the concept of genetic cues. We analyze a model of social evolution in a two-habitat situation with limited dispersal between habitats, in which the average relatedness at the time of helping and other benefits of helping can differ between habitats. An important result from the analysis is that alleles at a polymorphic locus play the role of genetic cues, in the sense that the pres- ence of a cue allele contains statistical information for an organism about its current environ- ment, including information about relatedness. We show that epistatic modifiers of the cue polymorphism can evolve to make optimal use of the information in the genetic cue, in anal- ogy with a Bayesian decision maker. Another important result is that the genetic linkage between a cue locus and modifier loci influences the evolutionary interest of modifiers, with tighter linkage leading to greater divergence between social traits induced by different cue alleles, and this can be understood in terms of genetic conflict. Introduction Traditional theories of social evolution in structured populations use reproductive value to describe the fitness effects of variation in helping and harming traits [1–4]. They are applied to population structures such as the two sexes [1], juveniles and adults [3], dispersers and non-dis- persers [5], and high- and low-quality individuals [4]. Individuals can, depending on their state, vary in their phenotype, which corresponds to a reaction norm [4], but genetic polymorphism in social traits is not explicitly included in the theory. Although it is recognized that frequency dependence is compatible with social evolution theory [6], questions of the emergence and maintenance of genetic polymorphism in social traits have not been given full attention. This absence is striking, as the possibility of such genetic polymorphism has attracted much interest. Examples of studies in the laboratory and the field span from work on cheater-cooperator poly- morphisms [7–15] to investigations of genetic variation in microbial pathogens [16, 17]. The possibility that population structure contributes to polymorphism also has support [18–22]. It is already well understood that a social trait, such as an individual’s investment in helping, can evolve to different equilibria depending on the relatedness in social groups in different hab- itats, with more helping in habitats where there is higher relatedness. We use the concept of genetic cues to extend this insight to situations where there is dispersal between habitats and where the social trait is influenced by several, linked or unlinked, genetic loci. The basic idea of genetic cues [23–26] is that alleles can function as statistical predictors of coming selective con- ditions for an individual. As a consequence of selection, allele frequencies can differ between local environments, such that possessing particular alleles correlates with local conditions in a manner analogous to environmental cues. Using this insight one can integrate genetic poly- morphism into theories of conditional phenotype determination. If the environmental heterogeneity includes characteristics that are important for social evo- lution, like the size or composition of social groups, the heterogeneity could favor genetic poly- morphism in social traits. If so, there will be a correlation between gene frequencies and social characteristics, and genes can act as cues of relatedness. To illustrate this general idea we develop a specific model with two habitats. Author Summary The theory of kin selection explains the evolution of helping when relatives interact. It can be used when individuals in a social group have different sexes, ages or phenotypic quali- ties, but the theory has not been worked out for situations where there is genetic polymor- phism in helping. That kind of polymorphism, for instance cheater-cooperator polymorphism in microbes, has attracted much interest. We include these phenomena into a general framework of social evolution. Our framework is built on the idea of genetic cues, which means that an individual uses its genotype at a polymorphic locus as a Funding: This work was supported by grants from the Swedish Research Council (621-2010-5437) and the Carl Trygger Foundation (CTS 15292) to OL and by a Leverhulme Trust International Network Grant to SRXD, PH, OL, and JMM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 1 / 14 PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 Genes as Cues of Relatedness Competing Interests: The authors have declared that no competing interests exist. statistical predictor of the current social conditions, including the expected relatedness in a social group. We allow for multilocus determination of the phenotype, in the form of mod- ifiers of the effects of the alleles at a cue locus, and we find that there can be genetic con- flicts between modifier loci that are tightly linked versus unlinked to the cue locus. Introduction We show that alleles at a cue locus can provide information about social circumstances, such as within-group relatedness and opportunities for cooperation, and that epistatic modifiers of the phenotypic effects of a genetic polymor- phism can evolve to make use of this information. We also show that the evolutionary interests of epistatic modifiers can differ depending on their degree of linkage to a polymorphic locus, and we interpret this phenomenon in terms of genetic conflict. Genes as Cues of Relatedness member has an equal and independent chance of producing each of the Ni offspring (model details are given in S1 Text). A smaller Ni thus corresponds to higher relatedness. For a pair of group members, the probability of being identical by descent since founding is member has an equal and independent chance of producing each of the Ni offspring (model details are given in S1 Text). A smaller Ni thus corresponds to higher relatedness. For a pair of group members, the probability of being identical by descent since founding is ri ¼ 1 Ni ; ð1Þ ri ¼ 1 Ni ; ð1Þ which follows [27] and [28]. The offspring group members engage in a social interaction, for instance a public goods game [29], and produce dispersing offspring in proportion to the pay- off in the game. An individual’s phenotype z represents an investment (strategy) in the game, and we assume 0  z  1. The payoff to an individual with phenotype z in habitat i is a func- tion wiðz; zÞ of z and the average investment z of the individual’s group. As a convenient exam- ple we will use wiðz; zÞ ¼ Wi þ biz  ciz2, where the benefit biz is proportional to the average investment and the cost ci z2 is assumed to increase quadratically with the individual’s invest- ment. For polymorphic populations the group compositions will vary, and we are particularly interested in the expected payoff in habitat i to a randomly chosen rare mutant player of the game with phenotype z0, in a population where the resident phenotypes z1 and z2 occur with frequencies pi1 and pi2 (where pi1 + pi2 = 1). We write this as w0 i ¼ E½wiðz0; zÞjz1; z2; pi1; pi2: ð2Þ ð2Þ Because a new group is founded by random dispersers, those groups containing mutant strate- gies will predominantly be founded by one mutant and Ni −1 resident types. Some basic aspects of the model are illustrated in Fig 1. To study the invasion of mutant traits, we need the derivative of the expected mutant payoff, which we write as dik ¼ @ w0 i @z0  z0¼zk ¼ bi Ni 1 þ ðNi  1Þri ð Þ  2cizk; ð3Þ ð3Þ for habitat i and phenotype zk, i = 1, 2, k = 1, 2. Model There are two habitats, each containing a large number of groups. They are formed and dis- solved by colonization followed by social interaction and the production of offspring that dis- perse, and again colonization. A group in habitat i, where i = 1, 2, is founded by Ni haploid individuals, randomly derived from a pool of dispersers in that habitat. To implement variation between habitats in average within-group relatedness, group members reproduce asexually fol- lowing founding, forming Ni haploid offspring group members, such that each founding group PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 2 / 14 PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 Genes as Cues of Relatedness Fig 1. Elements of the model. Panel (A) shows the population cycles in habitat 1 (color coded blue) and habitat 2 (red), including formation of social groups and playing the public goods game, resulting in the production of dispersing offspring, some of which go to the dispersal pool in their birth habitat and some go the pool in the other habitat. New social groups are then formed from the pool in each habitat. (B) The expected payoff Eq (2) for mutant trait z0 in habitat 1 (blue) and habitat 2 (red) in the limit of no between-habitat dispersal. The resident traits in habitats 1 and 2 are z1 and z2 (blue and red vertical lines). The gray curve shows mutant payoff when there is random dispersal, with the same two resident traits. (C) Illustration of group formation for two groups in habitat 1 with N1 = 3. First founding group members are randomly drawn from the dispersal pool, followed by asexual reproduction forming N1 offspring, each of which is a copy of a randomly selected parent in the founding group. (D) For a rare mutant (darker blue), founding groups with mutants will predominantly contain a single mutant. The offspring groups can contain from 0 to N1 mutants, and in expectation contain one mutant. doi:10.1371/journal.pcbi.1005006.g001 Fig 1. Elements of the model. Panel (A) shows the population cycles in habitat 1 (color coded blue) and habitat 2 (red), including formation of social groups and playing the public goods game, resulting in the production of dispersing offspring, some of which go to the dispersal pool in their birth habitat and some go the pool in the other habitat. New social groups are then formed from the pool in each habitat. (B) The expected payoff Eq (2) for mutant trait z0 in habitat 1 (blue) and habitat 2 (red) in the limit of no between-habitat dispersal. The resident traits in habitats 1 and 2 are z1 and z2 (blue and red vertical lines). The gray curve shows mutant payoff when there is random dispersal, with the same two resident traits. (C) Illustration of group formation for two groups in habitat 1 with N1 = 3. First founding group members are randomly drawn from the dispersal pool, followed by asexual reproduction forming N1 offspring, each of which is a copy of a randomly selected parent in the founding group. We study evolutionary change of a dimorphism z1, z2 by examining the invasion of mutant modifiers. Let x1 and x2 denote two alleles at the cue locus. In the resident population, the genetic cue xk induces the phenotype zk, and nik is the number of individuals in habitat i with phenotype zk at a population dynamical equilibrium. The epistatic effect of a mutant modifier is that xk instead induces the phenotype z0 k. Letting n0 ik denote the (small) number of mutant modifiers in habitat i with phenotype z0 k (i.e., linked to cue allele xk), we can write down a population projection matrix for the mutant invasion. The invasion fitness of the mutant modifier is Fðz0 1; z0 2; z1; z2Þ ¼ log l; ð4Þ ð4Þ where λ is the leading eigenvalue of the population projection matrix. Here we give an overview of the derivation of this matrix (details are given in S1 Text). For simplicity, we assume that individuals are haploid over most of the life cycle. However, to explore the consequences of recombination between cue and modifier loci, we introduce sex- ual reproduction by assuming there is a brief sexual phase in the dispersal pool in a habitat. This involves diploid individuals and crossing over, with a recombination rate ρ between cue and modifier loci, to produce the haploid individuals that found the groups as described above. Mating is random with respect to the dispersal pool and occurs before the forming of groups in the habitat. As a census point, we specify the population composition at a time after the sexual phase, when groups have formed and the public goods game is about to start. The sequence of events in the life cycle, starting right after the census point, is as follows: (i) public goods game 3 / 14 PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 Genes as Cues of Relatedness We compute a selection gradient from the invasion fitness Eq (4) using standard methodol- ogy of matrix population models [30]. Because we average over the group compositions Eq (2), our analysis is consistent with the structured population approach to adaptive dynamics [31], and it can also be seen as a direct fitness methodology for social evolution theory [1, 3], also referred to as a personal fitness methodology [6]. In order to check our analytical results, and to illustrate the effects of genetic conflict between cue and modifier loci, we have run individual-based evolutionary simulations corre- sponding to our model assumptions. As a genotype-phenotype mapping in these simulations, we used a sigmoid function z ¼ 1 1 þ exp a0  agx   ð5Þ ð5Þ of a ‘liability’ a0 + agx, where x is the effect of an allele at the genetic cue locus, and a0 and ag are parameters that are genetically determined by modifier loci (details are given in S1 Text). To compute evolutionary equilibria numerically, we developed a C++ program that follows a path of small steps through z1 z2–space, each of which increase the invasion fitness Eq (4), until reaching an equilibrium. We used the Eigen C++ library [32] to compute eigenvalues. For the individual-based evolutionary simulations, we developed C++ programs that directly implemented the sequence of events in the life cycle, using pseudo-random numbers to handle stochastic events, such as recombination and mutation. In the simulations, we used a total pop- ulations size of 40 000 and time periods of 40 000 full life cycles or more. (D) For a rare mutant (darker blue), founding groups with mutants will predominantly contain a single mutant. The offspring groups can contain from 0 to N1 mutants, and in expectation contain one mutant. doi:10.1371/journal.pcbi.1005006.g001 doi:10.1371/journal.pcbi.1005006.g001 doi:10.1371/journal.pcbi.1005006.g001 with offspring production in proportion to payoff, (ii) within- and between-habitat migration of these offspring, forming a dispersal pool in each habitat, (iii) mating and recombination, and (iv) the next episode of group formation, including one asexual generation. By putting these events together, one can write down the matrix (see S1 Text). Using the population dynamics we can also determine the region of coexistence of two phenotypes z1 and z2 for dif- ferent sets of parameters, by determining when each phenotype can invade a monomorphism of the other (the condition is given in equation (S16) in S1 Text). PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 4 / 14 Illustration Fig 2 shows how the migration rate m between habitats and the recombination rate ρ between cue and modifier loci influence dimorphic evolutionary equilibria, i.e. phenotypes where the selection gradient Eq (7) vanishes. The blue and red curves indicate phenotypes z1 and z2 suited to habitats with low and high relatedness. The selection gradient is illustrated in Fig 3 for a few values of m and ρ, and the shaded regions in this figure show where a polymorphism at the cue locus is maintained. In this example, the only difference between habitats is the number of founders of a social group, with N1 = 20 in habitat 1 and N2 = 2 in habitat 2, so it is appropriate to interpret the genetic cue as a cue of relatedness. As seen in Fig 2, there is an interaction between the migration rate and the recombination rate, such that for very low migration rate (m = 0.01) the recombination rate has little influence on the equilibrium dimorphism, whereas for a higher migration rate (m = 0.10) the difference between z1 and z2 varies considerably from tight linkage to free recombination. For even higher rates of between-habitat migration, genetic polymorphism is not maintained at the cue locus, regardless of the cue-modifier recombination rate ρ, and the outcome is instead a mono- morphism. For the parameter values in Fig 2, this happens for m = 0.15 or higher. Genes as Cues of Relatedness describes changes in payoff to a ‘Bayesian decision maker at the modifier locus’. Eq (7) is an extension of the direct fitness approach of social evolution theory to situations with genetic polymorphism at the cue locus. Note that this selection gradient refers to the invasion of mutant modifiers, and not to the invasion of alleles at the cue locus, except for the special case of full linkage (ρ = 0), for which cue and modifier form a unit. describes changes in payoff to a ‘Bayesian decision maker at the modifier locus’. Eq (7) is an extension of the direct fitness approach of social evolution theory to situations with genetic polymorphism at the cue locus. Note that this selection gradient refers to the invasion of mutant modifiers, and not to the invasion of alleles at the cue locus, except for the special case of full linkage (ρ = 0), for which cue and modifier form a unit. Completing the life cycle, through migration, mating and recombination, and group forma- tion, we can express Vik in terms of reproductive values vjl at our census point: Vik ¼ v111h11km1i þ v212h21km2i þ v121h12km1i þ v222h22km2i: ð8Þ ð8Þ Here, mji is the rate of migration from habitat i to j. The ‘cue inheritance’ is described by hjlk ¼ ð1  rÞdlk þ rpjl; ð9Þ ð9Þ so that with probability 1 −ρ the cue allele is passed to offspring and with probability ρ the off- spring receives its cue allele through recombination with a random individual in the dispersal pool. Finally, ϕj is the probability for an individual in the dispersal pool in habitat j to become a founding group member. We must also examine whether or not polymorphism can be maintained at the cue locus. This needs to be investigated as a separate question, by determining when each of the pheno- types z1 and z2 can invade a monomorphism of the other. The condition for this is given in equation (S16) in S1 Text. Selection gradient We use the methodology of adaptive dynamics and matrix population modeling [30, 33] to compute the derivative of invasion fitness for a mutant modifier. The details of the derivation are given on pp. 8–10 of S1 Text, and here we focus on the interpretations in terms of informa- tion in a cue. The genetic cue provides information to an individual about its current habitat. The prior probability of being in habitat i is qi = ni/(n1 + n2), where ni = ni1 + ni2 is the number of individuals in habitat i at a population dynamical equilibrium and nik is the number of indi- viduals in habitat i with phenotype zk. For an allele at a modifier locus, the probability of being in habitat i, conditional on being linked to allele xk at the cue locus is qik ¼ pikqi p1kq1 þ p2kq2 ¼ nik n1k þ n2k ; ð6Þ ð6Þ where pik = nik/ni. The selection gradient is the derivative of invasion fitness Eq (4) with respect to mutant traits, and can be written @F @z0 k  z0 k¼zk ¼ V1kd1kpkq1k þ V2kd2kpkq2k: ð7Þ ð7Þ To interpret this expression, note that q1k and q2k are the respective probabilities of being in habitat 1 or 2, conditional on being linked to cue allele xk. The factor pk = (n1k + n2k)/(n1 + n2) is a ‘dilution factor’ that appears because the mutant z0 k is only expressed in individuals with cue allele xk. The d1k and d2k are the derivatives of the expected payoff Eq (2) in habitats 1 and 2 with respect to the mutant trait, and are given in Eq (3). Finally Vik is the reproductive value of an offspring of a player in habitat i with cue allele xk. From the manner in which the condi- tional probability qik appears in the expression, we can conclude that the selection gradient PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 5 / 14 Genetic conflicts The divergence between z1 and z2 depends on ρ, as in Figs 2 and 3, because modifier alleles with different linkage to cue alleles have different demographic futures, and thus different evo- lutionary interests. A fully linked mutant modifier will remain more concentrated in one of the habitats, which tends to favor specialization to that habitat, whereas an unlinked one will fairly quickly become evenly distributed over cue alleles and habitats, which tends to favor less spe- cialized phenotypes. This difference in evolutionary interest between modifiers follows the logic of genetic conflicts [34], in the sense that the invasion of a loosely linked modifier, PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 6 / 14 Genes as Cues of Relatedness Fig 2. Evolutionary equilibrium dimorphisms. The equilibrium dimorphisms z1 and z2, color coded blue and red, are plotted as functions of the rate of recombination ρ between cue and modifier loci. The two habitats differ in the size of social groups, with N1 = 20 and N2 = 2, resulting in lower relatedness in habitat 1 (r1 = 0.05) than in habitat 2 (r2 = 0.5). Three examples are shown, labeled with the rate of migration between habitats: m12 = m21 = m = 0.01, 0.05, 0.10. The total population size is the same in both habitats, and the parameters for the public goods game are also the same: W1 = W2 = 0.5, b1 = b2 = 3.0, c1 = c2 = 1.5. The gray horizontal line shows the equilibrium of gradual evolution in a monomorphic population, which does not depend on m or ρ. The dark gray points (with error bars) at ρ = 0.0 and ρ = 0.5, shifted slightly left and right for visibility, show mean and standard deviation of the average phenotype over 10 replicate individual-based evolutionary simulations. In these simulations, ag in Eq (5) was encoded by a single locus whereas a0 was kept at a fixed value (see S1 Text for further explanation). d i 10 1371/j l bi 1005006 002 Fig 2. Evolutionary equilibrium dimorphisms. The equilibrium dimorphisms z1 and z2, color coded blue and red, are plotted as functions of the rate of recombination ρ between cue and modifier loci. Genetic conflicts The two habitats differ in the size of social groups, with N1 = 20 and N2 = 2, resulting in lower relatedness in habitat 1 (r1 = 0.05) than in habitat 2 (r2 = 0.5). Three examples are shown, labeled with the rate of migration between habitats: m12 = m21 = m = 0.01, 0.05, 0.10. The total population size is the same in both habitats, and the parameters for the public goods game are also the same: W1 = W2 = 0.5, b1 = b2 = 3.0, c1 = c2 = 1.5. The gray horizontal line shows the equilibrium of gradual evolution in a monomorphic population, which does not depend on m or ρ. The dark gray points (with error bars) at ρ = 0.0 and ρ = 0.5, shifted slightly left and right for visibility, show mean and standard deviation of the average phenotype over 10 replicate individual-based evolutionary simulations. In these simulations, ag in Eq (5) was encoded by a single locus whereas a0 was kept at a fixed value (see S1 Text for further explanation). doi:10.1371/journal.pcbi.1005006.g002 doi:10.1371/journal.pcbi.1005006.g002 reducing the divergence between phenotypes, creates the context for the invasion of a more tightly linked modifier that reverses this effect. The outcome of genetic conflicts can depend on such things as the of the availability of mutations, the genetic architecture of a trait, and the strength of selection. For modifiers of polymorphic effects, genetic conflicts can have the further consequence of changing selection acting on the additive effects of alleles at a locus from stabilizing to disrup- tive, potentially giving rise to selectively maintained polymorphism at that locus. For instance, for the case of m = 0.10 in Fig 2, unlinked modifiers favor a very small divergence between z1 and z2, but once this outcome has been achieved, the selection on alleles at other loci with addi- tive effects on z becomes disruptive (just as originally for the cue locus itself). Genetic polymor- phism might then be transferred from an original cue locus to a new locus. How this can happen is illustrated by the individual-based simulations in Fig 4. The geno- type-phenotype mapping Eq (5) from the genetic cue x to the trait z has been changed from that in Fig 2, where the parameter a0 was fixed, to one where both parameters a0 and ag are genetically determined and can evolve. PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 Genetic conflicts In Fig 4A, a0 and ag are each determined by a single locus, either fully linked or unlinked to each other and to the cue locus. When m is small or when ρ = 0, the outcome of the individual-based simulations remains in agreement with the predictions from the selection gradient Eq (7), but for m = 0.10 and ρ = 0.5, the outcome is instead the same as that for m = 0.10 and ρ = 0 (Fig 4B). The reason is that, starting with PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 7 / 14 Genes as Cues of Relatedness Fig 3. Trait evolution plots for dimorphisms. In each example, the shaded region shows where a dimorphism z1, z2 can be maintained, the arrows indicate the direction and magnitude of the selection gradient Eq (7), and the dots show evolutionarily equilibrium dimorphisms. The examples differ in between-habitat migration rate m12 = m21 = m and rate of recombination ρ. (A) m = 0.05, ρ = 0.001; (B) m = 0.05, ρ = 0.5; (C) m = 0.10, ρ = 0.001; (D) m = 0.10, ρ = 0.5. Other parameters: N1 = 20 and N2 = 2, W1 = W2 = 0.5, b1 = b2 = 3.0, c1 = c2 = 1.5. doi:10.1371/journal.pcbi.1005006.g003 Fig 3. Trait evolution plots for dimorphisms. In each example, the shaded region shows where a dimorphism z1, z2 can be maintained, the arrows indicate the direction and magnitude of the selection gradient Eq (7), and the dots show evolutionarily equilibrium dimorphisms. The examples differ in between-habitat migration rate m12 = m21 = m and rate of recombination ρ. (A) m = 0.05, ρ = 0.001; (B) m = 0.05, ρ = 0.5; (C) m = 0.10, ρ = 0.001; (D) m = 0.10, ρ = 0.5. Other parameters: N1 = 20 and N2 = 2, W1 = W2 = 0.5, b1 = b2 = 3.0, c1 = c2 = 1.5. doi:10.1371/journal.pcbi.1005006.g003 polymorphism at the cue locus, ag evolved to become small, reducing the divergence between the phenotypes from Eq (5), which in turn gave rise to disruptive selection on a0, causing poly- morphism to evolve at that locus, while the polymorphism at the original cue locus collapsed. The end result was that the locus coding for a0 became a polymorphic cue locus, with pheno- types z1, z2 in accordance with the evolutionary interests of fully linked modifiers of this new polymorphism (Fig 4B). Other conceivable evolutionary outcomes of disruptive selection on a0 are shown in Fig 4C and 4D. g In Fig 4C, 5 unlinked loci have small positive effects on a0 and 5 have small negative effects, and each of these loci became polymorphic in the simulation, while at the same time the origi- nal genetic cue locus remained polymorphic. The overall effect was a fairly broad distribution PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 8 / 14 Genes as Cues of Relatedness Fig 4. In (C) the modifiers a0 and ag in Eq (5) are each determined by several loci with small additive effects, and the loci contributing to a0 all became polymorphic. In (D) there is a more complex architecture for a0, with additive effects that in turn can be modified with an adjustable threshold limiting the amount of gene expression, and this threshold became polymorphic (see text and S1 Text for further explanation). g 4. Results from individual-based simulations, illustrating consequences of genetic conflict. (A) Same as the Fig 4. Results from individual-based simulations, illustrating consequences of genetic conflict. (A) Same as the simulations in Fig 2 except that a0, in addition to ag, in Eq (5) is determined by a single locus. The blue and red points (with error bars) show the deviating outcome for m = 0.10, ρ = 0.5, which is a consequence of genetic conflict between the cue locus and the locus encoding ag: ag became close to zero, but a0 became polymorphic, and the polymorphism at the original cue locus collapsed. The outcome is further illustrated in (B), showing a kernel-smoothed distribution of phenotypes in a typical simulation. The blue and red vertical lines show the prediction from Fig 3C, where ρ = 0, and the blue and red dashed lines the prediction from Fig 3D, where ρ = 0.5. The outcome where an unlinked modifier (a0) takes over the polymorphism depends on the genetic architecture, as illustrated in (B), (C) and (D). In (C) the modifiers a0 and ag in Eq (5) are each determined by several loci with small additive effects, and the loci contributing to a0 all became polymorphic. In (D) there is a more complex architecture for a0, with additive effects that in turn can be modified with an adjustable threshold limiting the amount of gene expression, and this threshold became polymorphic (see text and S1 Text for further explanation). doi:10.1371/journal.pcbi.1005006.g004 of values for the investment z. In Fig 4D, the maximum expression at the loci with positive and negative effects was controlled by two separate unlinked loci, and one of these became poly- morphic, giving rise to a bimodal distribution of values of z. In these examples, a notable amount of genetic variation in z evolved, but the width and shape of the distribution of z depended on the details of the genetic architecture of the trait. Results from individual-based simulations, illustrating consequences of genetic conflict. (A) Same as the simulations in Fig 2 except that a0, in addition to ag, in Eq (5) is determined by a single locus. The blue and red points (with error bars) show the deviating outcome for m = 0.10, ρ = 0.5, which is a consequence of genetic conflict between the cue locus and the locus encoding ag: ag became close to zero, but a0 became polymorphic, and the polymorphism at the original cue locus collapsed. The outcome is further illustrated in (B), showing a kernel-smoothed distribution of phenotypes in a typical simulation. The blue and red vertical lines show the prediction from Fig 3C, where ρ = 0, and the blue and red dashed lines the prediction from Fig 3D, where ρ = 0.5. The outcome where an unlinked modifier (a0) takes over the polymorphism depends on the genetic architecture, as illustrated in (B), (C) and (D). In (C) the modifiers a0 and ag in Eq (5) are each determined by several loci with small additive effects, and the loci contributing to a0 all became polymorphic. In (D) there is a more complex architecture for a0, with additive effects that in turn can be modified with an adjustable threshold limiting the amount of gene expression, and this threshold became polymorphic (see text and S1 Text for further explanation). d i 10 1371/j l bi 1005006 004 Fig 4. Results from individual-based simulations, illustrating consequences of genetic conflict. (A) Same as the simulations in Fig 2 except that a0, in addition to ag, in Eq (5) is determined by a single locus. The blue and red points (with error bars) show the deviating outcome for m = 0.10, ρ = 0.5, which is a consequence of genetic conflict between the cue locus and the locus encoding ag: ag became close to zero, but a0 became polymorphic, and the polymorphism at the original cue locus collapsed. The outcome is further illustrated in (B), showing a kernel-smoothed distribution of phenotypes in a typical simulation. The blue and red vertical lines show the prediction from Fig 3C, where ρ = 0, and the blue and red dashed lines the prediction from Fig 3D, where ρ = 0.5. The outcome where an unlinked modifier (a0) takes over the polymorphism depends on the genetic architecture, as illustrated in (B), (C) and (D). In all cases, an individual gains PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 9 / 14 Genes as Cues of Relatedness Fig 5. Illustration of the information contained in genetic cues. Panel (A) shows the conditional probability of being in habitat 1 (with r1 = 0.05) for an individual possessing cue allele x1 (blue curves, q11) versus cue allele x2 (red curves, q12). The probability is given as a function of the recombination rate ρ between cue and modifier loci. The three cases are from Fig 2, with different rates of between-habitat migration m12 = m21 = m = 0.01, 0.05, 0.10. The blue lines in panels (B) to (D) show logistic regressions of habitat 1 on the liability a0+ag x in eq (5), for the individual-based simulations in Fig 4B to 4D (with m = 0.10 and ρ = 0.5). The distributions of this liability are shown in gray, and the vertical blue and red lines indicate ‘typical’ low and high values (mean ± sd for (C) and (D)). See S1 Text for further explanation. doi:10.1371/journal.pcbi.1005006.g005 Fig 5. Illustration of the information contained in genetic cues. Panel (A) shows the conditional probability of being in habitat 1 (with r1 = 0.05) for an individual possessing cue allele x1 (blue curves, q11) versus cue allele x2 (red curves, q12). The probability is given as a function of the recombination rate ρ between cue and modifier loci. The three cases are from Fig 2, with different rates of between-habitat migration m12 = m21 = m = 0.01, 0.05, 0.10. The blue lines in panels (B) to (D) show logistic regressions of habitat 1 on the liability a0+ag x in eq (5), for the individual-based simulations in Fig 4B to 4D (with m = 0.10 and ρ = 0.5). The distributions of this liability are shown in gray, and the vertical blue and red lines indicate ‘typical’ low and high values (mean ± sd for (C) and (D)). See S1 Text for further explanation. doi:10.1371/journal.pcbi.1005006.g005 information about its current habitat from its genotype, and one can show that the clearcut polymorphism in Fig 4B is the most informative, with progressively less information on aver- age in Fig 4C and 4D, as illustrated in Fig 5. The latter cases are intermediate between the evo- lutionary interests of fully linked and unlinked modifiers. Genes as Cues of Relatedness structured populations [3, 6], with the distinction that the presence of a cue allele in an individ- ual’s genotype, rather than a phenotypic state, defines the class structure. In our model, indi- viduals use strategies that are conditional on a genetic cue, but our general approach can incorporate a combination of genetic, environmental and transgenerational cues [26, 35]. Just as is the case in standard social-evolution theory, relatedness enters into our model as a description of the genetic structure of social groups. The structure refers to genetic variation at epistatic modifier loci, rather than at genetic cue loci, so the relatedness parameter ri in the pay-off derivative Eq (3) refers to rare mutants at a modifier locus. This is in accordance with the general idea of treating genetic variation at a cue locus as input to a developmental or ‘deci- sion-making’ system, and then to examine long-term evolution of the developmental system [24, 26]. The value of this perspective is that it guides the analysis and interpretation by form- ing a link to the study of conditional strategies, such as the study of phenotypic plasticity. The different ways in which individuals gain information about themselves and their social partners has figured importantly in the study of social evolution [2]. For instance, migrant indi- viduals arriving in a local population have different expectations of relatedness to their neigh- bors than non-dispersers [5]. The possibility that individuals can recognize kin through similarity in genetically polymorphic traits has been carefully investigated, with the conclusion that kin recognition can evolve in spatially structured populations [36–38]. Yet another possi- bility is that individuals estimate their degree of inbreeding, and thus how likely they are to be related to their neighbors, using their relative homozygosity as an indicator of local relatedness [39]. Our analysis of genetic cues of relatedness contributes to this general emphasis on the role of information, but differs from the other examples through an affinity to the study of local adaptation in the face of gene flow, which has been given much attention in evolutionary ecology but rather little in theories of social evolution. We found that the genetic linkage between cue and modifier loci can influence the evolu- tionary outcome (Figs 2 and 3), and this gives rise to genetic conflicts. Discussion We have shown how adaptively maintained genetic polymorphism can be integrated into social evolution theory by making use of the concept of genetic cues. The selection gradient we derived (in eq (7)) parallels the direct, or personal, fitness approach to social evolution in class- PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 10 / 14 PLOS Computational Biology | DOI:10.1371/journal.pcbi.1005006 June 24, 2016 S1 Text. Details of model description, results and individual-based simulations. (PDF) S1 Text. Details of model description, results and individual-based simulations. (PDF) Genes as Cues of Relatedness small-effect mutant modifiers share their demographic future with the organism. Our results in Fig 4—that disruptive selection can act to diminish the control exercised by unlinked modi- fiers over the degree of phenotypic specialization—illustrate how individual optimization might be circumvented when there is genetic polymorphism. Furthermore, our individual- based simulations with multilocus genetic architectures resulted in evolutionary outcomes that were intermediate between the evolutionary interests of linked and unlinked modifiers (Figs 4C, 4D, 5C and 5D). This fits with the general idea of the organism as a compromise between different evolutionary interests [45, 46]. In conclusion, our framework broadens the scope of social evolution theory, by accounting for adaptively maintained genetic variation in heterogeneous environments and by incorporat- ing evolutionary outcomes over the range from genetic specialism to generalism. Many instances of interactions between relatives in nature are likely to be found somewhere between the extremes of such a spectrum. A major insight from our work is that positions along this spectrum can correspond to the degree of genetic linkage between polymorphic loci and epi- static modifiers of the phenotype in question. Our analysis thus delivers potentially testable predictions about the evolution of epistasis between modifiers and polymorphic loci and can inspire empirical investigation of the importance of genetic cues of relatedness. Acknowledgments We thank Angus Buckling and Vincent Jansen for helpful suggestions. Author Contributions Wrote the paper: OL SRXD PH JMM. Conceived and performed the modeling: OL. Designed the software for the model analysis: OL. Wrote the paper: OL SRXD PH JMM. Conceived and performed the modeling: OL. Designed the software for the model analysis: OL. Genes unlinked to a genetic cue locus tend to favor phenotypes that are less specialized to particular habitats com- pared to tightly linked genes, because unlinked genes become adapted to exist in all habitats, be transferred between them, and to use the information in a genetic cue to adjust the phenotype in an optimal way for this situation. Tightly linked genes, on the other hand, might be selected to perform well in only one of the habitats, even at the expense of performance in another habi- tat. The reason is that a modifier allele tightly linked to a cue locus allele can become concen- trated to one of the habitats, with the other habitat acting as a sink, to which little adaptation takes place [40, 41]. Our results on the role of genetic conflicts in giving rise to disruptive selection at modifier loci (Fig 4) extends the previous understanding of genetic conflicts when there is adaptively maintained genetic polymorphism [24]. Disruptive selection in heterogeneous environments can maintain genetic polymorphism [42], and genetic cue polymorphism is an example of this general phenomenon. So, if unlinked or loosely linked modifiers of a genetically polymorphic locus evolve to reduce or eliminate the divergence between phenotypes, there will be disruptive selection at loci with additive effects on the phenotype in question. Theoretical modeling has found that disruptive selection tends to favor genetic architectures where polymorphism is concentrated to a single locus [23, 43], but as we have shown, constraints on the set of geno- type-phenotype mappings can lead to intermediate outcomes between a single-locus polymor- phism and polygenic variation where each locus has a small effect (Fig 4). A basic question for evolutionary theory is whether evolutionary change can be seen as opti- mizing some form of fitness for the organism or individual [44]. Our analysis of genetic con- flicts throws new light on this issue. 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Evaluation of Hemorrhoid Outcomes for Pregnant Women
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Evaluation of Hemorrhoid Outcomes for Pregnant Women Evaluation of Hemorrhoid Outcomes for Pregnant Women Evaluation of Hemorrhoid Outcomes for Pregnant Women Dr. Ahmed Fakhri Omar1, Dr. Massar Raheem Abbas2, and Dr. Doaa Abbas khairullah3 1M.B.Ch.B \ C.A.B.S \ M.R.C.S. Ireland \ (General Surgeon), Ministry of Health of Kurdistan, Erbil Directory of Health, Roj Halat Emergency Hospital C.A.B.S \ M.R.C.S. Ireland \ (General Surgeon), Ministry of Health of Kurdistan, Erbil Directory of Health ergency Hospital 2M.B.Ch.B \ D.G.O. \ (Obstetrics and Gynecology), Iraqi Ministry of Health, Najaf Health Department, Al-Furat Al- Awsat Teaching Hospital, Najaf, Iraq 3 3M.B.Ch.B. \ D.O.G. \ (Obstetrician and Gynaecologist), Ministry of Health, Al-Russafa Health Directorate, Fatima Al- Zhraa Teaching for Women and Children Hospital, Baghdad, Iraq Abstract: Background: Hemorrhoids are defined as an aberrant downward movement in the anal cushions that results in venous dilatation. Hemorrhoids are commonly associated with burning, itching, perianal discomfort, and bleeding. Aim: This paper aims to evaluate of hemorrhoid outcomes for pregnant women. Patients and methods: This paper was interested to evaluate of hemorrhoid outcomes for pregnant women where include patients who suffered of hemorrhoids in different hospitals in Iraq from 19th July 2021 to 25th June 2022. This paper was focused on patients who have ages in between 25-40 years. This paper was included to groups. Where the first represented the patients' group who still suffered of hemorrhoids after the process outcomes of the operative, while the second group presented patients who successes of prevent hemorrhoids where it, represented as intervention group with 164 cases where each group has 64 patients. The data were examined and recovered the outcomes of health outcomes by the SPSS program. Results and Discussion: According to our findings, either ITT or PP analyses revealed that this intervention reduced hemorrhoids by about 60% of the overall rate. The prevalence of hemorrhoids following giving birth for the patient’s category (ITT-41%; PP-42%) was consistent with Poskus et al.'s observed rate of 40.7% in a comparable population. Conclusion: Due to the comparatively low miscarriage as well as hemorrhoid rates, small variations between research groups might have been ignored. Yet, the miscarriage rate was the most recognized result for assessing the safety of different prenatal procedures. Finally, our proposed method, which aims to change dietary and behavioral patterns, dramatically lowers the risk of hemorrhoids throughout pregnancy and may be safely advised to pregnant women. Keywords: hemorrhoids, Pregnancy, rate of spontaneous miscarriages, and rate of hemorrhoids. INTRODUCTION Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License *Corresponding Author: Dr. Ahmed Fakhri Omar DOI- https://doi.org/10.5281/zenodo.8066134 Sarcouncil Journal of Medicine and Surgery ISSN(Online): 2945-3534 Augie, M.A. et al. Volume- 02| Issue- 06| 2023 Research Article Received: 05-04-2023 | Accepted: `19-05-2023 | Published: 21-06-2023 Sarcouncil Journal of Medicine and Surgery ISSN(Online): 2945-3534 Augie, M.A. et al. Volume- 02| Issue- 06| 2023 Research Article Received: 05-04-2023 | Accepted: `19-05-2023 | Published: 21-06-2023 Sarcouncil Journal of Medicine and Surgery ISSN(O li ) 2945 3534 Received: 05-04-2023 | Accepted: `19-05-2023 | Published: 21-06-2023 INTRODUCTION birth weight in new-born > 3800 g, and constipation are all significant risk factors with hemorrhoids as well as anal fissures, according to Poskus et al. Constipation and a history of anal issues, according to Ferdinande et al., are important risk factors for getting perianal illness during pregnancy. Despite constipation is one of the most well-known modifiable risk factors significantly linked to the occurrence of hemorrhoids following pregnancy, research on the subject is limited. There are currently no research examining dietary and behavioural strategies to reduce the prevalence of chronic hemorrhoids in pregnancy. [Monika, S. et al., 2014- Davis, B.R. et al., 2018] Hemorrhoids are defined as an aberrant downward movement in the anal cushions that results in venous dilatation [Thomson, W.H.F, 1975]. Hemorrhoids are commonly associated with burning, itching, perianal discomfort, and bleeding. This ailment is very common during pregnancy, especially throughout the third trimester as well as the postpartum period. A few clinical investigations found an incidence of hemorrhoids ranging from 15% to 41%, or even 85%, in select groups, with the frequency increasing with age and parity. [Jakubauskas, M. et al., 2020- Medich, D.S. et al., 1995] Hemorrhoids in pregnancy are caused by a variety of physiological causes. Venous stasis of the perianal area is caused by an increase in circulating blood volume as well as an increase in intraabdominal pressure caused by uterine enlargement. Furthermore, the pregnancy hormone progesterone relaxes smooth muscles not just within the venous walls as well as in the colon, resulting in decreased motility as well as constipation. Several prospective studies have acknowledged some of these variables. [Gojnic, M. et al., 2005- Shin, G.H. et al., 2015] Hemorrhoids remain among the most prevalent adult illnesses globally, involving 4.4% up 36% of the world's population. Incomplete figures reveal that at least 50% of people over the age of 50 have hemorrhoids, with mixed hemorrhoids accounting for the great majority. Hemorrhoids symptoms and indicators involve frequent stools, itching, discomfort, prolapse, and bowel movement blood. These are frequently coupled alongside enlarged hemorrhoid pads, that might be a sign of various diseases. Hemorrhoids have a negative influence on one's quality of life. As a result, it is especially Personal history of perianal illness, straining throughout delivery with more than 20 minutes, 9 Sarc. Jr. Med. Sur. Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher PATIENTS AND METHODS PATIENTS AND METHODS This paper was interested to evaluate of hemorrhoid outcomes for pregnant women where include patients who suffered of hemorrhoids in different hospitals in Iraq from 19th July 2021 to 25th June 2022. This paper was focused on patients who have ages in between 25-40 years. This paper was included to groups. Where the first represented the patients' group who still suffered of hemorrhoids after the process outcomes of the operative, while the second group presented patients who successes of prevent hemorrhoids where it, represented as intervention group with 164 cases where each group has 64 patients. The data were examined and recovered the outcomes of health outcomes by the SPSS program. This paper was also examined of pregnancy outcomes with into hemorrhoid patients for pregnant women were had Newburn weight (kg), Newburn height (cm), and Head circumference (cm). It also studied examinations of birth of newborn outcomes with into hemorrhoid patients for pregnant women, where include Vaginal birth without assistance, Vaginal birth with assistance, and Caesarean delivery, which can be cleared in Figure 4 and Figure 5. This paper was presented Distributions of hemorrhoid patients for pregnant women based on age, BMI, and marital status, which contain within Married and Single, where the demographic outcomes were found in Table 1, Table 2, and Table 3. To further of results, this paper was evaluated of the rate of hemorrhoids in basics of Hemorrhoids rate (ITT) and Hemorrhoids rate (PP) and rate of spontaneous miscarriages in basics of Spontaneous miscarriage rate (ITT) and Spontaneous miscarriage rate (PP) into outcomes into hemorrhoid patients for pregnant women, which can be shown in Figure 6 and Figure 7. To follow-up, this paper was examined characteristics baselines into hemorrhoid patients for pregnant women based on symptoms which include aching anus, hard lumps near the anus, itching around the anus, Prolapsed hemorrhoid, and Rectal bleeding, which can be seen in Table 4. RESULTS INTRODUCTION vol-2, issue-6 (2023) pp-9-16 Omar, A.F.et al., In comparison of both groups, this paper studied Changes of the number of previous pregnancies into hemorrhoid patients for pregnant women, which have progressed with numbers which are 0, 1, 2, and >2, as well as Features of coloproctological outcomes with into hemorrhoid patients for pregnant women which History of hemorrhoids, Current perianal discomfort, Current perianal pain, Current perianal bleeding Current perianal lumps, History of perianal operations, and Family history of perianal disease, and Features of previous delivery outcomes with into hemorrhoid patients for pregnant women which get on Did not give birth, Vaginal delivery, and Caesarean delivery where can be seen in Figure 1, Figure 2, and Figure 3. important to create and carry out timely scientific and efficient treatment programs within clinical practice [Creasy, R.K. et al., 1984]. This paper aims to evaluate of hemorrhoid outcomes for pregnant women. important to create and carry out timely scientific and efficient treatment programs within clinical practice [Creasy, R.K. et al., 1984]. This paper aims to evaluate of hemorrhoid outcomes for pregnant women. The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License RESULTS Table 1: Distributions of hemorrhoid patients for pregnant women based on age N V 64 Mi 0 M 32.5000 SM .58078 Me 32.5000 Mo 25.00a SD 4.64621 Var 21.587 Sk .000 SES .299 Ra 15.00 Min 25.00 Max 40.00 S 2080.00 Table 1: Distributions of hemorrhoid patients for pregnant women based on age 10 Sarc. Jr. Med. Sur. vol-2, issue-6 (2023) pp-9-16 Omar, A.F.et al., Table 2: Distributions of hemorrhoid patients for pregnant women based on BMI F P(%) VP (%) CP (%) V <26.5 30 46.9 46.9 46.9 >26.5 34 53.1 53.1 100.0 T 64 100.0 100.0 Table 2: Distributions of hemorrhoid patients for pregnant women based on BMI Table 3: Distributions of hemorrhoid patients for pregnant women based on marital status F P(%) VP (%) CP (%) V Married 45 70.3 70.3 70.3 Single 19 29.7 29.7 100.0 T 64 100.0 100.0 Table 3: Distributions of hemorrhoid patients for pregnant women based on marital statu Table 3: Distributions of hemorrhoid patients for pregnant women based on marital status Table 4: Examinations of characteristics baselines into hemorrhoid patients for pregnant women based on physical activity Table 4: Examinations of characteristics baselines into hemorrhoid patients for pregnant women based on physical activity p y y F P(%) VP (%) CP (%) V Enough 26 40.6 40.6 40.6 Too low 38 59.4 59.4 100.0 T 64 100.0 100.0 Table 5: Examinations of characteristics baselines into hemorrhoid patients for pregnant women based on symptoms Table 5: Examinations of characteristics baselines into hemorrhoid patients for pregnant women based on symptoms Table 5: Examinations of characteristics baselines into hemorrhoid patients for pregnant women based symptoms F P (%) VP (%) CP (%) V aching anus 10 15.6 15.6 15.6 hard lumps near the anus 12 18.8 18.8 34.4 itching around the anus 18 28.1 28.1 62.5 Prolapsed hemorrhoid 9 14.1 14.1 76.6 Rectal bleeding 15 23.4 23.4 100.0 T 64 100.0 100.0 symptoms F P (%) VP (%) CP (%) V aching anus 10 15.6 15.6 15.6 hard lumps near the anus 12 18.8 18.8 34.4 itching around the anus 18 28.1 28.1 62.5 Prolapsed hemorrhoid 9 14.1 14.1 76.6 Rectal bleeding 15 23.4 23.4 100.0 T 64 100.0 100.0 Figure 1: Changes of the number of previous pregnancies into hemorrhoid patients for pregnant women. Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher RESULTS 0 5 10 15 20 25 30 35 40 45 Frequency Percentage Frequency Percentage patients (64) controls (64) previous pregnancies 0 1 2 >2 previous pregnancies Figure 1: Changes of the number of previous pregnancies into hemorrhoid patients for pregnant women. 11 Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher right © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher ( ) Publisher: SARC Publisher Sarc. Jr. Med. Sur. vol-2, issue-6 (2023) pp-9-16 Omar, A.F.et al., 1 mar, A.F.et al., Sarc. Jr. Med. Sur. Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher RESULTS vol-2, issue-6 (2023) pp-9-16 opyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License P bli h SARC P bli h Figure 2: Features of coloproctological outcomes with into hemorrhoid patients for pregnant women Figure 3: Features of previous delivery outcomes with into hemorrhoid patients for pregnant women 0 5 10 15 20 25 30 35 40 History of hemorrhoids Current perianal discomfort Current perianal pain Current perianal bleeding Current perianal lumps History of perianal operations Family history of perianal disease Coloproctological variable patients patients controls controls 0 10 20 30 40 50 60 Frequency Percentage Frequency Percentage patients (64) controls (64) previous delivery Did not give birth Vaginal delivery Cesarean delivery Fig re 2: F t f l t l i l t ith i t h h id ti t f t 0 5 10 15 20 25 30 35 40 History of hemorrhoids Current perianal discomfort Current perianal pain Current perianal bleeding Current perianal lumps History of perianal operations Family history of perianal disease Coloproctological variable patients patients controls controls Fi 3 F f i d li i h i h h id i f 0 10 20 30 40 50 60 Frequency Percentage Frequency Percentage patients (64) controls (64) previous delivery Did not give birth Vaginal delivery Cesarean delivery Figure 3: Features of previous delivery outcomes with into hemorrhoid patients for pregnant women 12 Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License ( ) Publisher: SARC Publisher Sarc. Jr. Med. Sur. Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher RESULTS vol-2, issue-6 (2023) pp-9-16 Omar, A.F.et al., Figure 4: Examinations of pregnancy outcomes with into hemorrhoid patients for pregnant women ure 5: Examinations of birth of new-born outcomes with into hemorrhoid patients for pregnant women 0 10 20 30 40 50 60 70 patients controls Birth assistance Birth assistance Vaginal birth without assistance Vaginal birth with assistance Cesarean delivery 0 10 20 30 40 50 60 Newborn weight (kg) Newborn height (cm) Head circumference (cm) Birth exaamination patients controls Fi 4 E i i f i h i h h id i f 0 10 20 30 40 50 60 70 patients controls Birth assistance Birth assistance Vaginal birth without assistance Vaginal birth with assistance Cesarean delivery ure 4: Examinations of pregnancy outcomes with into hemorrhoid patients for pregnant women Figure 4: Examinations of pregnancy outcomes with into hemorrhoid patients for pregnant women Figure 5: Examinations of birth of new-born outcomes with into hemorrhoid patients for pregnant women. 0 10 20 30 40 50 60 Newborn weight (kg) Newborn height (cm) Head circumference (cm) Birth exaamination patients controls 5 E i ti f bi th f b t ith i t h h id ti t f t 0 10 20 30 40 50 60 Newborn weight (kg) Newborn height (cm) Head circumference (cm) Birth exaamination patients controls Figure 5: Examinations of birth of new-born outcomes with into hemorrhoid patients for pregnant women. 13 Sarc. Jr. Med. Sur. vol-2, issue-6 (2023) pp-9-16 Omar, A.F.et al., Figure 6: Evaluations of the rate of hemorrhoid outcomes into hemorrhoid patients for pregnant women patients controls Rate of hemorrhoids Variables 0 0 0 0 0 Hemorrhoids rate (ITT) 34 53.13 11 17.19 4.24 Hemorrhoids rate (PP) 18 28.13 9 14.06 3.11 0 10 20 30 40 50 60 Rate of hemorrhoids Variables Hemorrhoids rate (ITT) Hemorrhoids rate (PP) patients controls Rate of hemorrhoids Variables 0 0 0 0 0 Hemorrhoids rate (ITT) 34 53.13 11 17.19 4.24 Hemorrhoids rate (PP) 18 28.13 9 14.06 3.11 0 10 20 30 40 50 60 Rate of hemorrhoids Variables Hemorrhoids rate (ITT) Hemorrhoids rate (PP) Figure 6: Evaluations of the rate of hemorrhoid outcomes into hemorrhoid patients for pregnant women. Figure 6: Evaluations of the rate of hemorrhoid outcomes into hemorrhoid patients for pregnant women. RESULTS Figure 7: Evaluations of the rate of spontaneous miscarriage outcomes into hemorrhoid patients for pregnant women 0 5 10 15 20 25 30 35 40 45 patients controls Rate of spontaneous miscarriages Rate of spontaneous miscarriages Variables Spontaneous miscarriage rate (ITT) Spontaneous miscarriage rate (PP) Figure 7: Evaluations of the rate of spontaneous miscarriage outcomes into hemorrhoid patients for pregnant women 0 5 10 15 20 25 30 35 40 45 patients controls Rate of spontaneous miscarriages Rate of spontaneous miscarriages Variables Spontaneous miscarriage rate (ITT) Spontaneous miscarriage rate (PP) Figure 7: Evaluations of the rate of spontaneous miscarriage outcomes into hemorrhoid patients for pregnant women Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher Omar, A.F.et al., Omar, A.F.et al., Implications for clinical and research Pregnant women are a particularly susceptible demographic. Consequently, the safety of patient group interventions was critical. We selected to examine the miscarriage rate to demonstrate whether it failed to result in poor pregnancy outcomes. The miscarriage incidence did not change substantially across groups, and patients weren't reporting any extra adverse effects that may be linked to the impact of an intervention. On research analysis, we discovered that a history of perianal illness as well as newborn height represented independent risk factors for developing hemorrhoids after delivery. [Wolff, B.G. et al., 2007] 4. Abramowitz, L., Sobhani, I., Benifla, J.L., Vuagnat, A., Daraï, E., Mignon, M. and Madelenat, P. "Anal fissure and thrombosed external hemorrhoids before and after delivery." Diseases of the colon & rectum 45.5 (2002): 650-655. 5. Ferdinande, K., Dorreman, Y., Roelens, K., Ceelen, W. and De Looze, D. "Anorectal symptoms during pregnancy and postpartum: a prospective cohort study." Colorectal Disease 20.12 (2018): 1109-1116. 6. Medich, D.S. and Fazio, V.W. "Hemorrhoids, anal fissure, and carcinoma of the colon, rectum, and anus during pregnancy." Surgical Clinics of North America 75.1 (1995): 77-88. The only preventive factor that significantly reduced the probability of hemorrhoids was in the control group. Our findings are comparable to those published by Ferdinande et al. and Poskus et al. [Avsar, A.F. et al., 2010; Mirhaidari, S.J. et al., 2016], who discovered that a history of perianal illness is strongly related with an increase in hemorrhoids during pregnancy. However, we did not discover that constipation before to the first trimester was linked to hemorrhoids after birth. Our intervention included dietary and behavioural adjustments, which are also advised for conservative hemorrhoid therapy in non-pregnant patients. 7. Gojnic, M., Dugalic, V., Papic, M., Vidaković, S., Milićević, S. and Pervulov, M. "The significance of detailed examination of hemorrhoids during pregnancy." Clinical and Experimental Obstetrics & Gynecology 32.3 (2005): 183-184. 8. MacLennan, A.H., Taylor, A.W., Wilson, D.H. and Wilson, D. "The prevalence of pelvic floor disorders and their relationship to gender, age, parity and mode of delivery." BJOG 107.12 (2000): 1460-1470. 9. Shin, G.H., Toto, E.L. and Schey, R. “Pregnancy and Postpartum Bowel Changes: Constipation and Fecal Incontinence.” American Journal of Gastroenterology 110.4 (2015):521–9. CONCLUSION Due to the comparatively low miscarriage as well as hemorrhoid rates, small variations between research groups might have been ignored. Yet, the miscarriage rate was the most recognized result for assessing the safety of different prenatal procedures. Finally, our proposed method, which aims to change dietary and behavioral patterns, dramatically lowers the risk of hemorrhoids throughout pregnancy and may be safely advised to pregnant women. 10. Monika, S. and Rutherford, J.D. “Cardiovascular Physiology of Pregnancy Circulation.” "Cardiovascular physiology of pregnancy." Circulation 130.12 (2014): 1003- 1008. 11. Folden, S.L. “Practice Guidelines for the Management of Constipation in Adults.” Rehabil Nurs. 27 (2002):169–75. 12. Marx, F.A. “Prevention of hemorrhoids by controlled defecation.” Dis Colon Rectum. 36 (1993):1084. DISCUSSION prevalence of hemorrhoids following giving birth for the patient’s category (ITT-41%; PP-42%) was consistent with Poskus et al.'s observed rate of 40.7% in a comparable population. prevalence of hemorrhoids following giving birth for the patient’s category (ITT-41%; PP-42%) was consistent with Poskus et al.'s observed rate of 40.7% in a comparable population. According to our findings, either ITT or PP analyses revealed that this intervention reduced hemorrhoids by about 60% of the overall rate. The 14 © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License ) Publisher: SARC Publisher Sarc. Jr. Med. Sur. vol-2, issue-6 (2023) pp-9-16 Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License P bli h SARC P bli h Omar, A.F.et al., Omar, A.F.et al., ASCRS Textbook of Colon and Rectal Surgery (2007). 16. Füzün, M. “Anorektal Benign Hastalıklar.” Klinik Gastroenteroloji ve Hepatoloji. (2007). 17. Place, R., Hyman, N. and Simmang, C, et al. “The standart task force is the ASCRS.” Dis Colon Rectum. 46 (2003):573-6. 20. Avsar, A.F. and Keskin, H.L. “Hemorrhoids during pregnancy.” J Obstet Gynaecol. 30(2010):231-7. 21. Mirhaidari, S.J., Porter, J.A. and Slezak, F.A. "Thrombosed external hemorrhoids in pregnancy: a retrospective review of outcomes." International journal of colorectal disease 31.8 (2016): 1557-1559. 18. Creasy, R.K. and Resnik, R. “Maternal-fetal medicine.” Philadelphia: WB saunders (1984). 19. Wolff, B.G., Pemberton, J.H. and Wexner, S.D, et al. “Hemorrhoidal Disease.” The Copyright © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License Publisher: SARC Publisher REFERENCES 1. Thomson, W.H.F. “The nature of hemorrhoids.” Br J Surg. 62 (1975):542–52. 1. Thomson, W.H.F. “The nature of hemorrhoids.” Br J Surg. 62 (1975):542–52. 13. van Tol, R.R., Kleijnen, J., Watson, A.J.M., Jongen, J., Altomare, D.F. and Qvist, N, et al. “European Society of ColoProctology (ESCP) Guideline for Haemorrhoidal Disease.” :93. 2. Jakubauskas, M. and Poskus, T. "Evaluation and management of hemorrhoids." Diseases of the Colon & Rectum 63.4 (2020): 420-424. 2. Jakubauskas, M. and Poskus, T. "Evaluation and management of hemorrhoids." Diseases of the Colon & Rectum 63.4 (2020): 420-424. 14. Davis, B.R., Lee-Kong, S.A., Migaly, J., Feingold, D.L. and Steele, S.R. "The American Society of Colon and Rectal Surgeons clinical practice guidelines for the management of hemorrhoids." Diseases of the Colon & Rectum 61.3 (2018): 284-292. 3. Poskus, T., Buzinskienė, D., Drasutiene, G., Samalavicius, N.E., Barkus, A., Barisauskiene, A., Tutkuviene, J., Sakalauskaite, I., Drasutis, J., Jasulaitis, A. and Jakaitiene, A. "Haemorrhoids and anal fissures during pregnancy and after childbirth: a prospective cohort study." BJOG 121.13 (2014): 1666- 1671. 3. Poskus, T., Buzinskienė, D., Drasutiene, G., Samalavicius, N.E., Barkus, A., Barisauskiene, A., Tutkuviene, J., Sakalauskaite, I., Drasutis, J., Jasulaitis, A. and Jakaitiene, A. "Haemorrhoids and anal fissures during pregnancy and after childbirth: a prospective cohort study." BJOG 121.13 (2014): 1666- 1671. 15. Abstracts P. Int J Gynecol Obstet. 155 (2021): 127–532. 15 ight © 2022 The Author(s): This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0) International License ) Publisher: SARC Publisher Sarc. Jr. Med. Sur. vol-2, issue-6 (2023) pp-9-16 Omar, A.F., Abbas, M.R. and khairullah, D.A. "Evaluation of Hemorrhoid Outcomes for Pregnant Women." Sarcouncil Journal of Medicine and Surgery 2.5 (2023): pp 9-16. Cite this article as: Cite this article as: Omar, A.F., Abbas, M.R. and khairullah, D.A. "Evaluation of Hemorrhoid Outcomes for Pregnant Women." Sarcouncil Journal of Medicine and Surgery 2.5 (2023): pp 9-16. Omar, A.F., Abbas, M.R. and khairullah, D.A. "Evaluation of Hemorrhoid Outcomes for Pregnant Women." Sarcouncil Journal of Medicine and Surgery 2.5 (2023): pp 9-16. 16
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Anterior Lamina Cribrosa Insertion in Primary Open-Angle Glaucoma Patients and Healthy Subjects
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RESEARCH ARTICLE Anterior Lamina Cribrosa Insertion in Primary Open-Angle Glaucoma Patients and Healthy Subjects Kyoung Min Lee1, Tae-Woo Kim1*, Robert N. Weinreb2, Eun Ji Lee1, Michae¨l J. A. Girard3,4, Jean Martial Mari5 1. Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea, 2. Department of Ophthalmology and Hamilton Glaucoma Center, University of California San Diego, La Jolla, California, United States of America, 3. Department of Bioengineering, National University of Singapore, Singapore, Singapore, 4. Singapore Eye Research Institute, Singapore, Singapore, 5. INSERM U1032, Universite´ de Lyon, Lyon, France *twkim7@snu.ac.kr Abstract Purpose: To determine using swept-source optical coherence tomography (SS- OCT) whether there are differences in the location of the anterior lamina cribrosa insertion (ALI) in primary open-angle glaucoma (POAG) patients and healthy subjects. OPEN ACCESS Citation: Lee KM, Kim T-W, Weinreb RN, Lee EJ, Girard MJA, et al. (2014) Anterior Lamina Cribrosa Insertion in Primary Open-Angle Glaucoma Patients and Healthy Subjects. PLoS ONE 9(12): e114935. doi:10.1371/journal.pone.0114935 Methods: Fifty three eyes from 53 patients with POAG, and 53 eyes from 53 age- matched healthy subjects were included prospectively in Seoul National University Bundang Hospital. Twelve radial line B-scans centered on the optic disc in every half-clock-hour meridian were acquired using SS-OCT. The ALI position was assessed by measuring two parameters: (1) ALI distance (ALID)—the distance from the anterior scleral canal opening (ASCO) to the ALI; and (2) marginal anterior lamina cribrosa surface depth (mALCSD)—the perpendicular distance from the ASCO plane to the anterior lamina cribrosa surface. These parameters were compared between the two groups for each meridian. Editor: Bang V. Bui, University of Melbourne, Australia Received: July 15, 2014 Copyright:  2014 Lee et al. This is an open- access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and repro- duction in any medium, provided the original author and source are credited. Results: Both ALID (256¡54 vs. 209¡37 mm, mean ¡ SD, p,0.001) and mALCSD (232¡63 vs. 187¡40 mm, p,0.001) were significantly greater in the POAG group than in the normal group. The largest difference was observed at the 6.5 o9clock and 11.5 o9clock meridians for both ALID and mALCSD. Multiple regression analysis revealed a negative correlation between age and both ALID and mALCSD in the control group, and a negative correlation between mean deviation of the visual field test and both ALID and mALCSD in the POAG group. Conclusions: The ALI was displaced posteriorly in eyes with POAG compared to those of healthy controls. This finding suggests that the posteriorly located lamina Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Funding: The work was supported by a grant from the National Research Foundation of Korea funded by the Korean Government (no. 2013R1A1A1A05004781) and an unrestricted grant from Research to Prevent Blindness (New York, NY). The funding organizations had no role in the design or conduct of this research. Anterior Lamina Cribrosa Insertion in POAG cribrosa insertion is an important component of glaucomatous optic nerve excavation. cribrosa insertion is an important component of glaucomatous optic nerve excavation. Introduction Glaucoma is characterized by the loss of retinal ganglion cells and their axons, which is accompanied by corresponding visual field defects [1]. It is generally considered that glaucomatous axonal damage occurs principally at the lamina cribrosa [2–4]. Compression and displacement of the lamina cribrosa are thought to contribute to or initiate the blockade of axoplasmic flow within the retinal ganglion cell axons that ultimately leads to the death of retinal ganglion cells [4]. Structural alteration of the lamina cribrosa and the resulting pre-laminar tissue loss cause cupping (excavation) of the optic nerve head. Strain within the lamina cribrosa also could compress the laminar capillaries, causing ischemic insult to the axons [5, 6]. Active cell mediated remodeling of the extracellular matrix [7, 8] has also been suggested as an important part/mechanism of glaucomatous excavation [9]. Yang et al. recently demonstrated the occurrence of posterior migration of the laminar insertion in a primate glaucoma model in which cupping was detected by confocal scanning laser tomography after exposure to moderate intraocular pressure (IOP) elevations [10]. This finding suggests that not only the compression and posterior bowing of the lamina cribrosa but also the posterior migration of the laminar insertion, which is attributable to physical disruption or remodeling or both [10], is involved in glaucomatous cupping. The advent of enhanced depth imaging spectral-domain optical coherence tomography (SD- OCT) has made it possible to examine the lamina cribrosa in vivo [11–15]. Using this technology, Park et al. reported that the anterior laminar insertion (ALI) was displaced more posteriorly in the superior and inferior regions than in the nasal and temporal regions in healthy subjects [16]. However, to the best of our knowledge, lamina insertion has never been evaluated in glaucoma patients. We hypothesized that posteriorly displaced ALI position is a component of optic nerve head remodeling in glaucoma. Although it was demonstrated in experimental glaucoma model, no study has addressed this issue in human patients. The purpose of the present study was to compare the ALI position of primary open angle glaucoma (POAG) patients and healthy subjects, and to determine factors associated with the more posteriorly located ALI. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 OPEN ACCESS Funding: The work was supported by a grant from the National Research Foundation of Korea funded by the Korean Government Competing Interests: The authors have declared that no competing interests exist. 1 / 17 PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Anterior Lamina Cribrosa Insertion in POAG from all subjects. This study was approved by the Seoul National University Bundang Hospital Institutional Review Board and followed the tenets of the Declaration of Helsinki. All participants underwent comprehensive ophthalmic examinations that included best-corrected visual acuity (BCVA), Goldmann applanation tonometry, refraction tests, slit-lamp biomicroscopy, gonioscopy, dilated stereoscopic examination of the optic disc, disc photographs (EOS D60 digital camera, Canon, Utsunomiyashi, Tochigiken, Japan), central corneal thickness measurement (Orbscan II, Bausch & Lomb Surgical, Rochester, NY, USA), axial length measurement (IOL Master version 5, Carl Zeiss Meditec, Dublin, CA, USA), SD- OCT (Spectralis, Heidelberg Engineering, Heidelberg, Germany), SS-OCT (DRI- OCT1, Topcon, Tokyo, Japan), and standard automated perimetry (Humphrey Field Analyzer II 750, 24–2 Swedish interactive threshold algorithm, Carl Zeiss Meditec). To be included, eyes had to have a BCVA of 20/40 or better, a spherical equivalent range from 26.0 diopters to +3.0 diopters, cylinder correction within ¡3.0 diopters, and no history of intraocular or corneal refractive surgery. The exclusion criteria were [17] a tilted disc (defined by tilt ratio – the ratio between the longest and shortest diameters of the optic disc – over 1.3 [18], torted disc (defined by the torsion angle – the deviation of the long axis of the optic disc from the vertical meridian – over 15˚ [19], retinal or neurologic diseases that could affect visual function, unreliable visual field tests (fixation loss rate .20%, false- positive or false-negative error rates .25%), and poor-quality SS-OCT images in which peripheral the anterior lamina cribrosa surface could not be imaged at more than 12 meridians. When both eyes were eligible, one eye was randomly chosen for data analysis. POAG was defined as the presence of an open iridocorneal angle, glaucomatous optic neuropathy with notching, rim thinning, and a retinal nerve fiber layer (RNFL) defect, and corresponding defects in the visual field. Glaucomatous visual field defect was defined as (1) outside normal limits on glaucoma hemifield test; or (2) three abnormal points, with a P,5% probability of being normal and one with P,1% by pattern deviation; or (3) pattern standard deviation of ,5% confirmed on two consecutive reliable tests (fixation loss rate #20%; false- positive and false-negative error rates #25%). The inclusion criteria for normal subjects were IOP was ,21 mmHg, the RNFL thickness as measured by SD-OCT was within the normal range, and normal visual field results. Normal range for SD-OCT was within 95 percentile of the normative database. Normal visual field was the absence of glaucomatous visual field defect and neurological defect. Patients and Methods This prospective study enrolled newly diagnosed glaucoma patients and age- matched healthy subjects who visited Seoul National University Bundang Hospital between March 2013 and March 2014. Written informed consent was obtained PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 2 / 17 Anterior Lamina Cribrosa Insertion in POAG The longer wavelength compared with SD-OCT enables deeper posterior penetration [20], which may be advantageous for visualizing the peripheral lamina cribrosa and its insertion site [21–23]. The SS-OCT scans were obtained using 6-mm, 12-radial line scans centered on the optic disc. Thirty-two single images were registered and averaged for each line scan. To enhance visibility of peripheral lamina cribrosa, all images were post-processed by adaptive compensation [24, 25], and the measurement was performed by a glaucoma specialist (K.M.L) using Image J (version 1.48, National Insitute of Health, Bethesda, Maryland, USA). The longer wavelength compared with SD-OCT enables deeper posterior penetration [20], which may be advantageous for visualizing the peripheral lamina cribrosa and its insertion site [21–23]. The SS-OCT scans were obtained using 6-mm, 12-radial line scans centered on the optic disc. Thirty-two single images were registered and averaged for each line scan. To enhance visibility of peripheral lamina cribrosa, all images were post-processed by adaptive compensation [24, 25], and the measurement was performed by a glaucoma specialist (K.M.L) using Image J (version 1.48, National Insitute of Health, Bethesda, Maryland, USA). The clock hour location of the medians for the radial scans was determined as the closest meridian to the fovea-Bruch’s membrane opening axis (foBMO axis) to be the 9 o9clock position in all patients (Fig. 1) [26]. This was to correct for potential cyclotorsion of the eye or head tilt during image acquisition. As the SS- OCT does not display the foBMO axis, the infrared fundus photograph of SS- OCT (which contains 12 lines indicating the location of the scan) was overlapped with a Spectralis IR (Heidelberg Engineering, Heidelberg, Germany) fundus photograph using commercial software (Photoshop CC, Adobe Systems). With this approach, the maximum degree of inconsistency in regionalization among patients would be 7.5˚. The clock hour was assigned based on right-eye orientation. ALI was defined as the intersection of the scleral canal wall or the base of border tissue of Elschnig and the anterior surface of the lamina cribrosa in each of the 12 radial scans. Using these 12 scans, the ALI position was assessed at every- half- clock hour (24 meridians, both sides of each scan) by measuring the following 2 parameters: (1) ALI distance (ALID) – defined as the distance from the anterior scleral canal opening (ASCO) to the ALI; and (2) marginal anterior lamina cribrosa surface depth (mALCSD) – defined as the perpendicular distance from the ASCO plane to the anterior lamina cribrosa surface (Fig. 1). To determine ASCO, the anterior scleral surface plane was traced and/or projected to the optic nerve head (Fig. 2). The ALID and mALCSD were measured by an observer (K.M.L.) who was masked to the clinical information using both original images and those processed by adaptive compensation. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Swept-source optical coherence tomography p p g p y SS-OCT was performed using the DRI-OCT1 (Topcon, Tokyo, Japan) [20–23]. This OCT uses a light source of a wavelength-sweeping laser centered at 1050 nm, with a repetition rate of 100,000 Hz, yielding an 8 mm axial resolution in tissue. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 3 / 17 Data analysis To measure the interobserver reproducibility of measurement of ALID and mALCSD, 2 observers (K.M.L. and T-W.K.) measured ALID and mALCSD in 21 randomly selected eyes (84 meridians; superior, inferior, nasal, and temporal meridians in each patient), and the intra-class correlation coefficients (ICC) were calculated. Intraobserver reproducibility was assessed based on the 2 measure- ments by one observer (K.M.L) in the same manner. ALID and mALCSD were compared between the POAG patients and healthy subjects using an independent t test. To overcome multiple comparisons of the 24 ALI positions, Bonferroni correction was applied and the cutoff for statistical significance was set at p,0.002. Factors associated with ALID and mALCSD were also assessed using PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 4 / 17 Anterior Lamina Cribrosa Insertion in POAG Fig. 1. Measurement of the anterior lamina cribrosa insertion (ALI) position and marginal anterior laminar cribrosa depth (mALCSD). A. SS-OCT image without labels. B. SS-OCT image after adaptive compensation. C. Measurement of ALI distance (ALID). The yellow line indicates the anterior lamina cribrosa surface, and the white lines indicate the choroidoscleral interface. ALID (red arrow lines) was defined as the distance from the anterior scleral canal opening (green dots) to the meeting point of the anterior laminar surface and the scleral canal wall (yellow dots). D. mALCSD (red arrow lines) was defined as the perpendicular distance from the anterior scleral canal opening plane (green dashed line) to the anterior lamina cribrosa surface (yellow line) at the location of the anterior scleral canal opening (green dots). E. Alignment of the SS-OCT scans to the fovea–Bruch’s membrane opening center axis (foBMO axis), obtained using Spectralis infrared (IR) fundus photography (upper left). The SS-OCT IR fundus photography (upper right), which contains 12 lines indicating the location of the scan, was overlapped with the Spectralis IR fundus photograph (lower). The SS-OCT radial scan line that was closest to the foBMO axis (thin arrow) was defined as the 9 o9clock meridian (thick arrow). Note that the numbers in the SS-OCT IR fundus photography represent the serial number of the scans, not the clock-hour meridian. Fig. 1. Measurement of the anterior lamina cribrosa insertion (ALI) position and marginal anterior laminar cribrosa depth (mALCSD). A. SS-OCT image without labels. B. SS-OCT image after adaptive compensation. C. Measurement of ALI distance (ALID). The yellow line indicates the anterior lamina cribrosa surface, and the white lines indicate the choroidoscleral interface. Data analysis ALID (red arrow lines) was defined as the distance from the anterior scleral canal opening (green dots) to the meeting point of the anterior laminar surface and the scleral canal wall (yellow dots). D. mALCSD (red arrow lines) was defined as the perpendicular distance from the anterior scleral canal opening plane (green dashed line) to the anterior lamina cribrosa surface (yellow line) at the location of the anterior scleral canal opening (green dots). E. Alignment of the SS-OCT scans to the fovea–Bruch’s membrane opening center axis (foBMO axis), obtained using Spectralis infrared (IR) fundus photography (upper left). The SS-OCT IR fundus photography (upper right), which contains 12 lines indicating the location of the scan, was overlapped with the Spectralis IR fundus photograph (lower). The SS-OCT radial scan line that was closest to the foBMO axis (thin arrow) was defined as the 9 o9clock meridian (thick arrow). Note that the numbers in the SS-OCT IR fundus photography represent the serial number of the scans, not the clock-hour meridian. doi:10.1371/journal.pone.0114935.g001 doi:10.1371/journal.pone.0114935.g001 Fig. 2. Schematic diagram and sample images for detecting the anterior scleral canal opening (ASCO) in various types of border tissue of Elschnig (BTE). (A,B) non-oblique BTE, (C,D) externally oblique BTE, (E,F) internally oblique BTE. B, D, F. Left column is SS-OCT image without label, and right column is SS-OCT image with label. Anterior scleral surface (red dashed lines) is followed to the optic nerve head, and projected to define the ASCO (green dots). / Fig. 2. Schematic diagram and sample images for detecting the anterior scleral canal opening (ASCO) in various types of border tissue of Elschnig (BTE). (A,B) non-oblique BTE, (C,D) externally oblique BTE, (E,F) internally oblique BTE. B, D, F. Left column is SS-OCT image without label, and right column is SS-OCT image with label. Anterior scleral surface (red dashed lines) is followed to the optic nerve head, and projected to define the ASCO (green dots). Fig. 2. Schematic diagram and sample images for detecting the anterior scleral canal opening (ASCO) in various types of border tissue of Elschnig (BTE). (A,B) non-oblique BTE, (C,D) externally oblique BTE, (E,F) internally oblique BTE. B, D, F. Left column is SS-OCT image without label, and right column is SS-OCT image with label. Anterior scleral surface (red dashed lines) is followed to the optic nerve head, and projected to define the ASCO (green dots). Anterior Lamina Cribrosa Insertion in POAG multiple linear regression analysis. Statistical analyses were performed with Statistical Package for Social Sciences version 18.0 for Windows (SPSS, Chicago, IL, USA). Except where stated otherwise, the data are presented as mean ¡ SD values. Results One eye from each of 53 patients with POAG (29 male and 24 female) and one eye from each of 53 age-matched normal subjects (23 male and 30 women) were included in the analysis. Of these, 5 eyes were excluded because the disc was tilted or torted, and 1 was excluded because the peripheral anterior lamina cribrosa could not be visualized in more than half of the meridians, leaving a final sample of 50 glaucoma eyes (22 female) and 50 control eyes (29 female). Comparisons between POAG and age-matched control groups yielded no significant differences in age, BCVA, refractive errors, central corneal thickness, and axial length. The untreated IOP (average of at least two measurements before initiating any IOP- lowering treatment) was higher in the POAG group than in healthy subjects (Table 1). Table 2 shows the number of eyes for which either ALID or mALCSD was not measurable in each meridian due to invisibility of the ALI or peripheral anterior laminar surface. The ALI position was more often undetectable in the POAG patients than in the healthy subjects. The mALCSD was measurable in nearly all cases in both the POAG and control groups (Table 2). The mALCSD showed good correlation with ALID (Pearson’s correlation 50.895, p,0.001). The ALI position was undetectable in eyes with a deeply located lamina cribrosa, as evidenced by a larger mALCSD for eyes with an undetectable ALI than for those in which the ALI was detectable (327¡106 vs 221¡79 mm, p,0.001). In eyes with an optic disc pit, the ALI was measured from the extension line of the anterior lamina cribrosa surface (Fig. 3). An acquired optic disc pit was observed in nine of the POAG cases. Table 2 shows the number of eyes for which either ALID or mALCSD was not measurable in each meridian due to invisibility of the ALI or peripheral anterior laminar surface. The ALI position was more often undetectable in the POAG patients than in the healthy subjects. The mALCSD was measurable in nearly all cases in both the POAG and control groups (Table 2). The mALCSD showed good correlation with ALID (Pearson’s correlation 50.895, p,0.001). The ALI position was undetectable in eyes with a deeply located lamina cribrosa, as evidenced by a larger mALCSD for eyes with an undetectable ALI than for those in which the ALI was detectable (327¡106 vs 221¡79 mm, p,0.001). PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Data analysis doi:10.1371/journal.pone.0114935.g002 doi:10.1371/journal.pone.0114935.g002 5 / 17 PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Anterior Lamina Cribrosa Insertion in POAG Table 1. Characteristics of the patients with primary open-angle glaucoma (POAG) and the normal healthy (control) subjects. POAG (N550) Control (N550) p Male:female 28:22 21:29 0.230* Right:left 24:26 25:25 1.000* Age 60.9¡11.2 61.0¡11.5 0.972{ logMAR 0.09¡0.09 0.11¡0.10 0.176{ Refractive errors (D) 20.07¡1.64 0.49¡1.88 0.123{ Central corneal thickness (mm) 553¡30 558¡31 0.438{ Untreated IOP (mmHg) 16.0¡3.6 13.5¡2.5 ,0.001{ IOP scan (mmHg) 12.1¡3.5 13.5¡2.6 0.023{ Axial length (mm) 23.8¡1.2 23.7¡1.1 0.794{ Mean deviation 26.68¡6.48 20.30¡1.38 ,0.001{ *Calculated using the chi-square test. {Calculated using the independent t test. LogMAR 5 logarithm of the minimum angle of resolution; D5 diopters; IOP 5 intraocular pressure; IOP scan 5 IOP at the time of SS-OCT. primary open-angle glaucoma (POAG) and the normal healthy (control) subjects. acteristics of the patients with primary open-angle glaucoma (POAG) and the normal healthy (control) subjects. Table 1. Characteristics of the patients with primary open-angle glaucoma (POAG) and the normal healthy ( {Calculated using the independent t test. LogMAR 5 logarithm of the minimum angle of resolution; D5 diopters; IOP 5 intraocular pressure; IOP scan 5 IOP at the time of SS-OCT. Comparison of ALID and mALCSD ALID was significantly greater in the POAG group than in the normal group (256¡54 vs 209¡37 mm, p,0.001; Table 4, Fig. 4). The greatest difference was observed in the 6.5 o9clock (285¡87 vs 207¡44 mm, p,0.001) and 11.5 o9clock (298¡80 vs 237¡64 mm, p,0.001; Table 4, Fig. 5) meridians. Similarly, mALCSD was significantly greater in the POAG group than in the normal group Comparison of ALID and mALCSD ALID was significantly greater in the POAG group than in the normal group (256¡54 vs 209¡37 mm, p,0.001; Table 4, Fig. 4). The greatest difference was observed in the 6.5 o9clock (285¡87 vs 207¡44 mm, p,0.001) and 11.5 o9clock (298¡80 vs 237¡64 mm, p,0.001; Table 4, Fig. 5) meridians. Similarly, ble 2. Number of cases for which either the anterior lamina cribrosa insertion distance (ALID) or the marginal anter s not measurable in each meridian. Table 2. Number of cases for which either the anterior lamina cribrosa insertion distance (ALID) or the marginal anterior laminar cribrosa depth (mALCSD) was not measurable in each meridian. Results In eyes with an optic disc pit, the ALI was measured from the extension line of the anterior lamina cribrosa surface (Fig. 3). An acquired optic disc pit was observed in nine of the POAG cases. The measurement of ALID showed excellent intraobserver reproducibility {ICC (1, 1) for the superior 50.995 (0.988–0.998); inferior 50.997 (0.992–0.999); nasal 50.994 (0.985–0.998); and temporal regions 50.992 (0.980–0.997)}, and interobserver reproducibility {ICC (2, 1) for the superior 50.993 (0.982–0.997); inferior 50.994 (0.985–0.998); nasal 50.992 (0.980–0.997); and temporal regions 50.992 (0.980–0.997)}. The measurement of mALCSD also yielded excellent intraobserver reproducibility {ICC (1, 1) for the superior 50.995 (0.987–0.998); inferior 50.987 (0.967–0.995); nasal 50.995 (0.987–0.998); and temporal regions 50.996 (0.990–0.998)}, and interobserver reproducibility {ICC (2, 1) for the superior 50.970 (0.926–0.988); inferior 50.990 (0.976–0.996); nasal 50.992 (0.979–0.997); and temporal regions 50.990 (0.975–0.996), Table 3}. 6 / 17 y q values were calculated by the Fisher’s exact test. y D 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POA {p values were calculated by the Fisher s exact test. ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glaucoma. values were calculated by the Chi-square test. e calculated by the Fisher s exact test. or lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 prima calculated by the Chi-square test. e calculated by the Fisher’s exact test. p a ues e e ca cu a ed by e s e s e ac es ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glaucoma. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribr doi:10.1371/journal.pone.0114935.t002 doi:10.1371/journal.pone.0114935.t002 p y q p values were calculated by the Fisher’s exact test. her’s exact test. rtion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glaucom Chi square test. Fisher’s exact test. nsertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glau r the anterior lamina cribrosa insertion distance (ALID) or the marginal anterior laminar cribrosa depth (mALCSD) Clock hour ALID mALCSD POAG (N550) Control (N550) p POAG (N550) Control (N550) p 3 12 10 0.629* 2 1 1.000{ 4 4 3 1.000{ 1 0 1.000{ 5 6 4 0.741{ 0 1 1.000{ 6 3 1 0.617{ 0 0 6.5 0 0 0 0 7 0 0 0 0 8 0 0 0 0 9 0 0 0 0 10 1 2 1.000{ 0 0 11 5 3 0.715{ 0 1 1.000{ 11.5 7 3 0.318{ 0 0 12 9 4 0.234{ 1 1 1.000{ 1 20 15 0.295* 2 1 1.000{ 2 17 14 0.517* 1 2 1.000{ PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 7 / 17 Anterior Lamina Cribrosa Insertion in POAG Fig. 3. ALID measurement in eyes with an acquired pit. A. SS-OCT image without labels. Note that the lamina cribrosa is disinserted from the adjacent sclera. B. SS-OCT image after adaptive compensation. C. ALI was defined using an imaginary extension line (yellow dashed line) in eyes with a pit. Fig. 3. ALID measurement in eyes with an acquired pit. A. SS-OCT image without labels. Note that the amina cribrosa is disinserted from the adjacent sclera. B. SS-OCT image after adaptive compensation. C. ALI was defined using an imaginary extension line (yellow dashed line) in eyes with a pit. doi:10.1371/journal.pone.0114935.g003 (232¡63 vs 187¡40 mm, p,0.001; Table 5). The differences were most prominent in the 6 o9clock (294¡92 vs 199¡47 mm, p,0.001) and 11.5 o9clock (316¡84 vs 233¡57 mm, p,0.001; Table 5, Fig. 5) meridians. (232¡63 vs 187¡40 mm, p,0.001; Table 5). The differences were most prominent in the 6 o9clock (294¡92 vs 199¡47 mm, p,0.001) and 11.5 o9clock (316¡84 vs 233¡57 mm, p,0.001; Table 5, Fig. 5) meridians. Factors associated with ALID and mALCSD In the healthy subjects, univariate linear regression analysis revealed that a greater ALID was associated with both a higher IOP and younger age. mALCSD was also positively associated with IOP and axial length, and negatively associated with age. In the multivariate analysis, only age was associated with ALID (Table 6). In the POAG patients, untreated IOP and visual field mean deviation showed significant association with ALID and mALCSD. In the multivariate analysis, the visual field mean deviation was associated with both ALID and mALCSD (Table 7). PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Anterior Lamina Cribrosa Insertion in POAG Table 4. Comparison of ALID between POAG patients and normal healthy (control) subjects. Clock hour POAG (mm) Control (mm) p* 3 240¡71 194¡51 0.001 4 242¡68 208¡56 0.009 5 261¡80 218¡53 0.003 6 281¡83 207¡44 ,0.001 6.5 285¡87 207¡47 ,0.001 7 252¡87 188¡48 ,0.001 8 197¡73 176¡57 0.102 9 201¡81 160¡50 0.003 10 242¡71 191¡53 ,0.001 11 293¡86 234¡55 ,0.001 11.5 298¡80 237¡64 ,0.001 12 318¡102 259¡46 ,0.001 1 285¡70 243¡52 0.008 2 269¡58 233¡62 0.015 Mean{ 256¡54 209¡37 ,0.001 *p values were calculated by the independent-t test. {Mean value was obtained by the average of every half clock hour meridian, although only half of the total measurements were displayed on this table. ALID 5 anterior lamina cribrosa insertion distance; POAG 5 primary open angle glaucoma. Table 4. Comparison of ALID between POAG patients and normal healthy (control) subjects. *p values were calculated by the independent-t test. {Mean value was obtained by the average of every half clock hour meridian, although only half of the total measurements were displayed on this table. ALID 5 anterior lamina cribrosa insertion distance; POAG 5 primary open angle glaucoma. doi:10.1371/journal.pone.0114935.t004 first report to compare ALID and mALCSD measured from the anterior scleral opening in POAG patients and healthy subjects. first report to compare ALID and mALCSD measured from the anterior scleral opening in POAG patients and healthy subjects. g y j Previous studies that measured the anterior laminar surface depth [14, 15] or ALID [16] used Bruch’s membrane termination plane as the reference. The Previous studies that measured the anterior laminar surface depth [14, 15] or ALID [16] used Bruch’s membrane termination plane as the reference. The Fig. 4. Comparison of ALI positions between eyes from a patient with primary open-angle glaucoma (POAG) and a normal control (both aged 62 years). The images are for the right eye in both patients. White arrows in the central circle indicate the meridians of the scans. The upper and lower images in each pair are from the normal control and POAG eyes, respectively. Yellow lines indicate the lamina cribrosa surface and white lines indicate the choroidoscleral interface. Note that ALID is greater in the POAG eye, with the most prominent differences being observed in the superotemporal and inferotemporal areas. Fig. 4. Discussion This prospective in-vivo case-control study found the ALI to be located more posteriorly in POAG patients than in normal controls in the inferotemporal (6–7 o9clock), superotemporal (9.5–12 o9clock), and nasal (2.5–3 o9clock) meridians (Fig. 5). Similarly, mALCSD was greater in the inferior (4.5–7 o9clock) and superior (9–3 o9clock) meridians (Fig. 5). To the best of our knowledge, this is the Table 3. Inter and intraobserver reliability of measuring ALID and mALCSD. ALID Intraobserver reliability Interobserver reliability Superior 0.995 (0.988–0.998) 0.993 (0.982–0.997) Inferior 0.997 (0.992–0.999) 0.994 (0.985–0.998) Nasal 0.994 (0.985–0.998) 0.992 (0.980–0.997) Temporal 0.992 (0.980–0.997) 0.992 (0.980–0.997) mALCSD Intraobserver reliability Interobserver reliability Superior 0.995 (0.987–0.998) 0.970 (0.926–0.988) Inferior 0.987 (0.967–0.995) 0.990 (0.976–0.996) Nasal 0.995 (0.987–0.998) 0.992 (0.979–0.997) Temporal 0.996 (0.990–0.998) 0.990 (0.975–0.996) ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth. Table 3. Inter and intraobserver reliability of measuring ALID and mALCSD. D 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth. ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 8 / 17 Comparison of ALI positions between eyes from a patient with primary open-angle glaucoma (POAG) and a normal control (both aged 62 years). The images are for the right eye in both patients. White arrows in the central circle indicate the meridians of the scans. The upper and lower images in each pair are from the normal control and POAG eyes, respectively. Yellow lines indicate the lamina cribrosa surface and white lines indicate the choroidoscleral interface. Note that ALID is greater in the POAG eye, with the most prominent differences being observed in the superotemporal and inferotemporal areas. doi:10.1371/journal.pone.0114935.g004 PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 9 / 17 Anterior Lamina Cribrosa Insertion in POAG Fig. 5. Comparison of ALID (A) and mALCSD (B) between subjects with POAG and healthy controls in each meridian. Significant differences after Bonferroni correction (p,0.002) are indicated with asterisks. doi:10.1371/journal.pone.0114935.g005 Fig. 5. Comparison of ALID (A) and mALCSD (B) between subjects with POAG and healthy controls in each meridian. Significant differences after Bonferroni correction (p,0.002) are indicated with asterisks. Fig. 5. Comparison of ALID (A) and mALCSD (B) between subjects with POAG and healthy controls in each meridian. Significant differences after Bonferroni correction (p,0.002) are indicated with asterisks. doi:10.1371/journal.pone.0114935.g005 doi:10.1371/journal.pone.0114935.g005 current study can be distinguished from those studies because the ALI position was measured using the anterior scleral opening level as the reference. The lamina cribrosa is a collagenous extension of the sclera. It is formed by ingrowth of the surrounding sclera after the optic nerve has already been formed in the fetal period [27, 28]. It is therefore reasonable to measure ALID from the anterior scleral opening and not from the level of Bruch’s membrane opening to assess the extent of posterior migration of the ALI. This matter is particularly important because choroidal thickness may vary among patients [29]. In eyes with a thick choroid, ALID would be overestimated even in eyes without any or only a small degree of posterior migration of the ALI. In contrast, ALID would be underestimated in eyes with a thin choroid, even with substantial posterior current study can be distinguished from those studies because the ALI position was measured using the anterior scleral opening level as the reference. The lamina cribrosa is a collagenous extension of the sclera. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Anterior Lamina Cribrosa Insertion in POAG Table 5. Comparison of mALCSD between POAG patients and normal healthy (control) subjects. Clock hour POAG (mm) Control (mm) p* 3 252¡94 194¡68 0.001 4 238¡81 198¡57 0.005 5 262¡95 199¡52 ,0.001 6 294¡92 199¡47 ,0.001 6.5 286¡95 201¡50 ,0.001 7 253¡98 184¡48 ,0.001 8 196¡80 167¡60 0.046 9 200¡83 148¡53 ,0.001 10 245¡77 190¡60 ,0.001 11 297¡84 226¡61 ,0.001 11.5 316¡84 233¡57 ,0.001 12 326¡101 252¡58 ,0.001 1 313¡105 236¡66 ,0.001 2 284¡97 220¡63 ,0.001 Mean{ 232¡63 187¡40 ,0.001 *p values were calculated by the independent-t test. {Mean value was obtained by the average of every half clock hour meridian, although only half of the total measurements were displayed on this table. mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glaucoma. Table 5. Comparison of mALCSD between POAG patients and normal healthy (control) subjects. *p values were calculated by the independent-t test. {Mean value was obtained by the average of every half clock hour meridian, although only half of the total measurements were displayed on this table. mALCSD 5 marginal anterior lamina cribrosa surface depth; POAG 5 primary open angle glaucoma. doi:10.1371/journal.pone.0114935.t005 doi:10.1371/journal.pone.0114935.t005 migration of the ALI (Fig. 6). Use of the anterior scleral opening level as the reference avoids these measurement errors. In addition to the ALID, the mALCSD was also measured in the present study because the ALID was not always visible. mALCSD is the summation of the vertical component of ALID and the effect of posterior bowing of the lamina cribrosa. However, given the short distance between the ALI and the lamina cribrosa surface where mALCSD was measured, the effect of posterior bowing may be small. Thus, we considered that mALCSD can be used as a surrogate parameter that may indirectly reflect ALID. Since mALCSD is measured Table 6. Factors affecting ALI in normal healthy subjects. ALID mALCSD Univariate Multivariate* Univariate Multivariate* b p b p b p b p Age 21.352 0.003 21.054 0.050 21.984 ,0.001 21.706 0.002 IOP 4.590 0.029 2.187 0.328 5.623 0.012 1.812 0.406 CCT 0.098 0.577 0.093 0.620 SEQ 22.575 0.376 23.212 0.294 AXL 8.093 0.101 1.899 0.711 11.399 0.030 2.332 0.642 ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; IOP 5 intraocular pressure; CCT 5 central corneal thickness; SEQ 5 spherical equivalent; AXL 5 axial length. It is formed by ingrowth of the surrounding sclera after the optic nerve has already been formed in the fetal period [27, 28]. It is therefore reasonable to measure ALID from the anterior scleral opening and not from the level of Bruch’s membrane opening to assess the extent of posterior migration of the ALI. This matter is particularly important because choroidal thickness may vary among patients [29]. In eyes with a thick choroid, ALID would be overestimated even in eyes without any or only a small degree of posterior migration of the ALI. In contrast, ALID would be underestimated in eyes with a thin choroid, even with substantial posterior PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 10 / 17 PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 0114935 December 22, 2014 11 / 17 p q ; g values of less than 0.10 in the univariate regression analysis were included in the multivariate analysis. ; p q ; g *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate doi:10.1371/journal.pone.0114935.t006 Anterior Lamina Cribrosa Insertion in POAG Table 7. Factors affecting anterior laminar cribrosa insertion in primary open angle glaucoma. ALID mALCSD Univariate Multivariate* Univariate Multivariate* b p b p b p B p Age 0.058 0.938 20.345 0.672 Untreated IOP 5.102 0.022 1.898 0.389 6.422 0.007 2.905 0.202 CCT 20.232 0.505 20.464 0.218 SEQ 4.657 0.361 1.106 0.843 AXL 25.694 0.592 23.607 0.751 MD 24.864 ,0.001 24.366 0.001 25.581 ,0.001 24.817 0.001 ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; IOP 5 intraocular pressure; CCT 5 central corneal thickness; SEQ 5 spherical equivalent; AXL 5 axial length; MD 5 mean deviation. *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate analysis. Table 7. Factors affecting anterior laminar cribrosa insertion in primary open angle glaucoma. ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; IOP 5 intraocular pressure; CCT 5 central corneal thickness; SEQ 5 spherical equivalent; AXL 5 axial length; MD 5 mean deviation. *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate analysis. ALID 5 anterior lamina cribrosa insertion distance; mALCSD 5 marginal anterior lamina cribrosa surface depth; IO corneal thickness; SEQ 5 spherical equivalent; AXL 5 axial length; MD 5 mean deviation. *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate perpendiculary from the the anterior sclera edge, it was more frequently measurable than ALID (Table 2). The difference of mALCSD between the POAG patients and healthy subjects was similar to that of ALI in each meridian. perpendiculary from the the anterior sclera edge, it was more frequently measurable than ALID (Table 2). The difference of mALCSD between the POAG patients and healthy subjects was similar to that of ALI in each meridian. In the healthy subjects, the ALID and mALCSD were negatively correlated with age. We speculate that it could be associated with age-related changes in the connective tissue. Maintaining a high rate of matrix remodeling with matrix metalloproteinase is an important mechanism for conserving the plasticity of the lamina cribrosa in physiologic conditions [30]. *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate analysis. doi:10.1371/journal.pone.0114935.t006 Table 6. Factors affecting ALI in normal healthy subjects. ; p q ; g *Variables with P values of less than 0.10 in the univariate regression analysis were included in the multivariate analysis. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 11 / 17 doi:10.1371/journal.pone.0114935.t007 Anterior Lamina Cribrosa Insertion in POAG [35]. This highlights the unique compliance and biomechanics of the aged lamina cribrosa [36, 37]. We speculate that thickening and stiffening of the lamina cribrosa would lead to a smaller ALID and mALCSD. Meanwhile, age was not associated with either ALID or mALCSD in the glaucoma patients. The effect of age might be masked by a more influential factor (e.g., glaucoma severity and IOP-related stress) in them. In the glaucoma patients, untreated IOP and mean deviation showed a significant association in the univariate analysis. However, only visual field mean deviation remained significant in the multivariate analysis. This finding suggests that the ALI position is not simply dependent on the level of IOP but associated with overall factors involved in the glaucomatous optic nerve damage. In the development of glaucomatous excavation, not only the IOP-related stress itself but also the active remodeling process which is controlled by ECM degrading enzymes (e.g, MMPs) contributed by reactive astrocytes are involved [8, 38]. Such process would continue throughout the disease up to the end stage of disease, thereby leading larger ALID found in eyes with more advanced disease [9]. The most prominent group difference was observed in the inferotemporal (6–7 o9clock) and superotemporal (9.5–12 o9clock) meridians, where glaucomatous damage occurs preferentially. It is generally considered that the lamina cribrosa is less dense superiorly and inferiorly, rendering those areas more susceptible to pressure-induced damage [39]. Our findings suggest that the connection between the lamina cribrosa and the peripapillary sclera is also weaker in these sectors than in the temporal and nasal sectors, thereby rendering them more susceptible to pressure-induced stress. Alternatively, this finding could suggest that tissue remodeling of the lamina cribrosa, which is largely mediated by astrocytes [8, 38, 40], is more vigorous in this region. It is also possible that astrocytes are more strongly activated in this region due to the greater strain on the laminar beams in this area. In the present study, 92% of the studied POAG patients had an untreated IOP of ,21 mmHg over multiple measurements on different days. This suggests that even though their IOP was within the statistically normal range, IOP-induced stress is associated with POAG. Recent computational modeling studies have demonstrated that the mechanical stress imposed on the optic nerve head may vary markedly in eyes with the same IOP, depending on ocular geometry factors such as scleral thickness [41–44]. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Since aging generally involves increased sequestration of matrix metalloproteinase (MMP) and a reduced turnover of the extracellular matrix [31], it can be supposed that older eyes would have a thicker and stiffer lamina cribrosa. Human ex-vivo studies have found that advancing age is associated with a thicker lamina cribrosa [32] and changes in the composition of the extracellular matrix [33, 34]. Being consistent with this, we have reported that the thickness of the central lamina cribrosa increases with aging Fig. 6. Comparison of ALID and mALCSD based on Bruch’s membrane opening (white dashed line) and the anterior scleral canal opening (green dashed line) in a glaucomatous eye (A, B, C) and a normal eye (D, E, F). A, D. SS-OCT images without labels. B, E. SS-OCT images after adaptive compensation. C, F. Yellow lines indicate the lamina cribrosa surface, and green lines indicate the anterior scleral surface. ALID measured from Bruch’s membrane opening would be a (red dashed line) +b (red line), while ALID from the anterior scleral canal opening would be a. Note that a+b is similar between C and F; however, a is noticeably smaller in F than in C. Similarly, mALCSD is much larger in F when it is measured from the level of BMO (longer double arrows), although the depths from the ASCO (shorter double arrows) are smaller in F than in C. Fig. 6. Comparison of ALID and mALCSD based on Bruch’s membrane opening (white dashed line) and the anterior scleral canal opening (green dashed line) in a glaucomatous eye (A, B, C) and a normal eye (D, E, F). A, D. SS-OCT images without labels. B, E. SS-OCT images after adaptive compensation. C, F. Yellow lines indicate the lamina cribrosa surface, and green lines indicate the anterior scleral surface. ALID measured from Bruch’s membrane opening would be a (red dashed line) +b (red line), while ALID from the anterior scleral canal opening would be a. Note that a+b is similar between C and F; however, a is noticeably smaller in F than in C. Similarly, mALCSD is much larger in F when it is measured from the level of BMO (longer double arrows), although the depths from the ASCO (shorter double arrows) are smaller in F than in C. doi:10.1371/journal.pone.0114935.g006 12 / 17 PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Anterior Lamina Cribrosa Insertion in POAG migration of the ALI may be considered an additional mechanism of optic-disc cupping. It may be particularly relevant in the presence of peripheral excavation and neural rim loss which are not explained by the posterior migration of the central lamina cribrosa alone [9]. Second, posterior migration of the lamina cribrosa would shorten the distance from the anterior laminar surface to the retrolaminar subarachnoid space. This would result in a steeper translaminar pressure gradient in the peripheral scleral canal, which may increase the impairment of the axoplasmic flow, especially in the peripheral scleral canal [47, 48]. Third, the blood supply to the optic nerve head enters largely from the periphery [5]. Thus, structural alterations in the lamina cribrosa insertion may be accompanied by a change in the vascular supply to the optic nerve. Fourth, disruption or remodeling of the laminar beams may occur during the process of posterior migration, which may in turn result in rupture of the capillaries inside the laminar beams and disc hemorrhage [9, 49]. In line with this concept, we recently demonstrated the occurrence of a structural alteration around the time of disc hemorrhage [49]. g This study has limitations. First, the ALI position was not always visible in all meridians. However, it is not likely that this we do not consider that this affected our conclusions. The ALI is likely to be invisible in eyes with a deeply located lamina cribrosa. Consistent with this notion, mALCSD was larger in eyes in which the ALI position was invisible. In addition, the ALI position was more often invisible in the POAG patients. This would lead to underestimation of the average ALID for the entire POAG patients. Thus, any potential bias derived from this limitation would actually reinforce our finding. We consider that the true difference between the POAG patients and healthy subjects is greater than was revealed by the present study. Second, in eyes with an optic disc pit, we measured ALID using an extension line. This measurement is probably inappropriate because the ALI does not exist in such eyes. However, an acquired pit is thought to be a result of optic nerve remodeling associated with lamina cribrosa disinsertion [23, 50, 51]. Postulating that an acquired pit is part of a spectrum of lamina cribrosa displacement, we could not exclude the POAG eyes with pits. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 Based on this notion, additional factors may amplify the IOP-derived stress imposed on the optic nerve head in normal- tension glaucoma. Alternatively, Ren et al. reported that the cerebrospinal fluid (CSF) pressure is lower in patients with a normal IOP [45]. Wang et al. subsequently reported that the orbital CSF space was narrower in patients with a normal IOP, consistent with their earlier study [46]. The presence of a low CSF pressure may increase the translaminar pressure gradient, leading the lamina cribrosa to the same condition as in patients with increased IOP and normal CSF pressure. p The existence of posterior migration may have several important implications for the pathogenesis of glaucomatous optic neuropathy [10]. First, posterior PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 13 / 17 Our measurement based on an extension line of the lamina cribrosa implicates the minimum approximation of ALI (i.e., the actual ALID would be the same or larger than our approximation in these eyes). Since acquired pits existed in only POAG patients, with an acquired pit, this limitation also reinforces our finding. Third, we excluded the eyes with tilted or torted optic disc. This was because those eyes might have distorted optic nerve head structure, and thus confounded our analysis. Due to this study design, our data cannot be applied to eyes with tilted or torted optic disc. In conclusion, the ALI position is located more posteriorly in POAG eyes than in healthy eyes, and this tendency is most prominent in the superotemporal and inferotemporal sectors. The ALI position is correlated with the visual field mean deviation. These findings support the notion that the posteriorly located lamina cribrosa insertion is an important component of glaucomatous optic nerve excavation. PLOS ONE | DOI:10.1371/journal.pone.0114935 December 22, 2014 14 / 17 Anterior Lamina Cribrosa Insertion in POAG Acknowledgments Author Contributions: Dr. Tae-Woo Kim had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data anaylsis. Financial Disclosure: RNW has received instruments form Heidelberg Engineering for use in research. Author Contributions Conceived and designed the experiments: KML TWK. Performed the experiments: KML TWK. Analyzed the data: KML TWK. Contributed reagents/materials/ analysis tools: MJAG JMM. Wrote the paper: KML TWK RNW EJL. Conceived and designed the experiments: KML TWK. Performed the experiments: KML TWK. Analyzed the data: KML TWK. Contributed reagents/materials/ analysis tools: MJAG JMM. Wrote the paper: KML TWK RNW EJL. 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What is the difference between perceived and actual risk of distracted driving? A field study on a real highway
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1. Introduction Distracted driving due to secondary tasks is the main cause of traffic accidents. These second- ary tasks include cognitive tasks (e.g., conversation and texting) and visual tasks (e.g., attend- ing to surrounding vehicles and billboards) [1–3]. Driving distractions reduce the lane- keeping performance of drivers, potentially leading to serious traffic crashes [4, 5]. In the United States, distracted driving caused 3,477 deaths in 2015, 14.5% of which were attributed to unstable lateral vehicle control [6, 7]. Data Availability Statement: All relevant data are within the manuscript. RESEARCH ARTICLE What is the difference between perceived and actual risk of distracted driving? A field study on a real highway RESEARCH ARTICLE a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Zhen Li, Chang WangID*, Rui Fu, Qinyu Sun, Hongjia Zhang School of Automobile, Chang’an University, Xi’an, Shaanxi, China * wangchang@chd.edu.cn * wangchang@chd.edu.cn OPEN ACCESS Citation: Li Z, Wang C, Fu R, Sun Q, Zhang H (2020) What is the difference between perceived and actual risk of distracted driving? A field study on a real highway. PLoS ONE 15(4): e0231151. https://doi.org/10.1371/journal.pone.0231151 Editor: Yanyong Guo, University of British Columbia, CANADA Copyright: © 2020 Li 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. PLOS ONE PLOS ONE Abstract Distracted driving is a leading cause of traffic accidents. It is influenced by driver attitude toward secondary tasks; however, field-based studies on the effects of low-perceived-risk tasks on lateral driving have rarely been reported. A total of 17 experienced non-profes- sional drivers were recruited to participate in two secondary tasks: a cognitive experiment (conversation) and a visual distraction experiment (observation of following vehicles), each representing low-perceived-risk secondary tasks. One-way analysis of variance (ANOVA) was conducted to evaluate the effects of low-perceived-risk tasks on lateral driving perfor- mance. ANOVA results indicated that compared with baseline (no task) lateral performance, lane-keeping ability was enhanced during cognitive distractions. In the visual distraction experiment, more than 50% of the distractions required 1–2 s. Lane deviation and its growth rate increased with the duration of distraction. Compared with cognitive distraction, lane deviation increased significantly with visual distraction, and lane-keeping performance was seriously impaired. For low-perceived-risk tasks, visual distractions impaired driving safety more seriously, compared with cognitive distractions, suggesting that drivers misjudge the risks associated with visual tasks. These results can contribute to the design of advanced driving-assistance systems and improve professional driver programs, potentially reducing the frequency of traffic accidents caused by distracted driving. a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Data Availability Statement: All relevant data are within the manuscript. Funding: This work is supported by National Key R&D Program of China (2018YFB1600501). Dangerous driving behaviors, including drunk driving and drowsy driving, have been pro- hibited by transportation laws and regulations in many countries. Use of mobile phones as a high-risk distraction task, has also been restricted in China since 2013; while driving, drivers Competing interests: The authors have declared that no competing interests exist. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 1 / 15 PLOS ONE What is the difference between perceived and actual risk of distracted driving? are not allowed to hold a phone and only use Bluetooth or headsets to make calls [8]. However, in addition to using mobile phones, various secondary tasks can cause distracted driving [1, 4, 9], which cannot be completely avoided by merely applying laws. These distractions impair driving performance, and numerous studies have been conducted to categorize driving dis- tractions. Cognitive distractions, visual distractions, and manual distractions comprise a widely used classification method [10]. Cognitive distractions occur when the driver is not entirely focused on the road (e.g., talking to passengers); visual distractions occur when the driver is distracted from keeping his or her eyes on the road (e.g., when concerned with the roadside environment or the rearview mirror); and manual distractions occur when the driver is distracted while operating certain devices (e.g., adjusting the radio). In addition to legal constraints, driver self-regulation can effectively reduce the influence of distracted driving [11]. Many drivers have reported that they often change their driving behav- ior during secondary tasks, such as reducing their speed or stopping the car [12]. Oviedo– Trespalacios et al. and Wandtner et al. [13, 14] observed that drivers tend to decelerate while engaging in high-risk secondary tasks in a driving simulation experiment. Stavrinos et al. [15] found that drivers prefer to select various safe speeds in different driving scenarios. Wang et al. [16] indicated that drivers reduce their distraction duration while driving under high-risk conditions. In self-regulation, crash risk perception plays a critical role, directly influencing driver atti- tude toward their level of self-regulation and road safety [17, 18]. Questionnaires have been used to investigate the subjective assessment by drivers of the risk associated with different dis- traction tasks. Patel et al. [19] distributed a subjective ranking survey that identified mobile phone use and makeup application as the riskiest behaviors. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 Data Availability Statement: All relevant data are within the manuscript. Meanwhile, the perceived risks associated with conversation and observing road signs or landscapes were low. Findings also suggest that drivers may not be more careful while engaging in conversation or observing driv- ing scenarios. Gentzler et al. [20] similarly reported that conversation with passengers and looking at vehicles on the roadside were rated as low-risk distraction tasks by drivers. How- ever, scenarios such as conversations and observing driving behaviors were common behaviors on actual roads [21, 22], classified as cognitive and visual distractions, respectively. Despite these findings, studies on whether perceived secondary tasks are low-risk during actual driving are rarely reported. In a previous study, some experienced drivers considered performing a secondary task to constitute a safe driving behavior; that is, they could perform secondary tasks while driving safely [23]. However, excessive self-confidence in driving skills may reduce driver self-regulation in performing secondary tasks [24], affecting driving perfor- mance and increasing the likelihood of an accident. Several driving metrics have been applied to evaluate the effects of distraction on driving performance. Steering wheel reversal rate (SRR) is a useful indicator for detecting visual and cognitive distraction. Kountouriotis et al. [25, 26] found that SRR increased during visual and cognitive distraction. In driving simulation experiments, the standard deviation of lane posi- tion (SDLP) was used to evaluate the lane-keeping performance of drivers during secondary tasks; research revealed that SDLP increased when dialing a mobile phone but decreased dur- ing a conversation [27, 28]. To evaluate the lane-keeping performance of the driver and the lat- eral position of the vehicle, lane deviation was considered as an intuitive indicator [29–31]. Despite numerous studies regarding the effects of driving distraction on lateral driving perfor- mance, research on the influence of driving duration on driving performance have rarely been reported. Ostlund et al. [32] demonstrated that task duration may influence lateral deviation; for the same driving task, the longer the time window duration, the greater the lane deviation. Thus, comparing the effects of different distraction tasks on lateral driving performance requires the selection of a fixed time or reference to the rate of lane deviation. 2 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Data Availability Statement: All relevant data are within the manuscript. To examine the difference between perceived and actual risks associated with secondary tasks, this study evaluated the effects of low-perceived-risk secondary tasks (i.e., cognitive and visual distractions) on the lane-keeping performance of the driver on a real highway. Informa- tion on the lane position of the vehicle was collected by a lane recognition system installed in the test vehicle, and a front camera was used to record the visual distraction time. The lane position of the vehicle was used to evaluate the lateral control of the driver while performing cognitive and visual distraction tasks (conversation and observing the road scenarios, respec- tively). To compare two low-perceived-risk secondary tasks, a lane deviation rate was selected; analysis of variance (ANOVA) tests were performed to evaluate the effects of two types of distraction. 2.1 Apparatus As shown in Fig 1, the high-fidelity test platform is a real vehicle: the 2008 Volkswagen Touran equipped with a lane mark recognition system (Mobileye C2-170) and multiple high-speed cameras. The lane mark recognition system measured the distance of the test vehicle to the left and right lane marks at a system frequency of 10 Hz and with an accuracy of 5 cm. Multiple high-speed cameras were used to monitor driver head motion, driving behavior, and traffic environment. 2.2 Participants Seventeen experienced drivers (15 males and 2 females) were recruited through an advertise- ment in Xi’an, China and were compensated for their participation. Each of the participants, aged 27–48 years (M = 34.7, SD = 7.7), had a valid driver’s license, normal or corrected-to-nor- mal vision, and driving experience for 3–23 years (M = 8.4, SD = 5.2). None had been involved in a traffic accident during the past 3 years. The participants, all non-professional drivers, per- formed two driving tasks on the same road in the same car. Each driver had about 30 min of rest between driving trials. 2. Methods This section describes three field trials to investigate the effects of two low-perceived-risk sec- ondary tasks on the lane-keeping ability of the driver. Two tasks—conversation and rear-vehi- cle observation—were selected as cognitive and visual tasks, respectively. Drivers considered each task to be of low perceived risk; these tasks represented the most common distractions on real roads [19, 20, 22]. All trials were performed on the same highway by using an instru- mented vehicle. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 2.4 Cognitive distraction Trial 1 examined the effect of a cognitive distraction task on the lane-keeping ability of the driver. In this trial, participants were required to perform a conversation task, which is consid- ered a low-risk distraction on the basis of a subjective ranking of distraction tests. An experi- mental staff member sat in the rear passenger seat, and participants communicated with the staff member by answering a series of calculation questions. Lane deviation were recorded to analyze the effects of cognitive distractions. Makishita [33] indicated that performing calculations can be considered as a serious con- versation. In this trial, drivers were subjected to calculation tasks involving addition and sub- traction of two positive two-digit numbers. In the addition task, the sum of the calculation was smaller than 100; in the subtraction task, the difference was not zero, and the answer could be either negative (e.g., 14 −26 = -12) or positive (42 −19 = 23). The drivers had to immediately answer orally the questions asked by the experimental staff member. If the participant responded correctly, the next question was asked; otherwise, the participant was again asked the same question. The staff member then asked the next question regardless of the correctness of the second answer. 2.3 Driving route The drivers were asked to drive on the G3001 highway from Sanqiao to Xinzhu, a two-way, six-lane highway with a speed limit of 100 km/h. The route was 38 km long to allow partici- pants to drive for roughly 30 min. Three trials were performed during nonpeak hours without traffic congestion. All tests were conducted under clear weather conditions to avoid any nega- tive effect of weather on driver performance. To prevent crashes, an experimental staff member with more than 20 years of driving expe- rience was seated in the front passenger seat. The task of this staff member was to focus on the driving environment during the experiment. He was expected to inform the participant during the secondary task when a potential risk arose. The research team purchased insurance for all participants. 3 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Fig 1. Instrumented vehicle. Fig 1. Instrumented vehicle. https://doi.org/10.1371/journal.pone.0231151.g001 https://doi.org/10.1371/journal.pone.0231151.g001 2.7 Lane deviation Lane deviation, the difference in the lateral position of the vehicle at the starting and end moments of the task, was used to evaluate the lane-keeping ability of the drivers. On the basis of [34], the lateral position of a vehicle represents the distance between the center of the vehicle and the center lane mark. The lateral position of the vehicle is presented in Fig 3, where H is the lane width, L1 is the distance from the left lane to the left side of the vehicle, L2 is the distance from the right side of the vehicle to the right lane, D is the width of the vehicle, and J is the distance from the lane center to the center of the vehicle. Vehicle lane-keeping characteristics can be represented by J. The formula to calculate J is shown in Eq (1): Ji ¼  1 2 jL1i L2ij ð1Þ ð1Þ where L1i and L2i denote the distance from the left and right lines (cm) at any time i, respec- tively; and ± represents the direction relative to the lane center (i.e., left is denoted by +, and right is denoted by −); and Ji is the vehicle lane position at any time i. where L1i and L2i denote the distance from the left and right lines (cm) at any time i, respec- tively; and ± represents the direction relative to the lane center (i.e., left is denoted by +, and right is denoted by −); and Ji is the vehicle lane position at any time i. The lane deviation during a driving task can be calculated as The lane deviation during a driving task can be calculated as LD ¼ jJ2 J1j ð2Þ ð2Þ where LD is the lane deviation (cm), J1 is the lane position at the start moment of the driving task, and J2 is the lane position at the end moment of the driving task. The rate of lane devia- tion was considered as the mean lane deviation during a driving task. where LD is the lane deviation (cm), J1 is the lane position at the start moment of the driving task, and J2 is the lane position at the end moment of the driving task. The rate of lane devia- tion was considered as the mean lane deviation during a driving task. 2.6 Normal driving Driving behavior during normal driving was explored in this trial. Before the trial, the partici- pants were required to drive the instrumented vehicle, using their typical driving style, on the test road for 30 min. The participants were not given any specific requirements when driving normally. 2.5 Visual distraction In Trial 2, we evaluated the effects of a visual distraction task on the lane-keeping ability of the driver. Before the test was conducted, participants were told that while driving, they would be estimating the relative distance and speed of a rear vehicle during the experiment, with no other requirements. Rear vehicles randomly approached the test vehicle and were not under experimental controls. Drivers were allowed to maintain their own driving styles and to avoid communicating with the experimental staff. In this test, each driver was asked to observe a rear vehicle through a rearview mirror whenever he/she felt doing so was safe. The driver was 4 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE What is the difference between perceived and actual risk of distracted driving? required to quickly estimate the rear-vehicle speed and relative distance as the rear vehicle approached the subject vehicle. Moreover, the driver orally reported this information to the staff. We distinguished the distraction time from his/her head motion and eye movement, as shown in the surveillance video. The start time was the moment the driving sight turned from the front to the rearview mirror, whereas the end time was the moment the driving sight turned from the rearview mirror to the front. Fig 2(A) shows driver sight and head position without visual distractions. Fig 2(B) shows the moment a driver checks the rearview mirror. Fig 2(C) shows the driver sight focused on the left-side rearview mirror. Fig 2(D) shows the moment the driver turns to look to the front. Fig 2(E) shows the driver sight returning to the front after visual distraction. The video consisted of 24 frames/s. Fig 2(B)–2(D) display 1 s of the time captured in 1 frame (the distraction duration is 1.042 s). PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 3. Result A total of 247 visual distraction segments were recorded. The minimum visual distraction duration was 0.13 s, the maximum duration was 5.63 s, the average duration was 1.90 s, and the standard deviation was 0.94 s. The distribution of visual distractions is presented in Fig 4. Among the visual distraction segments, the most frequent distraction duration was in the 1.0–1.5 s range. The distraction duration of 66 visual distraction segments was in the 1.0–1.5 s range, which comprising 26.3% of the total duration. When the distraction duration was shorter than 1.0 s, the duration was positively correlated with the number of distraction seg- ments; when the distraction time was longer than 1.5 s, the distraction duration was negatively correlated with the number of distraction segments. The visual distraction duration mainly ranged within 1.0–2.0 s, constituting 50.2% of the total distraction time. More than nine-tenths of the visual distraction tasks had a duration of 0.5–3.5 s. In assessing the trend of change in lane deviation with distraction duration, we used qua- dratic regression and linear regression to establish regression equations for lane deviation. The quadratic regression curve and scatterplot of lane deviation and distraction duration are pre- sented in Fig 5. The fit statistics for this model indicated that quadratic regression was a good fit to the data (p < 0.001). The linear regression and scatterplot of lane deviation and distrac- tion duration are presented in Fig 6. The fit statistics for this model indicated that linear regression was a good fit to the data (p < 0.001). Compared with linear fitting (R2 = 0.326), the quadratic regression (R2 = 0.363) were better. The comparison results showed that the change trend of lane deviation with the distraction duration is more in line with the quadratic change, suggesting that the growth rate of the lane deviation increases with an increase in distraction duration and that the safety of the vehicle decreases rapidly. Owing to the low number of partial-interval segments, we divided the distraction process into seven ranges and conducted ANOVA on lane deviation in SPSS. The main effect of dis- traction duration was significant, F(6, 240) = 16.326, p < 0.001 (Table 1). A post-hoc test revealed no significant difference in lane deviation between distraction durations in the [0.0, 1.0), [1.0, 1.5), and [1.5, 2.0) ranges. 2.8 Procedure Before the experiment, each driver completed a preparation phase of adaptive driving on a test road. Participants informed the staff once they had adapted to the experimental vehicle and the test road. Subsequently, the experiment officially began. The entire driving procedure 5 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Fig 2. Driver distraction. https://doi.org/10.1371/journal.pone.0231151.g002 Fig 3. Lane position of the vehicle. https://doi.org/10.1371/journal.pone.0231151.g003 Fig 2. Driver distraction. https://doi.org/10.1371/journal.pone.0231151.g002 Fig 2. Driver distraction. https://doi org/10 1371/journal pone 0231151 g002 Fig 2. Driver distraction. https://doi.org/10.1371/journal.pone.0231151.g002 Fig 3. Lane position of the vehicle. https://doi.org/10.1371/journal.pone.0231151.g003 Fig 3. Lane position of the vehicle. https://doi.org/10.1371/journal.pone.0231151.g003 Fig 3. Lane position of the vehicle. https://doi.org/10.1371/journal.pone.0231151.g003 https://doi.org/10.1371/journal.pone.0231151.g003 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 6 / 15 PLOS ONE What is the difference between perceived and actual risk of distracted driving? consisted of three stages: the normal driving stage, cognitive distraction stage, and visual dis- traction stage. These three trials were performed at random with 15 min intervals. In the cognitive distraction stage, the participants were asked questions continuously throughout the driving task, and the experimental staff recorded the answers. After the experi- ment, the driving status of the drivers was distinguished based on the recorded time and sur- veillance video. Information on lane departure was obtained by processing the data collected using the lane mark recognition system. In the visual distraction stage, the staff indicated when a rear vehicle was approaching, and the participant needed to quickly report the relative distance and driving speed of the rear vehicle. 2.9 Ethics and authorization statement The experimental protocol was approved by the research committee of Chang’an University. Informed consent was obtained from each participant. No permits were required for the described study, which complied with all relevant regulations. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 3. Result No significant difference in lane deviation was found between distraction durations in the [1.5, 2.0), [2.0, 2.5), and [2.5, 3.0) ranges. The lane devia- tions (15.69 and 15.95 cm) were significantly higher when the distraction duration were in the [2.0, 2.5), and [2.5, 3.0) than the lane deviations (9.50 cm, 10.30 cm) when the distraction dura- tion were in the [0.0, 1.0) and [1.0, 1.5) ranges. Moreover, the lane deviation was 36.76 cm 7 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Fig 4. Distraction duration distribution. https://doi.org/10.1371/journal.pone.0231151.g004 Fig 4. Distraction duration distribution. https://doi.org/10.1371/journal.pone.0231151.g004 when the distraction duration was in the [3.5, 6.0) range, which is significantly higher than those in the other six time intervals. The lane deviation was 21.67 cm when the distraction duration was in the [3.0, 3.5) range; a significant difference from lane deviations in the other six time intervals was indicated. when the distraction duration was in the [3.5, 6.0) range, which is significantly higher than those in the other six time intervals. The lane deviation was 21.67 cm when the distraction duration was in the [3.0, 3.5) range; a significant difference from lane deviations in the other six time intervals was indicated. Ostlund et al. [32] found that lateral deviation increased as task duration increased. To eliminate this effect, the rate of lane deviation was selected while comparing the effects of visual distractions with those of cognitive distractions on lateral performance. The rates of lane deviation during cognitive distractions, visual distractions, and normal driving are presented in Fig 7. Fig 5. Quadratic regression of lane deviation and distraction duration. https://doi.org/10.1371/journal.pone.0231151.g005 https://doi.org/10.1371/journal.pone.0231151.g005 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 8 / 15 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Fig 6. Linear fitting of lane deviation and distraction duration. https://doi.org/10.1371/journal.pone.0231151.g006 Fig 6. Linear fitting of lane deviation and distraction duration. https://doi.org/10.1371/journal.pone.0231151.g006 One-way ANOVA was conducted on the rate of lane deviation in SPSS. The main effects of secondary tasks are listed in Table 2. Findings indicated that the distraction task significantly influenced the lateral driving performance of the driver (F(2, 6053) = 349.363, p < 0.001). Post-hoc test results are listed in Table 3. 3. Result Compared with the rate of lane deviation during normal driving (5.00 cm), the rate of lane deviation during visual distraction (8.25 cm) is sig- nificantly higher; however, the cognitive distraction task significantly decreases the rate of lane deviation (4.38 cm). Moreover, the rate of lane deviation during visual distraction is higher than that during cognitive distractions—that is, twice as much as that during cognitive distrac- tions. These findings indicate that lane deviation is faster and more likely to cause traffic acci- dents during visually distracted driving. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 4. Discussion In this paper, we investigated the effects of two types of low-perceived-risk secondary tasks on the lateral performance of the drivers. With an instrumented vehicle, a normal driving task, a visual distraction task, and a cognitive distraction task were conducted on a real highway. Lane Table 1. Difference tests of lane deviations in different distraction duration districts. Factor N Subset for alpha = 0.05 1 2 3 4 [0.0,1.0) 30 9.50 [1.0,1.5) 66 10.30 [1.5,2.0) 56 11.70 11.70 [2.0,2.5) 36 15.69 [2.5,3.0) 21 15.95 [3.0,3.5) 21 21.67 [3.5,6.0) 17 36.76 Sig. .408 .106 1.000 1.000 https://doi.org/10.1371/journal.pone.0231151.t001 Table 1. Difference tests of lane deviations in different distraction duration districts. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 9 / 15 PLOS ONE What is the difference between perceived and actual risk of distracted driving? Fig 7. Comparison of lane deviation rates. https://doi.org/10.1371/journal.pone.0231151.g007 Fig 7. Comparison of lane deviation rates. https://doi.org/10.1371/journal.pone.0231151.g007 https://doi.org/10.1371/journal.pone.0231151.g007 deviation was used as an indicator to evaluate the lane-keeping ability of the drivers. In the cognitive distraction task, we evaluated lane deviations during conversation; in the visual dis- traction task, drivers had to identify and estimate information (i.e., speed and distance) about a rear vehicle. As low-perceived-risk secondary tasks, these distraction tasks exerted significantly different effects on the lateral performance of each driver. Results revealed that visual distractions signif- icantly increased the lane deviation rate, whereas cognitive distractions slightly decreased this rate. The higher the lane deviation rate, the poorer the lane-keeping ability of the driver. Such reduction could lead to increased likelihood of collision between the subject vehicle and a vehi- cle on the adjacent lane. Although both tasks were considered low-risk [19, 20], experimental results suggest that observing a rear vehicle during actual driving clearly impairs the lane-keep- ing ability of the drivers; thus, visual tasks are high-risk. This finding confirms that roadside billboards can lead to a high rate of traffic accidents [35] and further indicates that drivers tend to perceive high-risk visual tasks as low-risk tasks. Communicating with passengers did not impair the lane-keeping ability of the drivers. Consistent with previous experiments [36], the cognitive task slightly affected the driving performance but did not compromise the driving safety of the participants, suggesting that some cognitive tasks are relatively safe. y gg g g y The differential effects of visual and cognitive tasks may be explained as follows. PLOS ONE What is the difference between perceived and actual risk of distracted driving? PLOS ONE Table 3. Multiple Comparisons. (I) Task (J) Task Mean Difference (I-J) Std. Error Sig. 95% Confidence Interval Lower Bound Upper Bound Cognitive Normal -.6140 .13639 .000 -.8814 -.3466 Visual -3.8615 .14690 .000 -4.1495 -3.5736 Normal Cognitive .6140 .13639 .000 .3466 .8814 Visual -3.2475 .17104 .000 -3.5828 -2.9122 Visual Cognitive 3.8615 .14690 .000 3.5736 4.1495 Normal 3.2475 .17104 .000 2.9122 3.5828 through the rearview mirror and billboards; however, during cognitive distractions, drivers mostly continued looking at the lane in front of them, which helped them estimate the position of the vehicle. Notably, the conversation task could enhance the lane-keeping ability of the drivers, which is consistent with the naturalistic research that found cell phone conversations to reduce crash risk [37, 38]. In the current study, conversations may help the driver remain alert, preventing the driver from performing other distraction tasks because the driver needs to pay more attention to the road ahead. The second reason is that the drivers generally did not consider observing a rear vehicle to be dangerous; while performing this task, they were clearly focused on the rear car. Although the driver could perceive lane departure by the positional relationship between the lane mark- ing in the rearview mirror [39], a lack of risk awareness led to a higher lane deviation rate. However, during cognitive distractions, the drivers did not need to look at an object; they could continue looking at the lane in front of them, which helped them adjust the position of the vehicle. Muhrer and Kaber [40, 41] indicated that the drivers must adjust their driving behavior in accordance with the driving environment ahead. However, while performing a visual distraction task, the driver could not observe the curvature of the upcoming road; thus, the relative lane position of the car could not be adjusted promptly. Therefore, during driver training, the driver should be reminded of the danger of observing the surrounding environment for an extended period. Even when observing a rear vehicle through the rearview mirror, drivers should pay attention to lane keeping. Moreover, the results of the visual distraction task revealed two findings. More than 90% of the drivers could observe the rearview mirror within 0.5–3.5 s, and more than half of the tasks could be completed within 1–2 s, consistent with a previous study [42]. PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 4. Discussion Drivers tended to focus on visual distractors during most visual distraction tasks, such as observing The differential effects of visual and cognitive tasks may be explained as follows. Drivers tended to focus on visual distractors during most visual distraction tasks, such as observing Table 2. Tests of between-subjects effects. Table 2. Tests of between-subjects effects. Table 2. Tests of between-subjects effects. Source Type III Sum of Squares df Mean Square F Sig. Corrected Model 13173.986a 2 6586.993 349.363 .000 Intercept 168766.574 1 168766.574 8951.104 .000 Task 13173.986 2 6586.993 349.363 .000 Error 114124.929 6053 18.854 Total 295860.067 6056 Corrected Total 127298.916 6055 https://doi.org/10.1371/journal.pone.0231151.t002 PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 10 / 15 Based on observed means. The error term is Mean Square (Error) = 18.854. 5. Conclusion On the basis of an experiment on a real highway, this study presents a novel study on driving behaviors during low-perceived-risk secondary tasks. Moreover, this study compares the dif- ferences between the real risk and perceived risk of secondary tasks. The experiment findings emphasize that the perceived risk is not consistent with the actual risk of secondary tasks; in addition, drivers are inclined to underestimate the risk of visual distraction tasks. However, the actual risk of cognitive tasks at a low level of perceived risk is the same as the perceived risk of the driver. This study also demonstrates that lane deviation increases with distraction dura- tion. These findings can be applied in the design of advanced driving-assistance systems and in improving professional driver training programs. PLOS ONE The other notable finding is that lane deviations increased with an increase in distraction duration. This occurrence was similar to previous a finding [43], implying that distraction duration is positively correlated with the occurrence of an accident. Brumby and Salvucci [44, 45] found that lane deviation increased with phone-dialing duration while driving; this grow- ing trend of lane deviation supports the results in the present study. Moreover, the current study indicates that the relationship between lane deviation and distraction duration was not a simple linear association; rather, the increasing trend of lane deviation with distraction dura- tion could be categorized into three stages: 1) when the distraction duration was less than 2.0 s, the increase in lane deviation with distraction duration was not apparent; 2) when the distrac- tion duration was 2.0–3.0 s, lane deviation increased gradually; and 3) when the distraction duration was longer than 3.0 s, lane deviation increased rapidly. This finding may be attributed to working memory capacity [46, 47]. For a short-term visual distraction, the driver still PLOS ONE | https://doi.org/10.1371/journal.pone.0231151 April 2, 2020 11 / 15 PLOS ONE What is the difference between perceived and actual risk of distracted driving? remembers the lane ahead while performing the distraction task, which can help the driver maintain safe driving temporarily. However, for a long-term visual distraction, the load of the distraction task exceeds the working memory capacity of the driver; the longer the distraction time, the greater the lane deviation rate. Ahlstrom and Zhang [48, 49] discussed the influence of a distraction warning algorithm on driver attention. These results can help improve distrac- tion warning systems because a reasonable warning threshold can decrease false positives and improve driver acceptance of such systems. A large number of factors, such as driving environment, weather, and vehicle model, may affect driving behavior. To improve the internal validity, all experiments were conducted under the same conditions. Moreover, to ensure external fidelity, participants were recruited from the entire population rather than limiting the recruitment to only students or teachers. Factors such as age and educational background are not controlled, thereby ensuring diversity of the subjects. 6. Limitations This study has several limitations. The first limitation is that distraction duration cannot be further categorized because of insufficient experimental data. The effect of distraction duration on lateral vehicle deviation can be explored in greater detail in subsequent studies by using a shorter distraction time. In future research, we intend to further compare high-perceived-risk secondary tasks with low-perceived-risk secondary tasks. The second limitation is that the sample size is relatively small. Possible differences in lane- keeping ability during distracted driving across gender and age groups were neither evaluated nor controlled. Previous studies have indicated that the gender and age of the driver may affect driving behavior [50, 51]. However, the current experiment was conducted on a real highway with potential risks, resulting in a smaller number of female and old-age applicants. 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The impact of a naturalistic hands-free cellu- lar phone task on heart rate and simulated driving performance in two age groups. Transportation research part F: traffic psychology and behaviour. 2011, 14(1), 13–25. https://doi.org/10.1016/j.trf. 2010.09.002 15 / 15
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Bitcoin trading indicator: a machine learning driven real time bitcoin trading indicator for the crypto market
Bulletin of Electrical Engineering and Informatics
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Bulletin of Electrical Engineering and Informatics Vol. 12, No. 3, June 2023, pp. 1762~1772 ISSN: 2302-9285, DOI: 10.11591/eei.v12i3.4486 Bulletin of Electrical Engineering and Informatics Vol. 12, No. 3, June 2023, pp. 1762~1772 ISSN: 2302-9285, DOI: 10.11591/eei.v12i3.4486  1762 Bitcoin trading indicator: a machine learning driven real time bitcoin trading indicator for the crypto market Ashikur Rahaman1, Abu Kowshir Bitto1,6, Khalid Been Md. Badruzzaman Biplob1, Md. Hasan Imam Bijoy2, Nusrat Jahan3,4, Imran Mahmud1,5 j y 1Department of Software Engineering, Daffodil International University, Dhaka, Bangladesh 2Department of Computer Science and Engineering, Daffodil International University, Dhaka, Bangladesh 3Department of Information Technology and Management, Daffodil International University, Dhaka, Bangladesh 4Department of Computer Engineering, University Malaysia Perlis, Arau, Malaysia 5Graduate School of Business, Universiti Sains Malaysia, Penang, Malaysia 6MediprospectsAI Limited, London, United Kingdom Article Info Article history: Received Jul 29, 2022 Revised Sep 30, 2022 Accepted Oct 18, 2022 Keywords: Bitcoin Forex trading Machine learning Sentiment analysis Web scraping Corresponding Author: Abu Kowshir Bitto Department of Software Engineering, Daffodil International University Dhaka, Bangladesh Email: abu.kowshir777@gmail.com Corresponding Author: Abu Kowshir Bitto Department of Software Engineering, Daffodil International University Dhaka, Bangladesh Email: abu.kowshir777@gmail.com Corresponding Author: Abu Kowshir Bitto Department of Software Engineering, Daffodil International University Dhaka, Bangladesh Email: abu.kowshir777@gmail.com ABSTRACT As opposed to other fiat currencies, bitcoin has no relationship with banks. Its price fluctuation is largely influenced by fresh blocks, news, mining information, support or resistance levels, and public opinion. Therefore, a machine-learning model will be fantastic if it learns from data and tells or indicates if we need to purchase or sell for a little period. In this study, we attempted to create a tool or indicator that can gather tweets in real-time using tweepy and the Twitter application programming interface (API) and report the sentiment at the time. Using the renowned Python module "FBProphet," we developed a model in the second phase that can gather historical price data for the bitcoin to US dollar (BTCUSD) pair and project the price of bitcoin. In order to provide guidance for an intelligent forex trader, we finally merged all of the models into one form. We traded with various models for a very little number of days to validate our bitcoin trading indicator (BTI), and we discovered that the combined version of this tool is more profitable. With the combined version of the instrument, we quickly and with little error root mean square error (RMSE: 1,480.58) generated a profit of $1,000.71 USD. Keywords: Bitcoin Forex trading Machine learning Sentiment analysis Web scraping This is an open access article under the CC BY-SA license. 1. INTRODUCTION The foreign exchange rate for each currency is set by this market. It includes all transactions involving the buying, selling, and exchanging of currencies at set or prevailing rates. "Percentage in point" or "price interest point" is abbreviated as pip [6]. In the foreign exchange market, it is a tiny unit of measurement that denotes a change in a currency pair. Either the stated currency or the underlying currency may be used to represent it as a percentage. The smallest alteration in a currency quote is represented by a standardised unit called a pip. A lot [7] is a predetermined sum of money used along with pips to execute a trade in forex. Fortunately, a range of lot sizes are available to traders. Typically, in order to take a deal, traders must choose the lot size. On a normal trading account for excess, lots start at 0.0001 and can reach a maximum of 5. By putting more money into various accounts, you can raise the size of your lots. Natural language processing (NLP) is used in sentiment analysis [8], [9] to determine if data is favourable, negative, or neutral. Organizations typically employ sentiment analysis on textual data to analyse brand and product sentiment in consumer feedback and gain a better understanding of client wants. To evaluate and derive objective quantitative findings from unprocessed text, sentiment analysis uses NLP machine learning and other data analysis approaches. Sentiment analysis is a branch of text mining. g y pp y g In 1998, one of the earliest books on stock market forecasting [10] was published. Information was acquired by Wüthrich and associates from the Wall Street Journal, Financial Times, Reuters, and Bloomberg. According to Borges [11] any positive or negative news is immediately absorbed by the market, and stock prices change in accordance. Therefore, it is impossible to outperform the stock market because there are never any undervalued stocks to buy or overvalued stocks to sell. Over extended periods, many investors, including Warren Buffet, have been able to outperform the market. A single-layered convolutional neural network (CNN) model was created by Cavalli and Amoretti [12] to increase earnings when the trend is bullish and decrease losses when the market is bearish. Their creations were based on text from several social media profiles. A trading strategy test revealed that it had superior accuracy and return compared to a single source system [13]. 1. INTRODUCTION A person [1] going by the name of Satoshi Nakamoto originally published one of the finest cryptocurrencies, bitcoin, on January 9, 2009. Each bitcoin was only worth $2.26 when the bitcoin to US dollar (BTCUSD) pair first entered the currency market. The most volatile cryptocurrency now that demands more general attention is bitcoin. Everyone, from researchers to traders, is searching for a pricing pattern to invest in and make the biggest return they can. Bitcoin: a peer-to-peer (P2P) electronic cash system that was introduced as a forward-thinking electronic cash alternative on just nine pages. On the surface, cryptocurrencies like bitcoin [2] and others resemble fiat money a lot. As with regular money, a bitcoin can be broken into smaller pieces known as Satoshi's and used to make purchases from businesses that take bitcoin. To store bitcoins, a user must first build a wallet. On a computer or a mobile device, this wallet can be downloaded and installed. Some websites also offer access to online Journal homepage: http://beei.org 1763  ISSN: 2302-9285 Bulletin of Electr Eng & Inf wallets, and some hardware vendors sell USB sticks that are actual wallet devices. These wallets come with a bitcoin address that may be used to send or receive money. In technical terms, a bitcoin address is a hashed representation of a public key. The corresponding private key is retained in the wallet and is encrypted and secret [3]. The foundation of the entire bitcoin network is the blockchain, a decentralised public ledger. It records all previous exchanges between various bitcoin addresses, including the amounts sent. This makes it possible to determine how much money is available in each wallet. It also enables the ownership of the spent bitcoins to be confirmed. The integrity and chronological order of the blockchain are guaranteed by cryptography [3]. All transactions are published to the P2P network through mining [4]. Miners put a lot of time and effort into creating hashes that meet certain criteria. The process of adding new bitcoins to circulation is known as bitcoin mining. By resolving incredibly difficult math puzzles, new bitcoins are created through the process of mining, which also verifies bitcoin transactions. When a bitcoin is successfully mined, the miner is given a certain number of bitcoins. A decentralised or over-the-counter (OTC) market for trading foreign currencies is known as the foreign exchange market (forex, FX, or currency market) [5]. 1. INTRODUCTION In order to see the market trend and do a seasonal study, we also create a time series forecasting model. bitcoin on the foreign exchange market. The tone of the tweet from the day before is the main focus. In order to see the market trend and do a seasonal study, we also create a time series forecasting model. 2. RESEARCH METHOD In this segment, data collection, web scraping, data handling/pre-processing, time series generation, data analysis with forecasting, and developing BTI trading indicator has complied, which represent in Figure 1; the details explanation is given orderly. Figure 1. Workflow diagram of proposed study Figure 1. Workflow diagram of proposed study 1. INTRODUCTION An recurrent neural network (RNN)-based model was employed in a depth literature analysis [14] to forecast the price of bitcoin based on Twitter sentiment. By using analysis, we can predict the price of bitcoin based on the emotion of tweets that come from specific sources. I particularly like how they use gradient descent, another machine-learning method, to extract a significant price from Twitter sentiment analysis by using daily high and low prices from historical data. A number of machine learning techniques are detailed in the reference paper by Colianni et al. [15] that predict the price of bitcoin. Before using their model, they even conducted extensive literature research. They used two datasets to distribute their model. One was for hourly data followed by time series, and the other was for daily time series data. Additionally, they used supervised learning to classify Twitter sentiment using data from Twitter. The accuracy and maximum result they were able to achieve using Bayesian Naive Bayes was 95% for day-basis data and 76.59% for hour-basis data. Research by Garcia and Schweitzer [16] published a companion piece. The researchers used a trading simulation engine and two daily Twitter sentiment time series. The latter was based on a collection of positive and negative terms from the linguistic inquiry and word count (LIWC) lexicon, as well as the daily ratio between them. To trade in forex, we must do a market analysis, determine the present stance of the market pair, and make a prognosis or projection. It is difficult for one person to consider every angle because humans make mistakes, and doing so has so far taken a lot of time. Additionally, because of how quickly time passes, traders must act more quickly while making decisions. Therefore, our goal is to create a real-time "bitcoin" trading indicator for the currency market that is powered by machine learning. To be more precise, we want to predict whether we should "buy" or "sell" on the following day. We'll employ current market support and resistance in real-time to work toward this objective. We won't purchase actual bitcoin. But we'll deal in Bitcoin trading indicator: a machine learning driven real time bitcoin trading … (Ashikur Rahaman)  1764 ISSN: 2302-9285  1764 bitcoin on the foreign exchange market. The tone of the tweet from the day before is the main focus. 2.1. Data collection Tweet data extraction procedure diagram  1765 ISSN: 2302-9285  Bulletin of Electr Eng & Inf Table 1. Sample data for bitcoin data Date Close Volume 9/17/2014 457.3340149 21056800 9/18/2014 424.4400024 34483200 9/19/2014 394.79599 37919700 Table 2. Sample data for tweet data Index Tweets 1 RT @xZ3R0x_: $CPHX is pumping! 🠓ˆ#ETH gas fees are low! The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_ holders… 2 RT @BTC_Archive: The government just prints money...and doesn’t seem to have any consequences. They can’t make more #Bitcoin - Billionaire… 2.2. Data pre-processing Before the arrangement takes place, data pre-handling is an essential task. For bitcoin, "yfinance" [20] is a very rich library that provides those data in a suitable style, so we do not need to fill in any kind of rows with a simple imputer. Since the bitcoin market is open around-the-clock, there is no risk of seasonal statistics being broken. To normalise the data, it was standardised to convert from 0 to 1. Next, the tweet data that we are collecting through the Twitter application programming interface (API) is distorted by several superfluous symbols, capitalization, or even new lines and hyperlinks [21]. It will be horrible if we manually clean up by capturing each row of tweets. We developed a technique to extract a pandas data frame and apply a function to eliminate new lines, hashtags (#), letter formatting, and hyperlinks that contain the http symbol because of this. We must save every tweet in a new data column after the tweets have been cleansed. For that reason, we can create a new column to hold all cleaned-up tweets. Table 3 now includes the sample data with clean tweets following the preprocessing of the twitter data. Table 3. Tweet data after preprocess Index Raw tweets Clean tweets 1 RT @xZ3R0x_: $CPHX is pumping ! 📈#ETH gas fees are low !The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_holders… RT @xZ3R0x_: $CPHX is pumping ! 📈TH gas fees are low ! The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_holders… 2 RT @BTC_Archive: the government just prints money and doesn’t seem to have any consequences. They can’t make more #bitcoin-Billionaire… RT @BTC_Archive: the government just prints money and doesn’t seem to have any consequences. They can’t make more bitcoin-Billionaire… 1 RT @xZ3R0x_: $CPHX is pumping ! 📈#ETH gas fees are low !The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_holders… @ _ yp _ ¦ 2 RT @BTC_Archive: the government just prints money and doesn’t seem to have any consequences. They can’t make more #bitcoin-Billionaire… 2.3. Data feature generating We cleaned up the tweets, and as a result, several data columns about cleaned tweets have been generated. We first retrieve each row's subjectivity. The subjective scale ranges from (-1) to (+1). Higher subjectivity is indicated by a value near +1. A value nearer to -1 denoted less subjectivity. In order to shed insight on the subjectivity of tweets relating to bitcoin, this subjectivity column was pulled from the cleaned tweets column. More subjectivity means a bigger impact. The majority of tweets have subjectivity levels above 0.50 and significantly affect the market. Polarity is a different column that displays the strength of the subjectivity. Let's discuss the first tweet from our collection. As you can see, it has 0.1 subjectivity but 0.00 polarity. The tweet has less subjectivity and no market linkage, which is why polarity there displays as 0. We chose tweets that would be more polarising and subject to do an excellent sentiment analysis. 2.1. Data collection It is impossible to emphasise the significance of datasets in machine learning research [17]. This study uses two different forms of data: tweets from Twitter and quantitative bitcoin price data obtained using the Python module "tweepy" [18]. We construct the exact symbols of currency prices, such BTCUSD, using ticker parameters. This cost is expressed as a percentage of the US dollar per bitcoin. The current datetime for the last range of data pulling was generated using a Python datetime object. We run the programme using the Python package "yfinance" and extract the bitcoin data in USD as our bitcoin data for time series analysis from Figure 2. We first requested a "Twitter developer" [19] account based on Figure 3. Using a Python module named "tweepy," we later produced consumer key, consumerSecret, accessToken, and accessSecret to authenticate on Twitter. In this instance, the search phrase included the hashtags #bitcoin and #bitcoin. However, in order to balance my dataset and maintain data uniqueness, we filtered retweets. We still entered dates manually into our application. Users must enter the year, month, and day. Due to the bitcoin market's extreme volatility and frequent movements, we typically create 2,000 rows of pertinent tweets for the previous day. Tweets that are saved as string data with indexes ranging from 0 to 1,999. Tables 1 and 2 provide a sample dataset. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 Figure 2. Bitcoin data extraction procedure diagram Figure 2. Bitcoin data extraction procedure diagram Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 Bulletin of Electr Eng & Inf ISSN: 2302-9285  1765 Figure 3. Tweet data extraction procedure diagram Table 1. Sample data for bitcoin data Date Close Volume 9/17/2014 457.3340149 21056800 9/18/2014 424.4400024 34483200 9/19/2014 394.79599 37919700 Table 2. Sample data for tweet data Index Tweets 1 RT @xZ3R0x_: $CPHX is pumping! 🠓ˆ#ETH gas fees are low! The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_ holders… 2 RT @BTC_Archive: The government just prints money...and doesn’t seem to have any consequences. They can’t make more #Bitcoin - Billionaire… Bulletin of Electr Eng & Inf ISSN: 2302-9285  1765 Figure 3. Tweet data extraction procedure diagram Bulletin of Electr Eng & Inf ISSN: 2302-9285  1765 Figure 3. 2.4. Sentiment generating using TextBlob A Python package for text processing is called TextBlob [22]. It provides a fundamental API for doing common NLP tasks, such as part-of-speech tagging, noun phrase extraction, sentiment analysis, classification, and translation, among others [23]. It is easier to understand and more enticing. We use sentiment analysis to extract subjectivity, followed by polarity to determine the range of each subjective Bitcoin trading indicator: a machine learning driven real time bitcoin trading … (Ashikur Rahaman)  1766 1766  66  ISSN: 2302-9285 tweet. This is because, when performing our operation that will produce more realistic outcomes when it comes to conducting Forex or stock market trading, we require the total number of tweets. The movement of a currency like Bitcoin on the FX market is correlated with public opinion. Therefore, if a trader can in some way comprehend the current mood, they can in some way comprehend market tendencies to execute their transaction. tweet. This is because, when performing our operation that will produce more realistic outcomes when it comes to conducting Forex or stock market trading, we require the total number of tweets. The movement of a currency like Bitcoin on the FX market is correlated with public opinion. Therefore, if a trader can in some way comprehend the current mood, they can in some way comprehend market tendencies to execute their transaction. The sentiment polarity of the element, which decides whether the text conveys the user's positive, negative, or neutral feeling about the subject, defines the orientation of the stated emotion, which is between [-1,1]. Subjectivity [24] exists between [0, 1]. Subjectivity is a metric used to determine how much of a text is made up of fact and personal opinion. The text is more subjective than usual; therefore, it offers personal opinions rather than objective information. We can begin writing the function to create a Sentiment class once we have determined the subjectivity and polarity of a data collection. I utilised the sentiment classes positive, negative, and neutral in this instance. Polarity is defined as "positive" if it is greater than 0 and "negative" if it is less than 0. Sometimes it might be 0, in which case the sentiment class will be displayed as "neutral". For our tool, this sentiment class is crucial. since judgements made by the computer will be based on this class. 2.4. Sentiment generating using TextBlob The entire algorithm could deliver incorrect information if our sentiment analysis is flawed. If that occurs, we might suffer a large financial loss. We can filter tweets about subjectivity to get some more ordinal results. The outcome might be more appealing if we filter away tweets with more subjectivity. Table 4 details the Sentiment class and the filtered tweets dataset. Table 4. Subjectivity and polarity results for tweet dataset Index Tweets Cleaned tweets Subjectivity Polarity Sentiment 1 RT @intocryptoverse: #bitcoin great accumulation: lessons from the stock market https://t.co/XH4ao5KgZv RT @intocryptoverse: bitcoin great accumulation: lessons from the stock market 0.75 0.8 Positive 2 RT @xZ3R0x_: $CPHX is pumping ! 📈 #ETH gas fees are low ! The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_holders… RT @xZ3R0x_: $CPHX is pumping ! 📈TH gas fees are low ! The 1st January another airdrop of Phoenix Coin for all @Phoenix_Crypto_holders… 0.3 0 Neutral 3 RT @RepTedBudd: given @BrianBrooksUS's previous experience as head of the OCC, I asked him if the U.S. government is "behind the curve" whe… RT @RepTedBudd: Given @BrianBrooksUS's previous experience as head of the OCC, I asked him if the U.S. government is "behind the curve" whe… 0.433333 -0.28333 Negative Table 4. Subjectivity and polarity results for tweet dataset eets Cleaned tweets Subjectivity Polarity Table 4. Subjectivity and polarity results for tweet dataset 2.6. Performance measure (error/accuracy) The method of mean absolute error (MAE), mean squared error (MSE), root mean square error (RMSE), and model correctness are used to assess the performance of the models [26]. The MAE in a measurement is the sum of the errors. The same event is expressed by the measurement of errors between the paired observations. Additionally, it highlights the discrepancies between measured and real values. It is the arithmetic average of the total absolute error. Include variations between predicted and observed values in the Y versus X example. "(2)" is the formula for MAE. 𝑀𝐴𝐸= 1 𝑛 ∑ |𝑥𝑖−𝑥| 𝑛 𝑖=1 (2) 𝑀𝐴𝐸= 1 𝑛 ∑ |𝑥𝑖−𝑥| 𝑛 𝑖=1 (2) Here, n denotes the number of errors, |𝑥𝑖−𝑥| the absolute errors, and the summation sign (it means to add all). The MSE of the estimator determines the average squared error in statistics. The true value and the estimated value are contrasted using the average squared. It demonstrates how close a regression line must be to a group of points. The distance from the regression line point demonstrates this, followed by a square. All of the negative value is turned positive by this square. We determine the square of error using MSE. "(3)" is the formula for MSE. 𝑀𝑆𝐸= 1 𝑛 ∑ |𝐴𝑐𝑡𝑢𝑎𝑙−𝑓𝑜𝑟𝑐𝑎𝑠𝑡|2 𝑛 𝑖=1 (3) 𝑀𝑆𝐸= 1 𝑛 ∑ |𝐴𝑐𝑡𝑢𝑎𝑙−𝑓𝑜𝑟𝑐𝑎𝑠𝑡|2 𝑛 𝑖=1 (3) Here, n is the number of elements, is the sum, actual is the original y-value, and forecast is the regression y-value. The RMSE stands for the standard deviation of prediction error. We can determine the locations of the data points on the regression line using residuals or prediction error. The RMSE method determines how large these prediction mistakes are. It demonstrates how closely the data are related to the best fitting line. RMSE is typically used in climatology, regression analysis, and forecasting to validate experimental results. "(4)" is the formula for RMSE. 𝑅𝑀𝑆𝐸= √ 1 𝑛 ∑ |𝑠𝑖−𝑜𝑖|2 𝑛 𝑖=1 (4) 𝑅𝑀𝑆𝐸= √ 1 𝑛 ∑ |𝑠𝑖−𝑜𝑖|2 𝑛 𝑖=1 𝑅𝑀𝑆𝐸= √ 1 𝑛 ∑ |𝑠𝑖−𝑜𝑖|2 𝑛 𝑖=1 (4) (4) Here, oi =observations, si =variables predicted values, n=Observations number for analysis which is available. Here, oi =observations, si =variables predicted values, n=Observations number for analysis which is available. is available. 2.5. Facebook prophet p p A piecewise linear or logistic growth curve trend is one of the four fundamental parts of the Prophet process, an additive regression model. Prophet chooses change points from the data to automatically detect changes in trends. an annual seasonal element that is modelled using fourier series. The decomposable time series model used by FBProphet [25] has three main parts: seasonal, trends, holidays or events influence, and error, as shown in "(1)". 𝑓(𝑥) = 𝑔(𝑥) + 𝑠(𝑥) + ℎ(𝑥) + 𝑒(𝑡) (1) 𝑓(𝑥) = 𝑔(𝑥) + 𝑠(𝑥) + ℎ(𝑥) + 𝑒(𝑡) (1) FBProphet utilises a linear model to match the data, but by adjusting its parameters, it can convert to a nonlinear model (logistics growth). By default, FBProphet fits our model into a linear model. Some things will be fully realised as prediction technology advances. Carrying capacity is what it is known as, and the anticipated increase should reach it. Time-series forecasting is the process of building a model to forecast future values based on recent and historical time-series data. Therefore, the first thing we must do is to get the data. The Prophet demands that we change the name of the "date" column to "ds" and that we call our y-column just "y." Although Prophet does most of its work in the background, there are a few hyperparameters that let us easily adjust our models. To work with FB-Prophet in this instance, i used the "date" column as "ds" and the "close" column as "y". The intended data set's head portion is depicted in Figure 4(a). Once the data has been generated, we can now use Prophet's forecast method to obtain other forecasted variables. Figure 4(b) shows "yhat," which is the anticipated closing price, "yhat lower," which stands for the day's support, and "yhat upper," which stands for the day's resistance. The "ds" column, specifically, represents the future date. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 ISSN: 2302-9285 Bulletin of Electr Eng & Inf  1767 (a) (b) Figure 4. Data (a) preparation for FBProphet and (b) forecast data using FBProphet (a) (b) Figure 4. Data (a) preparation for FBProphet and (b) forecast data using FBProphet (a) (b) (a) Figure 4. Data (a) preparation for FBProphet and (b) forecast data using FBProphet 3. RESULTS AND DISCUSSION 3.1. Time series analysis The breakdown of the daily bitcoin price following "2014-09-17" is depicted in Figure 5. The first graph displays the recent increase in the price of bitcoin after 2018. The year is indicated on the x-axis, and the y-axis displays the daily "close" price of bitcoin. The tendency for a time series to generally increase, decrease, or get worse across the entire dataset. It is also known as the time series' gradual evolution. The "ds" chart displays the daily basis seasonal variation of the price of bitcoin. As we can see, when the market opened at 0:00 Greenwich mean time (GMT), or 6:00 AM Bangladesh time, the price was at its lowest point. It takes 4 hours for something to move up from one position, and the final 4 hours are when it moves down to the lowest position of the day. The yearly and weekly fluctuations in the price of bitcoin in relation to the dataset are displayed on two more random charts that are also random. If we examine the "day of the week" chart, we can see that its price increases most on friday. Bitcoin trading indicator: a machine learning driven real time bitcoin trading … (Ashikur Rahama ISSN: 2302-9285  1768 Figure 5. Decomposition of daily additive bitcoin price Figure 5. Decomposition of daily additive bitcoin price 3.2. Prediction target as close price The daily close price of bitcoin in USD is thought to be the main focus of this effort. The bitcoin trade marketplaces, which were considered to be the end of lengthy financial exchanges, are open every day of the week, 24/7, throughout the entire year. Temporary closures for support and updates are the main exception. As a result, the price of bitcoin fluctuates quickly between trade markets. The website coinmarketcap.com reported 16,123 distinct digital currency transaction markets as of January 2019. The significance of a local pricing could be incorrect due to the continually open business hours. On this record, the current price is equal to the maximum distance of the projected 23:59 coordinated universal time (UTC) last trading moment for every day. 3.3. Performance measurement Now, our constructed model can perform well with a low error rate in terms of model correctness. Table 5 shows the MAE, MSE, and RMSE. We created three different systems that geared up the final model after compiling the BTI into data. The results of a $1,000 USD cryptocurrency market deposit. Table 6 shows the deposit value, profit, and remaining balance for the four developed models. Table 5. Model performance metrics Model Name MAE MSE RMSE Bitcoin’s sentiment analysis using TextBlob 13140.41 220262701.56 14841.25 Time series forecasting using FBProphet 2084.47 12745971.02 3570.15 Web scrapping (by following internet) 2167.96 12661285.40 3758.27 The final model (combined version) 914.74 2192117.14 1480.58 Table 6. Findings of all implemented models Model Name Deposit ($) Profit ($) Remain Balance ($) Bitcoin’s sentiment analysis using TextBlob 1,000 439.65 1,439.65 Time series forecasting using FBProphet 1,000 -1000 000 Web scrapping (by following internet) 1,000 128 1128 The final model (combined version) 1,000 1,000.71 2,000.71 Table 6 demonstrates that the combined model's profitability is the highest. That implies that bitcoin's price movement is not only dependent on a single element; rather, there are a number of additional factors that might influence the market's direction. The first model only generates tweets and examines sentiment analysis of tweets using #bitcoin to see if it produces output in three categories. which are polar opposites, positive, and neutral. Although we can make some money there, it is insufficient for professional trading. Time series forecasting with FBProphet can provide market trends and other time series forecasting details, however employing this method exclusively would not be a suitable strategy because there are very few shortcomings in it. 3.2. Bitcoin trading indicator Our BTI was created by combining several techniques such as site scraping, sentiment analysis on Twitter, and cryptocurrency prediction values. The act of retrieving a website and gathering data from it is known as web scraping. When a user visits a website, a browser downloads the page, a process known as fetching. Web crawling is therefore a crucial component of web scraping because it enables us to gather pages for further processing. We utilised the well-known Python module "BeautifulSoup" version 4 to extract helpful data from numerous websites. Without using any machine learning models, we traded by using the ecrowdwisdom.live URL. This website is useful for making predictions about bitcoin and other cryptocurrencies. In the end, its forecasted outcome is favourable and is well received by many traders. Figure 6 illustrates the fundamental workings of Python-based web scraping. We combine our model with data from our sentiment analysis of tweets from earlier days, anticipated data visualisation, and web scraping technologies to create a useful tool that can provide a signal for short-term trading. Figure 7 shows an illustration of our whole model. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 Figure 6. Web page data scraping basic mechanism Figure 6. Web page data scraping basic mechanism Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772  1769 ISSN: 2302-9285 Bulletin of Electr Eng & Inf  Figure 7. The BTI Figure 7. The BTI 3.4. Prediction and indicator Figure 8 depicts the outcome after combining all trading logic into an if/else condition. A non- technical person may easily utilise it, and as i already indicated, we employed an online learning system to collect real-time qualitative and quantitative data sets. Even the support and resistance pip counts coming from a stable web platform. We attempted to signal trading using our bitcoin data from our BTI indicator. The trades in Table 7 are shown together with their open time, types, size, price, T/P value, and close time. We demonstrate the profit and highlight the buy or sell types using the BTI indicator. Bitcoin trading indicator: a machine learning driven real time bitcoin trading … (Ashikur Rahaman)  1770 ISSN: 2302-9285  1770  Figure 8. Bitcoin prediction and visualization from final model Figure 8. Bitcoin prediction and visualization from final model Table 7. Trading statement summary using BTI indicator No Trade Open time Type Size Price T/P Close time Profit BTI indicator 1 2183156 2021.11.06 11:16:22 buy 0.05 60437.95 61399.82 2021.11.06 21:22:20 46.48 Buy 2 1505512 2021.10.30 19:18:14 sell 0.2 61567.89 61450.19 2021.10.30 22:16:56 23.54 Sell 4. CONCLUSION We demonstrated that price movement can be predicted by the overall mood analysis. To accomplish our main objective, we added up all subjective polarity and divided it by the size of the data frame to maintain a polarity between -1 and +1. The final step of this analysis is a function that determines our options. In order to achieve our goal, we evaluated our model by combining it with other variables. In order to provide more details about the BTCUSD market, we generally gathered certain site material and extracted historical pricing data. Additionally, when needed, our model is able to detect and retrieve the current date. The study's most important finding was that we were able to profit by $1,000.71 USD in just 10 days with little error (RMSE: 1480.58) using the combined version of the programme. At a glance, we can state that Twitter sentiment analysis can provide sentiment towards the state of the market, and other data can provide entry and exit points for a certain trade. REFERENCES REFERENCES [1] S. Nakamoto, “Bitcoin: A peer-to-peer electronic cash system,” Decentralized Business Review. pp. 1–9, 2008. [2] R. Böhme, N. Christin, B. Edelman, and T. Moore, “Bitcoin: Economics, technology, and governance,” Journal of Economic Perspectives, vol. 29, no. 2, pp. 213–238, May 2015, doi: 10.1257/jep.29.2.213. 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Gupta, “Sentiment analysis: Concept, analysis and applications,” Towards data science, 2018. https://towardsdatascience.com/sentiment-analysis-concept-analysis-and-applications-6c94d6f58c17 (accessed May 12, 2022). p y p y pp ( y , [9] R. J. Lia, A. B. Siddikk, F. Muntasir, S. S. M. M. Rahman, and N. Jahan, “Depression detection from social media using T tweet,” in Big Data Intelligence for Smart Applications, 2022, pp. 209–226, doi: 10.1007/978-3-030-87954-9_9. R. J. Lia, A. B. Siddikk, F. Muntasir, S. S. M. M. Rahman, and N. Jahan, Depression detection from social media using Tw tweet,” in Big Data Intelligence for Smart Applications, 2022, pp. 209–226, doi: 10.1007/978-3-030-87954-9_9. [10] B. Wuthrich, V. Cho, S. Leung, D. Permunetilleke, K. Sankaran, and J. Zhang, “Daily stock market forecast from textual web data,” in SMC’98 Conference Proceedings. 1998 IEEE International Conference on Systems, Man, and Cybernetics (Cat. No.98CH36218), 1998, pp. 2720–2725, doi: 10.1109/ICSMC.1998.725072. [10] B. Wuthrich, V. Cho, S. Leung, D. Permunetilleke, K. Sankaran, and J. Zhang, “Daily stock market forecast from textual web data,” in SMC’98 Conference Proceedings. 1998 IEEE International Conference on Systems, Man, and Cybernetics (Cat. No.98CH36218), 1998, pp. 2720–2725, doi: 10.1109/ICSMC.1998.725072. ), , pp , [11] M. R. Borges, “Efficient market hypothesis in European stock markets,” The European Journal of Finance, vol. 16, no. 7, pp. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 REFERENCES Ravinder, “Real time sentimental analysis on Twitter,” in 2021 6th International Conference on Inventive Computation Technologies (ICICT), Jan. 2021, pp. 1030–1034, doi: 10.1109/ICICT50816.2021.9358772. [20] A. K. Bitto et al., “CryptoAR: scrutinizing the trend and market of cryptocurrency using machine learning approach on time series data,” Indonesian Journal of Electrical Engineering and Computer Science, vol. 28, no. 3, pp. 1684–1696, Dec. 2022, doi: 10.11591/ijeecs.v28.i3.pp1684-1696. j pp 1] K. Makice, Twitter API: Up and running: Learn how to build applications with the Twitter API. Sebastopol: "O’Reilly Media, Inc, 2009 [22] B. S. Shekhawat, “Sentiment classification of current public opinion on BREXIT: Naïve Bayes classifier model vs Python’s TextBlob approach,” M.S. thesis, Dept. Sci. in Data Analytics, National College of Ireland, Dublin, Ireland, 2019. [23] S Rahman N Jahan F Sadia and I Mahmud “Social crisis detection using Twitter based text mining a machine learning approach ” [23] S. Rahman, N. Jahan, F. Sadia, and I. Mahmud, Social crisis detection using Twitter based text mining-a machine learning ap Bulletin of Electrical Engineering and Informatics, vol. 12, no. 2, pp. 1069–1077, Apr. 2023, doi: 10.11591/eei.v12i2.3957. [24] A. Szabolcsi, “Positive polarity–negative polarity,” Natural Language & Linguistic Theory, vol. 22, no. 2, pp. 409–452, May 2004, doi: 10.1023/B:NALA.0000015791.00288.43. [25] R. K. Jana, I. Ghosh, and M. W. Wallin, “Taming energy and electronic waste generation in bitcoin mining: Insights from Facebook prophet and deep neural network,” Technological Forecasting and Social Change, vol. 178, p. 121584, May 2022, doi: 10.1016/j.techfore.2022.121584. j [26] M. A. Rubi, H. I. Bijoy, and A. K. Bitto, “Life expectancy prediction based on GDP and population size of Bangladesh using multiple linear regression and ANN model,” in 2021 12th International Conference on Computing Communication and Networking Technologies (ICCCNT), Jul. 2021, pp. 1–6, doi: 10.1109/ICCCNT51525.2021.9579594. REFERENCES 711–726, Oct. 2010, doi: 10.1080/1351847X.2010.495477. ), , pp , [11] M. R. Borges, “Efficient market hypothesis in European stock markets,” The European Journal of Finance, vol. 16, no. 7, pp. 711–726, Oct. 2010, doi: 10.1080/1351847X.2010.495477. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772  1771 Bulletin of Electr Eng & Inf  1771  ISSN: 2302-9285 2] S. Cavalli and M. Amoretti, “CNN-based multivariate data analysis for bitcoin trend prediction,” Applied Soft Computing, v 101, pp. 1–13, Mar. 2021, doi: 10.1016/j.asoc.2020.107065. pp j 3] Y. Zhai, A. Hsu, and S. K. Halgamuge, “Combining news and technical indicators in daily stock price trends prediction,” International Symposium on Neural Networks, 2007, pp. 1087–1096, doi: 10.1007/978-3-540-72395-0_132. y p pp [14] D. R. Pant, P. Neupane, A. Poudel, A. K. Pokhrel, and B. K. Lama, “Recurrent neural network based Bitcoin price prediction by Twitter sentiment analysis,” in 2018 IEEE 3rd International Conference on Computing, Communication and Security (ICCCS), Oct. 2018, pp. 128–132, doi: 10.1109/CCCS.2018.8586824. pp [15] S. Colianni, S. Rosales, and M. Signorotti, “Algorithmic trading of cryptocurrency based on Twitter sentiment analysis,” CS229 Project, vol. 1, no. 5, pp. 1–5, 2015. pp 6] D. Garcia and F. Schweitzer, “Social signals and algorithmic trading of Bitcoin,” Royal Society Open Science, vol. 2, no. 9, pp. 13, Sep. 2015, doi: 10.1098/rsos.150288. p [17] A. K. Bitto and I. Mahmud, “Multi categorical of common eye disease detect using convolutional neural network: a transfer learning h ” B ll i f El i l E i i d I f i l 11 4 2378 2387 A 2022 d i 10 11591/ i 11i4 3834 p [17] A. K. Bitto and I. Mahmud, “Multi categorical of common eye disease detect using convolutional neural network: a transfer learning approach,” Bulletin of Electrical Engineering and Informatics, vol. 11, no. 4, pp. 2378–2387, Aug. 2022, doi: 10.11591/eei.v11i4.3834. approach,” Bulletin of Electrical Engineering and Informatics, vol. 11, no. 4, pp. 2378–2387, Aug. 2022, doi: 10.11591/eei.v11i4.3834. [18] J. Abraham, D. Higdon, and J. Nelson, “Cryptocurrency price prediction using tweet volumes and sentiment analysis,” SMU Data Science Review, vol. 1, no. 3, pp. 1–21, 2018. [18] J. Abraham, D. Higdon, and J. Nelson, “Cryptocurrency price prediction using tweet volumes and sentiment analysis,” SM Science Review, vol. 1, no. 3, pp. 1–21, 2018. pp [19] K. S. Madhu, B. C. Reddy, C. Damarukanadhan, M. Polireddy, and N. BIOGRAPHIES OF AUTHORS Ashikur Rahaman received his undergraduate degree in Software Engineering Major in Data Science at Daffodil International University (DIU), Dhaka, Bangladesh. He is currently attending Universal Immigration and Education Consultancy Ltd as a Software Engineer. His research experience and interest now in crypto market and data science. He can be contacted at email: ashikur35-1575@diu.edu.bd. Abu Kowshir Bitto received his undergraduate degree in Software Engineering Major in Data Science at Daffodil International University (DIU), Dhaka, Bangladesh. He is currently attending MediprospectsAI as a Research and Development Engineer. He is member of International Association of Engineers. He is a Chief Human Resource Executive (CHRE) at Virtual Multidisciplinary Research Lab. He previously worked as a Research Assistant at the Data Science Lab DIU. He is an energetic, focused and hard working person since his student life. His research experience and interest now in computer vision, data science, and natural language processing. He can be contacted at email: abu.kowshir777@gmail.com. Khalid Been Md. Badruzzaman Biplob pursued his bachelor's degree and Master of Science in Computer Science and Engineering (CSE) at Daffodil International University (DIU), Dhaka, Bangladesh. Currently he is working as a Senior Lecturer in Software Engineering department at DIU. He is doing his Ph.D in Education from University Sains Islam, Malaysia. His area of interest includes machine learning, deep learning, and educational research. He can be contacted at email: Khalid@daffodilvarsity.edu.bd. Bitcoin trading indicator: a machine learning driven real time bitcoin trading … (Ashikur Rahaman)  1772 ISSN: 2302-9285 Md. Hasan Imam Bijoy pursued his bachelor's degree (B. Sc) in Computer Science and Engineering (CSE) at Daffodil International University (DIU), Dhaka, Bangladesh. Currently he is working as a Lecturer in CSE department at DIU. He is a Convener of the Virtual Multidisciplinary Research Lab. He is a research zealot, having published over 15 conference papers, 4 journal publications, and one programming book (A Handbook of C Programming with Example). His area of interest includes machine learning, deep learning, computer vision, natural language processing, image processing, internet of things, and so many field. He can be contacted at email: hasan15- 11743@diu.edu.bd. Md. Hasan Imam Bijoy pursued his bachelor's degree (B. Sc) in Computer Science and Engineering (CSE) at Daffodil International University (DIU), Dhaka, Bangladesh. Currently he is working as a Lecturer in CSE department at DIU. He is a Convener of the Virtual Multidisciplinary Research Lab. Bulletin of Electr Eng & Inf, Vol. 12, No. 3, June 2023: 1762-1772 BIOGRAPHIES OF AUTHORS He is a research zealot, having published over 15 conference papers, 4 journal publications, and one programming book (A Handbook of C Programming with Example). His area of interest includes machine learning, deep learning, computer vision, natural language processing, image processing, internet of things, and so many field. He can be contacted at email: hasan15- 11743@diu.edu.bd. Nusrat Jahan is Assitant Professor and head of Department of Information Technology and Management in Daffodil International University, Dhaka, Bangladesh. She is currently pursuing her Ph.D from School of Computer and Communication Engineering, Universiti Malaysia Perlis (UniMAP). Shecompleted her M.Sc. and B. Sc. in IT from Institute of Information Technology, Jahangirnagar University. Her research interests are distributed database system, machine learning, data mining, internet of things (IoT) and management information system (MIS). She can be contacted at email: nusrat.swe@diu.edu.bd. Dr. Imran Mahmud is an Associate professor and head of the Department of Software Engineering (SWE) at Daffodil International University. He is also an adjunct professor at the Graduate School of Business, Universiti Sains Malaysia. Dr. Imran is an expert in business analytics, technology management, and structural equation modeling. He can be contacted at email: imranmahmud@daffodilvarsity.edu.bd. Md. Hasan Imam Bijoy Nusrat Jahan is Assitant Professor and head of Department of Information Technology and Management in Daffodil International University, Dhaka, Bangladesh. She is currently pursuing her Ph.D from School of Computer and Communication Engineering, Universiti Malaysia Perlis (UniMAP). Shecompleted her M.Sc. and B. Sc. in IT from Institute of Information Technology, Jahangirnagar University. Her research interests are distributed database system, machine learning, data mining, internet of things (IoT) and management information system (MIS). She can be contacted at email: nusrat.swe@diu.edu.bd. Dr. Imran Mahmud is an Associate professor and head of the Department of Software Engineering (SWE) at Daffodil International University. He is also an adjunct professor at the Graduate School of Business, Universiti Sains Malaysia. Dr. Imran is an expert in business analytics, technology management, and structural equation modeling. He can be contacted at email: imranmahmud@daffodilvarsity.edu.bd. Dr. Imran Mahmud is an Associate professor and head of the Department of Software Engineering (SWE) at Daffodil International University. He is also an adjunct professor at the Graduate School of Business, Universiti Sains Malaysia. Dr. Imran is an expert in business analytics, technology management, and structural equation modeling. He can be contacted at email: imranmahmud@daffodilvarsity.edu.bd.
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Two new polytypes of 2,4,6-tribromobenzonitrile
Acta crystallographica. Section E, Crystallographic communications
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research communications Two new polytypes of 2,4,6-tribromobenzonitrile Doyle Britton,‡ Wayland E. Noland* and Kenneth J. Tritch ISSN 2056-9890 ISSN 2056-9890 Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431, USA. *Correspondence e-mail: nolan001@umn.edu Received 21 October 2015 Accepted 5 January 2016 Received 21 October 2015 Accepted 5 January 2016 Three polymorphs of 2,4,6-tribromobenzonitrile (RCN), C7H2Br3N, two of which are novel and one of which is a redetermination of the original structure first determined by Carter & Britton [(1972). Acta Cryst. B28, 945–950] are found to be polytypic. Each has a layer structure which differs only in the stacking of the layers. Each layer is composed of molecules associated through C N  Br contacts which form R2 2(10) rings. Two such rings are associated with each N atom; one with each ortho-Br atom. No new polytypes of 1,3,5-tribromo- 2-isocyanobenzene (RNC) were found but a re-determination of the original structure by Carter et al. [(1977). Cryst. Struct. Commun. 6, 543–548] is presented. RNC was found to be isostructural with one of the novel polytypes of RCN. Unit cells were determined for 23 RCN samples and 11 RNC samples. Polytypes could not be distinguished based on crystal habits. In all four structures, each molecule of the asymmetric unit lies across a mirror plane. Edited by A. J. Lough, University of Toronto, Canada ‡ Deceased July 7, 2015. ‡ Deceased July 7, 2015. ‡ Deceased July 7, 2015. Keywords: crystal structure; polytypes; poly- morphs; Sandmeyer; isocyanide; N  Br contacts; C  Br contacts CCDC references: 1445499; 1445498; 1445497; 1445496 Supporting information: this article has supporting information at journals.iucr.org/e Keywords: crystal structure; polytypes; poly- morphs; Sandmeyer; isocyanide; N  Br contacts; C  Br contacts CCDC references: 1445499; 1445498; 1445497; 1445496 Supporting information: this article has supporting information at journals.iucr.org/e research communications research communications RNC-II is the original Z = 8 structure. As the Z values suggest, RCN-II and RNC-II are isomorphs. 2. Structural commentary Molecules of RCN and RNC are nearly planar. The average distance of atoms from the plane of best fit is 0.025 A˚ in RCN- I. For RCN-II, the average distances are 0.037 and 0.010 A˚ , for the (N27) and (N37) molecules, respectively. In RNC-II, the molecules are slightly more distorted, with average deviations of 0.043 and 0.017 A˚ for the (N127) and (N137) molecules, respectively. For RCN-III, the average distances are 0.009, 0.018, and 0.032 A˚ for the (N47), (N57), and (N67) molecules, respectively. The bond lengths in RCN and RNC are generally similar (Fig. 4). They are also similar to the mean bond distances reported for bonds of each type (Allen et al., 1987). The N Figure 1 Synthesis of RCN and RNC. Figure 3 Molecular structure, with atom labeling, of RNC-II viewed along [120]. Displacement ellipsoids are drawn at the 50% probability level. Each molecule lies across a crystallographic mirror plane. Figure 4 Selected bond lengths (A˚ ) in RCN and RNC, averaged across all polytypes. The data shown in parentheses are the mean distances for each bond type reported by Allen et al. (1987). RNC-II is the original Z = 8 structure. As the Z values suggest, RCN-II and RNC-II are isomorphs. Figure 1 Synthesis of RCN and RNC. Figure Molecu Displa molecu RNC-II is the original Z = 8 structure. As the Z values suggest, RCN-II and RNC-II are isomorphs. Figure 1 Synthesis of RCN and RNC. Figure 3 Molecular structure, with atom labeling, of RNC-II viewed along [120]. Displacement ellipsoids are drawn at the 50% probability level. Each molecule lies across a crystallographic mirror plane. Figure 1 Synthesis of RCN and RNC. Figure 3 Molecular structure, with atom labeling, of RNC-II viewed along [120]. Displacement ellipsoids are drawn at the 50% probability level. Each molecule lies across a crystallographic mirror plane. Figure 4 Selected bond lengths (A˚ ) in RCN and RNC, averaged across all polytypes. The data shown in parentheses are the mean distances for each bond type reported by Allen et al. (1987). Figure 1 Synthesis of RCN and RNC. RNC-II is the original Z = 8 structure. As the Z values suggest, RCN-II and RNC-II are isomorphs. 2. Structural commentary Molecules of RCN and RNC are nearly planar. 1. Chemical context The reported structures of 2,4,6-tribromobenzonitrile (RCN, Figs. 1 and 2; Carter & Britton, 1972) and 1,3,5-tribromo-2- isocyanobenzene (RNC, Figs. 1 and 3; Carter et al., 1977) have two-dimensional layers of similarly arranged molecules, but the packing of adjacent layers is distinctly different. At the time, no explanation was offered. It was puzzling, given that the two compounds are isoelectronic, isosteric, and the prin- cipal intermolecular interactions, C N  Br and N C  Br, are similar. Recent reports of polytype organic structures, such as picryl bromide (Parrish et al., 2008) and 5,6-dimethyl- benzofurazan 1-oxide (Britton et al., 2012) led to the idea that RCN and RNC might occur as polytypes. Earlier, Bredig (1930) had determined the space group and unit cell of RCN with the same results as Carter & Britton. Bredig was trying to follow up on the goniometer studies of Jaeger (1909), but while he found the same a:b ratio as Jaeger in the RCN unit cell, he found a different b:c ratio. Accordingly, a search was made for polytypes of RCN, and to a lesser extent, of RNC. Four different structures were identified. RCN-I is the original Z = 2 structure of RCN; RCN- II is a new Z = 8 polytype; RCN-III is a new Z = 12 polytype. No RNC counterparts to RCN-I or RCN-III were observed. Accordingly, a search was made for polytypes of RCN, and to a lesser extent, of RNC. Four different structures were identified. RCN-I is the original Z = 2 structure of RCN; RCN- II is a new Z = 8 polytype; RCN-III is a new Z = 12 polytype. No RNC counterparts to RCN-I or RCN-III were observed. Accordingly, a search was made for polytypes of RCN, and to a lesser extent, of RNC. Four different structures were identified. RCN-I is the original Z = 2 structure of RCN; RCN- II is a new Z = 8 polytype; RCN-III is a new Z = 12 polytype. No RNC counterparts to RCN-I or RCN-III were observed. 178 Acta Cryst. (2016). E72, 178–183 doi:10.1107/S2056989016000256 research communications Figure 7 Translational (T) stacking of layers in Z = 2 RCN-I, viewed along [110]. If the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. Figure 7 Figure 5 II and RCN-III, respectively. Both are viewed along [100]. The molecules ectively Figure 7 Translational (T) stacking of layers in Z = 2 RCN-I, viewed along [110]. If the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. g View of one layer of RCN-I along [101]. Dashed blue lines represent short contacts. g Translational (T) stacking of layers in Z = 2 RCN-I, viewed along [110]. If the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. g Translational (T) stacking of layers in Z = 2 RCN-I, viewed along [110]. If the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. research communications atom in RNC is displaced toward the aryl ring compared to the literature distances for aryl isocyanides. research communications The average distance of atoms from the plane of best fit is 0.025 A˚ in RCN- I. For RCN-II, the average distances are 0.037 and 0.010 A˚ , for the (N27) and (N37) molecules, respectively. In RNC-II, the molecules are slightly more distorted, with average deviations of 0.043 and 0.017 A˚ for the (N127) and (N137) molecules, respectively. For RCN-III, the average distances are 0.009, 0.018, and 0.032 A˚ for the (N47), (N57), and (N67) molecules, respectively. Figure 4 Selected bond lengths (A˚ ) in RCN and RNC, averaged across all polytypes. The data shown in parentheses are the mean distances for each bond type reported by Allen et al. (1987). The bond lengths in RCN and RNC are generally similar (Fig. 4). They are also similar to the mean bond distances reported for bonds of each type (Allen et al., 1987). The N Figure 2 Figure 2 Figure 2 Figure 2 Figure 2 Molecular structures, with atom labeling, of RCN-I viewed along [111]; RCN-II viewed along [120]; RCN-III viewed along [120]. Displacement ellipsoids are drawn at the 50% probability level. In discussion, molecules are named by their respective nitrogen atoms. Each molecule lies across a crystallographic mirror plane Figure 2 Molecular structures, with atom labeling, of RCN-I viewed along [111]; RCN-II viewed along [120]; RCN-III viewed along [120]. Displacement ellipsoids are drawn at the 50% probability level. In discussion, molecules are named by their respective nitrogen atoms. Each molecule lies across a crystallographic mirror plane. Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N 179 Acta Cryst. (2016). E72, 178–183 Acta Cryst. (2016). E72, 178–183 Figure 7 Translational (T) stacking of layers in Z = 2 RCN-I, viewed along [110]. If the unit cell of RCN-I is transformed by the matrix [100/010/201], the dimensions of the projection become 10.247 (3)  12.480 (3) A˚ , which is similar to the corresponding b  c measurements, 10.2147 (10)  12.4754 (12) A˚ for RCN-II, and 10.2167 (18)  12.493 (2) A˚ for RCN-III. Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. research communications Figure 5 View of one layer of RCN-I along [101]. Dashed blue lines represent short contacts. research communications research communications Figure 5 View of one layer of RCN-I along [101]. Dashed blue lines represent short contacts. 2,4,6-Tribromoaniline was prepared from aniline according to the work of Coleman & Talbot (1943). 2,4,6-Tribromoaniline was prepared from aniline according to the work of Coleman & Talbot (1943). 2,4,6-Tribromoaniline was prepared from aniline according to the work of Coleman & Talbot (1943). RCN, adapted from the work of Toya et al. (1992): Diazo- tization: 2,4,6-Tribromoaniline (1.25 g), water (2.5 ml), and glacial acetic acid (4.4 ml) were combined in a round- bottomed flask. The resulting suspension was cooled in an ice bath, and then H2SO4 (98%, 1.0 ml) was added dropwise, followed by an ice-cold solution of NaNO2 (520 mg) in water (4 ml). The resulting mixture was warmed to 310 K for 1 h, and then cooled in an ice bath. Cyanide suspension: CuCN (680 mg) and NaCN (1.12 g) were dissolved in water (20 ml). RCN, adapted from the work of Toya et al. (1992): Diazo- tization: 2,4,6-Tribromoaniline (1.25 g), water (2.5 ml), and glacial acetic acid (4.4 ml) were combined in a round- bottomed flask. The resulting suspension was cooled in an ice bath, and then H2SO4 (98%, 1.0 ml) was added dropwise, followed by an ice-cold solution of NaNO2 (520 mg) in water (4 ml). The resulting mixture was warmed to 310 K for 1 h, and then cooled in an ice bath. Cyanide suspension: CuCN (680 mg) and NaCN (1.12 g) were dissolved in water (20 ml). NaHCO3 (10.9 g) and ethyl acetate (10 ml) were added, giving a suspension, which was cooled in an ice bath. Cyanation: The diazotization mixture was added dropwise to the cyanide suspension as quickly as possible without causing excessive foaming. The ice bath was removed and then the mixture was stirred overnight. The organic phase was set aside. The aqueous phase was extracted with ethyl acetate (3  10 ml). The combined organic portions were washed with brine (10 ml), dried with Na2SO4, and concentrated at reduced pressure, giving a brown powder, which was purified by column chromatography (SiO2, hexane–ethyl acetate, gradient from 1:0 to 10:1). The desired fraction (Rf = 0.61 in 8:1) was concentrated at reduced pressure, giving beige needles (760 mg, 59%). M.p. 400–400.5 K (lit. 402 K; Giumanini et al., 1996); 1H NMR (300 MHz, CD2Cl2)  7.853 (s, H13); 13C NMR (75 MHz, CD2Cl2)  135.3 (C13), 128.6 (C14), 127.4 (C12), 118.3 (C17), 116.0 (C11); IR (NaCl, cm1) 3095, 3068, 2921 (w), 2233 (s, C N; lit. research communications Figure 9 Pseudotranslational (T) and pseudocentric (C) stacking of layers in Z = 12 RCN-III, viewed roughly along [010]. Table 1 Short contact geometry (A˚ , ). X Y  Br X Y Y  Br X Y  Br C17 N17  Br12i 1.144 (10) 3.053 (4) 131.45 (9) C27 N27  Br32ii 1.132 (7) 3.059 (3) 131.76 (7) N127 C127  Br132ii 1.147 (6) 3.141 (4) 134.01 (8) C37 N37  Br22iii 1.156 (6) 3.077 (3) 130.68 (10) N137 C137  Br122iii 1.164 (6) 3.161 (4) 133.23 (11) C47 N47  Br52ii 1.146 (6) 3.072 (3) 130.95 (9) C57 N57  Br42iii 1.147 (6) 3.057 (3) 131.47 (7) C67 N67  Br62iv 1.139 (6) 3.065 (3) 131.96 (7) Symmetry codes: (i) x, 1  y, z; (ii) x, y, 1 + z; (iii) x, y, 1 + z; (iv) 1  x, 1  y, 1  z. rhenium (trichloroisocyanobenzene; Ko et al., 2011), and ruthenium (RNC; Leung et al., 2009). rhenium (trichloroisocyanobenzene; Ko et al., 2011), and ruthenium (RNC; Leung et al., 2009). 2,4,6-Tribromoaniline was prepared from aniline according to the work of Coleman & Talbot (1943). 2232), 1716 (w), 1563 (s), 1527 (s), 1431 (s), 1410 (s), 1370 (s), 1353 (s), 1328, 1191 (s), 1109 (s), 1087, 1063 (s), 854 (s), 809 (s), 748 (s); MS (EI, m/z) [M]+ calculated for C7H2Br3N 336.7732, found 336.7716. Figure 9 Pseudotranslational (T) and pseudocentric (C) stacking of layers in Z = 12 RCN-III, viewed roughly along [010]. The NC  Br contact distances in RNC-II are a smaller percentage of the van der Waals distance, 3.63 A˚ , versus corresponding atoms in RCN-II. The contacts in RNC-II occur at slightly wider angles than those in RCN-II (Table 1). In RCN-II, the planes of best fit of the two different mol- ecules are inclined by 6.5 to each other; in RNC-II this inclination is 7.5. In RCN-III, the relative inclination of planes of (N47) and (N57) molecules is 7.0. These two planes are approximately bisected by the planes of (N67) molecules. 3. Supramolecular features Fig. 5 shows a two-dimensional layer of RCN-I. All of the structures are composed of similar layers. Adjacent molecules are associated through C N  Br interactions, arranged in R2 2(10) rings (Etter, 1990; Bernstein et al., 1995). The CN  Br distances in these rings range between 3.053 and 3.077 A˚ (Table 1); these distances can be compared with the N  Br van der Waals distance of 3.40 A˚ (Bondi, 1964; Rowland & Taylor, 1996). Each layer in RCN-II is composed of alternating (N27) and (N37) molecules. RCN-III contains two layers of alternating (N47) and (N57) molecules for each layer composed entirely of (N67) molecules. Adjacent pairs of layers show translational or pseudotranslational, or pseudo- centric stacking (Fig. 6). RCN-I shows translational stacking between all adjacent layers (Fig. 7). In RCN-II, alternating pairs of layers show pseudocentric and pseudotranslational stacking (Fig. 8). In RCN-III, each layer of (N67) molecules pseudotranslationally overlaps both neighboring (N47/N57) layers, while pairs of adjacent (N47/N57) layers, every third pair of layers, overlap pseudocentrically (Fig. 9). Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. Figure 8 Pseudocentric (C) and pseudotranslational (T) stacking of layers in Z = 8 RCN-II, viewed roughly along [010]. Figure 6 Pseudotranslational (T) and pseudocentric (C) stacking of layers in RCN-II and RCN-III, respectively. Both are viewed along [100]. The molecules shown are the second pair of layers from the top, in Fig. 7 and Fig. 8, respectively. Figure 6 Pseudotranslational (T) and pseudocentric (C) stacking of layers in RCN-II and RCN-III, respectively. Both are viewed along [100]. The molecules shown are the second pair of layers from the top, in Fig. 7 and Fig. 8, respectively. Acta Cryst. (2016). E72, 178–183 180 Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N 180 4. Database survey A search of the Cambridge Structural Database (Version 5.36, update 3; Groom & Allen, 2014) for 2,4,6-trihalo-3,5-unsub- stituted benzonitriles found nine entries: RCN; its trichloro analog, Gol’der et al. (1952), Carter & Britton (1972), Pink et al. (2000); its trifluoro analog, Britton (2008); four mixed- halogen entries, Gleason & Britton (1978), Britton (2005), Britton et al. (2002), and Britton (1997). Searching for the corresponding isocyanides found two entries: RNC and its trichloro analog (Pink et al., 2000). Layers of the type observed in RCN were reported in 2,6- dibromo entries with Cl, Br, or I at the 4-position. Other entries exhibit short contacts between the cyano- or isocyano- group and one ortho-halogen atom of an intralayer molecule, with various interlayer contacts. Polymorphs are only reported for 2,4,6-trichlorobenzonitrile; those are not polytypic. 2,4,6-Tribromoformanilide, adapted from the work of Krishnamurthy (1982): Acetic anhydride (3.2 ml) and tetra- hydrofuran (THF, 5.0 ml) were combined in a round- bottomed flask. Formic acid (88% aq., 1.7 ml) was added dropwise. The resulting solution was stirred for 30 min at room temperature. A solution of 2,4,6-tribromoaniline (1.82 g) in Expanding the search to include organometallic complexes found three more entries, with the cyano N or isocyano C atom ligating gallium (trifluorobenzonitrile; Tang et al., 2012), 181 Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N 1 Acta Cryst. (2016). E72, 178–183 research communications Experimental details. RCN-I RCN-II RCN-III RNC-II Crystal data Chemical formula C7H2Br3N C7H2Br3N C7H2Br3N C7H2Br3N Mr 339.83 339.83 339.83 339.83 Crystal system, space group Monoclinic, P21/m Orthorhombic, Pnma Orthorhombic, Pnma Orthorhombic, Pnma Temperature (K) 173 173 173 173 a, b, c (A˚ ) 4.8742 (15), 10.247 (3), 8.683 (3) 13.6183 (13), 10.2147 (10), 12.4754 (12) 20.399 (4), 10.2167 (18), 12.493 (2) 13.5916 (18), 10.1464 (13), 12.6158 (16) , ,  () 90, 94.97 (1), 90 90, 90, 90 90, 90, 90 90, 90, 90 V (A˚ 3) 432.0 (2) 1735.4 (3) 2603.7 (8) 1739.8 (4) Z 2 8 12 8 Radiation type Mo K Mo K Mo K Mo K  (mm1) 13.93 13.88 13.87 13.84 Crystal size (mm) 0.50  0.15  0.10 0.25  0.20  0.07 0.50  0.15  0.10 0.40  0.35  0.20 Data collection Diffractometer Bruker 1K area detector Bruker 1K area detector Bruker 1K area detector Bruker APEXII CCD Absorption correction Multi-scan (SADABS; Bruker, 2002) Multi-scan (SADABS; Bruker, 2002) Multi-scan (SADABS; Bruker, 2002) Multi-scan (SADABS; Bruker, 2002) Tmin, Tmax 0.080, 0.248 0.06, 0.37 0.054, 0.337 0.170, 0.333 No. of measured, independent and observed [I > 2(I)] reflections 4093, 1024, 856 16607, 2093, 1692 22804, 2691, 2165 19459, 2105, 1638 Rint 0.127 0.052 0.055 0.078 (sin / )max (A˚ 1) 0.649 0.650 0.616 0.650 Refinement R[F 2 > 2(F 2)], wR(F 2), S 0.046, 0.116, 1.01 0.028, 0.063, 1.02 0.023, 0.046, 1.07 0.025, 0.055, 1.06 No. of reflections 1024 2093 2691 2105 No. of parameters 58 115 173 116 H-atom treatment H-atom parameters constrained H-atom parameters constrained H-atom parameters constrained H-atom parameters constrained  max,  min (e A˚ 3) 1.36, 1.28 0.44, 0.69 0.56, 0.49 0.44, 0.48 Computer programs: SMART, APEX2 and SAINT (Bruker, 2002), SHELXT (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b), Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008), enCIFer (Allen et al., 2004), and publCIF (Westrip, 2010). Computer programs: SMART, APEX2 and SAINT (Bruker, 2002), SHELXT (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b), Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008), enCIFer (Allen et al., 2004), and publCIF (Westrip, 2010). dropwise. The mixture was stirred for 18 h, cooled in an ice bath, and then filtered through neutral alumina (3 cm H  3 cm D), with addition of sufficient dichloromethane (DCM) to elute all product as indicated by TLC. The filtrate was concentrated at reduced pressure. research communications The resulting yellow residue was dissolved in DCM (25 ml), cooled in an ice bath, and washed with ice-cold acetic acid solution (0.025 M, 3  15 ml), and then ice-cold sat. NaHCO3 solution (15 ml). The organic phase was collected, dried with Na2SO4, and then concen- trated under a stream of nitrogen, giving beige needles upon filtration (630 mg, 34%). M.p. 390 K (lit. 394 K, Mironov & Mokrushin, 1999); Rf = 0.75 (Al2O3 in 2:1 hexane–ethyl acetate); 1H NMR (300 MHz, CD2Cl2)  7.827 (s, H123); 13C NMR (75 MHz, (CD3)2CO) 159.7 (C127), 135.8 (C123), 135.4 (C121), 124.5 (C124), 122.0 (C122); IR (NaCl, cm1) 3162, 3068, 2921, 2128 (s, N C; lit. 2125), 1660 (s), 1555 (s), 1370 (s), 856 (s), 701 (s); MS (EI, m/z) [M]+ calculated for C7H2Br3N 336.7732, found 336.7734. THF (20 ml) was added dropwise. The resulting mixture was stirred for 18 h. The resulting heterogeneous mixture was filtered through neutral alumina (Sigma–Aldrich 199974, 5 cm H  3 cm D), with addition of sufficient THF to elute all product, as indicated by TLC. The filtrate was concentrated at reduced pressure. The resulting residue was washed with sat. NaHCO3 solution (50 ml), and then filtered. The filter cake was recrystallized from acetone, giving white needles (1.72 g, 87%). M.p. 493–494 K (lit. 494.5 K; Chattaway et al., 1899); Rf = 0.48 (SiO2 in 1:1 hexane–ethyl acetate); 1H NMR (300 MHz, (CD3)2SO)  10.192 (s, NH, O-E conformer, 0.87H), 8.522 (s, NH, O-Z conformer, 0.13H), 8.260 (s, CHO, 1H), 8.018 (s, CH, 2H); 13C NMR (75 MHz, (CD3)2SO)  165.9 (CO, O-Z conformer), 159.8 (CO, O-E conformer), 134.6 (ipso-C), 134.4 (CH), 124.5 (ortho-CBr), 121.1 (para-CBr); IR (NaCl, cm1) 3201, 3166, 1661 (s, C O), 1558, 1154, 858, 810; MS (ESI, m/z) [M – H] calculated for C7H4Br3NO 355.7750, found 355.7758. Analysis (MHW Laboratories, Phoenix, AZ, USA) calculated for C7H4Br3NO: C 23.50, H 1.13, Br 66.99, N 3.91; found C 23.42, H 1.15, Br 66.71, N 3.57. THF (20 ml) was added dropwise. The resulting mixture was stirred for 18 h. The resulting heterogeneous mixture was filtered through neutral alumina (Sigma–Aldrich 199974, 5 cm H  3 cm D), with addition of sufficient THF to elute all product, as indicated by TLC. The filtrate was concentrated at reduced pressure. The resulting residue was washed with sat. NaHCO3 solution (50 ml), and then filtered. 6. Refinement Chattaway, F. D., Orton, K. J. P. & Hurtley, W. H. (1899). Ber. Dtsch. Chem. Ges. 32, 3635–3638. Crystal data, data collection, and structure refinement details for RCN and RNC are summarized in Table 2. H atoms were placed in calculated positions and refined as riding atoms, with C—H = 0.95 A˚ and Uiso(H) = 1.2Ueq(C). Coleman, G. H. & Talbot, W. F. (1943). Org. Synth, Coll. Vol. 2, 592– 595. Etter, M. C. (1990). Acc. Chem. Res. 23, 120–126. Giumanini, A. G., Verardo, G., Geatti, P. & Strazzolini, P. (1996). Tetrahedron, 52, 7137–7148. Gleason, W. B. & Britton, D. (1978). Cryst. Struct. Commun. 7, 365– 370. Acknowledgements Gol’der, G. A., Zhdanov, G. S. & Umanskij, M. M. (1952). Russ. J. Phys. Chem. 26, 1434–1437. The authors thank Victor G. Young, Jr. (X-Ray Crystal- lographic Laboratory, University of Minnesota) for assistance with unit cell and crystal determinations, and the Wayland E. Noland Research Fellowship Fund at the University of Minnesota Foundation for generous financial support of this project. y Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662– 671. Jaeger, F. M. (1909). Z. Kristallogr. 46, 268–269. Ko, C.-C., Siu, J. W.-K., Cheung, A. W.-Y. & Yiu, S.-M. (2011). Organometallics, 30, 2701–2711. Krishnamurthy, S. (1982). Tetrahedron Lett. 23, 3315–3318. Leung, C.-F., Ng, S.-M., Xiang, J., Wong, W.-Y., Lam, M. H.-W., Ko, C.-C. & Lau, T.-C. (2009). Organometallics, 28, 5709–5714. References Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470. Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335–338. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, S1–19. Mironov, M. A. & Mokrushin, V. S. (1999). Russ. J. Org. Chem. 35, 693–697. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, S1–19. Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. Parrish, D. A., Deschamps, J. R., Gilardi, R. D. & Butcher, R. J. (2008). Cryst. Growth Des. 8, 57–62. g Bondi, A. (1964). J. Phys. Chem. 68, 441–451. Pink, M., Britton, D., Noland, W. E. & Pinnow, M. J. (2000). Acta Cryst. C56, 1271–1273. Bredig, M. A. (1930). Z. Kristallogr. 74, 56–61. Britton, D. (1997). Acta Cryst. C53, 225–227. Rowland, R. S. & Taylor, R. (1996). J. Phys. Chem. 100, 7384–7391. Britton, D. (2005). Acta Cryst. E61, o1726–o1727. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Britton, D. (2008). Acta Cryst. C64, o583–o585. Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Britton, D., Noland, W. E. & Henke, T. K. (2002). Acta Cryst. E58, o185–o187. Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Tang, S., Monot, J., El-Hellani, A., Michelet, B., Guillot, R., Bour, C. Tang, S., Monot, J., El-Hellani, A., Michelet, B., Guillot, R., B & Gandon, V. (2012). Chem. Eur. J. 18, 10239–10243. Tang, S., Monot, J., El-Hellani, A., Michelet, B., Guillot, R., Bo & Gandon, V. (2012). Chem. Eur. J. 18, 10239–10243. Britton, D., Young, V. G., Noland, W. E., Pinnow, M. J. & Clark, C. M. (2012). Acta Cryst. B68, 536–542. ( ) Toya, Y., Takagi, M., Nakata, H., Suzuki, N., Isobe, M. & Goto, T. (1992). Bull. Chem. Soc. Jpn, 65, 392–395. ( ) y Bruker (2002). APEX2, SMART, SAINT, and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA. ( ) p Ugi, I., Fetzer, U., Eholzer, U., Knupfer, H. & Offermann, K. (1965). Ugi, I., Fetzer, U., Eholzer, U., Knupfer, H. Carter, V. B. & Britton, D. (1972). Acta Cryst. B28, 945–950. Angew. Chem. research communications The filter cake was recrystallized from acetone, giving white needles (1.72 g, 87%). M.p. 493–494 K (lit. 494.5 K; Chattaway et al., 1899); Rf = 0.48 (SiO2 in 1:1 hexane–ethyl acetate); 1H NMR (300 MHz, (CD3)2SO)  10.192 (s, NH, O-E conformer, 0.87H), 8.522 (s, NH, O-Z conformer, 0.13H), 8.260 (s, CHO, 1H), 8.018 (s, CH, 2H); 13C NMR (75 MHz, (CD3)2SO)  165.9 (CO, O-Z conformer), 159.8 (CO, O-E conformer), 134.6 (ipso-C), 134.4 (CH), 124.5 (ortho-CBr), 121.1 (para-CBr); IR (NaCl, cm1) 3201, 3166, 1661 (s, C O), 1558, 1154, 858, 810; MS (ESI, m/z) [M – H] calculated for C7H4Br3NO 355.7750, found 355.7758. Analysis (MHW Laboratories, Phoenix, AZ, USA) calculated for C7H4Br3NO: C 23.50, H 1.13, Br 66.99, N 3.91; found C 23.42, H 1.15, Br 66.71, N 3.57. Crystallization: RCN crystals were grown by slow evaporation of single-solvent solutions (290–295 K). RCN-I was obtained from acetonitrile, benzene, chloroform, or methylene chloride; RCN-II from mesitylene; RCN-III from benzene or chloroform. RNC-II crystals were obtained by sublimation (385 K, 0.05 torr), or by slow evaporation from the same solvents as RCN (268–295 K). Crystallization: RCN crystals were grown by slow evaporation of single-solvent solutions (290–295 K). RCN-I was obtained from acetonitrile, benzene, chloroform, or methylene chloride; RCN-II from mesitylene; RCN-III from benzene or chloroform. RNC-II crystals were obtained by sublimation (385 K, 0.05 torr), or by slow evaporation from the same solvents as RCN (268–295 K). RNC, adapted from the work of Ugi et al. (1965): 2,4,6- Tribromoformanilide (1.96 g) and N,N-diisopropylethylamine (DIPEA, 3.4 ml) were added to 1,2-dichloroethane (75 ml). The resulting suspension was refluxed for 5 min, and then cooled to room temperature. POCl3 (0.6 ml) was added Acta Cryst. (2016). E72, 178–183 182 Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N research communications Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N 183 References Int. Ed. Engl. 4, 472–484. Carter, V. B., Britton, D. & Gleason, W. G. (1977). Cryst. Struct. Commun. 6, 543–548. Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Acta Cryst. (2016). E72, 178–183 Britton et al.  C7H2Br3N, C7H2Br3N, C7H2Br3N and C7H2Br3N 183 supporting information supporting information Acta Cryst. (2016). E72, 178-183 [doi:10.1107/S2056989016000256] Two new polytypes of 2,4,6-tribromobenzonitrile Doyle Britton, Wayland E. Noland and Kenneth J. Tritch Acta Cryst. (2016). E72, 178-183 [doi:10.1107/S2056989016000256] Two new polytypes of 2,4,6-tribromobenzonitrile Doyle Britton, Wayland E. Noland and Kenneth J. Tritch Computing details Data collection: SMART (Bruker, 2002) for RCN-I, RCN-II, RCN-III; APEX2 (Bruker, 2002) for RNC-II. For all compounds, cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002). Program(s) used to solve structure: SHELXTL (Sheldrick, 2008) for RCN-I, RCN-II, RCN-III; SHELXT (Sheldrick, 2015a) for RNC-II. Program(s) used to refine structure: SHELXTL (Sheldrick, 2008) for RCN-I, RCN-II, RCN-III; SHELXL2014 (Sheldrick, 2015b) for RNC-II. For all compounds, molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), enCIFer (Allen et al., 2004), and publCIF (Westrip, 2010). (RCN-I) 2,4,6-Tribromobenzonitrile - polytype I Crystal data C7H2Br3N Mr = 339.83 Monoclinic, P21/m Hall symbol: -P 2yb a = 4.8742 (15) Å b = 10.247 (3) Å c = 8.683 (3) Å β = 94.97 (1)° V = 432.0 (2) Å3 Z = 2 F(000) = 312 Dx = 2.612 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2049 reflections θ = 2.4–27.4° µ = 13.93 mm−1 T = 173 K Needle, colorless 0.50 × 0.15 × 0.10 mm F(000) = 312 Dx = 2.612 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2049 reflections θ = 2.4–27.4° µ = 13.93 mm−1 T = 173 K Needle, colorless 0.50 × 0.15 × 0.10 mm 4093 measured reflections 1024 independent reflections 856 reflections with I > 2σ(I) Rint = 0.127 θmax = 27.5°, θmin = 2.4° h = −6→6 k = −13→13 l = −11→11 Refinement E72, 178-183 sup-2 supporting information (RCN-II) 2,4,6-Tribromobenzonitrile - polyt Crystal data C7H2Br3N Mr = 339.83 Orthorhombic, Pnma Hall symbol: -P 2ac 2n a = 13.6183 (13) Å b = 10.2147 (10) Å c = 12.4754 (12) Å V = 1735.4 (3) Å3 Z = 8 Data collection Bruker 1K area-detector diffractometer Radiation source: fine-focus sealed tube Graphite monochromator ω scans Absorption correction: multi-scan (SADABS; Bruker, 2002) Tmin = 0.06, Tmax = 0.37 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.028 wR(F2) = 0.063 S = 1.02 2093 reflections 115 parameters 0 restraints Primary atom site location: structure-invariant direct methods Fractional atomic coordinates and isotropic or (RCN-II) 2,4,6-Tribromobenzonitrile - polytype II F(000) = 1248 Dx = 2.601 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 3180 reflections θ = 2.9–27.2° µ = 13.88 mm−1 T = 173 K Plate, colorless 0.25 × 0.20 × 0.07 mm 16607 measured reflections 2093 independent reflections 1692 reflections with I > 2σ(I) Rint = 0.052 θmax = 27.5°, θmin = 2.2° h = −17→17 k = −13→13 l = −16→16 16607 measured reflections 2093 independent reflections 1692 reflections with I > 2σ(I) Rint = 0.052 θmax = 27.5°, θmin = 2.2° h = −17→17 k = −13→13 l = −16→16 Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.030P)2 + 1.560P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.44 e Å−3 Δρmin = −0.69 e Å−3 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq Br22 0.13341 (3) 0.52761 (3) 0.04244 (3) 0.02658 (11) Br24 0.14558 (4) 0.2500 0.43375 (4) 0.02477 (13) C21 0.1318 (3) 0.2500 0.0608 (4) 0.0197 (10) C22 0.1359 (2) 0.3683 (3) 0.1174 (3) 0.0206 (7) C23 0.1418 (2) 0.3697 (3) 0.2282 (3) 0.0217 (7) H23 0.1444 0.4500 0.2666 0.026* C24 0.1437 (3) 0.2500 0.2821 (4) 0.0190 (10) C27 0.1207 (4) 0.2500 −0.0545 (4) 0.0257 (11) N27 0.1115 (3) 0.2500 −0.1447 (4) 0.0332 (11) Br32 0.10699 (3) 0.47273 (3) 0.69146 (3) 0.02650 (11) Br34 0.12804 (4) 0.7500 0.29979 (4) 0.02786 (13) C31 0.1095 (3) 0.7500 0.6720 (3) 0.0175 (9) C32 0.1116 (2) 0.6320 (3) 0.6155 (3) 0.0195 (7) C33 0.1171 (2) 0.6315 (3) 0.5049 (3) 0.0201 (7) Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq Acta Cryst. Refinement Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained sup-1 Acta Cryst. (2016). E72, 178-183 supporting information w = 1/[σ2(Fo2) + (0.069P)2] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 1.36 e Å−3 Δρmin = −1.28 e Å−3 w = 1/[σ2(Fo2) + (0.069P)2] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 1.36 e Å−3 Δρmin = −1.28 e Å−3 Δρmax = 1.36 e Å−3 Δρmin = −1.28 e Å−3 (Δ/σ)max = 0.001 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq Br12 0.33356 (11) 0.47324 (5) 0.18676 (7) 0.0280 (2) Br14 1.11323 (14) 0.7500 0.57820 (9) 0.0256 (3) N17 −0.0263 (14) 0.7500 −0.0147 (8) 0.0313 (16) C11 0.3828 (14) 0.7500 0.1960 (8) 0.0204 (15) C12 0.4932 (10) 0.6324 (5) 0.2559 (6) 0.0224 (11) C13 0.7107 (10) 0.6313 (5) 0.3688 (6) 0.0244 (11) H13 0.7842 0.5512 0.4091 0.029* C14 0.8200 (14) 0.7500 0.4224 (8) 0.0197 (15) C17 0.1523 (16) 0.7500 0.0799 (9) 0.0241 (16) Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 Br12 0.0334 (4) 0.0160 (3) 0.0337 (4) −0.0043 (2) −0.0015 (2) −0.0016 (2) Br14 0.0229 (4) 0.0239 (4) 0.0295 (5) 0.000 −0.0018 (3) 0.000 N17 0.041 (4) 0.021 (3) 0.031 (4) 0.000 −0.006 (3) 0.000 C11 0.022 (3) 0.025 (4) 0.015 (4) 0.000 0.005 (3) 0.000 C12 0.023 (2) 0.016 (2) 0.029 (3) −0.0012 (19) 0.006 (2) 0.001 (2) C13 0.024 (2) 0.017 (3) 0.033 (3) 0.004 (2) 0.007 (2) 0.004 (2) C14 0.024 (3) 0.025 (4) 0.011 (3) 0.000 0.003 (3) 0.000 C17 0.030 (4) 0.011 (3) 0.032 (4) 0.000 0.004 (3) 0.000 Geometric parameters (Å, º) Br12—C12 1.883 (5) C12—C13 1.380 (8) Br14—C14 1.881 (7) C13—C14 1.391 (6) C11—C12 1.401 (6) C13—H13 0.9500 C11—C17 1.443 (10) N17—C17 1.144 (10) C12—C11—C12i 118.6 (6) C12—C13—H13 120.7 C12—C11—C17 120.7 (3) C14—C13—H13 120.7 C13—C12—C11 121.2 (5) C13—C14—C13i 121.9 (6) C13—C12—Br12 119.3 (4) C13—C14—Br14 119.0 (3) C11—C12—Br12 119.4 (4) N17—C17—C11 178.4 (9) C12—C13—C14 118.6 (5) C12i—C11—C12—C13 −1.6 (11) C11—C12—C13—C14 −0.2 (10) C17—C11—C12—C13 −178.9 (7) Br12—C12—C13—C14 −177.8 (5) C12i—C11—C12—Br12 176.0 (3) C12—C13—C14—C13i 2.0 (12) C17—C11—C12—Br12 −1.3 (9) C12—C13—C14—Br14 179.2 (5) Symmetry code: (i) x, −y+3/2, z. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) Geometric parameters (Å, º) Acta Cryst. (2016). Refinement (2016). E72, 178-183 sup-3 supporting information supporting information H33 0.1189 0.5511 0.4666 0.024* C34 0.1199 (3) 0.7500 0.4508 (4) 0.0196 (10) C37 0.1056 (3) 0.7500 0.7873 (4) 0.0200 (10) N37 0.1015 (3) 0.7500 0.8798 (3) 0.0255 (9) Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 Br22 0.0364 (2) 0.01742 (19) 0.0259 (2) −0.00058 (15) −0.00196 (15) 0.00451 (14) Br24 0.0303 (3) 0.0261 (3) 0.0179 (2) 0.000 0.00098 (19) 0.000 C21 0.018 (2) 0.021 (3) 0.021 (2) 0.000 0.0017 (19) 0.000 C22 0.0208 (16) 0.0182 (16) 0.0227 (17) 0.0016 (14) −0.0003 (13) 0.0017 (14) C23 0.0225 (16) 0.0186 (18) 0.0240 (17) −0.0012 (14) −0.0012 (14) −0.0017 (14) C24 0.021 (2) 0.021 (3) 0.015 (2) 0.000 0.0022 (18) 0.000 C27 0.028 (3) 0.020 (3) 0.029 (3) 0.000 0.000 (2) 0.000 N27 0.048 (3) 0.026 (2) 0.026 (3) 0.000 −0.002 (2) 0.000 Br32 0.0386 (2) 0.01618 (19) 0.02475 (19) −0.00117 (15) 0.00205 (14) 0.00374 (14) Br34 0.0418 (3) 0.0243 (3) 0.0174 (2) 0.000 −0.0003 (2) 0.000 C31 0.017 (2) 0.021 (2) 0.015 (2) 0.000 −0.0003 (17) 0.000 C32 0.0182 (15) 0.0163 (16) 0.0241 (17) 0.0004 (13) −0.0006 (13) 0.0044 (14) C33 0.0229 (17) 0.0157 (18) 0.0216 (17) 0.0015 (14) −0.0009 (13) −0.0018 (14) C34 0.025 (2) 0.018 (2) 0.015 (2) 0.000 −0.0001 (18) 0.000 C37 0.023 (2) 0.014 (2) 0.023 (3) 0.000 −0.0009 (19) 0.000 N37 0.030 (2) 0.024 (2) 0.023 (2) 0.000 −0.0002 (17) 0.000 Geometric parameters (Å, º) Br22—C22 1.877 (3) Br32—C32 1.884 (3) Br24—C24 1.892 (5) Br34—C34 1.887 (4) C21—C22 1.400 (4) C31—C32 1.396 (4) C21—C27 1.446 (7) C31—C37 1.439 (6) C22—C23 1.385 (5) C32—C33 1.382 (5) C23—C24 1.395 (4) C33—C34 1.387 (4) C23—H23 0.9500 C33—H33 0.9500 C27—N27 1.132 (7) C37—N37 1.156 (6) C22i—C21—C22 119.3 (4) C32ii—C31—C32 119.3 (4) C22—C21—C27 120.3 (2) C32—C31—C37 120.3 (2) C23—C22—C21 120.9 (3) C33—C32—C31 120.6 (3) C23—C22—Br22 119.3 (3) C33—C32—Br32 120.0 (3) C21—C22—Br22 119.8 (3) C31—C32—Br32 119.4 (2) C22—C23—C24 118.2 (3) C32—C33—C34 118.9 (3) C22—C23—H23 120.9 C32—C33—H33 120.5 C24—C23—H23 120.9 C34—C33—H33 120.5 C23i—C24—C23 122.4 (4) C33ii—C34—C33 121.6 (4) C23—C24—Br24 118.8 (2) C33—C34—Br34 119.2 (2) N27—C27—C21 179.7 (5) N37—C37—C31 179.3 (5) Atomic displacement parameters (Å2) Geometric parameters (Å, º) Acta Cryst. (2016). Refinement A t C t (2016) E72 178 183 (RCN-III) 2,4,6-Tribromobenzonitrile - polyty Crystal data C7H2Br3N Mr = 339.83 Orthorhombic, Pnma Hall symbol: -P 2ac 2n a = 20.399 (4) Å b = 10.2167 (18) Å c = 12.493 (2) Å V = 2603.7 (8) Å3 Z = 12 Data collection Bruker 1K area-detector diffractometer Radiation source: fine-focus sealed tube Graphite monochromator ω scans Absorption correction: multi-scan (SADABS; Bruker, 2002) Tmin = 0.054, Tmax = 0.337 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.023 wR(F2) = 0.046 S = 1.07 2691 reflections 173 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Fractional atomic coordinates and isotropic or eq x y Br42 0.340999 (16) 0.52705 Br44 0.32895 (2) 0.2500 (RCN-III) 2,4,6-Tribromobenzonitrile - polytype III Crystal data C7H2Br3N Mr = 339.83 Orthorhombic, Pnma Hall symbol: -P 2ac 2n a = 20.399 (4) Å b = 10.2167 (18) Å c = 12.493 (2) Å V = 2603.7 (8) Å3 Z = 12 F(000) = 1872 Dx = 2.601 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2928 reflections θ = 2.6–26.7° µ = 13.87 mm−1 T = 173 K Needle, colorless 0.50 × 0.15 × 0.10 mm Crystal data C7H2Br3N Mr = 339.83 Orthorhombic, Pnma Hall symbol: -P 2ac 2n a = 20.399 (4) Å b = 10.2167 (18) Å c = 12.493 (2) Å V = 2603.7 (8) Å3 Z = 12 F(000) = 18 Dx = 2.601 M Mo Kα radia Cell parame θ = 2.6–26.7 µ = 13.87 m T = 173 K Needle, colo 0.50 × 0.15 F(000) = 1872 Dx = 2.601 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2928 reflections θ = 2.6–26.7° µ = 13.87 mm−1 T = 173 K Needle, colorless 0.50 × 0.15 × 0.10 mm 22804 measured reflections 2691 independent reflections 2165 reflections with I > 2σ(I) Rint = 0.055 θmax = 26.0°, θmin = 2.6° h = −24→24 k = −12→12 l = −15→15 Refinement E72, 178-183 sup-4 supporting information C22i—C21—C22—C23 −1.4 (6) C32ii—C31—C32—C33 0.8 (6) C27—C21—C22—C23 176.8 (4) C37—C31—C32—C33 −178.9 (4) C22i—C21—C22—Br22 178.6 (2) C32ii—C31—C32—Br32 −179.2 (2) C27—C21—C22—Br22 −3.2 (5) C37—C31—C32—Br32 1.1 (5) C21—C22—C23—C24 0.1 (5) C31—C32—C33—C34 −0.3 (5) Br22—C22—C23—C24 −179.9 (3) Br32—C32—C33—C34 179.7 (3) C22—C23—C24—C23i 1.3 (7) C32—C33—C34—C33ii −0.2 (7) C22—C23—C24—Br24 −177.1 (2) C32—C33—C34—Br34 179.7 (2) Symmetry codes: (i) x, −y+1/2, z; (ii) x, −y+3/2, z. Acta Cryst. (2016). E72, 178-183 supporting information supporting information Br52 0.332551 (16) 0.47245 (3) 0.59427 (3) 0.02775 (9) Br54 0.32011 (2) 0.7500 0.20370 (3) 0.02542 (12) Br62 0.511839 (16) 0.52774 (3) 0.67598 (3) 0.02743 (10) Br64 0.50730 (2) 0.2500 1.06666 (4) 0.02435 (12) C41 0.33919 (19) 0.2500 −0.0353 (3) 0.0182 (9) C42 0.33772 (14) 0.3675 (3) 0.0214 (2) 0.0207 (7) C43 0.33432 (14) 0.3686 (3) 0.1321 (2) 0.0226 (7) H43 0.3331 0.4487 0.1706 0.027* C44 0.3328 (2) 0.2500 0.1851 (4) 0.0219 (10) C47 0.3440 (2) 0.2500 −0.1508 (4) 0.0218 (10) N47 0.34814 (18) 0.2500 −0.2423 (3) 0.0272 (9) C51 0.3338 (2) 0.7500 0.5758 (4) 0.0221 (10) C52 0.33096 (14) 0.6320 (3) 0.5193 (2) 0.0211 (7) C53 0.32641 (14) 0.6314 (3) 0.4085 (2) 0.0228 (7) H53 0.3246 0.5512 0.3701 0.027* C54 0.3245 (2) 0.7500 0.3549 (3) 0.0204 (10) C57 0.3399 (2) 0.7500 0.6908 (4) 0.0225 (10) N57 0.3445 (2) 0.7500 0.7823 (3) 0.0329 (10) C61 0.5080 (2) 0.2500 0.6942 (4) 0.0204 (10) C62 0.50889 (14) 0.3676 (3) 0.7509 (2) 0.0216 (7) C63 0.50886 (14) 0.3686 (3) 0.8618 (2) 0.0218 (7) H63 0.5092 0.4488 0.9002 0.026* C64 0.5083 (2) 0.2500 0.9155 (4) 0.0200 (10) C67 0.5049 (2) 0.2500 0.5783 (4) 0.0225 (10) N67 0.5024 (2) 0.2500 0.4872 (3) 0.0329 (10) Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 Br42 0.03864 (19) 0.01711 (17) 0.02545 (18) −0.00178 (14) 0.00143 (15) 0.00391 (15) Br44 0.0432 (3) 0.0252 (3) 0.0190 (3) 0.000 0.0007 (2) 0.000 Br52 0.03826 (19) 0.01818 (17) 0.02682 (18) −0.00040 (15) −0.00267 (15) 0.00467 (15) Br54 0.0309 (3) 0.0270 (3) 0.0184 (2) 0.000 0.0017 (2) 0.000 Br62 0.03877 (19) 0.01736 (17) 0.02617 (18) −0.00080 (15) −0.00036 (15) 0.00376 (15) Br64 0.0300 (2) 0.0243 (3) 0.0188 (2) 0.000 −0.00018 (19) 0.000 C41 0.016 (2) 0.017 (2) 0.022 (2) 0.000 −0.0010 (18) 0.000 C42 0.0214 (15) 0.0175 (17) 0.0233 (17) −0.0001 (14) −0.0011 (13) 0.0052 (14) C43 0.0269 (16) 0.0160 (17) 0.0248 (17) −0.0016 (14) −0.0003 (14) −0.0016 (15) C44 0.023 (2) 0.024 (3) 0.019 (2) 0.000 0.0000 (19) 0.000 C47 0.020 (2) 0.016 (2) 0.029 (3) 0.000 −0.004 (2) 0.000 N47 0.033 (2) 0.022 (2) 0.026 (2) 0.000 −0.0017 (19) 0.000 C51 0.016 (2) 0.026 (3) 0.024 (2) 0.000 0.001 (2) 0.000 C52 0.0244 (15) 0.0154 (17) 0.0234 (16) 0.0002 (14) −0.0002 (13) 0.0037 (14) C53 0.0255 (16) 0.0198 (18) 0.0232 (17) 0.0025 (14) 0.0024 (14) −0.0031 (15) C54 0.020 (2) 0.024 (3) 0.017 (2) 0.000 0.0021 (18) 0.000 C57 0.025 (2) 0.015 (2) 0.027 (3) 0.000 −0.003 (2) 0.000 N57 0.048 (3) 0.027 (2) 0.024 (2) 0.000 −0.001 (2) 0.000 C61 0.020 (2) 0.022 (2) 0.020 (2) 0.000 0.0041 (19) 0.000 Acta Cryst. Refinement Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0096P)2 + 3.390P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.56 e Å−3 Δρmin = −0.49 e Å−3 Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.00028 (3) Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0096P)2 + 3.390P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.56 e Å−3 Δρmin = −0.49 e Å−3 Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.00028 (3) Hydrogen site location: inferred from neighbouring sites Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0096P)2 + 3.390P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.56 e Å−3 Δρmin = −0.49 e Å−3 Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.00028 (3) sup-5 Acta Cryst. (2016). E72, 178-183 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq Br42 0.340999 (16) 0.52705 (3) −0.05464 (3) 0.02707 (10) Br44 0.32895 (2) 0.2500 0.33679 (4) 0.02913 (13) sup-5 supporting information supporting information (RNC-II) 1,3,5-Tribromo-2-isocyanobenzene - polytype II Crystal data C7H2Br3N Mr = 339.83 Orthorhombic, Pnma a = 13.5916 (18) Å b = 10.1464 (13) Å c = 12.6158 (16) Å V = 1739.8 (4) Å3 Z = 8 F(000) = 1248 Dx = 2.595 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2721 reflections θ = 3.0–27.4° µ = 13.84 mm−1 T = 173 K Block, colourless 0.40 × 0.35 × 0.20 mm Dx = 2.595 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2721 reflections θ = 3.0–27.4° µ = 13.84 mm−1 T = 173 K Block, colourless 0.40 × 0.35 × 0.20 mm 2105 independent reflections 1638 reflections with I > 2σ(I) Rint = 0.078 θmax = 27.5°, θmin = 2.2° h = −17→17 k = −13→13 l = −16→16 H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0121P)2 + 1.0004P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.44 e Å−3 Δρmin = −0.48 e Å−3 Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.00269 (12) H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0121P)2 + 1.0004P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.44 e Å−3 Δρmin = −0.48 e Å−3 Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.00269 (12) H-atom parameters constrained supporting information C57—C51—C52—C53 −178.7 (3) Br62—C62—C63—C64 −178.4 (3) C52ii—C51—C52—Br52 −178.48 (19) C62—C63—C64—C63i 1.0 (6) C57—C51—C52—Br52 1.9 (5) C62—C63—C64—Br64 −179.3 (2) Symmetry codes: (i) x, −y+1/2, z; (ii) x, −y+3/2, z. Symmetry codes: (i) x, −y+1/2, z; (ii) x, −y+3/2, z. (RNC-II) 1,3,5-Tribromo-2-isocyanobenzene - polytype II Acta Cryst. (2016). E72, 178-183 supporting information (2016). E72, 178-183 sup-6 supporting information supporting information C62 0.0199 (15) 0.0188 (17) 0.0261 (17) 0.0017 (13) 0.0011 (13) 0.0047 (15) C63 0.0236 (16) 0.0178 (18) 0.0239 (16) 0.0007 (14) 0.0018 (13) −0.0028 (15) C64 0.020 (2) 0.022 (2) 0.018 (2) 0.000 0.0017 (19) 0.000 C67 0.028 (2) 0.016 (2) 0.024 (3) 0.000 0.000 (2) 0.000 N67 0.055 (3) 0.021 (2) 0.024 (2) 0.000 −0.002 (2) 0.000 Geometric parameters (Å, º) Br42—C42 1.888 (3) C51—C52 1.399 (4) Br44—C44 1.897 (5) C51—C57 1.443 (6) Br52—C52 1.880 (3) C52—C53 1.387 (4) Br54—C54 1.892 (4) C53—C54 1.384 (4) Br62—C62 1.885 (3) C53—H53 0.9500 Br64—C64 1.889 (4) C57—N57 1.147 (6) C41—C42 1.394 (4) C61—C62 1.395 (4) C41—C47 1.447 (6) C61—C67 1.450 (6) C42—C43 1.384 (4) C62—C63 1.386 (4) C43—C44 1.381 (4) C63—C64 1.385 (4) C43—H43 0.9500 C63—H63 0.9500 C47—N47 1.146 (6) C67—N67 1.139 (6) C42—C41—C42i 118.9 (4) C54—C53—H53 120.6 C42—C41—C47 120.5 (2) C52—C53—H53 120.6 C43—C42—C41 121.0 (3) C53ii—C54—C53 122.1 (4) C43—C42—Br42 119.9 (2) C53—C54—Br54 119.0 (2) C41—C42—Br42 119.2 (2) N57—C57—C51 179.8 (5) C44—C43—C42 118.3 (3) C62i—C61—C62 119.0 (4) C44—C43—H43 120.9 C62—C61—C67 120.5 (2) C42—C43—H43 120.9 C63—C62—C61 120.9 (3) C43i—C44—C43 122.6 (4) C63—C62—Br62 119.4 (3) C43—C44—Br44 118.7 (2) C61—C62—Br62 119.8 (2) N47—C47—C41 179.7 (5) C64—C63—C62 118.6 (3) C52ii—C51—C52 119.1 (4) C64—C63—H63 120.7 C52—C51—C57 120.4 (2) C62—C63—H63 120.7 C53—C52—C51 120.7 (3) C63i—C64—C63 122.0 (4) C53—C52—Br52 119.7 (2) C63—C64—Br64 119.0 (2) C51—C52—Br52 119.7 (2) N67—C67—C61 180.0 (5) C54—C53—C52 118.7 (3) C42i—C41—C42—C43 −0.5 (6) C51—C52—C53—C54 −0.2 (5) C47—C41—C42—C43 −178.8 (3) Br52—C52—C53—C54 179.2 (3) C42i—C41—C42—Br42 179.07 (19) C52—C53—C54—C53ii −0.6 (6) C47—C41—C42—Br42 0.8 (5) C52—C53—C54—Br54 178.7 (2) C41—C42—C43—C44 0.4 (5) C62i—C61—C62—C63 −1.7 (6) Br42—C42—C43—C44 −179.2 (3) C67—C61—C62—C63 177.0 (3) C42—C43—C44—C43i −0.2 (6) C62i—C61—C62—Br62 177.1 (2) C42—C43—C44—Br44 179.4 (2) C67—C61—C62—Br62 −4.2 (5) C52ii—C51—C52—C53 0.9 (6) C61—C62—C63—C64 0.4 (5) C62 0.0199 (15) 0.0188 (17) 0.0261 (17) 0.0017 (13) 0.0011 (13) 0.0047 (15) C63 0.0236 (16) 0.0178 (18) 0.0239 (16) 0.0007 (14) 0.0018 (13) −0.0028 (15) C64 0.020 (2) 0.022 (2) 0.018 (2) 0.000 0.0017 (19) 0.000 C67 0.028 (2) 0.016 (2) 0.024 (3) 0.000 0.000 (2) 0.000 N67 0.055 (3) 0.021 (2) 0.024 (2) 0.000 −0.002 (2) 0.000 Acta Cryst. (2016). E72, 178-183 sup-7 Special details Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. sup 8 Acta Cryst (2016) E72 178 183 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq C121 0.3678 (3) 0.7500 0.5680 (3) 0.0162 (9) C122 0.3637 (2) 0.6315 (3) 0.6238 (2) 0.0176 (7) C123 0.3573 (2) 0.6306 (3) 0.7332 (2) 0.0182 (7) H123 0.3541 0.5499 0.7712 0.022* onal atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq sup-8 supporting information supporting information C124 0.3559 (3) 0.7500 0.7858 (4) 0.0173 (9) N127 0.3793 (3) 0.7500 0.4583 (3) 0.0215 (9) C127 0.3909 (4) 0.7500 0.3682 (4) 0.0285 (12) Br122 0.36763 (3) 0.47074 (3) 0.54952 (3) 0.02456 (11) Br124 0.35282 (4) 0.7500 0.93610 (4) 0.02254 (13) C131 0.3904 (3) 0.2500 0.1747 (3) 0.0161 (10) C132 0.3885 (2) 0.3685 (3) 0.1192 (3) 0.0169 (7) C133 0.3821 (2) 0.3691 (3) 0.0100 (2) 0.0179 (7) H133 0.3806 0.4499 −0.0281 0.021* C134 0.3781 (3) 0.2500 −0.0428 (4) 0.0190 (10) N137 0.3955 (3) 0.2500 0.2840 (3) 0.0180 (8) C137 0.3995 (3) 0.2500 0.3761 (4) 0.0246 (11) Br132 0.39399 (3) 0.52885 (3) 0.19404 (3) 0.02480 (11) Br134 0.36801 (4) 0.2500 −0.19267 (4) 0.02564 (14) Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 C121 0.013 (2) 0.019 (2) 0.016 (2) 0.000 0.0002 (19) 0.000 C122 0.0164 (16) 0.0157 (16) 0.0207 (17) 0.0016 (14) −0.0016 (14) −0.0031 (13) C123 0.0191 (17) 0.0152 (17) 0.0202 (17) 0.0013 (14) −0.0017 (14) 0.0039 (13) C124 0.017 (2) 0.017 (2) 0.018 (2) 0.000 0.0003 (19) 0.000 N127 0.026 (2) 0.018 (2) 0.021 (2) 0.000 0.0008 (17) 0.000 C127 0.035 (3) 0.025 (3) 0.026 (3) 0.000 0.002 (2) 0.000 Br122 0.0339 (2) 0.01579 (18) 0.0239 (2) −0.00052 (15) 0.00210 (15) −0.00522 (14) Br124 0.0290 (3) 0.0231 (3) 0.0155 (2) 0.000 −0.0005 (2) 0.000 C131 0.014 (2) 0.019 (2) 0.015 (2) 0.000 −0.0026 (17) 0.000 C132 0.0158 (16) 0.0138 (16) 0.0210 (17) 0.0001 (13) 0.0003 (13) −0.0042 (13) C133 0.0229 (18) 0.0132 (17) 0.0174 (17) 0.0014 (14) −0.0001 (13) 0.0035 (13) C134 0.018 (2) 0.024 (3) 0.015 (2) 0.000 −0.0016 (18) 0.000 N137 0.019 (2) 0.017 (2) 0.018 (2) 0.000 0.0008 (16) 0.000 C137 0.024 (3) 0.019 (3) 0.030 (3) 0.000 −0.001 (2) 0.000 Br132 0.0360 (2) 0.01500 (19) 0.0234 (2) −0.00111 (15) −0.00260 (14) −0.00427 (14) Br134 0.0393 (3) 0.0222 (3) 0.0154 (3) 0.000 0.0003 (2) 0.000 Geometric parameters (Å, º) C121—N127 1.393 (6) C131—N137 1.380 (6) C121—C122i 1.395 (4) C131—C132ii 1.392 (4) C122—C123 1.382 (4) C132—C133 1.380 (4) C122—Br122 1.882 (3) C132—Br132 1.883 (3) C123—C124i 1.381 (4) C133—C134ii 1.381 (4) C123—H123 0.9500 C133—H133 0.9500 C124—Br124 1.897 (5) C134—Br134 1.895 (4) N127—C127 1.147 (6) N137—C137 1.164 (6) Atomic displacement parameters (Å2) Geometric parameters (Å, º) Acta Cryst. (2016). Acta Cryst. (2016). E72, 178-183 supporting information E72, 178-183 sup-9 supporting information supporting information C123—C122—C121 120.8 (3) C133—C132—C131 120.5 (3) C123—C122—Br122 119.6 (2) C133—C132—Br132 119.9 (2) C121—C122—Br122 119.6 (2) C131—C132—Br132 119.5 (2) C124—C123—C122 118.3 (3) C132—C133—C134 118.7 (3) C124—C123—H123 120.8 C132—C133—H133 120.7 C122—C123—H123 120.8 C134—C133—H133 120.7 C123—C124—C123i 122.5 (4) C133ii—C134—C133 122.1 (4) C123i—C124—Br124 118.7 (2) C133ii—C134—Br134 118.9 (2) C127—N127—C121 178.5 (5) C137—N137—C131 179.8 (4) N127—C121—C122—C123 176.7 (3) N137—C131—C132—C133 −179.2 (3) C122i—C121—C122—C123 −1.0 (6) C132ii—C131—C132—C133 1.6 (6) N127—C121—C122—Br122 −3.0 (5) N137—C131—C132—Br132 0.6 (5) C122i—C121—C122—Br122 179.30 (19) C132ii—C131—C132—Br132 −178.6 (2) C121—C122—C123—C124 −0.5 (5) C131—C132—C133—C134 −0.2 (5) Br122—C122—C123—C124 179.2 (3) Br132—C132—C133—C134 −179.9 (3) C122—C123—C124—C123i 2.1 (7) C132—C133—C134—C133ii −1.3 (7) C122—C123—C124—Br124 −177.4 (2) C132—C133—C134—Br134 179.3 (3) Symmetry codes: (i) x y+3/2 z; (ii) x y+1/2 z Symmetry codes: (i) x, −y+3/2, z; (ii) x, −y+1/2, z. Hydrogen-bond geometry (Å, º) D—H···A D—H H···A D···A D—H···A C123—H123···Br134iii 0.95 3.08 3.976 (3) 157 C133—H133···Br124iv 0.95 3.10 3.995 (3) 157 Symmetry codes: (iii) x, y, z+1; (iv) x, y, z−1. Hydrogen-bond geometry (Å, º) Acta Cryst. (2016). E72, 178-183 sup-10 sup-10
https://openalex.org/W2736640449
https://repository.ubn.ru.nl//bitstream/handle/2066/177182/177182.pdf
English
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Prefrontal Glx and GABA concentrations and impulsivity in cigarette smokers and smoking polysubstance users
Drug and alcohol dependence
2,017
cc-by
7,880
Version of the following full text: Publisher’s version Downloaded from: http://hdl.handle.net/2066/177182 Download date: 2024-10-24 A B S T R A C T Keywords: Cocaine GABA Glutamate Impulsivity Smoking Substance dependence Keywords: Cocaine GABA Glutamate Impulsivity Smoking Substance dependence Glutamate and GABA play an important role in substance dependence. However, it remains unclear whether this holds true for different substance use disorders and how this is related to risk-related traits such as impulsivity. We, therefore, compared Glx (as a proxy measure for glutamate) and GABA concentrations in the dorsal anterior cingulate cortex (dACC) of 48 male cigarette smokers, 61 male smoking polysubstance users, and 90 male healthy controls, and investigated the relationship with self-reported impulsivity and substance use. Glx and GABA concentrations were measured using proton Magnetic Resonance Spectroscopy. Impulsivity, smoking, alcohol and cocaine use severity and cannabis use were measured using self-report instruments. Results indicate a trend towards group differences in Glx. Post-hoc analyses showed a difference between smokers and healthy controls (p = 0.04) and a trend towards higher concentrations in smoking polysubstance users and healthy controls (p = 0.09), but no differences between smokers and smoking polysubstance users. dACC GABA con- centrations were not significantly different between groups. Smoking polysubstance users were more impulsive than smokers, and both groups were more impulsive than controls. No significant associations were observed between dACC neurotransmitter concentrations and impulsivity and level and severity of smoking, alcohol or cocaine use or the presence of cannabis use. The results indicate that differences in dACC Glx are unrelated to type and level of substance use. No final conclusion can be drawn on the lack of GABA differences due to assessment difficulties. The relationship between dACC neurotransmitter concentrations and cognitive impair- ments other than self-reported impulsivity should be further investigated. (Schmaal et al., 2012a; Silveri et al., 2014). Several Magnetic Re- sonance Spectroscopy (1H-MRS) studies in humans have shown that glutamate is affected in substance dependence (e.g., Schmaal et al., 2012b; Yücel et al., 2007). However, the role of GABA in human addiction is less well studied and it remains to be investigated whether glutamate and GABA deviate between different substances of abuse. Moreover, very little is known about the relationship between these neurotransmitters and risk-related traits, including impulsivity, in people with (SUDs). However, glutamate levels in Prefrontal Glx and GABA concentrations and impulsivity in cigarette smokers and smoking polysubstance users Prefrontal Glx and GABA concentrations and impulsivity in cigarette smokers and smoking polysubstance users Mieke H.J. Schultea,b,1,⁎, Anne Marije Kaaga,b,1, Reinout W. Wiersa, Lianne Schmaalc, Wim van den Brinkb, Liesbeth Renemand,g, Judith R. Homberge, Guido A. van Wingenb,f,g,2, Anna E. Goudriaanb,h,2 a Addiction, Development, and Psychopathology (ADAPT) lab, Department of Psychology, University of Amsterdam, The Netherlands b Department of Psychiatry, Academic Medical Center, University of Amsterdam, The Netherlands c Department of Psychiatry and Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands d Department of Radiology and Nuclear Medicine, Academic Medical Center, University of Amsterdam, The Netherlands e Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, The Netherlands f Spinoza center for Neuroimaging, Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands g Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, The Netherlands h Arkin Mental Health, Amsterdam, The Netherlands http://dx.doi.org/10.1016/j.drugalcdep.2017.06.025 Received 10 February 2017; Received in revised form 12 June 2017; Accepted 12 June 2017 ⁎ Corresponding author at: University of Amsterdam, Department of Psychology, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands. 1 Shared first authorship. 2 Shared last authorship. E-mail address: m.h.j.schulte@uva.nl (M.H.J. Schulte). Available online 25 July 2017 0376-8716/ © 2017 The Authors. Published by Elsevier Ireland Ltd. This is an open access article under the CC BY license (http://creativecom m ons.org/licenses/BY/4.0/). Note: Note: To cite this publication please use the final published version (if applicable). To cite this publication please use the final published version (if applicable). Drug and Alcohol Dependence 179 (2017) 117–123 Contents lists available at ScienceDirect 1 Shared first authorship ⁎ Corresponding author at: University of Amsterdam, Department of Psychology, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands. 1 E-mail address: m.h.j.schulte@uva.nl (M.H.J. Schulte). 1. Introduction Neurobiological models of substance use disorders (SUDs) have mainly focused on the dopaminergic system (Berridge and Robinson, 1998; but see Nutt et al., 2015 for a critical appraisal). Glutamatergic and GABAergic mechanisms in substance depen- dence have recently become more prominent in models of addiction (e.g., Li et al., 2013). Glutamate and GABA play a key role in per- sonality traits associated with addiction, such as impulsivity . Published by Elsevier Ireland Ltd. This is an open access article under the CC BY license (http://creativecom m ons.org/licenses/BY/4.0/). M.H.J. Schulte et al. Drug and Alcohol Dependence 179 (2017) 117–123 the Anterior Cingulate Cortex (ACC) have been related to functions that are affected in SUDs such as delay discounting (e.g., Schmaal et al., 2012a). specifically, we expect that each substance-using group shows higher Glx concentrations and lower GABA concentrations compared to healthy controls. Furthermore, since the use of multiple substances has been shown to be associated with larger group differences in neuro- transmitter concentrations (Abé et al., 2013; Ke et al., 2004; Mason et al., 2006), our second hypothesis is that smoking polysubstance users will show larger neurotransmitter deviations from the healthy controls than smokers. In addition, neurotransmitter concentrations are hy- pothesized to be associated with self-reported substance use (reported as the level of substance use severity and the amount of substance use). Our fourth hypothesis is that there will be group differences with regard to self-reported impulsivity. More specifically, we expect that both smokers and smoking polysubstance users show higher impulsivity than healthy controls, and that smoking polysubstance users will show higher impulsivity compared to smokers. Finally, we hypothesize that higher self-reported impulsivity levels are associated with higher Glx and lower GABA concentrations across all three groups. The ACC has been a main region of interest for imaging studies on SUDs, as this brain region is suggested to play a key role in craving and relapse to drug-seeking, and impulsivity (Brand et al., 2014; Garavan and Hester, 2007; Myers and Carlezon, 2010). This region is highly suitable for 1H MRS studies due to its homogeneous structure, resulting in several human 1H MRS studies on ACC glutamate concentrations in SUDs. However, the results are inconsistent with regard to the existence and direction of ACC glutamate and GABA alterations in SUDs. 2.1. Participants Data (unpublished at time of submission) from two different studies were combined, hereafter referred to as Study A and Study B. Study A focused on the effects of N-acetylcysteine on dACC neurotransmitter concentrations of smokers, of which the baseline measures of smokers (S, n = 48) were included in the current analyses. Study B focused on neurocognitive measures in cocaine users, who reported the use of multiple substances and are therefore referred to as polysubstance users. Those who also smoked cigarettes were included in the current analyses (SP, n = 61). Healthy controls (HC, n = 90) who do not smoke or use any substances besides recreational alcohol use were in- cluded from both studies. GABA and glutamate concentrations may depend on the number of substances used. For instance, lower ACC GABA concentrations may be more pronounced in cocaine dependent subjects with a history of al- cohol dependence compared to cocaine dependent subjects without such a history (Ke et al., 2004). Similarly, GABA concentrations in the dorsolateral prefrontal cortex seem to be more pronounced in poly- substance users compared to alcohol dependent patients (Abé et al., 2013). Furthermore, Mason et al. (2006) did not find differences in glutamate and GABA concentrations between alcohol dependent sub- jects and healthy controls. However, they did find higher glutamate and lower GABA concentrations when comparing smoking with non- smoking alcohol dependent subjects. Therefore, we included a group of cigarette smokers as well as a group of smoking polysubstance users to investigate group differences in ACC Glx and GABA concentrations. This has been shown to be a sensitive method to detect the relation between the types of substances used and microstructural changes in the brain (Kaag et al., 2016). In study A, inclusion criteria were: male; 18–55 years old; smoking at least 15 cigarettes per day; a desire to quit smoking; a Fagerström Test Nicotine Dependence (FTND; Heatherton et al., 1991) score of at least 3, indicating at least a low degree of smoking dependence (Heatherton et al., 1991), and an Alcohol Use Disorder Identification (AUDIT) score lower than 13, indicating the absence of heavy alcohol use and/or an alcohol use disorder. In study B, inclusion criteria were: male; 18–50 years old; non-treatment seeking; and snorting cocaine at least once per week in the last 6 months. 2.1. Participants Healthy controls were also excluded if they reported a history of substance (ab)use or dependence including nicotine use, and in case of any psychotropic medication use. Exclusion criteria for all participants were: major medical or neu- rological disease; lifetime history of psychotic or bipolar disorder; the presence of contraindication to MRI scanning; and the use of anti- depressants or antipsychotics. Participants in study B were instructed not to use alcohol or cocaine ten hours before the session, but partici- pants from both studies were allowed to smoke ad libitum before the start of the studies. In addition, participants in study B were excluded if they ever used heroin, but were not excluded on the use of other sub- stances. All participants were recruited by means of advertisements and word of mouth. Written informed consent was acquired before the beginning of the session. Study A was approved by the Ethics Committee of the Psychology Department of the University of Amsterdam, and registered with the Netherlands Trial Registry (number: NTR3576). Study B was approved by the Ethical Review Board of the Academic Medical Centre of the University of Amsterdam, the Netherlands. SUDs have also been associated with impaired impulse control and deviant ACC functioning (Garavan and Hester, 2007; Hester and Garavan, 2004; Li et al., 2008; Moeller et al., 2001). Furthermore, higher impulsivity has been positively associated with deviating glu- tamate concentrations in rodents (see e.g., Pattij and Vanderschuren, 2008), and this association has also been found in cocaine dependent subjects (Schmaal et al., 2012a). However, no such data are available on other SUDs and therefore the relationship between neurotransmitter concentrations and cognitive abnormalities remains unknown. To address these issues, we compared Glx and GABA concentrations in the dorsal Anterior Cingulate Cortex (dACC) of cigarette smokers, smoking polysubstance users and healthy controls. We chose the dACC as a region of interest since it has been associated with impaired im- pulse inhibition in cocaine dependence (Garavan and Hester, 2007; Hester and Garavan, 2004). Furthermore, we examined the relationship of these neurotransmitter concentrations with self-reported impulsivity and the level of substance use. Our first hypothesis is that there will be group differences with regard to Glx and GABA concentrations. More 1. Introduction That is, both increased (Bauer et al., 2013; Lee et al., 2007; Mon et al., 2012; Schmaal et al., 2012b; Thoma et al., 2011), decreased (Durazzo et al., 2016; Ende et al., 2013; Hermann et al., 2012; Mashhoon et al., 2011; Prescot et al., 2013; Yang et al., 2009; Yücel et al., 2007), as well as no differences in ACC glutamate concentrations in substance users com- pared to non-substance using controls have been reported (Chang et al., 1999; Gallinat and Schubert, 2007). Similar to the latter findings, the literature on ACC GABA concentrations in substance dependent in- dividuals is also inconsistent. Both lower (Abé et al., 2013; Prescot et al., 2013; Silveri et al., 2014), as well as no differences in substance users compared to non-using controls have been reported (Mon et al., 2012). These contradictory findings may be the result of methodolo- gical differences, such as the location of the MRS voxel (e.g., dorsal (Schmaal et al., 2012) or rostral ACC (Yang et al., 2009)) It should be noted that 1H MRS studies are not always able to differentiate between glutamate, glutamine, and other components due to overlap in spectral assignment, for which the term Glx (a composite measure) is often used (Ramadan et al., 2013). Therefore, the term Glx is used henceforth as a proxy measure of glutamate when referring to data acquired in the current study. 3. Results In the current study, Glx concentrations are reported as the best available proxy measure of glutamate, due to overlap in spectral as- signment of glutamate, glutamine, and other components. The applied 1H MRS measurements allowed us to quantify the concentration of Glx and GABA in the dACC. The even and the J-difference (odd-even) ac- quisitions were analyzed using LCModel (Linear Combination of Model spectra; Provencher, 1993). Total creatine (Cre + PCr) and total N- acetyl aspartate (NAA + NAAG) were quantified from the even acqui- sitions, and Glx, GABA, and again NAA were quantified from the dif- ference acquisitions. Glx and GABA were normalized to the difference- spectra NAA, and the even-spectra NAA was normalized to creatine. This procedure calibrated signal amplitude across even and difference acquisitions within each subject, enabling Glx and GABA concentra- tions to be expressed in units of creatine (see for details Waddell et al., 2011, 2007). Cramer–Rao Lower Bounds (CRLBs) of 20% were used for each individual peak as a quality criterion (Provencher, 1993). All spectra were also visually inspected. Scans that did not meet de CRLB criterion or passed the visual inspection were excluded from analyses. CRLBs for all metabolites in all subjects were between 3 and 9%. Ad- ditional indicators for the quality of the spectra were mean ( ± SD) signal to noise ratio and mean ( ± SD) full width half maximum 2.3. Magnetic resonance spectroscopy acquisition and processing Participants of study A and B were scanned on the same scanner. First, a structural three-dimensional T1-weighted volume (TR = 8.2 ms; TE = 3.7 ms; 220 slices; voxel size 1 × 1 × 1 mm; ma- trix size 240 × 187) was acquired in the transverse plane using a SENSE 32-channel receiver head coil on an Achieva XT 3T head-only MRI scanner (Philips Healthcare, Best, The Netherlands) at the Spinoza Centrum of the University of Amsterdam. This structural image was used to place the MRS voxel in the dACC (see Fig. 1), based on each individual’s anatomical landmarks. The voxel was placed over the midline covering both hemispheres, since there was no prior expecta- tion of differences in Glx or GABA concentrations between hemispheres. GABA-edited 1H J-difference spectra were acquired using a MEGA- PRESS sequence (Waddell et al., 2007; TR = 2000 ms; TE = 73 ms; voxel size 35 mm × 20 mm × 15 mm, 384 transients). During the odd transients, a 15.64 ms sinc-center editing pulse (64 Hz full width at half maximum) was applied at 1.9 ppm and 4.6 ppm in an interleaved manner to specifically excite GABA and suppress water, respectively. 2.4. Statistical analyses Data were checked for outliers and normal distribution. Non- parametric tests were used if a variable did not meet the criterion of normal distribution after log-transformation. Differences between groups were analyzed using one-way ANOVAs, followed by planned pairwise comparisons to test for possible group differences. To ac- count for multiple testing, a Bonferroni correction of 2 was applied for the analyses on neurotransmitter concentrations (Glx and GABA). Since the results on Glx were trend significant, the post-hoc analyses were exploratory and therefore performed without cor- rection for multiple comparisons. Eta squared is reported as an index of effect size. Bivariate correlation analyses were used to investigate associations between neurotransmitters and im- pulsivity. For exploratory purposes, multiple regression analyses were used to investigate, per group, associations between neuro- transmitter concentrations and the level of substance use, as well as the severity of substance use disorders for alcohol, tobacco and cocaine, and cannabis used, as measured with the AUDIT, FTND, DUDIT, and TLFB, respectively. For each analysis, only the sub- stances that were used by that particular group were entered in the regression analyses. 2.2. Clinical assessments For all participants, the premorbid level of intellectual functioning was measured using the Dutch version of the National Adult Reading Test (NART; Schmand et al., 1991), the AUDIT (Babor et al., 1989) was used to assess the level of alcohol use and related problems, the Time Line Follow Back method (TLFB; Sobell and Sobell, 1992) was used to assess cannabis use in the preceding 6 months, and the Barratt Impulsiveness Scale (BIS-11; Patton et al., 1995) was administered to assess self-reported im- pulsivity. 2.2. Clinical assessments For the substance-using groups, the severity of smoking dependence was assessed using the FTND. For the SP group, the Drug Use Disorder Identification Test (DUDIT; Berman et al., 2005) was used to assess the 118 Drug and Alcohol Dependence 179 (2017) 117–123 M.H.J. Schulte et al. Fig. 1. Spectroscopy details. Left: placement of the MRS voxel in the dorsal Anterior Cingulate Cortex (dACC). Middle: Example spectrum for the difference acquisition from the dACC voxel. Right: Example spectrum for the even acquisition from the dACC voxel. Fig. 1. Spectroscopy details. Left: placement of the MRS voxel in the dorsal Anterior Cingulate Cortex (dACC). Middle: Example spectrum for the difference acquisition from the dACC voxel. Right: Example spectrum for the even acquisition from the dACC voxel. nt of the MRS voxel in the dorsal Anterior Cingulate Cortex (dACC). Middle: Example spectrum for the difference acquisition from the dACC en acquisition from the dACC voxel. Fig. 1. Spectroscopy details. Left: placement of the MRS voxel in the dorsal Anterior Cingulate Cortex (dACC). Middle: Example spectrum fo voxel. Right: Example spectrum for the even acquisition from the dACC voxel. (FWHM). The SNR for the heavy smokers was 4.20 (0.89), for smoking polysubstance users it was 4.16(1.13), and 4.32 (1.04) for the healthy controls. The FWHM for the heavy smokers was 0.05 (0.02), for the smoking polysubstance users it was 0.06 (0.02), and 0.05 (0.02) for the healthy controls. level of cocaine use and related problems. For all participants, the premorbid level of intellectual functioning was measured using the Dutch version of the National Adult Reading Test (NART; Schmand et al., 1991), the AUDIT (Babor et al., 1989) was used to assess the level of alcohol use and related problems, the Time Line Follow Back method (TLFB; Sobell and Sobell, 1992) was used to assess cannabis use in the preceding 6 months, and the Barratt Impulsiveness Scale (BIS-11; Patton et al., 1995) was administered to assess self-reported im- pulsivity. level of cocaine use and related problems. 3 There appeared to be a subtraction error at 3.2 ppm in a considerable proportion of the spectra (smokers: 80%, smoking polysubstance users: 69%, healthy controls: 60%), which might have led to a distortion in the quantification of GABA. However, there was no difference in proportion of subtraction error between groups (χ2(2) = 1.553, p = 0.460). 3.1. Sample characteristics After excluding participants due to unreliable MRS spectra, 30/ 48 (62.5%) from the S group, 38/61 (62.3%) from the SP group, and 61/90 (67.7%) from the HC group were included in the analyses. Demographic, clinical, and neurotransmitter information is dis- played in Table 1. The groups were of similar age (H2 = 3.00, p = 0.22), but differed in IQ (F2,126 = 4.20, p = 0.017). Post-hoc analyses showed that the S group did not differ from the HC group (p = 0.981), but that the SP group had lower IQ compared to the HC group (p = 0.008) and the S group (p = 0.023). Since IQ was not a matching criterion and represents a group characteristic, IQ was not entered as a covariate in the analyses on group differences in Glx and GABA. Moreover, IQ was not correlated with Glx (p = 0.71) or GABA (p = 0.69). There was no difference between the S and SP groups with regard to nicotine dependence as mea- sured with the FTND (t66 = 0.539, p = 0.59). There were sig- nificant group differences in alcohol use and related problems as measured with the AUDIT (F2,126 = 51.87, p < 0.001). Post-hoc 119 Drug and Alcohol Dependence 179 (2017) 117–123 M.H.J. Schulte et al. Table 1 Between group differences in demographic, clinical and neurobiological outcomes. 3.1. Sample characteristics HC S SP Fa/H(df)b/Uc P-value Effect size (η2) N = 61 N = 30 N = 38 Mean SD Mean SD Mean SD Age 32.10 9.69 35.87 10.48 32.66 7.45 3.00(2)b 0.22 0.02 IQ (NART) 104.9 8.60 105.00 8.90 99.90 9.60 4.196a 0.017ee 0.06 Alcohol (units/week) 4.87 6.36 7.23 6.39 25.98 25.49 47.34(2)b < 0.0001 0.29 AUDIT scores 5.67 3.75 6.10 2.91 13.37 4.58 51.87a < 0.0001 0.45 Cigarettes/week – – 155.24 67.79 115.22 61.35 6.504a 0.013 0.09 FTND scores – – 6.07 1.96 5.79 2.21 0.291a 0.59 0.004 DUDIT scores – – – – 18.19 5.00 – – – Cocaine/week (g) – – – – 2.29 1.32 – – – Cannabis/week (joints) – – 0.09 0.19 4.73 7.19 67.00c 0.01 0.18 BIS-11 59.27 7.92 64.89 9.85 72.94 9.96 26.83a < 0.001 0.31 Glx 0.62 0.11 0.68 0.13 0.67 0.13 2.71a 0.07 0.04 GABA 0.20 0.04 0.20 0.09 0.20 0.04 0.04a 0.96 0.001 Abbreviations: AUDIT, Alcohol Use Disorder Identification Test; BIS-11, Barratt Impulsiveness Scale version 11; DUDIT, Drug Use Disorder Identification Test; FTND, Fagerström Test for Nicotine Dependence; GABA, gamma-aminobutyric acid, referenced to creatine; Glx, composite measure of glutamate and glutamine, referenced to creatine; HC, Healthy Controls; NART, National Adult Reading Test; S, Smokers; SD, Standard Deviation; SP, Smoking Polysubstance Users. a p-values represent univariate ANOVAs. b p values represent non parametric univariate ANOVAs Abbreviations: AUDIT, Alcohol Use Disorder Identification Test; BIS-11, Barratt Impulsiveness Scale version 11; DUDIT, Drug Use Disorder Identification Test; FTND, Fagerström Test for Nicotine Dependence; GABA, gamma-aminobutyric acid, referenced to creatine; Glx, composite measure of glutamate and glutamine, referenced to creatine; HC, Healthy Controls; NART, National Adult Reading Test; S, Smokers; SD, Standard Deviation; SP, Smoking Polysubstance Users. a p-values represent univariate ANOVAs. b p-values represent non-parametric univariate ANOVAs. c p-values represent non-parametric t-test. Fig. 2. Concentration of Glx (left) and GABA (right) in the dorsal Anterior Cingulate Cortex per group 85(M ± SD). There was a trend significant between group difference with regard to Glx (p = 0.07), but no between group difference with regard to GABA (p = 0.96). analyses showed that the SP group had higher AUDIT scores com- pared to the HC (p < 0.001) and the S group (p < 0.001), but that there was no difference in AUDIT scores between the S and HC groups. 3.1. Sample characteristics However, AUDIT scores were not correlated with Glx (p = 0.45) or GABA (p = 0.72). Moreover, since cocaine use is highly related to alcohol use and therefore high AUDIT scores are inherently connected to cocaine use (EMCDDA, 2009; Connor et al., 2014; Tang et al., 2007), AUDIT scores were not included as a covariate in the analyses when comparing the S and SP groups to the HC group on brain Glx and GABA measures to avoid the risk of overcorrection resulting in a serious reduction of variance in Glx and GABA measures (Miller and Chapman, 2001). Also see section ‘substance use and neurotransmitter levels’ for the association be- tween neurotransmitter concentrations and AUDIT scores. group differences in GABA concentrations (F2,105 = 0.041, p = 0.96; see Fig. 2).3 Additionally, there were no between group differences with respect to total N-Acetyl Aspartate (NAA + NAAG; F2,126 = 0.334, p = 0.72, η2 = 0.005) and total creatine (Cre + PCr; F2,126 = 1.456, p = 0.24, η2 = 0.023). Also, there were no group differences in regional grey matter (F2,126 = 1.625, p = 0.20, η2 < 0.001) or white matter (F2, 126 = 0.849, p = 0.43, η2 < 0.001) volume within the dACC voxel for those individuals included in the analyses on Glx differences. In addition, there were no group differences in grey matter (p = F2,126 = 0.346, p = 0.71, η2 < 0.001) or white matter (F2,126 = 0.172, p = 0.84, η2 < 0.001) for those included in the analyses on GABA differ- ences. 3.2. Glx and GABA concentrations To account for multiple testing, a Bonferroni correction of 2 was applied for the analyses on neurotransmitter concentrations (Glx and GABA), resulting in an adjusted alpha level of 0.025. With re- gard to Glx concentrations, there was a trend significant group difference (F2,126 = 2.71, p = 0.07; see Fig. 2). Since this suggests the presence of individual group differences in Glx, planned group comparisons were performed to explore these potential differences. Since these analyses were exploratory, no correction for multiple comparisons was applied. In these post-hoc group comparisons the S group had higher dACC Glx concentrations compared to the HC group (p = 0.04; η2 = 0.05) and the SP group tended to have higher dACC Glx concentration than the HC group (p = 0.09; η2 = 0.03). No difference in dACC Glx concentrations was found between the S and SP groups (p = 0.67). There were no between The groups were significantly different from each other with regard to BIS-11 score (F2,122 = 26.83, p < 0.001; see Table 1). Planned comparisons showed that the HC group had the lowest BIS-11 scores, and that their score was significantly different from the S (p = 0.008) the SP group (p < 0.001). In addition, the SP group scored sig- nificantly higher on the BIS-11 than the S group (p = 0.001). However, there was no association between BIS-11 score and Glx (p = 0.85) or GABA concentrations (p = 0.34; see Fig. 3). 120 3.4. Substance use and neurotransmitter levels contradicts previous findings of larger differences in multiple versus single substance users (Abé et al 2013; Ke et al 2004; Mason et al Fig. 3. Correlation between Glx (left) and GABA (right) with BIS-scores per group. There was no as- sociation between BIS-11 score and Glx (p = 0.85) or GABA (p = 0.34). M.H.J. Schulte et al. Drug and Alcohol Dependence 179 (2017) 117–123 M.H.J. Schulte et al. M.H.J. Schulte et al. M.H.J. Schulte et al. Fig. 3. Correlation between Glx (left) and GABA (right) with BIS-scores per group. There was no as- sociation between BIS-11 score and Glx (p = 0.85) or GABA (p = 0.34). Fig. 3. Correlation between Glx (left) and GABA (right) with BIS-scores per group. There was no as- sociation between BIS-11 score and Glx (p = 0.85) or GABA (p = 0.34). 3.4. 3.2. Glx and GABA concentrations Substance use and neurotransmitter levels contradicts previous findings of larger differences in multiple versus single substance users (Abé et al., 2013; Ke et al., 2004; Mason et al., 2006). Since the substance using groups did not differ in the level of nicotine dependence, this may indicate that alterations in Glx con- centrations are possibly more related to smoking dependence than to other types of substance use. However, since there were no significant correlations between glutamate concentrations and nicotine use se- verity (or alcohol and cocaine use severity), higher glutamate con- centrations may be associated with the presence of (underlying pro- cesses related to) substance dependence in general, unspecific to the type of substance. Other explanations could be that there is a ‘threshold effect’ resulting in affected glutamate concentrations after someone has used for a certain period of time of with a specific intensity of substance use, or the cardiovascular effect of the used substances that cause a circulatory compromise in the dACC. More extensive studies should be performed to further disentangle this differential effect. Additional exploratory analyses were performed to investigate possible associations between substance use levels and substance use disorder severity with dACC neurotransmitter concentrations. In the HC group, multiple regression did not show a significant re- lation between AUDIT scores and Glx (F1,60 = 0.001, p = 0.97) or GABA concentrations (F1,47 = 0.166, p = 0.69), and no significant re- lations between the amount of alcohol used and Glx (F1,56 = 0.084, p = 0.77) or GABA concentrations (F1,44 = 0.303, p = 0.59). In the S group, there also was no significant relation between AUDIT and FTND scores and Glx (F2,29 = 0.120, p = 0.89) or GABA con- centrations (F2,33 = 0.203, p = 0.82), and no significant relation be- tween the amount of alcohol and the number of cigarettes and Glx (F2,29 = 0.186, p = 0.83) or GABA concentrations (F2,33 = 0.112, p = 0.90). As expected, we found between group differences in self-reported impulsivity with the highest impulsivity scores in smoking poly- substance users followed by smokers and the lowest in healthy controls. However, impulsivity was not significantly correlated to dACC Glx or GABA concentrations. This is not in line with previous studies showing a significant correlation between impulsivity and glutamate con- centrations (Pattij and Vanderschuren, 2008; Schmaal et al., 2012b). 4. Discussion This study investigated differences in dACC Glx and GABA con- centrations and impulsivity between cigarette smokers, smoking poly- substance users, and healthy controls. In line with our first hypothesis, there was a trend towards group differences in dACC Glx concentra- tions. Furthermore, in contrast to our first hypothesis, there were no between group differences in dACC GABA concentrations. Post hoc analyses showed that both substance using groups tended to have higher Glx concentrations compared to healthy controls, but that there was no difference between both substance using groups, which refutes our second hypothesis. It should be noted that no correction for mul- tiple comparison was applied since these comparisons were performed exploratory. In contrast to our third hypothesis, there were no sig- nificant correlations between dACC neurotransmitter concentrations and substance use severity, or the amount of substance use. In line with our fourth hypothesis, there were group differences with regard to impulsivity. Post hoc analyses showed that smokers and smoking polysubstance users had higher BIS-11 scores than healthy controls, and smoking polysubstance users showed higher scores than smokers. However, in contrast to our fifth hypothesis, there were no significant correlations between dACC neurotransmitter concentrations and self- reported impulsivity. In contrast to previous studies (Abé et al., 2013; Durazzo et al., 2016; Ke et al., 2004; Prescot et al., 2013; Silveri et al., 2014), we did not find differences in dACC GABA concentrations between the sub- stance using groups and healthy controls, or between smokers and smoking polysubstance users. Possible explanations include differences in methodology between the previous studies and the current study. For instance, previous studies recruited mainly non-smokers (Ke et al., 2004; Prescot et al., 2013; Silveri et al., 2014), whereas both substance using groups in the current study were smokers. Another explanation could be the duration of abstinence at the moment of testing since the aforementioned studies all tested GABA concentrations after at least one week of abstinence. In the current study, the substance using par- ticipants were allowed to smoke ad libitum until the session. However, Mon et al. (2012) also found no differences in GABA concentrations despite a period of abstinence. Although at trend level, our findings support the literature on de- viating glutamate concentrations and thus point to the potential of (anti)glutamatergic agents for the treatment of substance dependence. 3.2. Glx and GABA concentrations However, the review by Pattij and Vanderschuren (2008) is based on animal studies using different indicators for impulsivity. The study of Schmaal et al. (2012b) tested in only 8 treatment seeking cocaine de- pendent patients with similar BIS-11 scores but much higher AUDIT scores than the cocaine users in the current study (21.3 vs. 13.4). Finally, in the SP group there were no significant relations of AUDIT score, FTND score, DUDIT score, and cannabis use with Glx (F4,36 = 0.044, p = 0.99) or GABA concentrations (F4,24 = 0.86, p = 0.51), and no significant relations of alcohol, cigarette, cocaine and cannabis use with Glx (F4,37 = 0.712, p = 0.59) or GABA concentra- tions (F4,25 = 1.021, p = 0.42). References Abé, C., Mon, A., Durazzo, T.C., Pennington, D.L., Schmidt, T.P., Meyerhoff, D.J., 2013. Polysubstance and alcohol dependence: unique abnormalities of magnetic resonance- derived brain metabolite levels. Drug Alcohol Depend. 130, 30–37. http://dx.doi. org/10.1016/j.drugalcdep.2012.10.004. Babor, T.F., Kranzler, H.R., Lauerman, R.J., 1989. Early detection of harmful alcohol consumption: comparison of clinical, laboratory, and self-report screening proce- dures. Addict. Behav. 14, 139–157. http://dx.doi.org/10.1016/0306-4603(89) 90043-9. Bauer, J., Pedersen, A., Scherbaum, N., Bening, J., Patschke, J., Kugel, H., Heindel, W., Arolt, V., Ohrmann, P., 2013. Craving in alcohol-dependent patients after detox- ification is related to glutamatergic dysfunction in the nucleus accumbens and the anterior cingulate cortex. Neuropsychopharmacology 38, 1401–1408. http://dx.doi. org/10.1038/npp.2013.45. Berman, A.H., Bergman, H., Palmstierna, T., Schlyter, F., 2005. Evaluation of the Drug Use Disorders Identification Test (DUDIT) in criminal justice and detoxification set- tings and in a Swedish population sample. Eur. Addict. Res. 11, 22–31. http://dx.doi. org/10.1159/000081413. g Berridge, K.C., Robinson, T.E., 1998. What is the role of dopamine in reward: hedonic impact, reward learning, or incentive salience? Brain Res. Rev. 28, 309–369. http:// dx.doi.org/10.1016/S0165-0173(98)00019-8. g Brand, M., Young, K.S., Laier, C., 2014. Prefrontal control and internet addiction: a theoretical model and review of neuropsychological and neuroimaging findings. Front. Hum. Neurosci. 8, 1–13. http://dx.doi.org/10.3389/fnhum.2014.00375. Broos, N., Schmaal, L., Wiskerke, J., Kostelijk, L., Lam, T., Stoop, N., Weierink, L., Ham, J., de Geus, E.J.C., Schoffelmeer, A.N.M., van den Brink, W., Veltman, D.J., de Vries, T.J., Pattij, T., Goudriaan, A.E., 2012. The relationship between impulsive choice and impulsive action: a cross-species translational study. PLoS One 7, 1–9. http://dx.doi. org/10.1371/journal.pone.0036781. Chang, L., Ernst, T., Strickland, T., Mehringer, C.M., 1999. Gender effects on persistent cerebral metabolite changes in the frontal lobes of abstinent cocaine users. Am. J. Psychiatry 156, 716–722. Connor, J.P., Gullo, M.J., White, A., Kelly, A.B., 2014. Polysubstance use: diagnostic challenges, patterns of use and health. Curr. Opin. Psychiatry 27, 269–275. http://dx. doi.org/10.1097/YCO.0000000000000069. In conclusion, the current study found indications of dACC Glx differences between substance using groups and healthy controls, but not between the substance using groups. Moreover, Glx concentrations were not associated with the level of substance use and therefore the observed increase in Glx in substance users is not just a consequence of substance use itself. Furthermore, no differences in dACC GABA con- centrations were found. There were group differences in self-reported impulsivity, but self-reported impulsivity was not significantly corre- lated with dACC Glx or GABA concentrations. Contributors other substance use disorders (for reviews, see Deepmala et al., 2015; McClure et al., 2014). More research is needed to investigate the exact mechanisms underlying the efficacy of such glutamatergic agents. MHJS and AMK collected and analyzed the data, and wrote the first draft of the paper. RWS, LS, WvdB, LR, JRH, GAvW, and AEG were involved in the design of the studies and actively participated in writing and revising the manuscript for publication. All authors critically re- viewed the manuscript for content and approve the final version for publication. y g y g g g Major strengths of this study are the relatively large samples and the direct comparison of neurotransmitter concentrations and impulsivity between smokers with or without concurrent polysubstance use and non-substance using healthy controls. Another strength of this study is the simultaneous assessment of neurobiological and behavioral mea- sures. The current study also has limitations. First, only male partici- pants were recruited in both studies. Although this may lead to more homogeneous groups and thereby strengthens the results of the study, this also limits the generalizability of the results to the general popu- lation. Second, as mentioned before, the subjects were recruited as part of two individual studies to answer study-specific research questions. However, all participants were recruited in the same way and scanned in the same period with the same MRI scanner. Third, there is the issue of the use of multiple substances, especially in the group of smoking polysubstance users. Even though this resembles most cocaine users in the community and in treatment (EMCDDA, 2009; Connor et al., 2014), who are suggested to be also dependent on alcohol and/or tobacco (Tang et al., 2007), it could be that different substances have a different or even opposite effect on glutamate concentrations. This may also play an important role in the treatment of polysubstance users. In addition, for cannabis only the effect of the amount of cannabis use was analyzed, due to the lack of a questionnaire assessing problematic cannabis use in the original studies. Even though our sample size was fairly large for an imaging study, even larger (possibly multi-site) studies would be needed to study the neurobiological effects of polysubstance use. Fourth, to ensure overall good quality of the MRS data some partici- pants had to be excluded from the analyses on Glx and GABA con- centrations, due to unreliable MRS spectra. References More research is needed to investigate the relationship between dACC neurotransmitter con- centrations and aspects of cognitive impairment other than self-re- ported impulsivity. Deepmala, Slattery, J., Kumar, N., Delhey, L., Berk, M., Dean, O., Spielholz, C., Frye, R., 2015. Clinical trials of N-acetylcysteine in psychiatry and neurology: a systematic Deepmala, Slattery, J., Kumar, N., Delhey, L., Berk, M., Dean, O., Spielholz, C., Frye, R., 2015. Clinical trials of N-acetylcysteine in psychiatry and neurology: a systematic review. Neurosci. Biobehav. Rev. 55, 294–321. http://dx.doi.org/10.1016/j. neubiorev.2015.04.015. Durazzo, T.C., Meyerhoff, D.J., Mon, A., Abé, C., Gazdzinski, S., Murray, D.E., 2016. Chronic cigarette smoking in healthy middle-aged individuals is associated with decreased regional brain N-acetylaspartate and glutamate levels. Biol. Psychiatry 79, 481–488. http://dx.doi.org/10.1016/j.biopsych.2015.03.029. Ende, G., Hermann, D., Demirakca, T., Hoerst, M., Tunc-Skarka, N., Weber-Fahr, W., Wichert, S., Rabinstein, J., Frischknecht, U., Mann, K., Vollstädt-Klein, S., 2013. Loss of control of alcohol use and severity of alcohol dependence in non-treatment-seeking heavy drinkers are related to lower glutamate in frontal white matter. Alcohol. Clin Exp. Res. 37, 1643–1649. http://dx.doi.org/10.1111/acer.12149. European Monitoring Centre for Drugs and Drug Addiction. Polydrug use: Patterns and Responses (2009). Available at http://www.emcdda.europa.eu. Gallinat, J., Schubert, F., 2007. Regional cerebral glutamate concentrations and chronic tobacco consumption. Pharmacopsychiatry 40, 64–67. http://dx.doi.org/10.1055/s- 2007-970144. Garavan, H., Hester, R., 2007. The role of cognitive control in cocaine dependence. Neuropsychol. Rev. 17, 337–345. http://dx.doi.org/10.1007/s11065-007-9034-x. Acknowledgements Study A was supported by a grant from the NWO (Dutch National Science Foundation), awarded to the Dutch-Flemish Research School Experimental Psychopathology (grant number 022.003.038). Study B was supported by a grant provided by ZonMW (grant number 91211002). Conflict of interest No conflict declared. 4. Discussion For instance, acamprosate (commonly used in the treatment of alcohol dependence) and N-acetylcysteine (commonly used as a mucolytic agent in cough medicine) have both been found to reduce glutamate concentrations in alcohol and cocaine dependent individuals, respec- tively (Schmaal et al., 2012b; Umhau et al., 2010). In addition, several studies indicate that N-acetylcysteine is effective in the treatment of The trend towards increased Glx concentrations in smokers and smoking polysubstance users versus healthy controls are in line with previous research showing higher dACC glutamate concentrations (Bauer et al., 2013; Lee et al., 2007; Schmaal et al., 2012b; Thoma et al., 2011). However, no difference in dACC Glx concentrations between smokers and smoking polysubstance users were found, which 121 M.H.J. Schulte et al. Drug and Alcohol Dependence 179 (2017) 117–123 Drug and Alcohol Dependence 179 (2017) 117–123 Contributors However, similar propor- tions had to be excluded in all three groups and there was no difference in sociodemographic and clinical characteristics between those ex- cluded and those included in the current analyses. In addition, we were unable to verify if potential head movement during scanning affected scan quality. This should be taken into account in future studies. Fur- thermore, the results concerning GABA should be interpreted with caution, due to the presence of a choline peak at 3.2 ppm that might have distorted the quantification of GABA. This did not influence the quantification of Glx. Fifth, even though the BIS-11 is widely used to assess impulsivity, additional measures of behavioral impulsivity may capture different aspects of impulsivity unrelated to self-reported im- pulsivity (Broos et al., 2012; Kräplin et al., 2014). 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Embolia gordurosa: uma revisão para a prática ortopédica atual
Acta Ortopédica Brasileira
2,005
cc-by
24,205
SUMMARY Fat embolism (FE) is the occlusion of small blood vessels by fat droplets originated mainly from femur, tibia and pelvis fractures, as well as from knee and hip arthroplasty. It usually does not cause damage to the involved organs, unless when it is massive. In a few cases, FE evolves to the ‘fat embolism syndrome’ (FES), affecting most often the lungs and the brain, although any organ or structure of the body can be damaged. A embolia gordurosa (EG) é a oclusão de pequenos vasos por gotículas de gordura, geralmente originadas nas fraturas do fêmur, tíbia e bacia, e nas artroplastias do joelho e quadril. Nor- malmente não causa danos aos órgãos atingidos, a menos que seja maciça. Em poucos casos a EG evolui para a “síndrome da embolia gordurosa” (SEG) a qual afeta principalmente os pulmões e o cérebro, embora qualquer órgão ou estrutura do organismo possa ser afetada. y g Fat embolisms are hydrolyzed by lipase, forming free fatty acids (FFA), which cause a toxic effect to capillary endothelium, intensify- ing integrins activity, which, in turn, intensify neutrophils’ adherence to endothelial cells, making easier the activity of the proteolytic enzymes of such neutrophils’ lysosomes on the endothelium. p A gordura embolizada é hidrolizada pela lipase, originando os ácidos graxos livres (AGL) que agem toxicamente sobre o endotélio capilar e que intensificam a ação das integrinas as quais acentuam a adesividade dos neutrófilos às células endoteliais, facilitando a ação das enzimas proteolíticas dos lisossomas desses neutrófilos sobre o endótelio. y p y The result of those reactions is the capillary meshwork rupture, followed by hemorrhage and edema on affected organs. The FES presents many conditions, ranging from respiratory failure and variable neurological changes, to convulsions and deep coma. The diagnosis of FES is essentially made on clinical basis only, since there are no laboratory tests to validate it. Among imaging tests, only brain magnetic resonance clearly shows the perivascular edema and infarction areas. O resultado dessas reações é a ruptura da rede capilar seguida de hemorragia e edema nos órgãos afetados. A SEG apresenta desde insuficiência respiratória e alterações neurológicas varia- das até convulsões e coma profundo. O diagnóstico da SEG é puramente clínico, não existindo nenhum exame laboratorial que o confirme. Dentre os exames de imagens, apenas a ressonância magnética cerebral demonstra claramente as áreas do edema perivascular e dos infartos. ARTIGO DE REVISÃO ARTIGO DE REVISÃO EMBOLIA GORDUROSA: UMA REVISÃO PARA A PRÁTICA ORTOPÉDICA ATUAL FAT EMBOLISM: A REVIEW FOR CURRENT ORTHOPAEDICS PRACTICE LUIZ TARCISIO B. FILOMENO1, CLARA R. CARELLI2, NUNO C. L. FIGUEIREDO DA SILVA3, TARCISIO ELOY PESSOA DE BARROS FILHO4, MARCO MARTINS AMATUZZI5. SUMMARY FE treatment with uncountable drugs did not present positive re- sults; however, the most required measure to FES is mechanical ventilation. Mortality rate is almost 100% in fulminant forms; ap- proximately 20% in the sub acute forms, and there is no mortality in a sub clinical form. p O tratamento da EG com inúmeras drogas não apresentou re- sultados positivos; no entanto, a medida mais requisitada para a SEG é a assistência ventilatória. A mortalidade é quase de 100% nas formas fulminantes; aproximadamente de 20% nas formas sub-agudas e não há mortalidade na forma sub-clínica. In order to prevent FES is crucial to avoid shock and hypoxia from the accident scenery, and to proceed to the early fixation of fractures, which reduces the incidence of SARA and post-trauma mortality. g Para prevenir a SEG é fundamental evitar o choque e a hipóxia desde a cena do acidente, e proceder à fixação precoce das fraturas, o que diminui a incidência de SARA e a mortalidade pós-trauma. Keywords: Embolism, fat; Arthroplasty; Fractures. Descritores: Embolia gordurosa; Artroplastia; Fraturas Trabalho realizado no Instituto de Ortopedia e Traumatologia do Hospital das Clínicas da FMUSP Endereço: Dr. Luiz Tarcisio B. Filomeno - Rua Ovídio Pires de Campos, 333 Cerqueira Cesar São Paulo - CEP 05403 010 - e-mail: luiztbf@usp.br 1. Cirurgião Torácico, Prof. Assistente Doutor do Serviço de Cirurgia da Coluna Vertebral do Instituto de Ortopedia e Traumatologia do Hospital das Clínicas da FMUSP 2. Professora Livre-Docente, Coordenadora da Equipe de Clínica Médica do Instituto de Ortopedia e Traumatologia do Hospital das Clínicas da FMUSP. 3. Médico-Chefe da UTI do Instituto de Ortopedia e Traumatologia do Hospital das Clínicas da FMUSP 4. Professor Titular do Departamento de Ortopedia e Traumatologia da FMUSP e Chefe da Disciplina da Coluna Vertebral da FMUSP. 5. Professor Titular e Chefe do Departamento de Ortopedia e Traumatologia da FMUSP Trabalho recebido em: ACTA ORTOP BRAS 13(4) - 2005 ACTA ORTOP BRAS 13(4) - 2005 INTRODUÇÃO No caso de fraturas do fêmur, da tíbia e da bacia, principalmente, é comum a formação de trombos mistos, constituídos por gordura, plaquetas e hemácias. Já nos casos das artroplastias, foram descritas ainda as embolizações de micro fragmentos de osso, de medula óssea de ar e do cimento acrílico(7,11). Entretanto, nenhum desses fenômenos está relacionado ao desenvolvimento da SEG que, como veremos, é desencadeado pela ação dos ácidos graxos que se segue à hidrólise da gordura embolizada. reqüentes de EG e SEG. Tabela1- Causas mais freqüentes de EG e SEG. INTRODUÇÃO Seria ainda importante ressaltar que na EG os êmbolos gordurosos não são formados por fragmentos macro ou microscópicos de tecido adiposo, mas sim por gotículas de gor- dura neutra, dos mais variados diâmetros, mas medidos em micra, as quais circulam em suspensão no sangue até obstruir arteríolas il d l ã d t ó ã P t l d ã é eqüentes de EG e SEG. p p g Embora a SEG costume ocorrer principalmente após fraturas de ossos longos e da bacia em traumas e alta energia(8,22,32,36,38), também têm sido descritos, embora raramente, casos de SEG grave ou mesmo fatal, após traumas relativamente leves que causaram fratura de úme- ro, de tornozelo, de corpo vertebral, de costelas e de esterno(8,38-40). Aliás, vale aqui salientar que até mesmo a massagem cardíaca externa gera consideráveis graus de EG, a qual foi detectada em 40 a 85% de casos autopsiados(8,35). Outros procedimentos ortopédicos ainda mais leves, como a manipulação do alongador de Wagner, por exemplo, também já chegaram a causar SEG fatal(13). De modo semelhante, aqui, em nosso Serviço, tivemos a oportunidade de surpreender dois casos de SEG grave após a simples injeção de aspirado medular em foco de pseudoartrose. Recentemente a SEG foi descrita até mesmo após procedimentos estéticos, como a lipoaspiração(41,42) e a injeção de gordura autóloga peri-nasal(43), porém em um número muito restrito de casos. Apesar do extenso traumatismo provocado pela gravidade(Tabela 1). A “Síndrome da Embolia Gordurosa” rência de lesão e disfunção de um ou aos êmbolos gordurosos, ou seja, ou evolução atípica da EG. Os órg são, portanto, os mesmos atingidos o cérebro são as vísceras mais ating dominantes são a insuficiência respiratória aguda (nos pa- drões da Síndrome da Angústia Respiratória do Adulto -SARA-) e o acometimento cerebral, o qual pode variar desde uma simples ansiedade até o coma irreversível e morte(28). A SEG é uma afecção relativamente rara mas de extrema gravidade, com índices de mortalidade que variam entre 10 e 36%(18,29- 32), e que ocorre, na grande maioria dos casos, em pacien- tes ortopédicos(8,16,20,22,24,32). g ( ) A “Síndrome da Embolia Gordurosa” (SEG) é definida como a ocor- rência de lesão e disfunção de um ou mais órgãos , causadas pelos aos êmbolos gordurosos, ou seja, trata-se de uma complicação ou evolução atípica da EG. Os órgãos comprometidos pela SEG são, portanto, os mesmos atingidos pela EG. INTRODUÇÃO essas novas informações, como também comentá-las e discuti-las frente às evidências anteriores. Inicialmente, achamos oportuno enfatizar as definições das duas entidades essas novas informações, como também comentá-las e discuti-las frente às evidências anteriores. essas novas informações, como também comentá-las e discuti-las frente às evidências anteriores. Inicialmente, achamos oportuno enfatizar as definições das duas entidades Nesta revisão sobre o fenômeno da “Embolia Gordurosa” pudemos constatar que o assunto não só ainda apresenta relevantes pontos obscuros, como, por ser multidisciplinar, vem acarretando contro- vérsias em praticamente todas as especialidades médicas. Isto se deve ao fato de que os êmbolos gordurosos, embora se propaguem inicialmente através da circulação venosa, acometendo primaria- mente os pulmões, em muitos casos podem atravessar a circulação pulmonar(1-3) ou mesmo o septo inter-atrial(4-6) e, por via arterial, afetar qualquer órgão ou estrutura do organismo. Assim sendo, procuramos sintetizar aqui tanto os conhecimentos básicos mais relevantes, como os advindos das pesquisas clínicas e laboratoriais mais recentes. Ainda nos pareceu pertinente e útil, porém, não apenas reproduzir Inicialmente, achamos oportuno enfatizar as definições das duas entidades nosológicas que, embora intimamente relacionadas, têm significados clínico e patológico completamente diferentes: a “Embolia Gordurosa” (EG) e a “Síndrome da Embolia Gordurosa” (SEG). ( ) ( ) A “Embolia Gordurosa” é definida como a ocorrência de bloqueio mecânico da luz vascular por gotículas circulantes de gordura cujos diâmetros ultrapassam 8 a 10u e geralmente ficam retidas na rede capilar. Além de gordura, esses êmbolos freqüentemente carregam também células hematopoiéticas da medula óssea, o que confirma a sua origem (7-11). Sendo a EG um fenômeno de origem inicialmente venosa, é natural e esperado que os pulmões sejam não só seus Trabalho recebido em: ACTA ORTOP BRAS 13(4) - 2005 196 primeiros alvos como também os órgãos mais atingidos. Isso, de fato, é o que acontece na maioria dos casos. Existem, entretanto, alguns mecanismos pelos quais os êmbolos gordurosos podem lesar outros órgãos, de maneira tão grave quanto os pulmões, mas pela circulação arterial: 1o.) Através de micro-fístulas artério-venosas pulmonares anatômicas. Segundo Goslling et al.(12,13), esferas de vidro com diâmetro 20 a 40 vezes maior que o do capilar pulmonar ganham acesso à circulação sistêmica após passar por essas fístulas. 2o.) Pela deformação da própria gotícula de gordura que, assumindo uma forma mais alongada, lograria atravessar os capilares pulmo- nares(3). 3) Pelo septo inter-atrial, através do “Forame Oval”. INTRODUÇÃO Por outro lado, não é raro que se formem também trombos hemáticos, como pode ocorre após qualquer trauma grave ou cirurgia de grande porte. No caso de fraturas do fêmur, da tíbia e da bacia, principalmente, é comum a formação de trombos mistos, constituídos por gordura, plaquetas e hemácias. Já nos casos das artroplastias, foram descritas ainda as embolizações de micro fragmentos de osso, de medula óssea de ar e do cimento acrílico(7,11). Entretanto, nenhum desses fenômenos está relacionado ao desenvolvimento da SEG que, como veremos, é desencadeado pela ação dos ácidos graxos que se segue à hidrólise da gordura embolizada. reqüentes de EG e SEG. p p g Embora a SEG costume ocorrer principalmente após fraturas de ossos longos e da bacia em traumas e alta energia(8,22,32,36,38), também têm sido descritos, embora raramente, casos de SEG grave ou mesmo fatal, após traumas relativamente leves que causaram fratura de úme- ro, de tornozelo, de corpo vertebral, de costelas e de esterno(8,38-40). Aliás, vale aqui salientar que até mesmo a massagem cardíaca externa gera consideráveis graus de EG, a qual foi detectada em 40 a 85% de casos autopsiados(8,35). Outros procedimentos ortopédicos ainda mais leves, como a manipulação do alongador de Wagner, por exemplo, também já chegaram a causar SEG fatal(13). De modo semelhante, aqui, em nosso Serviço, tivemos a oportunidade de surpreender dois casos de SEG grave após a simples injeção de aspirado medular em foco de pseudoartrose. Recentemente a SEG foi descrita até mesmo após procedimentos estéticos, como a lipoaspiração(41,42) e a injeção de gordura autóloga peri-nasal(43), porém em um número muito restrito de casos. Apesar do extenso traumatismo provocado pela cânula de lipoaspiração, a EG resultante quase sempre é de pequena monta, quando comparada à que ocorre nas fraturas. O motivo desta diferença é que nos ossos as vênulas e si- nusóides, por terem suas paredes acoladas às trabéculas do osso, tendem a permanecer abertas após sua ruptura, ao passo que no tecido subcutâneo esses vasos tendem a se colabar, o que dificulta a embolização(8,44,45). Por outro lado, enquanto que nas fraturas e artroplastias os êmbolos gordurosos sejam originários da gordura do canal medular, nos traumatismos de partes moles eles provêm, como seria de se esperar, da própria gordura subcutânea. Do ponto de vista bioquímico, entretanto, tanto as células da gordura medular quanto as do tecido subcutâneo apresentam o mesmo tipo de gordura, assim chamada “neutra”(5,6,8,16,22,46). INTRODUÇÃO Como os pulmões e o cérebro são as vísceras mais atingidas, as manifestações clínicas dominantes são a insuficiência respiratória aguda (nos pa- drões da Síndrome da Angústia Respiratória do Adulto -SARA-) e o acometimento cerebral, o qual pode variar desde uma simples ansiedade até o coma irreversível e morte(28). A SEG é uma afecção relativamente rara mas de extrema gravidade, com índices de mortalidade que variam entre 10 e 36%(18,29- 32), e que ocorre, na grande maioria dos casos, em pacien- tes ortopédicos(8,16,20,22,24,32). Tabela1- Causas mais g ( ) A “Síndrome da Embolia Gordurosa” (SEG) é definida como a ocor- rência de lesão e disfunção de um ou mais órgãos , causadas pelos aos êmbolos gordurosos, ou seja, trata-se de uma complicação ou evolução atípica da EG. Os órgãos comprometidos pela SEG são, portanto, os mesmos atingidos pela EG. Como os pulmões e o cérebro são as vísceras mais atingidas, as manifestações clínicas dominantes são a insuficiência respiratória aguda (nos pa- drões da Síndrome da Angústia Respiratória do Adulto -SARA-) e o acometimento cerebral, o Tabela1- Causas mais freqüentes de EG e SEG. Tabela1- Causas mais freqüentes de EG e SEG. traumatismo provocado pela cânula de lipoaspiração, a EG resultante quase sempre é de pequena monta, quando comparada à que ocorre nas fraturas. O motivo desta diferença é que nos ossos as vênulas e si- nusóides, por terem suas paredes acoladas às trabéculas do osso, tendem a permanecer abertas após sua ruptura, ao passo que no tecido subcutâneo esses vasos tendem a se colabar, o que dificulta a embolização(8,44,45). Por outro lado, enquanto que nas fraturas e artroplastias os êmbolos gordurosos sejam originários da gordura do canal medular, nos traumatismos de partes moles eles provêm, como seria de se esperar, da própria gordura subcutânea. Do ponto de vista bioquímico, entretanto, tanto as células da gordura medular quanto as do tecido subcutâneo apresentam o mesmo tipo de gordura, assim chamada “neutra”(5,6,8,16,22,46). Seria ainda importante ressaltar que na EG os êmbolos gordurosos não são formados por fragmentos macro ou microscópicos de tecido adiposo, mas sim por gotículas de gor- dura neutra, dos mais variados diâmetros, mas medidos em micra, as quais circulam em suspensão no sangue até obstruir arteríolas e capilares do pulmão ou de outros órgãos. Por outro lado, não é raro que se formem também trombos hemáticos, como pode ocorre após qualquer trauma grave ou cirurgia de grande porte. INTRODUÇÃO Estudos recentes, utilizando a ecocardiografia trans-esofágica (ECO-TE), têm demonstrado que em cerca de 20 a 34% dos indivíduos adultos de uma população normal esse forame se encontra patente(6,8,14-17). Foi também observado que mesmo em indivíduos nos quais esse forame estava fechado, este poderia ser aberto na vigência de uma hipertensão pulmonar aguda como as que podem se instalar numa EG maciça(5,6,8). Na EG por via arterial os principais órgãos atingidos são o cérebro (1,2,5,6,18-21) a pele (petéquias) e as retinas(13,19,20,22-25). Em autópsias cuidadosas de vítimas de acidente automobilístico, toda- via, freqüentemente se encontram êmbolos gordurosos também nos rins, baço, fígado, adrenais e miocárdio(20,24-27). Neste ponto é necessário enfatizar que, apesar de ser grande o número de pa- cientes acometidos por episódios muitas vezes maciços de embolia gordurosa pós-traumática ou peri-operatórias, somente uma pequena fração deles desenvolverá manifestações clínicas de menor ou maior gravidade(Tabela 1). soldados mortos na Guerra da Coréia (1951-52) encontrou-se algum grau de EG, embora não fosse esta, necessariamente, a causa mortis de todos eles. Na pesquisa de Mudd et al.(35), a ocorrência de EG em autópsias realizadas após traumas graves foi de 68%. Capan et al.(22), em sua extensa e recente revisão, observaram que a EG fora detectada em até 95% das mortes por trauma com fratura de ossos longos e/ou de bacia. Já Estébe(8), numa outra ampla e também recente revisão de literatura, observou que o achado de EG em autópsias de mortes por trauma variava entre 40 e 100% (média = 80%). Por outro lado, Saldeen et al.(36) verificaram que a EG era também encontrada em cerca de 30% das autópsias de mortes não traumáticas, embora os êmbolos aqui ocorressem em menor quantidade e nunca maciçamente como nos casos de SEG. Esse aspecto será discutido mais adiante em “Fisiopatologia”, mas podemos adiantar que nesses casos os êmbolos gordurosos se formam no próprio plasma em virtude das alterações hormonais que sucedem as “situações de estresse” como as extensas cirurgias, por exemplo. É importante salientar aqui que nem sempre a detecção de EG à autópsia implica em que esta tenha sido a causa do óbito. Na imensa maioria dos casos supracitados de “situações de estresse”, a causa do óbito era bem definida e a EG foi apenas um achado incidental e pouco significativo(8,22,26,32,34). êmbolos gordurosos se formam no próprio plasma em virtude das alterações hormonais que sucedem as “situações de estresse” como as extensas cirurgias, por exemplo. INTRODUÇÃO É importante salientar aqui que nem sempre a detecção de EG à autópsia implica em que esta tenha sido a causa do óbito. Na imensa maioria dos casos supracitados de “situações de estresse”, a causa do óbito era bem definida e a EG foi apenas um achado incidental e pouco significativo(8,22,26,32,34). Embora a SEG costume ocorrer principalmente após fraturas de ossos longos e da bacia em traumas e alta energia(8,22,32,36,38), também têm sido descritos, embora raramente, casos de SEG grave ou mesmo fatal, após traumas relativamente leves que causaram fratura de úme- ro, de tornozelo, de corpo vertebral, de costelas e de esterno(8,38-40). Aliás, vale aqui salientar que até mesmo a massagem cardíaca externa gera consideráveis graus de EG, a qual foi detectada em 40 a 85% de casos autopsiados(8,35). Outros procedimentos ortopédicos ainda mais leves, como a manipulação do alongador de Wagner, por exemplo, também já chegaram a causar SEG fatal(13). De modo semelhante, aqui, em nosso Serviço, tivemos a oportunidade de surpreender dois casos de SEG grave após a simples injeção de aspirado medular em foco de pseudoartrose. Recentemente a SEG foi descrita até mesmo após procedimentos estéticos, como a lipoaspiração(41,42) e a injeção de gordura autóloga peri-nasal(43), porém em um número muito restrito de casos. Apesar do extenso traumatismo provocado pela cânula de lipoaspiração, a EG resultante quase sempre é de pequena monta, quando comparada à que ocorre nas fraturas. O motivo desta diferença é que nos ossos as vênulas e si- nusóides, por terem suas paredes acoladas às trabéculas do osso, tendem a permanecer abertas após sua ruptura, ao passo que no tecido subcutâneo esses vasos tendem a se colabar, o que dificulta a embolização(8,44,45). Por outro lado, enquanto que nas fraturas e artroplastias os êmbolos gordurosos sejam originários da gordura do canal medular, nos traumatismos de partes moles eles provêm, como seria de se esperar, da própria gordura subcutânea. Do ponto de vista bioquímico, entretanto, tanto as células da gordura medular quanto as do tecido subcutâneo apresentam o mesmo tipo de gordura, assim chamada “neutra”(5,6,8,16,22,46). Seria ainda importante ressaltar que na EG os êmbolos gordurosos não são formados por fragmentos macro ou microscópicos de tecido adiposo, mas sim por gotículas de gor- dura neutra, dos mais variados diâmetros, mas medidos em micra, as quais circulam em suspensão no sangue até obstruir arteríolas e capilares do pulmão ou de outros órgãos. ETIOPATOGENIA A simples fresagem do canal medular já causa grandes elevações da PIM, a qual pode atingir valores de até 650 mmHg(9). Neste mesmo estudo os autores observaram que com PIM maior que 150 mmHg a intensidade da EG era dez vezes maior que quando a PIM era menor que 150 mmHG. Conseqüentemente, em todo paciente submetido à fresagem do canal medular ocorre EG já nesta fase da operação(7,48,50,52,53). Em condições experimentais foi ainda verificado que o grau de EG decorrente da fresagem era até maior que o causado pela própria fratura(52). Do ponto de vista de função pulmonar (medidas do ‘shunt’ e da PaO2), entretanto, esse grau de EG não chegou a provocar alterações relevantes(7,9,50). Se por um lado a fixação de fraturas com placas praticamente não causa EG, já que não requer manipulação do canal medular, as fixações com pino intramedular são importante causa de EG(8,9,16,51,54,55). Embora a EG que ocorre durante a fresagem geralmente seja de pequena intensidade, durante a inserção de um pino intramedular, entretanto, ocorre acentuada EG em até 87% dos casos(16). Esse fato, embora já reconhecido, foi também recentemente comprovado pela ECO-TE(7). Por este motivo, tendo em vista que no restante da operação (pino ou prótese intramedular) certamente ocorrerá intensa EG, a maioria dos autores têm recomendado a utilização de fresas ‘acaneladas’ ou “sulcadas” (“fluted rods”, na literatura inglesa) que evitam grandes aumentos da PIM e, portanto, menor quantidade de êmbolos nesta fase da operação(8,9,16,51,54,55). Finalmente, devemos esclarecer que embora a EG e a SEG ocorram predominantemente em pacientes ortopédicos(8,16,22,32), existe uma vasta gama de situações clínicas nas quais elas podem se manifestar espontaneamente, isto é, independentemente de trauma externo ou cirúrgico. Apesar de se tratar de eventos raros, essas possibilidades não poderiam deixar de ser aqui mencionadas: septicemias, infusão de Intralipid, crises da anemia falciforme, pancreatites, diabetes, es- teatose hepática, corticoterapia prolongada, queimaduras extensas, descompressão atmosférica súbita, transfusões de sangue maciças, transplante de medula óssea, transplante renal, circulação extra-cor- pórea, e neoplasias ósseas intramedulares que aumentam a pressão dentro desse canal(8,16,22,32). O primeiro fato que nos chama a atenção nesta tabela é que em praticamente todos os pacientes com fratura de ossos longos ou bacia, assim como naqueles submetidos a artroplastias do joelho ou do quadril, ocorre embolia gordurosa. Por outro lado, é igualmente notável que em apenas uma pequena percentagem deles a EG evolui para SEG. “Fase Mecânica”: Esta é a fase em que os êmbolos gordurosos (gotículas de gordura neutra) entram na circulação venosa e se alojam nos capilares pulmonares. A quantidade de êmbolos varia muito, dependendo da energia e extensão do trauma, do osso envolvido, do tipo de fratura (as expostas causam menos EG) e dos procedimentos ortopédicos utilizados (fresagem, pinos e próteses). Como já mencionado, a gran- de maioria dos pacientes sujeitos à EG não apresenta sintomatologia grave, a despeito de intensas embolias, pois nesses pacientes o efeito é apenas mecânico, ou seja, a simples oclusão temporária de parte da rede capilar pulmonar(5-7,11,27,48,49). Por outro lado, se a EG for maciça a ponto de obstruir cerca de 80% da rede capilar pulmonar(13) haverá grande elevação da pressão da artéria pulmonar e, conse- qüente, insuficiência aguda do ventrículo direito (“cor-pulmonale” agudo), com rápida evolução para o óbito(1,2,5,10,15,49,50). Isso, num jovem normal, ao passo que num paciente idoso e/ou com menor reserva cardio-pulmonar, o ‘cor-pulmonale’ provavelmente se instale após embolias bem menos extensas(1,2,11,48). Estudos clínicos e expe- rimentais demonstraram amplamente que os êmbolos gordurosos aparecem nos capilares pulmonares poucos segundos após uma fratura ou manipulação do canal medular(22,32). Recentemente, com o uso da ECO-TE trans-operatória, observou-se que mesmo leves toques de martelo ou cinzel na diáfise de um osso já são suficientes para iniciar pequenos graus de EG. A causa primária de toda EG de origem óssea é o súbito aumento que se verifica na pressão que existe dentro do canal medular, ou seja, a pressão intra-medular (PIM). Quando um indivíduo é sujeito a um trauma de alta energia, ocorre uma grande deformidade dinâmica do osso e, conseqüente- mente, um grande aumento da PIM, logo antes da fratura(18). Nesse momento rompem-se também os vasos da medula óssea, bem como suas células adiposas, do que resulta a liberação de uma grande quantidade de gotículas de gordura que serão embolizadas através das vênulas e sinusóides do canal medular. Os sinusóides parecem mais propensos a receber os êmbolos pois, tendo suas paredes aderidas às trabéculas ósseas, permanecem sempre abertos e não sofrem colapso como as vênulas(8,45,51). Medições da PIM em huma- nos anestesiados mostram valores normais que oscilam entre 30 a 50 mmHg(16,51). Sabe-se, entretanto, que com valores da PIM entre 50 e 100mmHg já pode ocorrer EG(8,9). ETIOPATOGENIA As principais causas de EG e, conseqüentemente, de SEG, são as fraturas metafisárias do fêmur, e da tíbia e as da pelvis (Tabela 1). Na prática cirúrgica atual, entretanto, são também freqüentes os casos de EG e de SEG durante ou após as artroplastias do joelho e do quadril (Tabela 1), bem como nas instrumentações da coluna vertebral, sobretudo quando se utilizam os parafusos pediculares(33). Mais recentemente, tem-se dado maior importância também à EG derivada dos traumatismos graves do tecido subcutâneo, como soe acontecer nos ferimentos descolantes extensos, bem como nos traumas fechados de partes moles (quedas e espancamentos), os quais podem evoluir com SEG até mesmo fatal(2,8,35,36,44). Num estudo de autópsias realizadas em 53 casos de morte por espancamento (apenas quatro tinham fraturas) Hiss et al.(34)concluíram que a causa do óbito foi EG maciça em 32 casos (60%) e que em apenas 28% deles (15 casos) a morte se deveu a hemorragias internas. Por esses achados, os autores não só chamaram a atenção para a freqüência e gravidade da EG nos casos de espancamento, como reforçaram a observação de que a EG só não é encontrada em autópsias pós- trauma quando a morte sobrevém na cena do acidente ou até 4h após. A incidência de EG pós-trauma, entretanto, varia muito entre as experiências publicadas, provavelmente em função desse ‘fator-tem- po’, bem como da apreciação que se faz do grau da EG encontrada nas autópsias. Segundo Masson et al.(37), em 93% das autópsias dos 197 SEG(4-6,15,33). A intensidade da EG depende da manobra cirúrgica em questão: fresagem (‘reaming’), na literatura inglesa), pinos intrame- dulares (‘nailing’, na literatura inglesa) ou a inserção de próteses de joelho ou de quadril, com ou sem cimentação. Através da ECO-TE observa-se que enquanto não há manipulação do canal medular as câmaras cardíacas mostram-se preenchidas apenas com sangue. Com o início da fresagem, todavia, aparecem sinais hiperecóicos, que dão uma imagem comparável à de uma “tempestade de neve”, ao passo que durante a cimentação tanto o átrio como o ventrículo direito tornam-se totalmente opacificados pelos êmbolos gorduro- sos(5,6,14,15,33). Muito recentemente foi constatado, também através da ECO-TE trans-operatória, que mesmo a simples inserção de parafu- sos pediculares nas operações sobre a coluna vertebral provocavam EG de intensidade comparável às observáveis durante a inserção de próteses de joelho e de quadril, embora neste estudo pioneiro não tenham ocorrido efeitos tão deletérios quanto os já observados nas artroplastias(33). FISIOPATOLOGIA Embora a gênese da SEG seja um fenômeno extremamente com- plexo, seu desenvolvimento pode ser encarado como se ocorresse em duas fases distintas, porém interligadas: a primeira seria a “Fase Mecânica”, e a segunda seria a “Fase Bioquímica” (1,2,8,22,25,46,47). ETIOPATOGENIA O porquê deste fato, todavia, ainda não foi esclarecido, isto é: “por quê tanta EG e tão pouca SEG?”. Um outro fato que nos chama bastante a atenção nesta tabela é a enorme variação na incidência de SEG entre os diferentes autores: 0,25 a 30% de SEG nas fraturas múltiplas, por exemplo. Conforme veremos mais adiante, parece que a melhor explicação para essas discrepâncias seja a utilização de diferentes critérios para se diagnosticar essa síndrome. ACTA ORTOP BRAS 13(4) - 2005 “FASE BIOQUÍMICA” Curiosamente, “como se a EG fora um fenômeno fisiológico espera- do”, as células alveolares dos pulmões foram dotadas da capacidade de produzir lipase. Assim, mal as gotículas de gordura chegam e obstruem os capilares pulmonares, já começam a ser hidrolisadas pela lipase pulmonar que, em geral, elimina os êmbolos gordurosos em cerca de três dias(25,47). A hidrólise da gordura embolizada nos pulmões, entretanto, libera ácidos graxos (palmítico, esteárico e oleico), os quais normalmente são neutralizados e transportados pela albumina. Talvez essa neutralização pela albumina sérica contribua para que a grande maioria dos pacientes que sofreram EG não apresentem sintomas, isto é, não desenvolvam a SEG. Por motivos ainda não bem esclarecidos, contudo, numa pequena porcentagem de pacientes com fraturas de ossos longos ou bacia, assim como naqueles submetidos a artroplastias, a hidrólise da gordura retida nos capilares pulmonares libera aqueles mesmos ácidos graxos que, inesperadamente, acabam por provocar graves lesões nos alvéolos e capilares pulmonares. Tanto isso é verdade que, uma das maneiras mais eficientes de se provocar e reproduzir uma ‘SARA’ em animais de laboratório, é exatamente através da injeção intravenosa de ácido oléico(8,16,32,67-69). Já em 1956 Peltier(25) postulava que os ácidos graxos exerceriam uma ação lesiva direta sobre as células alveolares e en- doteliais. Como existe uma grande concentração de ions cálcio nas junções intercelulares, e como os ácidos graxos têm grande afinidade por este elemento, Peltier(25) sugeriu que os ácidos se uniriam aos ions Ca++, do que resultaria a ruptura das junções intercelulares e, conseqüentemente, a instalação de áreas difusas de hemorragia e edema no interstício e alvéolos pulmonares. O papel dos neutrófilos na gênese dessas lesões, contudo, é imprescindível, conforme se verificou mais tarde(3,14,34,67). Estudos recentes a esse respeito vieram não só comprovar aquelas observações como acrescentar dados histoquímicos de grande relevância: Mastrangelo et al.(70) observaram que as beta-2 integrinas CD11b/CD18 (proteínas que aumentam a adesividade entre membranas celulares) dos neutrófilos pulmonares tinham sua ‘expressão’ bastante aumentada após a injeção intra- venosa de ácido oléico. Isto é, na presença de ácidos graxos livres ocorria acentuação da aderência entre os neutrófilos e o endotélio do capilar pulmonar às custas daquelas integrinas. A seguir, o que se A ocorrência de EG em reoperações de prótese de quadril é as- sunto ainda pouco conhecido. “Fase Mecânica”: Considerando- se que quanto maior a PIM, maior a intensidade da EG detectada à ECO-TE, bem como maior a quantidade de gordura encontrada no sangue colhido da veia femoral do lado operado(16,27,39), é de se esperar que justamente na fase de cimentação das próteses é que ocorram as alterações cárdio-respiratórias mais intensas, o que de fato acontece. Na literatura consultada são numerosos os relatos de parada cardíaca e/ou de morte secundárias à EG no intra-operatório de artroplastias, tendo-se observado que a descompensação dos pacientes sempre se iniciava no momento da cimentação da prótese(8,10,11,19,48,53). Woo et al.(49) ao reverem a experiência com artroplastia total de quadril (ATQ) de diversos centros e analisando casuísticas que variavam entre 400 e 2012 operações, encontraram uma incidência de parada cardíaca intra-operatória de 0,6 a 10%, e uma mortalidade de 0.02 a 0,5%. Já Pitto et al.(11), em sua revisão, observaram que num grupo de14469 casos de ATQ com cimento houve 23 óbitos (0,16%), enquanto que no grupo de 15411 operações de ATQ sem cimento não houve nenhum óbito. Esses mesmos autores observaram ainda um outro aspecto que se mostrou de grande importância prática: 21 dos 23 pacientes que faleceram, no grupo de próteses cimentadas, tinham doença cardíaca e/ou pulmonar pré-existentes. Ou seja, embora a EG que inevitavelmente ocorre nas artroplastias seja geralmente bem tolerada pelos pacientes com boa função cardíaca e respiratória, ela pode ser fatal em pacientes com grave comprometimento dessas funções. Existem, todavia, táticas e técnicas cirúrgicas que podem atenuar esse risco, as quais serão discutidas mais adiante no item sobre prevenção. uma significativa diminuição da função do ventrículo esquerdo nos pacientes que receberam próteses cimentadas, alterações essas que persistiram por cerca de 2h após a cimentação(57). Além disso, um desses cinco pacientes acabou desenvolvendo franca SEG, predo- minantemente cerebral (confusão mental e insuficiência respiratória) 3h após a operação. Vários estudos clínicos e experimentais mais re- centes têm confirmado que a ATJ bilateral causa maior sangramento, mais arritmias cardíacas e mais EG que as operações unilaterais. A utilização de novas táticas cirúrgicas, como a prática do alargamento do orifício de entrada no fêmur distal (“overdrill”) associadas às fresas ranhuradas (“fluted rods”), entretanto, têm diminuído sensivelmente a gravidade da EG nos pacientes submetidos à ATJ bilateral, embora essa complicação não tenha sido de todo abolida(48,53,55,62). ACTA ORTOP BRAS 13(4) - 2005 “Fase Mecânica”: Deve ainda ser mencionado que mesmo nos pacientes submetidos à colocação de próteses condilares (que são extramedulares) persiste o risco de ocorrer EG, a qual, nesses casos, é desencadeada pela inserção das hastes de alinhamento(66). Considerando-se que essas hastes são usadas para manipulação intra-medular, elas também provocam aumento da PIM e, conse- qüentemente, podem desencadear EG(55,62,63). Finalmente, vale aqui mencionar a recomendação desses autores a de que a indicação de ATJ, uni ou bilateral, depende da capacidade do paciente tolerar ou não os efeitos do sangramento e da EG que são inevitáveis nessas operações. Noutras palavras, a indicação depende da reserva car- diovascular e respiratória de cada paciente. Kolettis et al.(55) relataram que chegaram mesmo a suspender o prosseguimento de uma ATJ bilateral depois que graves alterações hemodinâmicas ocorreram durante a colocação da prótese em um dos joelhos. Essa mudança de conduta intraoperatória só foi possível porque o paciente estava monitorizado com um cateter de Swan-Ganz, que permitia a medi- ção contínua da pressão da artéria pulmonar e do débito cardíaco. Desde então, esse tipo de monitorização passou a fazer parte da rotina desses autores ao realizar uma artroplastia em todo e qualquer paciente de alto risco. Ainda com relação às próteses, um outro aspecto que permaneceu em controvérsia durante longo tempo foi o do possível papel do cimento acrílico (metilmetacrilato) na gênese das graves alterações hemodinâmicas e respiratórias que acompanham as artroplas- tias(10,48,49,53). De fato, é sabido que o metilmetacrilato pode exercer ações vasodilatadora periférica e depressora do miocárdio(48,50,53), mas Homsy et al.(63) demonstraram tanto em cães como em seus pacien- tes, que nas quantidades habitualmente utilizadas nas artroplastias (2g/Kg de peso), o cimento acrílico atinge concentrações séricas que são 40 a 50 vezes menores que as necessárias para desencadear efeitos tóxicos cardiovasculares. Outros autores relataram ainda que em muitos de seus pacientes nos quais a concentração sérica de metilmetacrilato foi pesquisada no intra operatório de ATQ ou de ATJ o resultado foi negativo, isto é, não havia metilmetacrilato detectável em circulação(3,48,53,60,63). “Fase Mecânica”: Embora as fraturas de ossos longos e bacia sejam as principais causas de EG e SEG, estudos recentes utilizando a (ECO-TE) trans-operatória têm demonstrado que toda e qualquer manipulação cirúrgica do canal medular é seguida de EG, de maior ou menor grau, a qual pode ou não evoluir para Com efeito, medições intra-operatórias da PIM(9,48,55), bem como a uti- lização da ECO-TE(1,2,7,11,14,15,56) têm permitido observar que episódios maciços e prolongados de embolização gordurosa ocorrem princi- palmente na fase de inserção e cimentação das próteses de joelho ou de quadril, em todos os casos estudados(1,2,9-11,48,53,57). Durante a cimentação das próteses a PIM pode chegar a atingir valores de 650 a 1500 mmHg(7-9) e a embolização pode persistir por mais que 20 min(5,6,15,33). Embora, felizmente, a grande maioria desses pacientes acabe não desenvolvendo o ‘cor-pulmonale’ agudo durante a fase mais intensa da EG, eles invariavelmente apresentam profundas alterações hemodinâmicas e respiratórias nesse período, tais como: hipotensão arterial severa, arritmias cardíacas, aumento da pressão da artéria pulmonar e da resistência vascular pulmonar, aumento do ‘shunt’ arterio-venoso pulmonar e, conseqüente, diminuição da PaO2(6,7,9,15,17,30,99). Esses efeitos podem durar apenas alguns minutos, ou persistir por muitas horas no pós-operatórios(5-7,55,58). Também é interessante assinalar que essas alterações cardiopulmonares variam de acordo com a intensidade das imagens de embolismo mostradas pelo ECO-TE(5,6,14,59). Em termos de morbi-mortalidade, são muitas as evidências de que as próteses cimentadas são as que oferecem os maiores riscos de EG maciça per-operatória e de SEG grave no pós-operatório(1,2,7,11,17,46,48,53,58). Já as próteses não cimentadas, por aumentarem muito pouco a PIM, são raramente acompanhadas de EG de grande monta e, conseqüentemente, causam muito menos alterações cárdio-respiratórias e SEG(9,11,17,48,53,60). Em estudo clínico bem controlado, Ries et al.(48) observaram que em seus nove casos de próteses cimentadas o ‘shunt’ intrapulmonar aumentou 28%, em média, enquanto que nos 23 casos de próteses não cimentadas não houve alterações significativas daquele parâmetro. Na experiência de Pitto et al.(11), as alterações do ‘shunt’ foram de 24% e de 2%, respectivamente aos dois tipos de prótese. Trabalhos experimentais em cães(61), bem como o monitoramento pré-operatório com ECO- TE permitiram demonstrar ainda que na inserção das próteses de 198 quadril cimentadas, a EG não só é mais volumosa como também bastante mais prolongada que a verificada com as próteses não cimentadas(7,11,27,48,49,53,61). “Fase Mecânica”: Experimentos ‘in vitro’ permitiram constatar que na inserção das próteses com cimento a ‘PIM’ chegava a atingir valores de até 3190 mmHg, enquanto que na inserção das hastes não cimentadas a ‘PIM’ atingia, no máximo, 125 mmHG(11). Considerando- se que quanto maior a PIM, maior a intensidade da EG detectada à ECO-TE, bem como maior a quantidade de gordura encontrada no sangue colhido da veia femoral do lado operado(16,27,39), é de se esperar que justamente na fase de cimentação das próteses é que ocorram as alterações cárdio-respiratórias mais intensas, o que de fato acontece. Na literatura consultada são numerosos os relatos de parada cardíaca e/ou de morte secundárias à EG no intra-operatório de artroplastias, tendo-se observado que a descompensação dos pacientes sempre se iniciava no momento da cimentação da prótese(8,10,11,19,48,53). Woo et al.(49) ao reverem a experiência com artroplastia total de quadril (ATQ) de diversos centros e analisando casuísticas que variavam entre 400 e 2012 operações, encontraram uma incidência de parada cardíaca intra-operatória de 0,6 a 10%, e uma mortalidade de 0.02 a 0,5%. Já Pitto et al.(11), em sua revisão, observaram que num grupo de14469 casos de ATQ com cimento houve 23 óbitos (0,16%), enquanto que no grupo de 15411 operações de ATQ sem cimento não houve nenhum óbito. Esses mesmos autores observaram ainda um outro aspecto que se mostrou de grande importância prática: 21 dos 23 pacientes que faleceram, no grupo de próteses cimentadas, tinham doença cardíaca e/ou pulmonar pré-existentes. Ou seja, embora a EG que inevitavelmente ocorre nas artroplastias seja geralmente bem tolerada pelos pacientes com boa função cardíaca e respiratória, ela pode ser fatal em pacientes com grave comprometimento dessas funções. Existem, todavia, táticas e técnicas cirúrgicas que podem atenuar esse risco, as quais serão discutidas mais adiante no item sobre prevenção. quadril cimentadas, a EG não só é mais volumosa como também bastante mais prolongada que a verificada com as próteses não cimentadas(7,11,27,48,49,53,61). Experimentos ‘in vitro’ permitiram constatar que na inserção das próteses com cimento a ‘PIM’ chegava a atingir valores de até 3190 mmHg, enquanto que na inserção das hastes não cimentadas a ‘PIM’ atingia, no máximo, 125 mmHG(11). “FASE BIOQUÍMICA” Antes e após um teste de estresse com bicicleta ergométrica, foram colhidas amostras de sangue para cerca de 50 análises, as quais incluíram uma minuciosa avaliação dos sistemas da coagulação sangüínea, bem como um completo estudo do meta- bolismo hormonal, glicídico, lipídico, proteico e mineral. Dentre todos os testes avaliados, foram poucas as diferenças significativas: 1) A glicemia dos pacientes que haviam tido SEG tendia a aumentar, e não a diminuir, como seria o esperado durante o esforço. Foi ainda observado que dentre os 10 que tiveram SEG, cinco tinham ascen- dentes com diabetes, 2) a relação entre as lipoproteinas alfa e beta era menor nos casos que tiveram SEG, 3) o número de plaquetas era maior nos casos que tiveram SEG, 4) o teste de fragilidade ca- pilar foi anormal apenas nos pacientes que haviam tido SEG. 5) o nível de cortisol era menor nos casos que não tiveram SEG. Embora o estudo não tenha sido conclusivo, já se pôde ter a suspeita de que alterações metabólicas intrínsecas a determinados indivíduos podem torná-lo susceptível ao desenvolvimento da SEG após um episódio de EG. A diminuição do volume alveolar funcionante torna-se ainda mais extensa em virtude da formação de áreas de atelectasia, já que os pneumócitos lesados deixam de produzir o surfactante(25,68). Ainda com respeito às lesões pulmonares, Gossling e Pellegrini(13) obser- varam ser comum a formação de trombos mistos, constituídos por gordura + plaquetas + leucócitos + fibrina, que também obstruíam capilares pulmonares. Sugeriu, então, que a partir desses trombos ocorreria a liberação de serotonina pelas plaquetas, a qual, por cau- sar venoconstrição, provocaria congestão pulmonar. Por outro lado, lembrou que a partir dos mastócitos ocorreria também a liberação de histamina, o que causaria broncoconstrição, dificultando ainda mais a ventilação pulmonar(1,2,13). O resultado final de toda essa complexa cadeia de alterações celulares e fisicoquímicas é, portanto, o esta- belecimento de extensas áreas de pulmão nas quais os alvéolos são perfundidos mas não ventilados (“efeito shunt”) e outras nas quais ocorre o inverso, isto é, existem alvéolos que são ventilados mas não perfundidos (“efeito espaço-morto”). A conseqüência direta do ‘efeito shunt’, como se sabe, é a queda progressiva da PO2 arterial (PaO2), enquanto que o ‘efeito espaço-morto’ tende a aumentar progressivamente a PaCO2. A fisiopatologia da SEG, entretanto, não se limita às alterações acima descritas. “FASE BIOQUÍMICA” Como esta síndrome geralmente ocorre em decorrência de um trauma externo ou cirúrgico, que por si só já é acompanhado de inúmeras alterações hormonais, celulares, hemodinâmicas, imu- nológicas e da coagulação sangüínea, muitas das manifestações associadas à SEG podem, na verdade, decorrer do próprio trauma e não da EG per se(3,8,16,22,35,54). As alterações metabólicas pós-trauma, genericamente conhecidas como “Resposta Inflamatória Sistêmica”(69) ou “Resposta Metabólica ao Trauma”(71) têm, de fato, provocado sérias controvérsias em seus vários aspectos. No confronto com a fisiopa- tologia da EG, a primeira controvérsia em relação à do trauma vem do fato de a adrenalina, liberada em qualquer situação de estresse, ter entre suas ações a capacidade de mobilizar gordura depositada e daí liberar ácidos graxos na circulação. Embora este fato já tenha sido usado como um argumento a favor da “Teoria da Origem Sé- rica” da SEG, logo ficou comprovado que não só a quantidade de gordura mobilizada pelas catecolaminas era insuficiente para causar a SEG(64,72,73) como foi reiteradamente comprovado que a gordura embolizada provinha mesmo da medula óssea(23). As evidências a esse favor são: 1) O encontro freqüente de tecido medular em meio aos êmbolos gordurosos(7-11), 2) A observação constante de êmbolos gordurosos no sangue aspirado do átrio direito ou da veia femoral do lado que está sendo operado(2,5-7,9,51). 3) Experimentalmente, pela marcação da gordura medular com isótopos radioativos, os quais são detectados nos pulmões segundos após qualquer manipulação intra-medular(23), 4) A coincidência das manipulações intra-medulares com as imagens trans-operatórias da ECO-TE, conforme já ampla- mente comentado. á é “FASE BIOQUÍMICA” Antes e após um teste de estresse com bicicleta ergométrica, foram colhidas amostras de sangue para cerca de 50 análises, as quais incluíram uma minuciosa avaliação dos sistemas da coagulação sangüínea, bem como um completo estudo do meta- bolismo hormonal, glicídico, lipídico, proteico e mineral. Dentre todos os testes avaliados, foram poucas as diferenças significativas: 1) A glicemia dos pacientes que haviam tido SEG tendia a aumentar, e não a diminuir, como seria o esperado durante o esforço. Foi ainda observado que dentre os 10 que tiveram SEG, cinco tinham ascen- dentes com diabetes, 2) a relação entre as lipoproteinas alfa e beta era menor nos casos que tiveram SEG, 3) o número de plaquetas era maior nos casos que tiveram SEG, 4) o teste de fragilidade ca- pilar foi anormal apenas nos pacientes que haviam tido SEG. 5) o nível de cortisol era menor nos casos que não tiveram SEG. Embora o estudo não tenha sido conclusivo, já se pôde ter a suspeita de que alterações metabólicas intrínsecas a determinados indivíduos podem torná-lo susceptível ao desenvolvimento da SEG após um episódio de EG. complicação freqüente em politraumatizados, independentemente de estes terem ou não apresentado EG(22,75). Hoje em dia, portanto, considera-se que a CIVD e a SEG sejam duas condições mórbidas independentes, mas que podem coexistir num mesmo paciente, o que certamente compromete seu prognóstico. observou foi que os neutrófilos fixados ao endotélio liberavam enzimas proteolíticas de seus lisossomos (especialmente a mieloperoxidase) as quais acabavam por ‘digerir’ as células endoteliais e alveolares. Desta forma, temos aqui a ação lesiva indireta dos ácidos graxos, que fecha o que se poderia chamar de ‘teoria atual’ da gênese da lesão pulmonar na SEG(13,25,47,67,68,70). q p p g Embora muito já se saiba a respeito da fisiopatologia da SEG, um longo caminho de pesquisas ainda deve ser percorrido antes que se possa responder à intrigante pergunta: “Se todos os pacientes com fratura de ossos longos e bacia apresentam EG, por que apenas uma minoria deles desenvolve a SEG?”. Na tentativa de encontrar essa resposta. Avikainen et al.(77) exploraram extensivamente o perfil metabólico de 20 pacientes jovens que haviam sofrido fratura de fêmur um ano antes, sendo que 10 deles haviam desenvolvido SEG, mas os outros 10, não. “FASE BIOQUÍMICA” Woo et al.(49) relataram o caso de um paciente hígido que foi a óbito durante uma reoperação de ATQ na qual a remoção do cimento estava sendo feita com aparelho de ultrassom. Na autópsia deste paciente foi constatada a presença de EG maciça em seus pulmões. Como não encontraram literatura a respeito, esses autores perpetraram um estudo experimental de ATQ em cães com a finalidade de testar três diferentes técnicas de remoção do cimento: com osteótomo, com “drill” de alta rotação, com ultrassom. Observaram não ter havido diferenças entre os dois primeiros grupos, mas que o uso do ultrassom de fato provocava uma quantidade de EG substancialmente maior quando comparada aos outros métodos. Enfatizaram ainda que a ocorrência de EG não está associada propriamente à composição do cimento (metilmetacrilato), mas sim ao aumento da PIM por ele causada, já que “a EG também ocorre quando o canal medular é preenchido por cera, plastilene ou goma de mascar”, sic(49). Outro ponto a ser analisado diz respeito à viabilidade ou não de se fazer a artroplastia total de joelho(ATJ) bilateralmente, num único tem- po cirúrgico. Samii et al.(57) em 1979, foram os primeiros a estudar as alterações hemodinâmicas e respiratórias nesse tipo de intervenção, baseados tanto nas já conhecidas alterações que ocorriam nas ATQ, bem como em relatos de casos de hipotensão, parada cardíaca e óbito durante as ATJ(48,53,57,64,65) . Nos dez casos de seu estudo (cin- co próteses com cimento e cinco sem) os autores observaram ter ocorrido um acentuado aumento na pressão da artéria pulmonar e 199 complicação freqüente em politraumatizados, independentemente de estes terem ou não apresentado EG(22,75). Hoje em dia, portanto, considera-se que a CIVD e a SEG sejam duas condições mórbidas independentes, mas que podem coexistir num mesmo paciente, o que certamente compromete seu prognóstico. Embora muito já se saiba a respeito da fisiopatologia da SEG, um longo caminho de pesquisas ainda deve ser percorrido antes que se possa responder à intrigante pergunta: “Se todos os pacientes com fratura de ossos longos e bacia apresentam EG, por que apenas uma minoria deles desenvolve a SEG?”. Na tentativa de encontrar essa resposta. Avikainen et al.(77) exploraram extensivamente o perfil metabólico de 20 pacientes jovens que haviam sofrido fratura de fêmur um ano antes, sendo que 10 deles haviam desenvolvido SEG, mas os outros 10, não. ACTA ORTOP BRAS 13(4) - 2005 QUADRO CLÍNICO E DIAGNÓSTICO A SEG é uma afecção que pode acometer tanto os adultos jovens, mais propensos às fraturas advindas de acidentes no trânsito, no trabalho e nos esportes, como os idosos, estes mais sujeitos às fraturas patológicas e às artroplastias. Todavia, embora de ocorrên- cia rara, a SEG tem sido descrita também em crianças entre 5 e 14 anos que sofreram fraturas de ossos longos e bacia(35,40,78). Estima-se, entretanto, que a incidência da SEG em crianças seja cerca de 100 vezes menor que nos adultos, e que isso se deva ao fato de que sua gordura medular apresente uma concentração de trioleina muito menor que a dos adultos(13). q Dependendo do tempo do início dos sintomas em relação ao trauma, e da gravidade destes, a SEG foi classificada em “Aguda Fulminante”, “Sub-Aguda”, ou “Sub-Clínica”(22). A “Aguda Fulminante” é caracterizada pelo quadro acima descrito em ‘Fisiopatologia’, e que ocorre quando pacientes politraumatizados, ou submetidos a artroplastias, são acometidos por uma volumosa carga de EG, gran- de o suficiente para determinar a instalação de um ‘cor-pulmonale’ agudo, o qual geralmente culmina com o óbito(2,9,10,15,34,35,47,49). Caso esses pacientes estejam monitorizados com cateter de Swan-Ganz, observar-se-à o súbito aumento da pressão da artéria pulmonar, da resistência vascular pulmonar e, em decorrência disso, a queda do débito cardíaco(5,6,7,9,12,15). Quando existe forame oval patente, entre- tanto, a morte súbita pode advir de EG cerebral maciça, que causa infartos múltiplos na substância branca da base do encéfalo, bem como do tronco cerebral e do cerebelo(2,5,6,20,22,28,) Outra grande área de controvérsia dentro da fisiopatologia da SEG diz respeito às alterações na coagulação sangüínea. Considerando-se que a gordura tem atividade tromboplástica própria, que as gotícu- las de gordura são rapidamente ligadas a plaquetas, e que o foco de fratura libera tromboplastina tecidual, formulou-se a hipótese de que na EG existiria sempre um estado de coagulação intravascular disseminada (CIVD), e que os trombos mistos, formados por Gor- dura + Plaquetas + Hemácias + Fibrina + Leucócitos, seriam os responsáveis pelo desencadeamento da SEG(4,8,22,32). De fato, não é incomum encontrarem-se alterações laboratoriais com- patíveis com a síndrome da CIVD em alguns casos de SEG(22,27,45,74), embora seja extremamente rara a ocorrência da síndrome hemorrá- gica secundária a esta coagulopatia de consumo(13). Por outro lado, existem séries de casos de SEG bem estabelecidas nas quais os autores não lograram detectar nem mesmo as alterações laboratoriais que caracterizam a CIVD, em nenhum de seus pacientes(30,75). QUADRO CLÍNICO E DIAGNÓSTICO Finalmente, é importante relembrar que pacientes submetidos a transfusões de sangue maciças, ou então sujeitos a longos períodos de hipóxia, tam- bém podem apresentar petéquias, dado este que ganha importante papel nos diagnósticos diferenciais de um politraumatizado(8). p p g p Além de pulmões, encéfalo, pele e conjuntivas, a SEG pode acome- ter gravemente muitos outros órgãos ou estruturas. As retinas são envolvidas em praticamente 50% dos casos (12,13,22). A obstrução dos capilares da retina pelos êmbolos gordurosos pode levar à ocorrência de microinfartos, hemorragias e edema. Embora na grande maioria dos casos essas alterações sejam reversíveis, quando as lesões se instalam na área peripapilar é comum que deixem seqüelas per- manentes, tais como a diminuição da acuidade visual e a presença de escotomas(8,22). Os rins são freqüentemente acometidos na EG, mas a instalação de insuficiência renal aguda é um evento bastante raro(8,22). Gurd e Wilson(20) e Gurd(24) em sua vasta casuística de EG e SEG, detectou oligúria em 17% de seus pacientes, mas anúria em apenas três, os quais necessitaram de hemodiálise. p O cérebro é o segundo órgão mais atingido pela SEG, sendo afe- tado em 70 a 89% dos casos(8,18,22,29,32). As alterações neurológicas, contudo, podem aparecer entre10 a 120h após o trauma(18), e são extremamente variáveis: irritabilidade, ansiedade, agitação, confusão, delírio, convulsões, coma, hipertonia e descerebração são todos qua- dros já descritos, quer de maneira progressiva num mesmo paciente, quer isoladamente entre os diferentes casos. As alterações patoló- gicas responsáveis por esses sintomas são as obstruções capilares difusas provocadas pelos êmbolos gordurosos. Dessas obstruções resultam áreas de hipóxia, isquemia e hemorragias petequiais, estas em virtude da rotura dos capilares que sofreram a ação dos ácidos graxos e neutrófilos, à semelhança das lesões que ocorrem nos pulmões(8,21,22,51). Essas alterações são sempre seguidas de edema cerebral, podendo ainda haver o estabelecimento de verdadeiros infartos cerebrais nas regiões mais afetadas, que são a substância branca da base do cérebro, do tronco cerebral e do cerebelo. Embora as manifestações neurológicas geralmente denotem acometimento difuso em cerca de 12 a 25% dos casos, a SEG cerebral se manifesta por sinais de localização como anisocoria, afasia, apraxia, hemiplegia, paraplegia, tetraplegia, escotomas e desvio conjugado dos olhos(8,80). QUADRO CLÍNICO E DIAGNÓSTICO em T1 e alto sinal em T2 nas áreas acometidas, podendo detectar lesões a partir de 2mm de diâmetro(8,16,21) e em tempo tão hábil quanto o de 4h após um trauma(8,16,21,76). Na RMC, as áreas de alto sinal em T2 são tidas como características da SEG e indicam a presença de edema perivascular secundário à isquemia e à hipóxia(21,80). Outro importante aspecto da RMC diz respeito ao seu alto valor preditivo- negativo, ou seja, se o exame for normal a hipótese diagnóstica de SEG pode ser afastada(21). As petéquias cutâneas representam o terceiro sinal mais importante para o diagnóstico para o diagnóstico clínico da SEG. Essas diminutas lesões (1 a 2mm)são na verdade pequenas hemorragias originadas pela ruptura dos capilares da pele(1,2,19,20,24,31,79). De acordo com exames histológicos, os capilares seriam primeiro distendidos pelos êmbolos gordurosos e a seguir lesados pela ação dos ácidos graxos liberados(16,22,45). Assim, ao contrário do que se pensava inicialmente, a ocorrência das petéquias não guarda relação com a de plaquetopenia, que ocorre em cerca de 30% dos casos de SEG(8,20,22,24,32). As petéquias são bastante mais comuns, mas a menção de seu encontro tem variado entre 25% a 95% dos casos, segundo a extensa e recente revisão de Estebe et al.(8). Na maioria dos estudos publicados, contudo, essa incidência fica geralmente entre 40 e 60% dos casos(1,2,8,18-20,24,31,32,79). Também o tempo de aparecimento das petéquias em relação ao trauma varia bastante. São descritos intervalos de 12h até 96h após fraturas de ossos longos ou de bacia(22), embora seja mais característico que elas sejam detectadas entre 36 e 72h após o trauma(8). A localização das petéquias na SEG também demonstra um padrão característico, pois quase sempre são encontradas nas axilas, na região pré-esternal alta, nas faces laterais do pescoço e nas conjuntivas oculares(20,22,24,79). Em se tratando de lesões tão diminutas, porém, somente através de um exame clínico muito atento e suspeitoso, e num ambiente bem iluminado, é que as petéquias poderão ser detectadas. Mesmo assim, muitas vezes o seu encontro pode requerer até mesmo o uso de uma lupa(20). Outro importante dado clínico em relação às petéquias é que elas não duram muito tempo, sendo geralmente reabsorvidas em cerca de uma semana após o seu aparecimento(8,22). ACTA ORTOP BRAS 13(4) - 2005 QUADRO CLÍNICO E DIAGNÓSTICO Tipicamente, no tipo de SEG ‘Sub-Aguda’, o quadro clínico se inicia por taquipnéia, que passa a dispnéia e, se não trata- da a tempo, pode logo levar à cianose e finalmente causar a morte do paciente em menos de 24h. A radiografia (RX) do tórax nesses casos mostra um infiltrado bilateral difuso, mas que predomina nas regiões basais e peri-hilares, e costuma aparecer apenas cerca de 24h a 48h após o trauma. Esse aspecto radiológico, embora ‘típico’ da SEG, é encontrado em apenas 30 a 50% dos casos(18,22) e não pode ser considerado patognomônico dessa síndrome, pois pode ocorrer também na congestão pulmonar (por ICC ou hiperhidrata- ção), na contusão pulmonar, nas aspirações traqueobrônquicas do conteúdo gástrico e na SARA. O diagnóstico diferencial geralmente pode ser feito levando-se em conta os antecedentes imediatos e pregressos de cada paciente. A diferenciação com a congestão pulmonar é sugerida quando não há história de cardiopatia, quando o paciente é jovem, a área cardíaca é pequena, e desde que se tenha tido um bom controle sobre o balanço hidreletrolítico, quer se trate de uma ressuscitação pós-trauma, quer de uma artroplastia, por exemplo(8,16,22). Infiltrados semelhantes aos da SEG podem ocorrer em casos de contusão pulmonar, um outro achado freqüente em politraumatizados. Na contusão pulmonar, entretanto, as alterações radiológicas costumam estar presentes já nas primeiras 6h após o trauma, quase sempre são unilaterais, não respeitam a cisura entre os lobos e em geral situam-se diretamente sob a área externa do trauma. Quando o infiltrado da contusão pulmonar aparece bilateralmente, quase sempre existe uma nítida predominância da contusão em um dos pulmões(22,23). O infiltrado pulmonar da SEG deve ainda ser diferenciado aquele que aparece na SARA, que é uma complicação freqüente em politraumatizados, independentemente de terem tido ou não episódios de EG. A SARA, contudo, tende a se instalar mais tarde, aparecendo geralmente dois ou mais dias após o trauma. Existe, portanto, um período de coincidência, já que a SEG também pode iniciar suas manifestações até quatro dias após o trauma(74). A tomografia computadorizada do tórax (TCT) não acrescenta muito à radiografia comum em termos de diagnóstico, embora mostre infil- trados menores e mais precocemente que o RX simples. Obviamente que delimita melhor as áreas pulmonares comprometidas e se presta muito bem a fazer um completo inventário das vísceras intratorácicas e das cavidades pleurais(19,20,22,23). QUADRO CLÍNICO E DIAGNÓSTICO Para a grande maioria dos pesquisadores, portanto, a CIVD é tida como um fenômeno inconstante, que pode ou não ocorrer em conjunto com a SEG(13,27,74,76). Além disso, é bastante conhecido o fato da CIVD ser uma Outra grande área de controvérsia dentro da fisiopatologia da SEG diz respeito às alterações na coagulação sangüínea. Considerando-se que a gordura tem atividade tromboplástica própria, que as gotícu- las de gordura são rapidamente ligadas a plaquetas, e que o foco de fratura libera tromboplastina tecidual, formulou-se a hipótese de que na EG existiria sempre um estado de coagulação intravascular disseminada (CIVD), e que os trombos mistos, formados por Gor- dura + Plaquetas + Hemácias + Fibrina + Leucócitos, seriam os responsáveis pelo desencadeamento da SEG(4,8,22,32). O tipo “Sub-Agudo” é o mais freqüentemente relatado, pois, além se ser bem mais comum que o ‘Agudo Fulminante’, em geral se apresenta com quadro clínico bastante sugestivo. A característica tríade de sintomas é representada pela dificuldade respiratória pro- gressiva, pelas alterações da consciência e/ou do comportamento, e pelas petéquias cutâneas(13,19,20,22,23,31,39,47,74,79). De fato, não é incomum encontrarem-se alterações laboratoriais com- patíveis com a síndrome da CIVD em alguns casos de SEG(22,27,45,74), embora seja extremamente rara a ocorrência da síndrome hemorrá- gica secundária a esta coagulopatia de consumo(13). Por outro lado, existem séries de casos de SEG bem estabelecidas nas quais os autores não lograram detectar nem mesmo as alterações laboratoriais que caracterizam a CIVD, em nenhum de seus pacientes(30,75). Para a grande maioria dos pesquisadores, portanto, a CIVD é tida como um fenômeno inconstante, que pode ou não ocorrer em conjunto com a SEG(13,27,74,76). Além disso, é bastante conhecido o fato da CIVD ser uma Classicamente, os sintomas se iniciam entre 12 e 24h após o trauma, embora não sejam raros os casos em que isto só ocorra após 36 a 72h(8,16,22,23). Gurd et al.(20,24), todavia, num estudo minucioso de 100 casos de SEG, observaram que o tempo de latência entre trauma e sintomas variou entre 4h e 15 dias (média = 46h). Como seria de se esperar, os pulmões comumente são os órgãos mais atingidos, sendo muito raro que isto não aconteça (5,6,8,20,22,24). Conforme já men- cionado, o envolvimento pulmonar decorre do progressivo número 200 de alvéolos que vão sendo preenchidos por sangue e/ou exsudato, ou que sofrem atelectasia, do que resulta um quadro de hipóxia generalizada. QUADRO CLÍNICO E DIAGNÓSTICO Por outro lado, observaram ainda que muitos dos seus pacientes que tinham PaO2 normal também apresentavam plaquetopenia. Ganong et al.(31), em sua série de 100 pacientes com fratura de fêmur ou de tíbia por trauma direto, obser- varam que em nenhum dos seus 21 casos que evoluíram com SEG tinha ocorrido plaquetopenia. Nem, tampouco, queda acentuada do Ht. Enquanto que anemia e plaquetopenia eram anteriormente con- siderados como achados ‘típicos’ de SEG(20,24) os estudos acima co- mentados não só contrariaram os antigos conceitos, como reforçaram a idéia de que tais alterações decorrem mais obviamente do trauma propriamente dito que de uma possível SEG. Em nosso meio, Engel et al.(18) tampouco lograram detectar a ocorrência de plaquetopenia em 61% de seus 19 casos de SEG comprovada , 3) COAGULOPA- TIAS: Embora alguns casos de SEG possam apresentar alterações laboratoriais compatíveis com a CIVD (coagulação intra-vascular disseminada), a síndrome hemorrágica que às vezes se segue a esta coagulopatia de consumo raramente ocorreria na SEG(13). De fato, diversos autores têm encontrado alterações laboratoriais sugestivas de CIVD em muitos de seus pacientes com SEG. As alterações mais freqüentemente descritas têm sido a diminuição da calcemia e das plaquetas, o aumento da adesividade plaquetária, o prolongamento dos tempos de protrombina e de tromboplastina parcial ativada, o aparecimento dos PDF (produtos de degradação da fibrina) e a dimi- nuição do fibrinogênio circulante(8,16,17,20,22,24,27,39,74). Essas alterações, todavia, não ocorrem em todos os casos de SEG(27,30,75) e, quando ocorrerem, em geral são discretas(27,76). Assim sendo, a maioria dos autores mais recentes é da opinião que as alterações laboratoriais sugestivas de CIVD devem ser atribuídas principalmente às alterações da coagulação que usualmente acompanham um trauma grave do que a uma possível SEG(22,74,75). 4) COMPLEMENTO: No passado chegou-se a suspeitar que o “Complemento” estivesse envolvido na gênese da SEG(8,22). Conforme acima comentado, num paciente politraumatizado tanto os sintomas respiratórios quanto os neurológicos podem ter origens outras que não a SEG. A contusão pulmonar e o trauma crânio-en- cefálico, respectivamente, são os exemplos mais comuns dessas situações. Assim, no momento de se pensar nos diagnósticos dife- renciais, o tempo de aparecimento dos sinais e sintomas é um fator de grande importância. Num caso típico de SEG, tanto os sintomas respiratórios (que o correm em praticamente 100% dos casos) como os neurológicos (que ocorrem em cerca de 80% dos casos(8,22,29,32) começam a se manifestar entre 12 e 48h após o trauma. QUADRO CLÍNICO E DIAGNÓSTICO Esse lapso de tempo é atribuído à demora na conversão dos triglicérides da gordura neutra em ácidos graxos livres(23). O aparecimento de petéquias, 24h a 48h após o trauma, praticamente assegura o diagnóstico SEG, principalmente se levarmos em conta que todo esse quadro clínico está sendo considerado em situações bastante específicas, tais como as fraturas de ossos longos ou de bacia, as artroplastias de joelho ou de quadril e os extensos traumas de parte moles. Deve sempre ser lembrado, contudo, que como o quadro clínico da SEG pode ser superponível ao de outras condições pós-traumáticas, e como não existe nenhum teste laboratorial que possa assegurar ou “fechar” esse diagnóstico, a confirmação de uma SEG torna-se muitas vezes difícil, senão impossível. Atualmente, considerando-se um paciente em “situação de risco” para desenvolver SEG, a maioria dos autores tende a já firmar esse diagnóstico desde que o paciente apresente comprometimento respiratório e/ou cerebral, uma vez excluídas as causas mais evidentes para tais sintomas(19,21,29,51,56,79,81,82, 83). p Finalmente, dentro da classificação dos tipos de SEG, existe a forma “Sub-Clínica”, que segundo a revisão de Estebe et al.(8), ocorre em mais de 60% dos casos de fratura de ossos longos. Na opinião de Hoffman(51), entretanto, a SEG Sub-Clínica ocorreria, na verdade, em 100% desses casos, mas que, em virtude de sua extrema benigni- dade, geralmente passa despercebida ou nem mesmo é relatada. A denominação “Sub-Clínica” se deve ao fato de os pacientes apresen- tarem praticamente as mesmas alterações da “forma Sub-Aguda”, mas em intensidade tão menor que geralmente nem se manifestam através de sinais e sintomas. As alterações mais encontradas são um leve a moderado aumento da freqüência respiratória, da freqüência cardíaca e da temperatura, uma discreta diminuição da PaO2, que oscila em torno de 80mmHg. Quanto a PaCO2, que na forma “Sub- Aguda” tende a subir acima de 50mmHg, na forma “Sub-Clínica” tende a baixar até cerca de 30mmHg, em virtude da hiperventilação causada por taquipnéia. Não se observa, portanto, a dispnéia, e os exames laboratoriais demonstram poucas alterações. Quanto a parte neurológica, geralmente há leve sonolência, confusão ou irritabilida- de(74). Por essas razões é que o diagnóstico da SEG “Sub-Clínica é considerado como ‘difícil’ de ser feito, a menos que pesquisado com insistência e observado em detalhes(20,22,24). A SEG ‘Sub-Clínica’ é também muito freqüente após osteossínteses e artroplastias, manifes- tando-se de modo semelhante às observadas após as fraturas(9,56). QUADRO CLÍNICO E DIAGNÓSTICO A exemplo da forma Sub-Aguda, o quadro clínico da forma Sub-Clínica pode se iniciar entre 12 e 72h após o trauma(8), embora o intervalo mais comumente descrito seja o de 12 a 24h(23). Conforme já assi- nalado, a evolução da forma Sub-Clínica é extremamente benigna e sua mortalidade é virtualmente zero(22). g Inúmeros estudos mais recentes, porém, têm demonstrado que em- bora exista um aumento na atividade do “Complemento” após uma EG, esta também ocorre, da mesma forma e intensidade, noutras situações de trauma em que não existem fraturas. Trata-se, portanto, de mais uma alteração laboratorial inespecífica e sem valor para o diagnóstico de SEG(79,84). 5) ÁCIDOS GRAXOS LIVRES (AGL): Boa parte da resposta metabólica hormonal após um trauma grave ou cirurgia extensa consiste numa grande liberação de atecolaminas, cortisol, hormônio do crescimento, prolactina, insulina e glucagon(69). Paralelamente ocorre também um aumento dos níveis séricos de tri- glicérides e de AGL, os quais têm aqui função de aumentar a oferta calórica ao organismo seriamente traumatizado(22,39,73). Quando em circulação, os AGL estão ligados a moléculas de albumina, sendo, portanto, inertes. Apesar de todas as alterações metabólicas pós- traumáticas, porém, freqüentemente surpreendem-se níveis séricos normais ou mesmo diminuídos dos AGL em casos de SEG(8,74). Em- bora o padrão mais típico seja o de aumento dos AGL circulantes após um trauma com fraturas graves, o nível sérico dos AGL não QUADRO CLÍNICO E DIAGNÓSTICO Lindeque et al.(79) valorizaram sobretudo as alterações respiratórias pós-trauma, considerando já haver SEG estabelecida se pelo menos um dos seguintes sinais estivesse presente: 1 ) PaO2 < 60mmHg, 2) PaCO2 > 55mmHg, 3) Dispnéia intensa: freqüência respiratória > 35rpm, respiração laboriosa exigindo o uso de mús- culos acessórios. essas alterações sejam ‘características’ da SEG, elas não são ex- clusivas e muito menos sendo contestados pela experiência ulterior de outros autores. Em 1987, Lindeque et al.(79)publicaram sua experiência com o tratamento de 55 pacientes politraumatizados e com fraturas de ossos longos, dos quais 16 desenvolveram SEG. Puderam então constatar que se tivessem se baseado somente nos “Critérios de Gurd” para firmar o diagnóstico de SEG, apenas sete de seus 16 casos teriam sido identificados. Lindeque et al.(79) valorizaram sobretudo as alterações respiratórias pós-trauma, considerando já haver SEG estabelecida se pelo menos um dos seguintes sinais estivesse presente: 1 ) PaO2 < 60mmHg, 2) PaCO2 > 55mmHg, 3) Dispnéia intensa: freqüência respiratória > 35rpm, respiração laboriosa exigindo o uso de mús- culos acessórios. clusivas e muito menos diagnósticas dessa síndrome: 1) ANEMIA: Como é básico e bem sabido, a diminuição do hematócrito (Ht) é um dos achados mais precoces e esperados após um trauma grave. Nos casos de SEG sem hemorragia aparente, o Ht costuma chegar a níveis de 30% em cerca de 3/4 dos pacientes, já no primeiro ou no segundo dia após o trauma(22,83). Quando na admissão de um paciente o Hematócrito (Ht) não se encontra muito alterado, mas no primeiro ou segundo dia após o trauma este sofre uma queda súbita, esta queda pode se dever tanto às hemorragias pulmonares secundárias à toxicidade dos ácidos graxos, como também advir de muitas outras complica- ções pós-traumáticas como as tromboses extensas, ou as próprias hemorragias intracavitárias, musculares e subcutâneas Embora essas considerações pareçam óbvias, elas estão aqui colocadas frente à tendência de logo se pensar apenas em SEG na vigência de uma que- da súbita do Ht passados um ou dois dias após um trauma(20,25,34,74), 2) PLAQUETOPENIA: É também uma alteração classicamente tida como ‘característica’ da SEG, embora estudos mais numerosos e recentes tenham observado que a plaquetopenia ocorra somente em cerca de 30% dos casos(8,22,32). Riseborough et al.(74)observaram uma diminuição consistente e coincidente das plaquetas com a da PaO2 em seus pacientes com SEG. ACTA ORTOP BRAS 13(4) - 2005 QUADRO CLÍNICO E DIAGNÓSTICO Considerando-se que muitos desses pacientes são politraumatizados e que o encontro de sinais de localização geralmente falem a favor de trauma crânio-encefálico (TCE), é claro que nesses casos uma tomografia computadorizada cerebral (TCC) deverá sempre ser solici- tada para o diagnóstico diferencial com hematomas intracranianos(22). Ao contrário do que ocorre no TCE, todavia, na SEG a TCC não tem qualquer valor diagnóstico, pois mesmo nos casos de SEG cerebral comprovada, a TCC costuma mostrar-se normal ou acusar apenas edema cerebral inespecífico(16,21,22,56,80). Já a ressonância magnética cerebral (RMC) tem se mostrado bastante útil devido a sua alta sen- sibilidade e alta especificidade em detectar as lesões encefálicas da SEG. Caracteristicamente, a RMC mostra alterações de baixo sinal p , q Apesar de típicas, as três principais alterações clínicas da SEG (Insu- ficiência Respiratória, Alterações Neurológicas e Petéquias)não são patognomônicas dessa síndrome, já que ocorrem também amiúde em pacientes politraumatizados não sujeitos à EG. Em 1970, Gurd e Wilson(20) e Gurd(24), baseados no estudo de 100 casos de SEG que trataram num período de quatro anos, estabeleceram uma lista de critérios para o diagnóstico clínico dessa síndrome. De acordo com a análise de sua experiência sugeriram que o diagnóstico de SEG só deveria ser feito quando houvesse pelo menos um sintoma “Major” associado a pelo menos quatro sintomas “Minor”. Os “Sinto- mas Major” seriam a Insuficiência Respiratória Aguda, as Alterações Neurológicas e as Petéquias, ao passo que os “Sintomas Minor” seriam: taquicardia, febre (de 38° a 39°C) alterações da retina, alte- rações urinárias, queda súbita do hematócrito e/ou das plaquetas, aumento na velocidade de hemossedimentação e gordura positiva no escarro. Numa análise mais ampla e tardia desses casos, em 1974(24), esses autores confirmaram suas recomendações quanto àqueles critérios diagnósticos. Apesar de terem trazido importantes contribuições quanto à tentativa de se normatizar os critérios diagnós- ticos na SEG, os trabalhos de Gurd e Wilson(20) e Gurd(24) acabaram 201 sendo contestados pela experiência ulterior de outros autores. Em 1987, Lindeque et al.(79)publicaram sua experiência com o tratamento de 55 pacientes politraumatizados e com fraturas de ossos longos, dos quais 16 desenvolveram SEG. Puderam então constatar que se tivessem se baseado somente nos “Critérios de Gurd” para firmar o diagnóstico de SEG, apenas sete de seus 16 casos teriam sido identificados. EXAMES DE IMAGEM Concluíram também que a positividade de macrófagos com gordura era um achado ines- pecífico, já que esse achado foi muito semelhante tanto entre os 15 pacientes que não desenvolveram SEG como naqueles cinco em que a síndrome se instalou. Por outro lado, chamaram a atenção para o fato de o valor preditivo-negativo desse exame ser bastante elevado. Ainda nesse estudo os autores verificaram fatos novos que poderão vir a ter importância se futuramente confirmados. Observaram que nos cinco pacientes com SEG o número de neutrófilos intra-alveolares era nove vezes maior e que a concentração de albumina no LBA era 12 vezes maior que os respectivos valores dos 15 pacientes sem SEG. Isso mostra, segundo esses autores, que para haver SEG após uma EG, é necessária a participação de agentes tanto humorais como celulares, especialmente dos neutrófilos, conforme já referido por outros autores(67,68,70). 9) PaO2: Embora sejam muitas as causas que podem causar baixa da PaO2 após um trauma, existem situações clínicas específicas e bastante comuns nas quais o encontro de uma PaO2 < 60mmHg praticamente fecha o diagnóstico de SEG. É o que ocorre, p. ex., após fraturas isoladas de ossos longos (fêmur e tíbia) e da bacia(9,22,39,79). Na histórica série de Gurd et al.(20) a PaO2 medida em 50 casos mostrou os seguintes resultados: era menor que 50mmHg em 24 casos, situava-se entre 51 e 80mmHg em 17 casos, e era maior que 80mmHg em 9 casos. Portanto, para os casos recém internados e sob suspeita de SEG, a monitorização da gasometria arterial e/ou da saturação arterial transcutânea da hemoglobina são medidas indispensáveis para se acompanhar a evolução desses pacientes(12,15,30,39,74). O cérebro, o segundo órgão nobre mais freqüentemente atingido numa EG, geralmente é avaliado pelos seguintes exames: 1) To- mografia Computadorizada do Crânio (TCC)- Embora represente um exame de inestimável valor em muitas condições neurológicas, incluindo-se os traumas de crânio, não acrescenta informações de valor para o diagnóstico da SEG. Isto porque nesses casos a TCC mostra apenas edema cerebral difuso, que é inespecífico, mas não localiza nem delimita as lesões isquêmicas causadas pelos êmbolos gordurosos(16,21,22,56). g 2) RESSONÂNCIA MAGNÉTICA CEREBRAL (RMC)- A RMC logo se mostrou superior à TCC na avaliação de casos de SEG com envol- vimento cerebral por detectar, de maneira precoce e específica, os danos causados pelos êmbolos gordurosos. EXAMES DE IMAGEM Nesses sete casos, contudo, a PaO2 já era inferior a 80mmHg, demonstrando que mesmo que o paciente apresente um RX de tórax aparentemente normal, pode haver já lesão pulmonar significativa. Observação semelhante foi feita por Fraser et al.(23), que classificou como normais os RX de tórax de pacientes com SEG do tipo Sub-Clínico. Na TCT de pacientes com SEG é comum encontrarem-se infiltrados sub-segmentares múltiplos, também localizados mais nas regiões basais e peri-hilares(22,23). 3) Cintilografia Pulmonar de Perfusão: Dada a sua natureza, na EG esse exame possibilita detectar áreas pulmonares com falhas de perfusão, mesmo quando o RX de tórax é normal(22). Todavia, situamo-nos aqui no velho impasse, isto é, embora os defeitos de perfusão possam se dever à EG, o exame não tem o poder de fechar o diagnóstico de SEG, já que o mesmo tipo de imagem pode ser encontrado no tromboembolismo pulmonar(22). tem qualquer valor isolado no diagnóstico de SEG . 9. GORDURA no LAVADO BRONCO-ALVEOLAR (LBA): O LBA é ob- tido por um broncofibroscópio locado num brônquio subsegmentar através do qual se injetam cerca de 100ml de soro fisiológico que são aspirados logo seguir. O líquido obtido é então analisado quanto a sua celularidade e composição química. Na primeira investigação sobre o papel do LBA na SEG, na qual ao autores avaliaram apenas 10 pacientes, Chastre et al.(89) concluíram que se tratava de um exame positivamente diagnóstico, pois observaram que 30% a 82% dos macrófagos de oito daqueles pacientes apresentavam gordura neutra fagocitada, enquanto que nos casos sem SEG esse valor era menor que 2%. Chegaram então a sugerir que o diagnóstico de SEG poderia ser firmado toda vez que houvesse pelo menos 5% de macrófagos alveolares com gordura. Outros estudos sobre o assunto, todavia, não confirmaram essa impressão, pois mostraram ser comum o achado de alta percentagem de macrófagos alveola- res com gordura fagocitada (média de 40% - REIDER), no LBA de várias situações clínicas não relacionadas a fraturas, ou mesmo a traumas. Tratava-se de casos de SARA de diversas outras etiologias. Além disso, em muitos casos com o diagnóstico de SEG, o LBA nem sempre mostrava os macrófagos com gordura(8,16,23,39,90,91). Macrófagos alveolares com gordura fagocitada significam apenas que gotículas de gordura passaram pela circulação pulmonar, quer tenha havido trauma, EG, ou nenhuma dessas intercorrências. Mais recentemente, Aoki et al.(14)estudaram o LBA em 20 pacientes com fraturas de ossos longos, dos quais cinco desenvolveram SEG. ALTERAÇÕES LABORATORIAIS A ocorrência de SEG, principalmente quando secundária a trauma grave, acompanha-se sempre de profundas alterações metabólicas e hematológicas que em geral podem ser detectadas pelos exames laboratoriais. Deve-se ressaltar desde logo, contudo, que embora 202 ACTA ORTOP BRAS 13(4) - 2005 EXAMES DE IMAGEM tem se correlacionado nem com o diagnóstico nem com a gravidade da SEG(8,22,74,85). 6) LIPASE: Peltier et al.(25,47,86) que estudaram de- talhadamente esse assunto, observaram que os níveis de lipasemia aumentavam entre o 3o. e o 5o. dia após o trauma, e atingiam seu pico por volta do 8o. dia, fatos esses recentemente confirmados por Riseborough et al.(74). A dosagem da lipasemia, entretanto, carece de toda e qualquer importância diagnóstica na SEG, visto que tanto não chega a se alterar em muitos dos pacientes que desenvolvem essa síndrome, como também porque comumente se eleva em casos de trauma, mesmo quando não existem fraturas(8,16,22,27,46). 7) GOTAS de GORDURA no SANGUE: Em casos de extensos traumas de par- tes moles, bem como após fraturas de ossos longos ou de bacia, é comum surpreender-se gotículas de gordura nas veias centrais, átrio direito ou artéria pulmonar(37,87). Como vimos no início, esta é a condição que define a EG, mas que não faz o diagnóstico da SEG, já que a imensa maioria desses pacientes evolui sem sinais dessa síndrome(1,2,5-9,16,22,87). 8. GOTAS de GORDURA na URINA: Segundo a revisão de Capan et al.(22), a presença de gotículas de gordura na urina geralmente significa a ocorrência de uma EG maciça, mas não necessariamente acompanhada de SEG. Além disso, em muitos pacientes que desenvolvem a SEG não existe gordura detectável na urina(22,84). Trata-se, portanto, de mais um achado laboratorial que não tem qualquer valor isolado no diagnóstico de SEG(1,2,8,16,74,83,88). Considerando-se que na EG os pulmões são sempre os primeiros órgãos a serem atingidos e que em geral são também os mais gra- vemente acometidos(5,6,8,16,23,31,38), a investigação de uma possível SEG geralmente se inicia pelas imagens do tórax. 1) RADIOGRAFIA do TÓRAX (RX de tórax): Constitui-se num exame obrigatório em todo caso de politrauma, mas nem sempre é rotina após artroplastias, por exemplo. Quando, cerca de 6h após um trauma, um paciente apresen- ta infiltrado pulmonar difuso, é praticamente certo que essas imagens sejam decorrentes de contusão pulmonar ou de aspiração brônquica maciça(23,32,84). Como a lesão pulmonar da SEG decorre da ação dos ácidos graxos e como essas reações levam muitas horas para se completar, as imagens radiológicas da lesão pulmonar na SEG costumam aparecer somente 12h a 24h após o trauma. EXAMES DE IMAGEM 3) Cintilografia Pulmonar de Perfusão: Dada a sua natureza, na EG esse exame possibilita detectar áreas pulmonares com falhas de perfusão, mesmo quando o RX de tórax é normal(22). Todavia, situamo-nos aqui no velho impasse, isto é, embora os defeitos de perfusão possam se dever à EG, o exame não tem o poder de fechar o diagnóstico de SEG, já que o mesmo tipo de imagem pode ser encontrado no tromboembolismo pulmonar(22). Considerando-se que na EG os pulmões são sempre os primeiros órgãos a serem atingidos e que em geral são também os mais gra- vemente acometidos(5,6,8,16,23,31,38), a investigação de uma possível SEG geralmente se inicia pelas imagens do tórax. 1) RADIOGRAFIA do TÓRAX (RX de tórax): Constitui-se num exame obrigatório em todo caso de politrauma, mas nem sempre é rotina após artroplastias, por exemplo. Quando, cerca de 6h após um trauma, um paciente apresen- ta infiltrado pulmonar difuso, é praticamente certo que essas imagens sejam decorrentes de contusão pulmonar ou de aspiração brônquica maciça(23,32,84). Como a lesão pulmonar da SEG decorre da ação dos ácidos graxos e como essas reações levam muitas horas para se completar, as imagens radiológicas da lesão pulmonar na SEG costumam aparecer somente 12h a 24h após o trauma. Conforme já comentado na seção ‘Quadro Clínico e Diagnóstico’, infiltrados um pouco mais tardios (entre 24h e 48h ou mais) podem tanto decorrer de SARA pós-traumática como da SEG, ou mesmo de ambas as condições. Também já foi referido que na SEG o infiltrado pulmonar geralmente é bilateral e simétrico, acometendo principalmente as regiões peri-hilares e as bases dos pulmões(23). A clássica imagem em “tempestade de neve”, considerada como “típica” da SEG, contudo, aparece em apenas cerca de 30% a 50% desses pacientes(2,16,22,30,31). N hi t ló i d l õ btid d tó i d p p p Nos exames histológicos dos pulmões, obtidos de autópsias de pacientes que morreram na fase Sub-Aguda da doença, mostram, além das gotículas de gordura obstruindo numerosos capilares e ar- teríolas, hemorragia e edema nos alvéolos, o que explica a acentuada hipóxia que os levou à morte (8,74). 2) Tomografia Computadorizada do Tórax (TCT): Este exame provê informações semelhantes às do RX, porém bastante mais detalhadas. Gurd e Wilson(20) observa- ram que dentre seus 43 casos de SEG com TCT anormal havia sete pacientes com RX de tórax normal. EXAMES DE IMAGEM Quando, cerca de 6h após um trauma, um paciente apresen- ta infiltrado pulmonar difuso, é praticamente certo que essas imagens sejam decorrentes de contusão pulmonar ou de aspiração brônquica maciça(23,32,84). Como a lesão pulmonar da SEG decorre da ação dos ácidos graxos e como essas reações levam muitas horas para se completar, as imagens radiológicas da lesão pulmonar na SEG costumam aparecer somente 12h a 24h após o trauma. Conforme já comentado na seção ‘Quadro Clínico e Diagnóstico’, infiltrados um pouco mais tardios (entre 24h e 48h ou mais) podem tanto decorrer de SARA pós-traumática como da SEG, ou mesmo de ambas as condições. Também já foi referido que na SEG o infiltrado pulmonar geralmente é bilateral e simétrico, acometendo principalmente as regiões peri-hilares e as bases dos pulmões(23). A clássica imagem em “tempestade de neve”, considerada como “típica” da SEG, contudo, aparece em apenas cerca de 30% a 50% desses pacientes(2,16,22,30,31). Nos exames histológicos dos pulmões, obtidos de autópsias de pacientes que morreram na fase Sub-Aguda da doença, mostram, além das gotículas de gordura obstruindo numerosos capilares e ar- teríolas, hemorragia e edema nos alvéolos, o que explica a acentuada hipóxia que os levou à morte (8,74). 2) Tomografia Computadorizada do Tórax (TCT): Este exame provê informações semelhantes às do RX, porém bastante mais detalhadas. Gurd e Wilson(20) observa- ram que dentre seus 43 casos de SEG com TCT anormal havia sete pacientes com RX de tórax normal. Nesses sete casos, contudo, a PaO2 já era inferior a 80mmHg, demonstrando que mesmo que o paciente apresente um RX de tórax aparentemente normal, pode haver já lesão pulmonar significativa. Observação semelhante foi feita por Fraser et al.(23), que classificou como normais os RX de tórax de pacientes com SEG do tipo Sub-Clínico. Na TCT de pacientes com SEG é comum encontrarem-se infiltrados sub-segmentares múltiplos, também localizados mais nas regiões basais e peri-hilares(22,23). 3) Cintilografia Pulmonar de Perfusão: Dada a sua natureza, na EG esse exame possibilita detectar áreas pulmonares com falhas de perfusão, mesmo quando o RX de tórax é normal(22). Todavia, situamo-nos aqui no velho impasse, isto é, embora os defeitos de perfusão possam se dever à EG, o exame não tem o poder de fechar o diagnóstico de SEG, já que o mesmo tipo de imagem pode ser encontrado no tromboembolismo pulmonar(22). EXAMES DE IMAGEM O é b d ó ã b i f ü i id Considerando-se que na EG os pulmões são sempre os primeiros órgãos a serem atingidos e que em geral são também os mais gra- vemente acometidos(5,6,8,16,23,31,38), a investigação de uma possível SEG geralmente se inicia pelas imagens do tórax. 1) RADIOGRAFIA do TÓRAX (RX de tórax): Constitui-se num exame obrigatório em todo caso de politrauma, mas nem sempre é rotina após artroplastias, por exemplo. Quando, cerca de 6h após um trauma, um paciente apresen- ta infiltrado pulmonar difuso, é praticamente certo que essas imagens sejam decorrentes de contusão pulmonar ou de aspiração brônquica maciça(23,32,84). Como a lesão pulmonar da SEG decorre da ação dos ácidos graxos e como essas reações levam muitas horas para se completar, as imagens radiológicas da lesão pulmonar na SEG costumam aparecer somente 12h a 24h após o trauma. Conforme já comentado na seção ‘Quadro Clínico e Diagnóstico’, infiltrados um pouco mais tardios (entre 24h e 48h ou mais) podem tanto decorrer de SARA pós-traumática como da SEG, ou mesmo de ambas as condições. Também já foi referido que na SEG o infiltrado pulmonar geralmente é bilateral e simétrico, acometendo principalmente as regiões peri-hilares e as bases dos pulmões(23). A clássica imagem em “tempestade de neve”, considerada como “típica” da SEG, contudo, aparece em apenas cerca de 30% a 50% desses pacientes(2,16,22,30,31). Nos exames histológicos dos pulmões, obtidos de autópsias de pacientes que morreram na fase Sub-Aguda da doença, mostram, além das gotículas de gordura obstruindo numerosos capilares e ar- teríolas, hemorragia e edema nos alvéolos, o que explica a acentuada hipóxia que os levou à morte (8,74). 2) Tomografia Computadorizada do Tórax (TCT): Este exame provê informações semelhantes às do RX, porém bastante mais detalhadas. Gurd e Wilson(20) observa- ram que dentre seus 43 casos de SEG com TCT anormal havia sete pacientes com RX de tórax normal. Nesses sete casos, contudo, a PaO2 já era inferior a 80mmHg, demonstrando que mesmo que o paciente apresente um RX de tórax aparentemente normal, pode haver já lesão pulmonar significativa. Observação semelhante foi feita por Fraser et al.(23), que classificou como normais os RX de tórax de pacientes com SEG do tipo Sub-Clínico. Na TCT de pacientes com SEG é comum encontrarem-se infiltrados sub-segmentares múltiplos, também localizados mais nas regiões basais e peri-hilares(22,23). EXAMES DE IMAGEM Conforme já comentado na seção ‘Quadro Clínico e Diagnóstico’, infiltrados um pouco mais tardios (entre 24h e 48h ou mais) podem tanto decorrer de SARA pós-traumática como da SEG, ou mesmo de ambas as condições. Também já foi referido que na SEG o infiltrado pulmonar geralmente é bilateral e simétrico, acometendo principalmente as regiões peri-hilares e as bases dos pulmões(23). A clássica imagem em “tempestade de neve”, considerada como “típica” da SEG, contudo, aparece em apenas cerca de 30% a 50% desses pacientes(2,16,22,30,31). Nos exames histológicos dos pulmões, obtidos de autópsias de pacientes que morreram na fase Sub-Aguda da doença, mostram, além das gotículas de gordura obstruindo numerosos capilares e ar- teríolas, hemorragia e edema nos alvéolos, o que explica a acentuada hipóxia que os levou à morte (8,74). 2) Tomografia Computadorizada do Tórax (TCT): Este exame provê informações semelhantes às do RX, porém bastante mais detalhadas. Gurd e Wilson(20) observa- ram que dentre seus 43 casos de SEG com TCT anormal havia sete pacientes com RX de tórax normal. Nesses sete casos, contudo, a PaO2 já era inferior a 80mmHg, demonstrando que mesmo que o paciente apresente um RX de tórax aparentemente normal, pode haver já lesão pulmonar significativa. Observação semelhante foi feita por Fraser et al.(23), que classificou como normais os RX de tórax de pacientes com SEG do tipo Sub-Clínico. Na TCT de pacientes com SEG é comum encontrarem-se infiltrados sub-segmentares múltiplos, também localizados mais nas regiões basais e peri-hilares(22,23). 3) Cintilografia Pulmonar de Perfusão: Dada a sua natureza, na EG esse exame possibilita detectar áreas pulmonares com falhas de perfusão, mesmo quando o RX de tórax é normal(22). Todavia, situamo-nos aqui no velho impasse, isto é, embora os defeitos de perfusão possam se dever à EG, o exame não tem o poder de fechar o diagnóstico de SEG, já que o mesmo tipo de imagem pode ser encontrado no tromboembolismo pulmonar(22). Considerando-se que na EG os pulmões são sempre os primeiros órgãos a serem atingidos e que em geral são também os mais gra- vemente acometidos(5,6,8,16,23,31,38), a investigação de uma possível SEG geralmente se inicia pelas imagens do tórax. 1) RADIOGRAFIA do TÓRAX (RX de tórax): Constitui-se num exame obrigatório em todo caso de politrauma, mas nem sempre é rotina após artroplastias, por exemplo. g 6) Aprotinina (“Trasylol”): g 6) Aprotinina (“Trasylol”): ”Doença com fisiopatologia indefinida acarreta tratamento inespecífico”. Foi com esta frase que Estebe et al.(8) definiram a situação do tratamento atual da SEG. De fato, como veremos a seguir, inúmeros tratamentos, os mais díspares, já foram propostos para se tentar combater a SEG nas últimas décadas, sem que nenhum deles tinha se mostrado efetivo. 1) Álcool Etílico: A essa droga são atribuídas as ações de inibir a agregação de plaquetas, diminuir a liberação de serotonina e bloquear a ação de proteases, como aquelas presentes nos lisossomas dos neutrófilos. Embora estudos retrospectivos tenham indicado que pacientes que receberam aprotinina tenham evoluído melhor que os que não a receberam, nenhum estudo controlado (prospectivo e randomizado) foi feito para que se comprovasse ou não o valor dessa droga no tratamento da SEG(8,20,22,32). Sari et al.(58), que mais recentemente testaram a aprotinina, confirmaram que, de fato, a droga diminuiu a agregação plaquetária, mas não evitou a queda da PaO2, que seria o efeito mais desejado. 7) Aspirina: Segundo as revisões de Capan et al.(22)e de Mellor et al.(16), o uso dessa droga jamais trouxe quaisquer benefícios no tratamento da SEG. ó Na década de 1960, foi observado que politraumatizados em estado de embriagues geralmente tinham menor incidência de SEG que os acidentados sóbrios(8,22,38). A partir dessa observação foi constatado, em laboratório, que o álcool tinha o poder de diminuir a atividade da lípase sérica e, conseqüentemente, diminuir a liberação de ácidos graxos. Foi com essa premissa que se indicou o uso do álcool etílico no tratamento da SEG, com a suposição de que diminuindo-se a formação de ácidos graxos livres haveria menor chance de ocorrer lesão pulmonar. Apesar de ter sido testado na prática clínica, as ex- periências com o álcool foram poucas, aleatórias e descontroladas. E como jamais se realizou um estudo prospectivo e randomizado que provasse ou não a utilidade dessa terapêutica, o uso do álcool etílico logo foi abandonado(8,16,19,22). Alguns autores foram até bem mais categóricos, chegando mesmo a afirmar que o uso do álcool etílico não tinha qualquer efeito benéfico na SEG(12,31). 8) Corticosteróides: Por suas reconhecidas e comprovadas ações anti-inflamatórias, tanto locais quanto sistêmicas (inibindo a liberação das enzimas proteo- líticas dos lisossomas dos neutrófilos, a ativação do complemento, a resposta inflamatória sistêmica e a agregação plaquetária), os corticóides obviamente que já foram testados no tratamento da SEG. EXAMES DE IMAGEM Com este método é possível demonstrar lesões a partir de 2mm de diâmetro, as quais geralmente correspondem a edema perivascular(8,21,76). Por conse- guinte, logo se acumularam casos de SEG nos quais a TCC era absolutamente normal e a RMC demonstrava a presença de peque- nos infartos cerebrais(21,80). Os achados típicos da RMC na SEG são os sinais de baixa intensidade em T1 e de alta intensidade em T2. Quando aparecem sinais de alta intensidade em T1, isso significa que houve infarto hemorrágico, lesão muito incomum na SEG, uma vez que os êmbolos são pequenos e portanto raramente obstruem vasos de grande calibre(21). A lesão mais comum na SEG cerebral é o edema perivascular que acaba comprimindo os capilares e pre- judicando ainda mais a circulação local. Esse fenômeno pode ser indiretamente avaliado através do Doppler trans-craniano que tem a propriedade de detectar a lentidão do fluxo sanguíneo cerebral se- 203 4) Heparina: cundária ao aumento da resistência vascular(21). A RMC pode acusar as lesões da SEG já a partir de 3h a 4h após a ocorrência de um trauma. Caracteristicamente, as lesões da SEG cerebral situam-se sempre na substância branca profunda dos gânglios da base, do tronco cerebral e do cerebelo(76). Outra utilidade da RMC pode ser constatada no próprio seguimento imediato e tardio desses pacientes, pois a melhora nas imagens desse exame estão sempre associadas à melhora clínica dos pacientes. Por outro lado, verificou-se ainda que nos casos em que a RMC é normal, o diagnóstico de SEG cerebral pode ser totalmente descartado(21). cundária ao aumento da resistência vascular(21). A RMC pode acusar as lesões da SEG já a partir de 3h a 4h após a ocorrência de um trauma. Caracteristicamente, as lesões da SEG cerebral situam-se sempre na substância branca profunda dos gânglios da base, do tronco cerebral e do cerebelo(76). Outra utilidade da RMC pode ser constatada no próprio seguimento imediato e tardio desses pacientes, pois a melhora nas imagens desse exame estão sempre associadas à melhora clínica dos pacientes. Por outro lado, verificou-se ainda que nos casos em que a RMC é normal, o diagnóstico de SEG cerebral pode ser totalmente descartado(21). Tanto experimental quanto clinicamente, o uso da heparina em casos de SEG mostrou-se uma medida totalmente ineficaz, quando não desastrosa(19,25,42,45). Teoricamente, as funções da heparina na SEG seriam as de reverter o quadro de CIVD e estimular a lipase para diminuir a lipemia. 5) Dextran-40: Trata-se de uma solução constituída por polímeros de glicose com peso molecular igual a 40.000, os quais aumentam bastante o poder osmótico do plasma. Foi introduzido no tratamento da SEG com a suposição de que ao promover hemodiluição, diminuiria a agregação de plaquetas e eritrócitos(12). Embora seu uso se mostrasse útil na ma- nutenção ou recuperação da volemia em politraumatizados, nenhum benefício foi demonstrado quanto à diminuição da incidência ou à evolução de pacientes com SEG, e seu uso com esses propósitos logo foi abandonado(8,16,18,19,22,32,83). EXAMES DE IMAGEM Tais efeitos, entretanto, são altamente indesejá- veis, pois, de um lado, causa um indesejável aumento nos ácidos graxos circulantes e, por outro cria um alto risco de hemorragia em pacientes politraumatizados ou em pós-operatório de artroplastias(16). Em virtude dessas possíveis e graves complicações e considerando que o uso da heparina aumentou consideravelmente a mortalidade em animais de experimentação, seu uso passou a ser formalmente contra-indicado no tratamento da SEG(12,16,41,42,59). p Como se pôde constatar, pelo que revimos até aqui, não existe nem quadro clínico patognomônico, nem exame laboratorial ou imagi- nológico que possa fechar o diagnóstico de SEG. Na verdade, as petéquias são tidas como um achado “específico” da SEG num paciente com fraturas ou em pós-operatório de artroplastias. Entre- tanto, como essas lesões só aparecem 48h a 72h após o trauma ou operação, elas obviamente não se prestam ao estabelecimento de um diagnóstico precoce(20,21,22,24,84). O diagnóstico da SEG depende, portanto, de toda uma conjuntura de dados, devendo sempre ser levados em conta a história, os sinais e sintomas, e os exames de imagem(18,19,21-23,51,54,81,82,84,91). Considerando-se que não existe tratamento específico para a SEG, resta-nos tratar Considerando-se que não existe tratamento específico para a SEG, resta-nos tratar diretamente cada uma das conseqüências orgânicas dessa sín- drome(1,2,8,18,22,51,84). Como a SEG geralmente ocorre após um grave trauma ou extensa operação, é praticamente certo que se necessite restaurar a volemia (sangue e derivados, soro fisiológico, Ringer-lac- tato, Dextran etc) para manter o débito cardíaco, sobretudo quando há sinais de falência do ventrículo direito. Da mesma forma, caso a reposição volêmica não seja suficiente, devem ser usadas drogas vasoativas (Dopamina, Dobutamina, Nor-adrenalina) com os mesmos objetivos. Assim como o estado de choque piora o prognóstico da SEG, o mesmo ocorre se houver hipóxia. Por isso se recomenda a monitorização contínua da saturação de O2, procurando mantê-la sempre acima de 95%. Em alguns casos de SEG sub-clínica ou sub-agudas leves é possível manter essa saturação apenas com um cateter nasal de O2 (3 a 6 lpm)(38,79,94,95). Para os pacientes em franca insuficiência respiratória, entretanto, a ventilação mecânica se impõe(8,22,29,96). Apesar do comprometimento pulmonar ser gra- ve, nos pacientes que respondem bem à assistência ventilatória o processo inflamatório da SEG costuma clarear em 3 a 7 dias(16). Por outro lado, a hipertensão pulmonar que geralmente ocorre nos casos de SEG não costuma responder às drogas vasodilatadoras específicas para a pequena circulação (Nitroglicerina, Isoproterenol, Prostaglandinas). Estas, além de não terem demonstrado qualquer g 6) Aprotinina (“Trasylol”): Sua eficácia, contudo, jamais foi comprovada por estudos controlados e seu uso deixou de ser considerado(8,22,32,93). Por outro lado, como veremos mais adiante em “Profilaxia”, existem favoráveis indícios de que os corticóides possam realmente ser eficientes em prevenir ou diminuir a gravidade e a mortalidade da SEG. 2) Glicose Hipertônica ( GH ): ) p ( ) A infusão de 50g de glicose, VO ou IV, diminui a concentração de ácidos graxos circulantes cerca de 30min após(16). Nunca se soube, entretanto, que efeito isso poderia ter sobre a liberação dos ácidos graxos a partir da gordura embolizada nos capilares pulmonares. Quando a GH é dada junto com insulina, a inibição da lipólise pós- trauma é ainda maior(8,83). Embora alguns autores tenham observado menor incidência de SEG nos seus pacientes que receberam GH(46,83), tampouco neste caso jamais houve estudos controlados que afian- çassem o seu uso, que também logo foi abandonado(8,18,22). Freeman e Enneking(19), que chegaram a experimentar esse tratamento, foram levados a afirmar que a GH não melhorava nem evolução nem a sobrevida dos pacientes com SEG. ACTA ORTOP BRAS 13(4) - 2005 te são pu o a Medidas Ortopédicas: Embora o diagnóstico e o tratamento de suporte da SEG geral- mente estejam a cargo da equipe de terapia intensiva, a parte mais importante, que é a sua prevenção, é de inteira competência e res- ponsabilidade do cirurgião ortopédico. Em termos de fraturas, é claro que a modernização dos acessórios dos veículos e as campanhas de educação no trânsito são de grande importância para a diminui- ção daquelas lesões. Restam, entretanto, muitas outras causas de fraturas sobre as quais não se tem controle. Assim, uma vez frente a um paciente com fratura de ossos longos e/ou da pelve, cabe ao ortopedista tomar as decisões mais adequadas para se evitar uma SEG(32). É bem sabido que fraturas instáveis permitem a fricção en- tre os cotos ósseos e que isso provoca novas chuvas de êmbolos gordurosos, além daquela já ocorrida no momento do trauma(1,2,22). Esses fatos, entre outros, levaram ao conceito da “fixação precoce” das fraturas, com o intuito de se evitar a SEG e outras complicações como infecções, pseudoartrose, dor e dificuldades para manipular Considerando-se especialmente os politraumatizados, muitas vezes é difícil, senão impossível, estabelecer-se com precisão a causa mortis numa vítima que acaba sendo acometida por diversas e graves injú- rias tais como hemorragia maciça, choque, SARA, lesões torácicas, cranianas e abdominais(12,22,23,24,31). Ganong et al.(31) referiram que num estudo de autópsia de 5265 fatalidades por trauma a SEG foi considerada como causa mortis em 16% dos casos. A incidência de mortalidade na SEG, entretanto, varia muito entre os diversos autores, independentemente da época em que os estudos foram realizados. Capan et al.(22), em sua excelente revisão de 1993, referiu que a mortalidade da SEG variava entre 10% a 20% até o final da década de 1970, mas que em virtude da melhor e mais rápida ressuscitação e transporte dos acidentados, bem como ao uso da fixação precoce das fraturas e dos modernos cuidados das U0TIs, as fatalidades por SEG passaram a ocorrer em menos de 10% dos casos. Takahashi et al.(76), bem como Estebe et al.(8), por outro lado, em suas respectivas revisões de 1990 e 1997, referiram taxas de mortalidade entre 14% e 87% na SEG ocorrida em politraumatizados. Na revisão de Robinson et al.(32) em 2001, os autores encontraram taxas de mortalidade que variavam entre 5% e15% na maioria dos estudos, embora também tenham encontrado taxas mais altas, de até 36%. te são pu o a Medidas Ortopédicas: Ganong et al.(31) constataram que até a década de 1960 a mortalidade citada nos diferentes estudos variava entre 10% e 35%, mas que a partir da década de 1970 esses valores tinham baixado, oscilando entre 0% e 20%. Em nosso meio encontramos os recentes relatos de Araújo et al(29) que referiram uma mortalidade de 33% (3/9 casos), e de Engel et al.(18) que relataram uma mortalidade de 26% (5/19 casos). p o paciente no leito. Na década de 1990, diversos autores relataram sua experiência com a fixação precoce das fraturas, comprovando de forma reprodutível seus inúmeros benefícios. De um modo geral, esses estudos mostraram ter havido uma sensível diminuição na incidência de insuficiência respiratória (SEG/SARA), no tempo de ventilação mecânica e de permanência na UTI, menor ocorrência de febre e de infecções ósseas ou generalizadas, menor mortali- dade, menor permanência hospitalar e, portanto, menor custo do tratamento(1,2,8,22,31,32,78,81-83,97,98). Embora alguns desses estudos sejam retropectivos e não controlados, Robinson(32) publicou recentemen- te uma meta-análise dos “estudos controlados” sobre os efeitos da fixação precoce das fraturas, a qual confirmou plenamente as vantagens acima enumeradas. Essa revisão incluiu ainda uma meta-análise sobre a controvérsia na indicação da osteossíntese precoce com pino intramedular em pacientes com fratura e trauma torácico concomitante. De acordo com essa análise Robinson(32) pôde concluir que a osteossíntese não aumentava a incidência de insuficiência respiratória nesses pacientes, já que o trauma pulmonar inicial é que era o verdadeiro responsável pelas alterações que às vezes levavam o paciente à SARA. Schemitsch et al.(3), num elegante estudo experimental em cães chegaram às mesmas conclusões, isto é, que a fixação da fratura com pino intramedular não era um fator de importância decisiva na gênese da SARA, já que a EG que ocorria no momento do trauma era muito mais intensa que a observada du- rante a osteossíntese. Bosse et al.(99), que recentemente publicaram uma extensa revisão sobre “A Ortopedia do Século XX” chegou a conclusões semelhantes, ou seja, que a fixação precoce melhorava o prognóstico dos pacientes com fraturas graves, mesmo naqueles com trauma torácico concomitante. Controvérsia semelhante existe com relação à indicação da fixação precoce em pacientes com fratura e TCE. Numa série recentemente publicada, englobando 119 casos com fratura de fêmur ou tíbia associadas a TCE, Bhandari et al.(100) compararam os resultados dos casos cuja fratura foi tratada através de pino intramedular com os tratados por fixação através de placa. te são pu o a Medidas Ortopédicas: Ao final desse estudo, que foi prospectivo e randomizado, concluíram que as osteossínteses com pino intramedular em nada comprometeram a evolução neurológica desses pacientes, a qual dependeu unicamente do grau na escala de Glasgow em que cada paciente se encontrava ao ser admitido. E b i i d t id “fi ã Por tudo o que revimos até aqui, acreditamos que a tamanha dispari- dade que se observa entre os índices de mortalidade relatados pelos diferentes autores se deva, em grande parte, aos critérios usados para se diagnosticar o que é ou não SEG. Isto é, existe a SEG “típica”, assim como existe a SEG associada a outras complicações graves (Choque, TCE, p. ex.), e existem os casos eventualmente rotulados como SEG, mas que são de outra natureza, como a SARA pós-traumática, por exemplo. Portanto, enquanto não hou- ver um método de diagnóstico específico para a SEG, muitos dos dados e conhecimentos sobre a fisiopatologia, o quadro clínico, o diagnóstico, a terapêutica, o prognóstico e a profilaxia dessa síndrome permanecerão, em grande parte, empíricos. 3) Albumina Humana 3) Albumina Humana Uma das propriedades da albumina é a de quelar os ácidos graxos livres e evitar sua toxicidade(22). Baseando-se nessa constatação, o uso de Albumina IV foi proposto e testado no tratamento da SEG, mas nunca chegou a ser adotado em virtude da falta de evidências benéficas(8,16,22). Mesmo em condições experimentais ótimas, isto é, absolutamente controladas, Hoffman(54) não foi capaz de diminuir o grau de lesão pulmonar em cães quando neles injetou altas doses de imediatamente após a injeção de ácido oléico. Quando injetou ambas as substâncias ao mesmo tempo, todavia, referiu ter cons- tatado menor extensão da lesão pulmonar. Nesse sentido, pode ser que a infusão de albumina durante as artroplastias possa diminuir a incidência e gravidade da SEG que ocorre nessas operações. Todavia, até onde pudemos pesquisar, não encontramos na literatura estudos prospectivos e randomizados que recomendem essa conduta. Tais estudos seriam muito bem vindos, portanto. 204 a hiperoxigenação e a expansão da volemia antes de se iniciar a cimentação das próteses. Nos pacientes mais graves, com doença cardiovascular e/ou pulmonar debilitante (ASA 3 e 4), recomenda-se ainda a monitorização intra-operatória da pressão da artéria pulmo- nar e do débito cardíaco através do cateter de Swan-Ganz(19,51). Um dos óbices desses pacientes, sobretudo naqueles com enfisema pulmonar avançado, é que seu leito capilar já se encontra muito diminuído. Em condições normais de experimentação, a pressão da artéria pulmonar geralmente começa a se elevar somente quando mais de 50% do leito capilar encontra-se obstruído. Já na EG, como geralmente também existe vasoconstrição pulmonar, basta uma obstrução de cerca de 20% do leito capilar para que ocorra hiper- tensão pulmonar(22). efeito benéfico, muitas vezes foram responsáveis pela instalação ou piora de hipotensão arterial sistêmica(8,16, 32). p p Pelo que pudemos averiguar com relação ao tratamento da SEG, pode-se concordar integralmente com as observações de Murray et al.(95), segundo os quais “se até o final da década de 1960 a terapêu- tica da SEG era dirigida à diminuição da lipemia e das alterações da coagulação, atualmente os alvos do tratamento são a manutenção da oxigenação e do débito cardíaco”. ACTA ORTOP BRAS 13(4) - 2005 PROGNÓSTICO A principal causa de óbito nos pacientes com SEG é a insuficiência respiratória progressiva, ou seja, uma lesão pulmonar que evolui para SARA(22), embora nos casos com predomínio de sintomas neurológi- cos também possa sobrevir a morte, seja em virtude de infarto cerebral maciço ou de edema cerebral generalizado(16,28). Felizmente, porém, o prognóstico dos pacientes com envolvimento cerebral na SEG é geralmente favorável(20,22,24,31,32) e a evolução da melhora clínica pode ser acompanhada ou antecipada pelo desaparecimento das altera- ções na RMC(21,76,80). Nos casos em que houve infarto hemorrágico, entretanto, a lesão evolui para atrofia cerebral irreversível, deixando o paciente com seqüelas localizadas, ou com invalidez, ou até mesmo em estado vegetativo(76). PREVENÇÃO Ao reverem os exames laboratoriais desses pacientes, hipotensão sistêmica, hipertensão pulmonar, aumento do ‘shunt’ pulmo- nar e conseqüente queda da PaO2 arterial(1,2,7,11,60), além da embolização cerebral que ocorre em cerca de 80% dos casos(8,22,25,32,47,51). No intuito de diminuir a carga de EG durante a cimentação das próteses, várias táticas cirúrgicas foram introduzidas: 3.1) “RESPIRO” (“Venting”): A simples abertura de um orifício de 4 a 6mm de diâmetro na porção da diáfise situada poucos centímetros além da extremidade da prótese, por si só não ajuda na diminuição da PIM durante a cimentação(9,10,11), porém, quando acompanhada de outras medidas, como o uso de fresa ranhurada, do “overdrill” (orifício de entrada de 12mm) e do vácuo proximal (vide abaixo) tem sido considerada como útil na diminuição da PIM e, portanto, da EG(11,51,55). 3.2) ENCHIMENTO RETRÓGRADO: Preencher o canal medular com cimento, a partir da extremidade distal da prótese, não só ajuda a atenuar o aumento da PIM, como a evitar embolias gasosas(48). 3.3) VISCOSIDADE: O uso de cimentos de baixa viscosidade também têm sido apontados como úteis para se evitar maiores aumentos da PIM(10,11). 3.2) ENCHIMENTO RETRÓGRADO: Preencher o canal medular com cimento, a partir da extremidade distal da prótese, não só ajuda a atenuar o aumento da PIM, como a evitar embolias gasosas(48). g 3.3) VISCOSIDADE: O uso de cimentos de baixa viscosidade também têm sido apontados como úteis para se evitar maiores aumentos da PIM(10,11). entretanto, observaram que no grupo que teve complicações os valores da Proteina-C- Reativa e da Elastase eram muito superiores, e que o número de plaquetas era muito inferior aos respectivos va- lores do grupo que evoluiu sem complicações. Esse fato alertou os autores para o fato de que na época da osteossíntese os pacientes do primeiro grupo encontravam-se em pleno “estado inflamatório pós-traumático”, isto é, ainda sujeitos às alterações metabólicas, bioquímicas e hormonais do período pós-trauma ou pós-operatório de uma grande cirurgia(71,78,102). Os autores passaram a recomendar, portanto, que a fixação tardia de uma grande fratura não seja efetuada enquanto o paciente demonstrar sinais de insuficiência orgânica, ou exames laboratoriais que demonstrem que o estado inflamatório pós-traumático ainda esteja em curso. PREVENÇÃO Medidas Gerais: T i Tanto no paciente politraumatizado como naquele que está sendo operado, é de crucial importância que se evitem a hipovolemia e a hipóxia, pois esses são fatores que pioram sobremaneira o prognóstico de uma EG(8,22,51,79,95). Assim sendo, em ambas as situações se recomenda monitorar, muito de perto, especialmente a pressão arterial e a PaO2, corrigindo-se os seus desvios tão logo sejam detectados(8,22,51,79,95). Ainda no sentido de se prevenir ou diminuir os efeitos da EG sobre os sistemas respirató- rio e cardiovascular no intra-operatório, Orsini et al.(60) recomendam Embora a maioria dos autores pareça considerar que “fixação pre- coce” seja aquela feita dentro de 24h após o trauma, Behrman et al.(101) incluíram em sua publicação casos operados até 48h depois. Diamond, na discussão desse artigo, expressou a opinião de que 205 “qualquer fixação feita além de 6h a 8h deveria ser considerada tar- dia”. Pelo visto, parece existir ainda uma falta de consenso absoluto sobre a definição de ‘fixação precoce’. Outro importante ponto com relação ao assunto diz respeito à situação geral do paciente, isto é, se ele está ou não em condições de ser submetido a esse procedi- mento. Na excelente revisão histórica de Bosse et al.(99), ao discorrer sobre a introdução e a aceitação da fixação precoce das fraturas, o autor primeiramente relembra o desconforto, os sofrimentos e as complicações experimentados pelos pacientes submetidos à tração prolongada no leito. A seguir, apresenta e discute os benefícios da fixação precoce, enfatizando principalmente a significativa queda na incidência da insuficiência respiratória pós-traumática, assim como da mortalidade em geral. Segundo sua opinião(99), hoje compartilhada pela maioria dos autores, toda fratura de ossos longos e/ou de bacia deve, idealmente, ser fixada precocemente. Quando o paciente é politraumatizado, é claro que se deve esperar pelo esclarecimento e resolução de eventuais traumas de crânio, tórax ou abdome, além da reanimação inicial. Uma vez resolvidos esses problemas, contudo, a fratura deverá ser fixada o mais rapidamente possível, indepen- dentemente de o paciente ter ou não sido submetido a uma grande operação. Ainda segundo Bosse et al.(99), a fixação precoce só estaria formalmente contra-indicada nas situações de extrema gravidade, como nos casos de choque profundo e resistente ao tratamento, ou de anóxia irresponsiva à ventilação com O2 a 100%, ou de hipotermia e coagulopatia acentuadas. da aspiração do conteúdo medular . ACTA ORTOP BRAS 13(4) - 2005 PREVENÇÃO 2) FRESA RANHURADA: Na literatura, muito já se discutiu e ainda se discute sobre a utilização ou não da fresagem e também sobre qual tipo de fresa deveria ser utilizada. Já de há muito ficou com- provado que a fresagem é causadora de EG, pois essa manobra eleva sobremaneira a PIM(7,11,14,18,48,53) que pode atingir níveis de até 1500mmHg(8,18). Embora esse grau de EG nem sempre se traduza numa queda da PaO2(50), a EG causada pela fresagem pode e deve ser minimizada, pois maiores cargas de êmbolos gordurosos sempre ocorrerão nos tempos cirúrgicos subseqüentes. A tentativa de se utilizar pinos intramedulares de menor diâmetro com o intuito de se evitar a fresagem não tem ganhado muitos adeptos, já que esses pinos têm implicado num tempo muito maior de consolidação das fraturas, além de estarem associados a uma maior incidência de pseudoartrose e, portanto, da necessidade de procedimentos secundários para se resolver esses casos(99,104). Com relação aos dois tipos de fresa mais comuns, cilíndricas e ranhuradas, existem inúmeras evidências, clínicas e experimentais de que as cilíndricas aumentam muito mais a PIM e, portanto, causam muito mais EG que as fresas ranhuradas(8,9,18,51,55,64,73). 3) CIMENTAÇÃO: Conforme já discutido na seção sobre Fisiopato- logia, esta é a fase das artroplastias em que ocorre a maior carga de êmbolos gordurosos, do que pode resultar Um outro problema nessa área diz respeito aos pacientes que, por um daqueles motivos, não pode ser operado na fase aguda do trauma. Quando seria então o momento oportuno de operá-lo? A conduta geral é ditada pelo bom senso, isto é, a operação costu- ma ser indicada quando os pacientes se encontram ‘clinicamente estáveis’ e sem sinais de disfunção orgânica. Waydhas et al.(102) mostraram recentemente que a “Reação Sistêmica ao Trauma” tem profunda influência na evolução desses casos. Em seu grupo de 106 pacientes com trauma multi-sistêmico, em que todos tiveram que ser submetidos à osteossíntese muitos dias após o trauma, 40 deles (38%) desenvolveram insuficiência orgânica grave (respiratória, hepática ou renal) após a fixação da fratura, enquanto que os outros 60 casos (56%) nada tiveram. Todos haviam sido avaliados pelo intensivista, pelo anestesista e pelo cirurgião, os quais considera- ram cada paciente ‘em condições estáveis’ e sem nenhum sinal de qualquer insuficiência orgânica. CONSIDERAÇÕES FINAIS Fazer uma revisão absolutamente completa sobre a “Embolia Gor- durosa” é uma tarefa praticamente inexeqüível a um pequeno grupo de investigadores, considerando-se que apenas nos arquivos atuais da MEDLINE (1950 a 2004) existem 2622 artigos sobre esse assun- to. Tampouco acreditamos que a revisão de todos aqueles artigos pudesse elucidar os numerosos pontos obscuros dessa síndrome. Conforme demonstrado ao longo do texto, existem inúmeros aspectos controversos ou pouco esclarecidos sobre os fenômenos da EG e da SEG. A impressão que nos ficou, portanto, foi a de que, mais importante que se obter uma revisão completa desse assunto, seria a realização de diferentes estudos prospec- tivos e randomizados, e com casuísticas representativas, especificamente desenhados a j p 4) CORTICOSTERÓIDES: Embora não tenham se mostrado úteis tratamento da SEG já estabelecida, existem vários estudos sugerin que os corticosteróides possam exercer importante ação protet quando administrados antes que a SEG esteja completame instalada. Dentre as mais importantes ações anti-inflamatórias d corticóides destacam-se: o bloqueio da ativação do Compleme (C5a), a inibição da agregação plaquetária e, principalmente estabilização da membrana dos lisossomos, evitando assim o derrame de enzimas proteolíti- cas sobre as células endoteliais e alveolares(8,16,22,32,105). Apesar das apresentarem casuísticas relativamente baixas, existem pelo menos quatro estudos prospectivos e randomizados que demonstraram a eficácia dos corticóides em diminuir a incidência da SEG em pacien- tes com fratura de fêmur e/ou de tíbia, quando administrados profilaticamente, isto é, logo após a admissão do paciente ao hospital. Os dados mais relevantes desses estudos encontram-se resumidos na Tabela 2. Tabela 2 - * = Metilpredn estatisticamente significativa q grupos, mas sim uma ‘tendê corticóide. Nos diferença existiu e foi a Tabela 2 - * = Metilprednisolona, ** = Não houve diferença estatisticamente significativa quanto à incidência de SEG entre os três grupos, mas sim uma ‘tendência’ apontando para os benefícios do corticóide. Nos outros três estudos essa diferença existiu e foi aqui indicada pelo respectivo “p”. Tabela 2 - * = Metilprednisolona, ** = Não houve diferença estatisticamente significativa quanto à incidência de SEG entre os três grupos, mas sim uma ‘tendência’ apontando para os benefícios do corticóide. Nos outros três estudos essa diferença existiu e foi aqui indicada pelo respectivo “p”. PREVENÇÃO 3.4) VÁCUO PROXIMAL: Num interessante estudo prospectivo e randomizado sobre ATQ, Koessler et al.(15) aplicaram um vácuo de 600mmHg através de uma cânula metálica introduzida na linha intertrocanteriana em 60 pacientes, durante a cimentação da pró- tese, enquanto que em outros 60 casos não se fez o uso do vácuo. Todos os pacientes foram monitorados através da ECO-TE e de gasometrias arteriais. Puderam então observar que no grupo sem vácuo a incidência de EG ‘grau-2’ foi de 93% e a de ‘grau-3’ foi de 51%, enquanto que no grupo que recebeu a proteção do vácuo a EG ‘grau-2’ foi de 13% e a de ‘grau-3’ foi de apenas 8% (p < 0.5). Observaram ainda que no momento da ocorrência da EG, detectada pela ECO-TE, havia hipotensão arterial, aumento do ‘shunt’ e queda da PaO2. Resultados semelhantes foram depois reproduzidos por Pitto et al.(11) no grupo sem vácuo, a EG ocorreu em 85% dos casos, enquanto que no grupo com vácuo a incidência foi de apenas 5%. Em virtude do grande efeito protetor do vácuo, aplicado no fêmur proximal durante a cimentação das próteses, esses autores chegaram a con- siderar o uso dessa manobra até mesmo como uma boa alternativa à indicação de próteses sem cimento. Herndron et al.(27) também observaram significativa diminuição na intensidade e gravidade da EG Com relação à SEG que pode ocorrer após artroplastias ou osteos- sínteses, existem hoje diversas manobras ou táticas cirúrgicas que podem diminuir esse risco. Como seria de se esperar, todas elas visam evitar o aumento da pressão dentro do canal medular (PIM) durante a operação. As técnicas cirúrgicas atualmente utilizadas com esta finalidade são: 1) ESVAZIAMENTO DO CANAL MEDULAR.: Obviamente que quanto menor a quantidade de gordura intramedular, menor a chance de ocorrer EG. Das técnicas atualmente utilizadas, as que parecem fornecer melhores resultados são a lavagem do canal medular, com 206 com o uso do vácuo, só que ao invés de usarem a cânula metálica inter-trocanteriana, utilizaram um cateter intramedular. com o uso do vácuo, só que ao invés de usarem a cânula metálica inter-trocanteriana, utilizaram um cateter intramedular. que as medidas de PaO2 eram maiores naquele grupo porque, pro- vavelmente, o corticóide teria protegido os pulmões desses pacientes de danos maiores. Outro fato interessante que se pode observar nos dados dessa tabela é que a dose de Metilprednisolona administrada variou acentuadamente entre os diferentes autores. ACTA ORTOP BRAS 13(4) - 2005 PREVENÇÃO ona, ** = Não houve diferença nto à incidência de SEG entre os três a’ apontando para os benefícios do tros três estudos essa indicada pelo respectivo “p”. PREVENÇÃO Respectivamente à ordem de sua citação na tabela, essas doses foram de 40mg/Kg, 90mg/kg, 60mg/kg e 9mg/Kg. 3.5) “OVERDRILL” DISTAL: Num elaborado estudo sobre ATJ, Fahmy et al.(9) experimentaram cinco diferentes técnicas destinadas a evitar o inevitável aumento da PIM que ocorre nessas operações. Dentre as diversas combinações de manobras utilizadas, observaram que as menores alterações na PIM ocorriam quando se ampliava o orifí- cio de entrada no fêmur distal, dos habituais 8mm, para 12,7mm, o que eles denominaram de “overdrill”. Observaram ainda que com a utilização das fresas ranhuradas o aumento da PIM era bem menor. Dentre os cinco grupos testados, constatou que a associação da fresa ranhurada com o “overdrill” permitia manter a PIM entre em torno de seus valores normais (40 a 50mmHg), enquanto que com as outras técnicas esses valores variaram entre 180mmHg a 650mmHg. Com exceção do estudo de No.1, em todos os outros os resultados indicaram importante ação profilática dos corticóides quanto à ocor- rência de SEG após fraturas de fêmur e tíbia, apesar de as doses terem variado de 9mg/Kg a 90mg/Kg. Um dos maiores temores dos cirurgiões quanto ao uso de corticóides é a sua reconhecida associa- ção imunodepressora. A ocorrência de infecções oportunistas ou de super-infecções, entretanto, costumam ocorrer apenas nos casos de uso prolongado dessas drogas, situação muito diferente de seu ‘uso profilático’, o qual é feito por apenas um, dois ou três dias(84,106). Apesar das boas evidências(79,84,106) e sugestões(46) de que a Metilprednisolona, quando administrada logo após a admissão dos pacientes poderia evitar ou diminuir a incidência de SEG após fraturas de ossos longos e bacia, essa conduta não foi ainda aceita ou adotada como rotina. De acordo com os autores que reviram e discutiram esse assunto, isto se deve ao fato de que todos os estudos feitos até agora apresentam pequenas casuísticas, diferentes critérios de seleção dos pacientes e diferentes dosagens do corticóide utilizado, tornando a análise dos resultados não totalmente confiável. Ressaltam, portanto, a necessi- dade de se fazerem novos estudos prospectivos e randomizados e com grande número de pacientes, antes que se possa assumir uma conclusão definitiva a esse respeito(8,12,13,16,22,32,96). 3.6) PRÓTESES SEM CIMENTO: Foram introduzidas em virtude das graves e freqüentes complicações observadas com o crescente uso das próteses cimentadas, em especial a ocorrência de maciça e prolongada EG. PREVENÇÃO Através de observações clínicas e experimentais pôde-se, de fato, constatar que sua utilização diminuía considera- velmente a gravidade da EG durante as artroplastias(7,9,11,48,53,57,60). Por outro lado, as próteses sem cimento também apresentam des- vantagens, o que torna este tema extremamente polêmico. Pitto et al.(11), recentemente sumarizaram o assunto com uma boa dose de bom senso e experiência clínica. Segundo esses autores, “A decisão quanto ao uso de prótese cimentada ou não cimentada deve levar em conta a experiência do cirurgião e as seguintes características do paciente: idade, sexo, peso, atividade física, qualidade dos os- sos e anatomia do fêmur proximal”. Apesar de todas as técnicas e manobras até aqui discutidas, contudo, evitar-se completamente a ocorrência de EG, quer seja traumática ou peri-operatória, é ainda um objetivo impossível(48, 53). Ó conclusão definitiva a esse respeito( ). CONSIDERAÇÕES FINAIS Fazer uma revisão absolutamente completa sobre a “Embolia Gor- durosa” é uma tarefa praticamente inexeqüível a um pequeno grupo de investigadores, considerando-se que apenas nos arquivos atuais da MEDLINE (1950 a 2004) existem 2622 artigos sobre esse assun- to. Tampouco acreditamos que a revisão de todos aqueles artigos pudesse elucidar os numerosos pontos obscuros dessa síndrome. Conforme demonstrado ao longo do texto, existem inúmeros aspectos controversos ou pouco esclarecidos sobre os fenômenos da EG e da SEG. A impressão que nos ficou, portanto, foi a de que, mais importante que se obter uma revisão completa desse assunto, seria a realização de diferentes estudos prospec- tivos e randomizados, e com casuísticas representativas, especificamente desenhados a esclarecer as dúvidas e contro- vérsias que ora se impõem(92). O possível papel diagnóstico do lavado bronco-alveolar, o provável efeito profilático dos corticóides, o real benefício de cada uma das diferentes téc- nicas usadas nas artroplastias com vistas à diminuição da EG, seriam alguns exemplos dessa proposição. Não há dúvida de que tais estudos certamente trariam informações mais confiáveis e, portanto, de maior utilidade à prática ortopédica. A questão fundamental, entretanto, ainda não estaria resolvida. Ou seja, por que somente uma pequena fração dos pacientes que sofrem EG desenvolve SEG? 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Fat embolism syndrome in a case of abdominal lipectomy with liposuction. Md Med J 1999; 48:116-8. g p 95. Murray DG, Racz GB. Fat-embolism syndrome (respiratory insufficiency syndrome). J Bone Joint Surg Am 1974; 56:1338-49. 95. Murray DG, Racz GB. Fat-embolism syndrome (respiratory insufficie Am 1974; 56:1338-49. 43. Danesh-Meyer H, Savino PJ, Sergott RC. Case reports and small case series: ocular and cerebral ischemia 43. Danesh-Meyer H, Savino PJ, Sergott RC. Case reports and small case series: ocular and cer following facial injection of autologous fat. Arch Ophthalmol 2001; 119:777-8. 43. Danesh-Meyer H, Savino PJ, Sergott RC. REFERÊNCIAS BIBLIOGRÁFICAS Fat embolization and fatal cardiac arrest during hip arthroplasty with methylmethacrylate. Can J Anaesth 48:626-629, 2001. y g condylar prosthesis: report of two cases. Clin Orthop 1981; 160:106-8 y with methylmethacrylate. Can J Anaesth 48:626-629, 2001. y p p p 66. Caillouette JT, Anzel SH. 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Chest 1998; 113:178-81. 14. Aoki N, Soma K, Shindo M, Kurosawa T, Ohwada T. CONSIDERAÇÕES FINAIS No estudo de número um (46), apesar de não ter havido diferença estatisticamente significativa quanto à incidência de SEG entre os três grupos de pacientes, no grupo que recebeu corticóide a inci- dência de SEG foi zero. Além disso, houve, sim, diferença bastante significativa entre os valores das medidas de PaO2 dos pacientes dos diferentes grupos, notando-se aí que aqueles que receberam corticóide tiveram sempre uma PaO2 superior a dos outros grupos (p<0,03). A interpretação desse fato, segundo os autores, foi a de 207 tomography: case report. J Trauma 1997; 43:345-8. Case reports and small case series: ocu following facial injection of autologous fat. Arch Ophthalmol 2001; 119:777-8. y , , g p following facial injection of autologous fat. Arch Ophthalmol 2001; 119:777-8. ; 96. Richards RR. Fat embolism syndrome. Can J Surg 1997; 40:334-9. 96. Richards RR. Fat embolism syndrome. Can J Surg 1997; 40:334-9. g j g p 44. Hulman G. The pathogenesis of fat embolism. J Pathol 1995; 176: 3-9. 97. Goris RJA. Early osteosynthesis and prophylatic mechanical ventilation in the multitrauma patient. J Trauma 1982; 22:895-903. 97. Goris RJA. Early osteosynthesis and prophylatic mechanical ventilation in t 1982; 22:895-903. 45. Nogueira MP, Leme RJA, Fernandes TD. Embolia gordurosa. Acta Ortop Bras 1987; 5:166-74 g , , g p ; 46. Stoltenberg JJ, Gustilo RB. The use of methylprednisolone and hypertonic glucose in the prophylaxis fat embolism syndrome. Clin Orthop 1979; 143:211-21. g g p 6. Stoltenberg JJ, Gustilo RB. The use of methylprednisolone and hypertonic glucose in the 46. Stoltenberg JJ, Gustilo RB. The use of methylprednisolone and hyperto 46. Stoltenberg JJ, Gustilo RB. The use of methylprednisolone and hypertonic glucose in the prophylaxis of fat embolism syndrome Clin Orthop 1979; 143:211 21 46. Stoltenberg JJ, Gustilo RB. The use of methylprednisolon fat embolism syndrome. Clin Orthop 1979; 143:211-21. 98. Tscherne H, Regel G, Pape HC, Pohlemann T, Krettek C. Internal fixation of multiple fractures in patients with polytrauma. Clin Orthop 1998; 347:62-78. g yp fat embolism syndrome. Clin Orthop 1979; 143:211-21. 47. Peltier LF. Fat embolism: a current concept. Clin Orthop 1969; 66: 241-53 p y p 99. Bosse MJ, Mackenzie EJ, Riemer BL, Brumback RJ, McCarthy ML, Burgess AR et al. Adult respiratory distress syndrome, pneumonia, and mortality following thoracic injury and a femoral fracture treated either with intramedullary nailing with reaming or with a plate. A comparative study. J Bone Joint Surg Am 1997; 79:799-809. p p 48. Ries MD, Lynch F, Rauscher LA, Richman J, Mick C, Gomez M. Pulmonary p p 48. Ries MD, Lynch F, Rauscher LA, Richman J, Mick C, Gomez M. Pulmonary function during and after total 48. Ries MD, Lynch F, Rauscher LA, Richman J, Mick C, Gomez M. Pulmonary function during and after total hip replacement. J Bone Joint Surg Am 1993; 75:581-7. 48. Ries MD, Lynch F, Rauscher LA, Richman J, Mick C, Gomez M. Pulmonary function during and after total hip replacement. REFERÊNCIAS BIBLIOGRÁFICAS Síndrome da embolia gordurosa. Rev Bras Ortop 1994; 29: 767-72. p p pathogenesis of fat embolism. J Thorac Cardiovasc Surg 1972; 63: 968-72 pp ; p 18. Engel EE, Barbieri CH. Síndrome da pp p 18. Engel EE, Barbieri CH. Síndrome da embolia gordurosa. Rev Bras Ortop 1994; 29: 767-72. p g g ; 74. Riseborough EJ, Herndon JH. Alterations in pulmonary function, coag patients with fractures of the lower limbs. Clin Orthop 1976; 15: 248-67. p g g 74. Riseborough EJ, Herndon JH. Alterations in pulmonary function, coagu g g p 19. Freeman JI, Enneking FK. Orthopedic complications. In: Civetta JM, Taylor RW, Kirby RR. Critical care. 3rded. Philadelphia:Lippincot-Raven;1996.p.1231-52. 74. Riseborough EJ, Herndon JH. 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Satoh H, Kurisu K, Ohtani M, Arita K, Okabayashi S, Nakahara T et al. Cerebral fat emb 21. Satoh H, Kurisu K, Ohtani M, Arita K, Okabayashi S, Nakahara T et al. Cerebral fat embolism studie magnetic resonance imaging, transcranial doppler sonography, and single photon emission comp t h t J T 1997 43 345 8 21. Satoh H, Kurisu K, Ohtani M, Arita K, Okabayashi S, Nakahara T et al. Cerebral fat embolism studied by magnetic resonance imaging, transcranial doppler sonography, and single photon emission computed tomography: case report. J Trauma 1997; 43:345-8. 21. Satoh H, Kurisu K, Ohtani M, Arita K, Okabayashi S, Nakahara T et al. REFERÊNCIAS BIBLIOGRÁFICAS Evaluation of potential fat emb p of intramedullary nails after orthopedic fractures. Chest 1998; 113:178-81. 70. Mastrangelo AM, Jeitner TM, Eaton JW. Oleic acid increases cell surface expression and activityof CD11b 70. Mastrangelo AM, Jeitner TM, Eaton JW. 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Description of a new species of Apterotoxitiades Adlbauer, 2008 (Cerambycidae, Dorcasominae, Apatophyseini) and the female of A. vivesi Adlbauer, 2008, with notes on the biology of the genus
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08... 9 Launched to accelerate biodiversity research A peer-reviewed open-access journal 08... 9 Launched to accelerate biodiversity research A peer-reviewed open-access journal Descrip ZooKeys 482: 9–19 (2015) doi: 10.3897/zookeys.482.8901 http://zookeys.pensoft.net pecies of Apterotoxitia RESEARCH ARTICLE Abstract Following the description of the Apatophyseini genus Apterotoxitiades Adlbauer, 2008 (Cerambycidae: Dorcasominae) from South Africa, a new species has now been discovered in the eastern Drakensberg range of the country. The holotype female is here described as A. aspinosus sp. n. Also, a small series col­ lected at Hogsback, in the Amathole range, has allowed the description of the previously unknown female of the type species, A. vivesi Adlbauer, 2008. Both species are high altitude dwellers, occurring above 1300 m asl and their habitat consists mainly of mountain grassland interspersed with mistbelt forest pockets. All specimens were recorded in the austral winter to early spring, when these mountain ranges are occasion­ ally covered in snow and night temperature plummet below 0 °C. They appear to be nocturnal and their complete lack of wings indicates a remarkable adaptation to cold conditions at high altitude. http://zoobank.org/5E7A81DB-32AC-42B3-ACDE-C1B78D99477E Citation: Adlbauer K, Bjørnstad A, Perissinotto R (2015) Description of a new species of Apterotoxitiades Adlbauer, 2008 (Cerambycidae, Dorcasominae, Apatophyseini) and the female of A. vivesi Adlbauer, 2008, with notes on the biology of the genus. ZooKeys 482: 9–19. doi: 10.3897/zookeys.482.8901 Copyright Karl Adlbauer 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. Description of a new species of Apterotoxitiades Adlbauer, 2008 (Cerambycidae, Dorcasominae, Apatophyseini) and the female of A. vivesi Adlbauer, 2008, with notes on the biology of the genus Karl Adlbauer1, Anders Bjørnstad2, Renzo Perissinotto3 1 Kasernstraße 84, A-8041 Graz, Austria 2 Høyåsstien 12, NO-3727 Skien, Norway 3 School of Life Sciences, University of KwaZulu-Natal, P. Bag X54001, Durban 4001, South Africa Corresponding author: Renzo Perissinotto (renzo.perissinotto@nmmu.ac.za) c editor: S. Lingafelter  |  Received 5 November 2014  |  Accepted 23 January 2015  |  Published 11 February 2015 Keywords Cerambycidae, Dorcasominae, Apatophyseini, Apterotoxitiades, new species, habitat, South Africa Copyright Karl Adlbauer 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. Karl Adlbauer et al. / ZooKeys 482: 9–19 (2015) 10 Introduction The genus Apterotoxitiades Adlbauer, 2008 was described on the basis of a single male from Hogsback in the Amathole mountains of the Eastern Cape Province of South Africa. It was collected in August 1992, under a large log on gently sloping grassland terrain. In early September 2014, the type locality was revisited, resulting in several new specimens including the hitherto unknown female of the only described species, A. vivesi Adlbauer, 2008. This survey also provided further details on the habitat char­ acteristics and ecology of this species. A female specimen of what is obviously a representative of the genus Apterotoxitia­ des has for some time been in the ABPC collection. It had been collected in the Drak­ ensberg mountains of KwaZulu-Natal in October 1972, by an unknown collector. Because of a lack of knowledge of the degree of sexual dimorphism within the genus prior to the new Amathole collection, it was not possible to conclude with confidence as to whether this was the unknown female of A. vivesi or a different species. The new material from Hogsback however, clearly shows that the Drakensberg specimen repre­ sents an entirely different species which is hereby described.h f A brief outline of the generic diagnostic characters is given below. The generic description of Apterotoxitiades was provided by Adlbauer (2008), but the discovery of the new species, A. aspinosus sp. n. necessitates a slight amendment of the original description, mainly in virtue of a total absence of lateral pronotal spines in the new species. Methods Specimen length was measured from the anterior margin of the head to the elytral apex. Specimen width represents the maximum width of the elytra. Photos of set spe­ cimens were taken using a Canon Eos 5D camera fitted with a Canon MP-E 65 Macro 2.8-1.5× objective. Components of male genitalia were photographed under a Nikon SMZ 25 stereomicroscope, using a Nikon Digital Sight DS-Fi2 camera. In situ photos were taken using a Ricoh CX1 camera with macro setting. Collections are abbreviated as follows: TMSA, Ditsong National Museum of Nat­ ural History (formerly Transvaal Museum), Pretoria, South Africa; ISAM, Iziko South African Museum, Cape Town, South Africa; NHMO, Natural History Museum, Oslo, Norway; ABPC, Anders Bjørnstad Private Collection, Skien, Norway; KAPC, Karl Adlbauer Private Collection, Graz, Austria; RPPC, Renzo Perissinotto & Lynette Clennell Private Collection, Port Elizabeth, South Africa. Geographical abbreviations are as follows: RSA, Republic of South Africa; KZN, KwaZulu-Natal Province, South Africa; EC, Eastern Cape Province, South Africa. Description of a new species of Apterotoxitiades Adlbauer, 2008... 11 Genus Apterotoxitiades Adlbauer, 2008 The major characters are the wingless body with strongly atrophic (nearly absent) shoul­ ders, short head with small, coarsely facetted eyes and long palpi with terminal segment expanded in male. Pronotum armed or not (amended from the original description). Legs are long and slender, coxae are rather large and prominent. In the light of the recent work undertaken by Villiers et al. (2011), on the Dorcasominae of Madagascar, it is clear that the male genitalia of Apterotoxitiades fall within the range described for this subfamily. Only a single male of the remarkable type species A. vivesi, which seemingly oc­ curs rarely and locally, was hitherto known from the genus. The new material recently found allows the description of the female. Apterotoxitiades vivesi Adlbauer, 2008 Figures 1–4 Material examined. Four female and two male specimens: South Africa, EC, Hogs­ back, 1300 m, 7 Sep 2014, R. Perissinotto & L. Clennell leg. (TMSA, ISAM, KAPC, RPPC). Only one male and one female were found alive, while the other four speci­ mens were dead, two with soft tissue consumed by spiders. Description. ♀. Length: 10–11.5 mm; width: 3.5–4 mm (n = 4). General habitus as in male (Figure 2), but with shorter antennae and legs and wider elytra (Figures 1–3). Coloration. Dark greyish brown, apices of the elytra slightly lighter brown. Palpi, antennae, legs and ventral side light yellow brown. Mandibles light yellow brown, with the exception of the apices which are black. Body surface. Whole surface covered in short depressed silky tomentum. Long, thin, hairlike whitish grey bristles present especially on the lateral side of the mandi­ bles, scapus and pronotal sides (Figure 1A). Head. Broad with strong, falciform mandibles. Palpi moderately long, terminal segment only very weakly enlarged. Eyes coarsely facetted, strongly protuberant and broadly separated, small, oblique, not emarginate and far behind antennal tubercles. Frons between the eyes broad and flat. Antennae reaching to the second half of the elytra. Antennomeres becoming shorter towards the end, but not very different in length from each other. Pronotum. As long as wide with long, rather acute lateral spines pointed strongly obliquely upwards (Figure 1A). Surface like in male (Figure 2). Disc convex in the middle. Unlike in male, the anterior edge is not broader than the posterior. Scutellum. Very small, hardly visible, wider than long. Elytra. Fused, somewhat broader than in male, widest in the anterior third. Strongly convex, both laterally and dorsally. Slightly more than half of the anterior part sparsely punctate. Apices broadly rounded. Karl Adlbauer et al. / ZooKeys 482: 9–19 (2015) 12 Figure 1. Apterotoxitiades vivesi: Female dorsal (A) and ventral (B) habitus, 11 mm TL (photos Lynette Clennell). A B A Figure 1. Apterotoxitiades vivesi: Female dorsal (A) and ventral (B) habitus, 11 mm TL (photos Lynette Clennell). Legs. Long and slender, but shorter than in male (Figures 2 and 3). Coxae large and projecting (Figure 1B). Ventral surface. All coxae well separated from each other, especially the metacoxae. The first visible abdominal sternite is the longest, with the following becoming pro­ gressively shorter until the fifth visible (Figure 1B). i Male. A general description is provided in Adlbauer (2008). Apterotoxitiades vivesi Adlbauer, 2008 Figures 1–4 Only further details of the genitalia, along with photos of whole genitalia as well as tegmen and aedeagus separately are provided here (Figure 4A–C). Aedeagus with heavily sclerotized acute dorsal lobe bearing an acuminate apex. Ventral lobe with a rounded, weakly truncate apex, much shorter than dorsal lobe, and decidedly less sclerotized. Apophyses long, strap-shaped and constituting more than 50% of total aedeagus length (Figure 4B). Tegmen with relatively long and slender, slightly diverging parameres with apical brus­ hes of very long setae (Figures 4A, C). Presence of sheath-like appendage between the base of the parameres and the “tegmen ring”, on both sides.When the aedeagus is in its position inside the tegmen, the apex of the dorsal lobe reaches almost to the apices of the parameres, while the ventral lobe reaches just beyond the point of diversion of the parameres (Figure 4A). Description of a new species of Apterotoxitiades Adlbauer, 2008... 13 Figure 2. Apterotoxitiades vivesi: Male specimen in its natural habitat, Hogsback Forestry, September 2014 (photo Lynette Clennell). Figure 2. Apterotoxitiades vivesi: Male specimen in its natural habitat, Hogsback Forestry, September 2014 (photo Lynette Clennell). Figure 3. Apterotoxitiades vivesi: Female specimen in its natural habitat, Hogsback Forestry, September 2014 (photo Lynette Clennell). Figure 3. Apterotoxitiades vivesi: Female specimen in its natural habitat, Hogsback Forestry, September 2014 (photo Lynette Clennell). 14 Karl Adlbauer et al. / ZooKeys 482: 9–19 (2015) A B C Figure 4. Apterotoxitiades vivesi: Dorsal view of whole male genitalia (A), aedeagus (B) and tegmen (C) (photos Lynette Clennell). B Figure 4. Apterotoxitiades vivesi: Dorsal view of whole male genitalia (A), aedeagus (B) and tegmen (C) (photos Lynette Clennell). Apterotoxitiades aspinosus Björnstad, sp. n. http://zoobank.org/704D5D2E-5099-43E7-9478-5EBE9EC9B30A Figure 5 Apterotoxitiades aspinosus Björnstad, sp. n. http://zoobank.org/704D5D2E-5099-43E7-9478-5EBE9EC9B30A Figure 5 Apterotoxitiades aspinosus Björnstad, sp. n. http://zoobank.org/704D5D2E-5099-43E7-9478-5EBE9EC9B30A Figure 5 Type. Holotype (HT) ♀: RSA, Natal 1500/2000 m [Royal] Nat[al] Nat. Park X/1972 [collector unknown] (NHMO).hf Diagnosis. The most obvious difference from A. vivesi is the total lack of lateral spines on the pronotum. Both sexes of A. vivesi have pronotum with “langen, zahn­ förmigen Seitendornen” (Adlbauer 2008). The new species also differs by its greater size (17 mm vs. 10–11 mm in A. vivesi female), and by the somewhat more elongate body outline. Diagnosis. The most obvious difference from A. vivesi is the total lack of lateral spines on the pronotum. Both sexes of A. vivesi have pronotum with “langen, zahn­ förmigen Seitendornen” (Adlbauer 2008). The new species also differs by its greater size (17 mm vs. 10–11 mm in A. vivesi female), and by the somewhat more elongate body outline. Etymology. The word “aspinosus” refers to the lack of lateral spines on the prono­ tum, which are very prominent in the type species, A. vivesi. Etymology. The word “aspinosus” refers to the lack of lateral spines on the prono­ tum, which are very prominent in the type species, A. vivesi. Description. HT ♀. Length: 17 mm; width 5.8 mm. Habitus rather slender, long legged, flightless with fused elytra (Figure 5). Description. HT ♀. Length: 17 mm; width 5.8 mm. Habitus rather slender, long legged, flightless with fused elytra (Figure 5). l Coloration. Head and pronotum dark reddish brown, elytra slightly lighter. Legs, antennae and palpi yellow to brownish yellow. Eyes black with bronze lustre.i Body surface. Head and pronotum finely, but densely punctate/granulate. Elytra with scattered, shallow pit-like punctation, each pit bearing a pale yellowish bristle. Description of a new species of Apterotoxitiades Adlbauer, 2008... 15 A B Figure 5. Apterotoxitiades aspinosus sp. n.: Holotype female dorsal (A) and ventral (B) habitus, 17 mm TL (photos Karsten Sund and Hallvard Elven). Figure 5. Apterotoxitiades aspinosus sp. n.: Holotype female dorsal (A) and ventral (B) habitus, 17 mm TL (photos Karsten Sund and Hallvard Elven). Elytra surface with short, curved ± adpressed silky tomentum. The same type of tomen­ tum occurs on palpi, head, scape and pronotum, but there with interspersed long, stiffly erect pale yellowish-hyaline bristles, particularly distinct on anterior part of head and lateral part of pronotum. Head. Both labial and maxillary palpi long and slender and with ultimate joints narrowly triangular. Apterotoxitiades aspinosus Björnstad, sp. n. http://zoobank.org/704D5D2E-5099-43E7-9478-5EBE9EC9B30A Figure 5 Mandibles strong, sickle-shaped with curved, glabrous and shiny apices. Front of head with moderately raised antennal tubercles, and without a longitu­ dinal furrow between them. Eyes small, strongly protuberant, far apart from antennal socket, only sligthly emarginate. Antennae reaching elytral midlength; scapus widened apically; pedicellus almost globular, but shorter than wide. Antennomere 5 of same length as scape, following antennomeres shorter than these and gradually tapering and shortening distally; antennomeres 5–11 with minute, but dense greyish tomentum. g g Pronotum. Shorter than wide (length/width ratio = 0.8) and with posterior margin wider than anterior. Both edges are only weakly thickened or rimmed. Small constric­ tion on anterior end, at about one fifth of the length, otherwise smoothly convex both dorsally and laterally. y y Scutellum. Short, broadly triangular with a broad, slightly thickened black border. 16 Karl Adlbauer et al. / ZooKeys 482: 9–19 (2015) Elytra. Fused, strongly convex both laterally and dorsally and with evenly rounded apices. Shoulders only weakly marked. Legs. Long and slender with only weakly thickened femora; straight tibiae gradu­ ally widening apically; tarsi long and slender, especially the metatarsi. Ventral surface. Gula glabrous, all other parts finely granulate and rather densely cov­ ered in curved, silky, adpressed tomentum as on dorsal side (Fig. 5B). Procoxae strong and conical, separated by a narrow prosternal process slightly widened and truncate at apex. Procoxal cavities more or less circular in outline but antero-laterally with a small and short acute extension. Metasternum narrow with a truncated triangular process (Fig. 5B). Visible abdominal sternites 1–5 with a finely granulate microstructure and progressively narrowing posteriorly. Sternite 5 with a straight to weakly concave truncation apically. Male. Unknown. Biology of the genus Apterotoxitiades Both Apterotoxitiades species currently known have been collected in grassland terrain at high altitudes, above 1300 m asl, in the Amathole range of the Eastern Cape (Figure 6) and the eastern Drakensberg of KwaZulu-Natal (Figure 7). The vegetation units that characterize these areas are typically Amathole Montane Grassland (Gd 1, habitat of A. vivesi) and Northern Drakensberg Highland Grassland (Gd 5, presumed habitat of A. aspinosus sp. n.). Both are part of the Drakensberg Grassland Bioregion (Mucina and Rutherford 2006). The Amathole Montane Grassland unit exhibits short grassland dominated by a variety of grass species, mainly Themeda triandra, and a high species richness of forbs, especially those of the family Asteraceae (e.g. Helychrysum spp., Se­ necio spp.) (Mucina and Rutherford 2006). Although this vegetation unit is generally not regarded as highly threatened, in the area of Hogsback, which consitutes the only known habitat of A. vivesi, most of it has already experienced large-scale transformati­ on to pine plantations (Figure 6). The generally steep slopes of the Northern Drakensberg Highland Grassland sup­ port short sour grassland rich in forbs. Scattered trees of Protea caffra and P. roupel­ liae are also a typical feature of this vegetation unit, as are small patches of mistbelt forest occasionally growing in wet ravines. Unlike the previous unit, the Northern Drakensberg Highland Grassland vegetation currently faces little conservation threat, particularly in the relatively large uKhahlamba Drakensberg Park, which enjoys status of UNESCO World Heritage Site since 2000 (Mucina and Rutherford 2006). The Royal Natal National Park, where the holotype of A. aspinosus sp. n. was collected in 1972 (Figure 7), currently falls within this wider Park. g y All specimens of A. vivesi, including the holotype male collected in August 1992 (Adlbauer 2008), have so far been found under 1–2 year old pine logs lying on the ground, adjacent to the grassland (Figure 6). Three pine species are cultivated in the area by the Amathole Forestry Company, including Pinus elliottii, P. patula and P. radiata (Chapman 2011). However, no evidence of A. vivesi using this pine wood as Description of a new species of Apterotoxitiades Adlbauer, 2008... 17 Figure 6. Apterotoxitiades vivesi: Typical habitat of mountain grassland with shrub pockets and pine plantations on the slopes of the Hogsback mountain range (photo Lynette Clennell). Figure 6. Biology of the genus Apterotoxitiades Apterotoxitiades vivesi: Typical habitat of mountain grassland with shrub pockets and pine plantations on the slopes of the Hogsback mountain range (photo Lynette Clennell). boring or larval development medium could be found. All adult specimens were sim­ ply hiding under the logs, at the interface between bark and grass or leaf litter, where moisture levels were significantly higher than elsewhere and no light penetration oc­ curred. It is likely that larval development may occur either on the stems of the short shrubs that occur within the grassland, or on the roots of the grass itself. The larvae of some Palearctic genera of Cerambycidae, such as Vesperus and Dorcadion for instance, are well known for their underground development, feeding on the roots of a variety of grasses and shrubs (Pesarini and Sabbadini 1994). g Given their extremely reduced compound eyes, adult A. vivesi are probably noctur­ nal in activity. During the period of their activity, this area does not receive any major rainfall, but some surface moisture is maintained by night-time mist and/or fog. As this dries out in the heat of the day, however, the beetles would need to return under­ ground or find a suitable shelter for the day at the surface, ideally rich in moisture and protected from light and visual predators. Thus, tree logs lying on the ground at the edge of the grassland, and possibly also large stones, may provide an ideal hideout for adults to spend the day. However, this habitat is also shared by ground beetles (Car­ abidae) and spiders, with the latter actually consuming A. vivesi, judging by the state of the carcasses retrieved in their silk wrapping. Karl Adlbauer et al. / ZooKeys 482: 9–19 (2015) 18 Figure 7. Apterotoxitiades aspinosus: The Amphitheatre of the Royal Natal National Park, as a likely representative of the typical Drakensberg habitat of this species (photo Gerald Camp). Figure 7. Apterotoxitiades aspinosus: The Amphitheatre of the Royal Natal National Park, as a likely representative of the typical Drakensberg habitat of this species (photo Gerald Camp). The following observations were made directly in the field by R.P. during the survey of September 2014. Remarkably, the only two specimens found still alive in their habitat (all the other specimens were already dead and partly decomposed) died very rapidly once removed from their wet and dark hideout under the wood. Acknowledgements We are grateful to the Eastern Cape Department of Economic Affairs, Environmental Affairs and Tourism for granting permits to undertake collections in the study area. We also thank Riccardo Mourglia of Rivoli, Italy, for providing the holotype specimen of A. aspinosus and Karsten Sund and Hallvard Elven of the Natural History Museum in Oslo for the photos of the same. Lynette Clennell is thanked for photographic and observational support throughout the survey of the Hogsback area. Biology of the genus Apterotoxitiades They im­ mediately entered a state of muscular spasm, developing a shivering-type of reaction followed by the folding of their legs and death within a period of less than 1 hour. This reaction could possibly have been caused by sudden exposure to intense light, as their compound eyes are extremely reduced (Figures 1, 3, 5) and reminiscent of those observed in some cave beetles. A more likely possibility is, however, that they may have suffered thermal shock, by being suddenly exposed to temperatures much higher than those prevailing under the logs. The air temperature on the day of the collection was in fact partricularly high in comparison to seasonal averages, with almost 30 °C attained around midday. Even more intriguing appears to be the period of adult activity during mid-late winter. The already dead specimens, and a few more consumed carcasses found on site, clearly indicate that adults were already on their way out in early September and prob­ ably at peak activity about a month earlier. This is unusual for high altitude areas of southern Africa, where adult cerambycids generally start emerging only in the spring, after substantial rainfall events. At Hogsback, in particular, rainfall exhibits a bimod­ al pattern, with spring and late summer peaks, and annual precipitation can reach 1000 mm. Minimum temperatures often plummet below zero in winter and frost occurs with frequency of up to 80 days per year (Leroux 1994, Mucina and Ruther­ ford 2006). Occasional, light snowfalls are also a regular feature of the winter season. Thus, the winter activity of A. vivesi, combined with its apparent intolerance for high temperatures, may be indicative of an unusual adaptation to cold climatic conditions. Description of a new species of Apterotoxitiades Adlbauer, 2008... 19 Unfortunately, no habitat data was reported on the label accompanyng the holotype specimen of A. aspinosus sp. n., and thus it is not possible to draw conclusions about its ecology. Nevertheless, it seems likely that its main traits may be similar to those observed in A. vivesi, with the exception that in this case the period of adult activity is clearly in the spring, as the fresh holotype specimen was found in October. References Adlbauer K (2008) Neues zur Taxonomie von Cerambyciden der Äthiopischen Region (Coleoptera, Cerambycidae). Les Cahiers Magellanes 80: 1–20. Chapman C (2011) Practicing sustainable forestry in a tough environment. SA Forestry Magazine Dec 2011: 14–17. Leroux V (1994) Secret Southern Africa. AA The Motorist Publications (Pty) Limited, Cape Town, 320 pp. Mucina L, Rutherford MC (2006) The Vegetation of South Africa, Lesotho and Swaziland. Strelitzia 19. South African National Biodiversity Institute, Pretoria, 807 pp. Pesarini C, Sabbadini A (1994) Insetti della Fauna Europea: Coleotteri Cerambicidi. Natura, Rivista di Scienze Naturali 85(1/2): 1–132. Villiers A, Quentin R-M, Vives E (2011) Cerambycidae Dorcasominae of Madagascar (Coleop­ tera, Cerambycidae, Dorcasominae). Magellanes Collection Ex Natura 3: 1–387.
https://openalex.org/W3009897744
https://ruc.udc.es/dspace/bitstream/2183/25185/3/AlvesCarlos_FigueiredoCarlos_SanjurjoSanchezJorge_Rock_features_alteration_stone_materials_used_built_environment.pdf
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Rock Features and Alteration of Stone Materials Used for the Built Environment: A Review of Recent Publications on Ageing Tests
Geosciences
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Carlos Alves 1,*, Carlos Figueiredo 2 and Jorge Sanjurjo-Sánchez 3 1 LandS/Lab2PT-Landscapes, Heritage and Territory laboratory (FCT-AUR/04509) and Earth Sciences Department/School of Sciences, University of Minho, 4710-057 Braga, Portugal 2 CERENA—Centro de Recursos Naturais e Ambiente, FCT- UID/ECI/04028/2019, DEcivil, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; carlos.m.figueiredo@ist.utl.pt 3 University Institute of Geology, Universidade da Coruña, ESCI, Campus de Elviña, 15071 A Coruña, Spain; jorge.sanjurjo.sanchez@udc.es * C d d h 1 LandS/Lab2PT-Landscapes, Heritage and Territory laboratory (FCT-AUR/04509) and Earth Sciences Department/School of Sciences, University of Minho, 4710-057 Braga, Portugal 2 CERENA—Centro de Recursos Naturais e Ambiente, FCT- UID/ECI/04028/2019, DEcivil, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; carlos.m.figueiredo@ist.utl.pt 3 University Institute of Geology, Universidade da Coruña, ESCI, Campus de Elviña, 15071 A Coruña, Spain; jorge.sanjurjo.sanchez@udc.es * Correspondence: casaix@dct uminho pt j g j j * Correspondence: casaix@dct.uminho.pt Received: 30 December 2019; 26 February 2020; Published: 28 February 2020 Received: 30 December 2019; 26 February 2020; Published: 28 February 2020 Abstract: This work presents a review of recent publications, with publication date between 2017 and 2019, with information on the relation between rock characteristics and the effects of diverse agents associated with alteration of stone materials in the built environment. It considers information obtained from ageing tests performed under laboratory conditions and by exposure to outdoor agents. Several lithological groups were considered, with sedimentary carbonate rocks being the most frequently studied lithotypes and silicate metamorphic rocks being the group with scarcer information. In terms of ageing tests, salt weathering was the most frequent one while there was a noticeable lesser amount of information from tests with biological colonization. The collected data showed the influence of diverse features, from specific minerals to whole-rock properties and the presence of heterogeneities. These information are discussed in the context of formulating a general framework for stone decay. Keywords: salt weathering; mineralogy; structural-textural characteristics; porous media Rock Features and Alteration of Stone Materials Used for the Built Environment: A Review of Recent Publications on Ageing Tests Carlos Alves 1,*, Carlos Figueiredo 2 and Jorge Sanjurjo-Sánchez 3 Geosciences 2020, 10, 91; doi:10.3390/geosciences10030091 1. Introduction The potential interest of this line of research is, in our opinion, two-fold: p p To help in the diagnosis of the causes promoting the alteration of natural stone in the built environment, in order to help in the design of suitable intervention measures; To contribute to define criteria for the selection of suitable stone materials for application in the built environment, also according to the alteration agents that could affect these materials. 2. Dataset This review considers publications found in the Scopus database, with publication date from 2017 onward and that present empirical results from ageing tests with natural stone. We considered only studies performed under laboratory conditions or by exposure to outdoor conditions given that in these cases there would be information regarding time and some control in relation to the initial conditions. While there were many other publications concerning the alteration of stones in the built environment during the aforementioned period, we collected information from 74 publications [8– 81] that presented experimental results on the interaction between rock features and ageing agents, and that will be discussed in the following sections. This document was prepared with Google online software (Google Docs and Google Sheets) and with additional editing with the open-source freeware LibreOffice (https://www.libreoffice.org) and Inkscape (https://inkscape.org). 3. Rocks and Tests Here is presented a first analysis of the considered dataset with some general information in relation to the types of rocks and the tests that were used for simulating the alteration processes. 1. Introduction Stone is an important component of the cultural heritage and still going strong as a building material, with around 2.8 million tons of dimension stone sold in 2018 in the United States alone [1]. The interactions between stone materials and diverse agents in the built environment can lead to, in general, unwanted alteration features. The term “alteration” is used here in a wide sense to encompass all unintended transformations that the stone suffers because of the agents in the built environment such as salts, water, ice, biological colonization, atmospheric pollution, etc. The alteration of stone after emplacement in built structures has been noticed at least since the time of Herodotus, who reported the occurrence of efflorescence of salt in Egypt and remarked that "even the pyramids are being eaten away by it" [2]. Comments on stone characteristics relevant to their performance in buildings were also presented in Vitruvius classic work [3], which has what was possibly the first proposal for tests to assess stone durability using an exposure test. While the test proposed by Vitruvius used field conditions, the time range proposed by this author is not compatible with building projects and diverse accelerated ageing tests have been devised using the agents usually identified in the alteration of building materials. General concepts concerning the alteration processes that affect stone applied in the built environment can be found in Siegesmund and Snethlage [4]. While there are several reviews Geosciences 2020, 10, 91; doi:10.3390/geosciences10030091 www.mdpi.com/journal/geosciences www.mdpi.com/journal/geosciences Geosciences 2020, 10, 91 2 of 13 concerning alteration agents such as atmospheric pollution [5], soluble salts [6], and biological agents [7], the effects of rock characteristics have deserved less attention. concerning alteration agents such as atmospheric pollution [5], soluble salts [6], and biological agents [7], the effects of rock characteristics have deserved less attention. This review attempts to present a snapshot of recent trends in what can be called the petrological side of natural stone alteration and we did not consider results from tests with artificial stone. 3.1. Lithological Diversity The rocks mentioned in the publications were distributed (Figure 1) by the following general lithological groups: • SC, sedimentary carbonate rocks (mostly diverse types of limestones and including, travertines, carbonate tufas and dolostones); • SD, sedimentary detrital rocks, a group that in the studied set corresponds to arenaceous rocks; • P, pyroclastic rocks; • M, magmatic rocks (which include plutonic and lava rocks); , magmatic rocks (which include plutonic and lava rocks); C, metamorphic carbonate rocks (in the data collected all occurrences correspond to marbles); S, metamorphic silicate (with diverse crystals-sizes and composition, from slates to gneiss, and l d ) • MC, metamorphic carbonate rocks (in the data collected all occurrences correspond to marbles); • MS, metamorphic silicate (with diverse crystals-sizes and composition, from slates to gneiss, and including serpentinites). The plot represents the percentage of the studied publications that consider a given group, hence some publications will be counted more than once (e.g., if they studied a granite and a limestone) and the sum of the values will be higher than 100. More petrological details will be given in the discussion of the relations with alteration tests. It is clear that sedimentary carbonate rocks are dominant in this dataset while, on the other extreme, silicate metamorphic rocks are scarcely represented. While the plot of Figure 1 gives an indication of the lithological diversity of the studied dataset, it does not show the specific rocks considered in each publication. This will be more developed in the discussion of section 4 but even that might fail to reveal the extension of some works such as, e.g., Ahmad et al. [8], which consider 12 types of plutonic and metamorphic rocks and Pötzl et al. [47], which studied 14 types of tuff. 3 of 13 Geosciences 2020, 10, 91 eosciences 2020, 10, 91 3 of Figure 1. Lithological diversity of the analyzed publications considering the following broad groups: SC: sedimentary carbonate rocks; SD: sedimentary detrital rocks; P: pyroclastic rocks; M: magmatic rocks; MC: metamorphic carbonate rocks; MS: metamorphic silicate. Figure 1. Lithological diversity of the analyzed publications considering the following broad groups: SC: sedimentary carbonate rocks; SD: sedimentary detrital rocks; P: pyroclastic rocks; M: magmatic rocks; MC: metamorphic carbonate rocks; MS: metamorphic silicate. 3.2. Ageing Tests Figure 2 presents a plot that attempts to show the kind of agents that were used in the analyzed publications to promote the alteration of the rock specimens, again as a percentage of the dataset. The sum of the frequency values, again, gives a value above 100, since some publications consider more than one agent, such as salt weathering and freeze-thaw. In this general review, we are considering under "S" all salt weathering tests, regardless of the variations in terms of the type of salt, salt content, imbibition procedure, and environmental conditions, namely drying temperature. The groups "F" (freeze-thaw), "T" (thermal cycles), and "H" are all related to temperature variations but the first one mostly concerns the effects of volumetric variations of water in pores and, therefore, is akin of the salt weathering tests. The group referred to as "CR" (chemical reactants) corresponds to diverse tests where, nonetheless, chemical reactions are dominant, whether related to atmospheric pollution (solution, gases, and particles) or to dissolution and leaching by solutions, including slake tests. In this organization, we are assuming that water or salt solutions do not cause significant chemical changes. The group represented as "B" corresponds to tests designed to promote biological colonization but exposure tests, "E", can also promote this kind of result. As will be seen below, the kind of effects resulting from heating ("H") and thermal shocks and cycling ("T") are quite different, given, namely, that the first kind of test involves higher temperatures. We are assuming that the thermal effects of wet-dry tests (“W”) and salt weathering tests were negligible, which can be controversial, especially for the later. Of course, one can also posit that both salt weathering tests and freeze-thaw tests include a wetting-drying component. osciences 2020, 10, 91 4 of Figure 2. Ageing tests of which data were collected from the publications considered, S: salt weathering; F: freeze-thaw; W: wetting-drying; CR: chemical reactants; B: biological colonization; (see text for more information); T: thermal cycles; H: heating; U: exposure to ultraviolet radiation; E: exposure to weathering agents in the outdoors. 4 of 13 Geosciences 2020, 10, 91 Figure 2. Ageing tests of which data were collected from the publications considered, S: salt weathering; F: freeze-thaw; W: wetting-drying; CR: chemical reactants; B: biological colonization; (see text for more information); T: thermal cycles; H: heating; U: exposure to ultraviolet radiation; E: exposure to weathering agents in the outdoors. 3.2. Ageing Tests Salt weathering is clearly the most frequent kind of ageing test considered in the publications analyzed, followed by freeze-thaw. It is also noteworthy the relatively small proportion of publications concerning the effects of chemical pollutants and, most strikingly, the proportion that considers tests promoting biological colonization (however, tests involving the exposure to outdoor agents might be influenced by both). 4. Effects of Ageing Tests on Rock Features This section presents the information collected on the effects of ageing tests on specific rock features, including mineralogical, textural, structural, and pore system characteristics, as well as (bulk) physical properties, including mechanical properties. In some cases, results concern one feature but in others, the authors propose potential relations to several factors. 4.1. Minerals and Other Phase Constituents The characteristics of some minerals and other constituent phases have been indicated as contributing to the alterations of stone materials. Some mineral phases are particularly susceptible to dissolution such as calcite, which was studied by tests with acid rain solutions [30] and the occurrence of high magnesium calcite and aragonite was considered to favor dissolution of limestones [17]. Also in limestones, there is reference to the susceptibility of calcite to biological action [63]. The anisotropic behavior to the dissolution of calcite has been reported as having an impact on the surface reactivity of marbles [69]. Some studies have also found etching of calcite crystals resulting from limestone heating [22]. Experiments with burying in guano, which can have saline and acid effects, have described reactivity of lithologies with calcium phases in limestone and basalt [9]. According to Deng et al. [36], clay minerals can react with acid solutions, enhancing the microporosity and susceptibility to freeze-thaw of sandstones. There are also references to the reactivity of non-crystalline constituents, such as the dissolution of organic matter in limestone under salt weathering [35] and the susceptibility of carbon-rich slates to microorganisms [19]. In a somewhat opposite direction, there are indications that dolomite crystals in marbles were less susceptible to the action of microorganisms [11] and that the presence of dolomite in limestones contributed to higher resistance to dissolution with water [17]. The higher resistance to salt Geosciences 2020, 10, 91 5 of 13 weathering tests of dolomitic marbles, in relation to calcitic ones, has been attributed to the lower solubility of dolomite, when compared with calcite, in salt solutions [23]. weathering tests of dolomitic marbles, in relation to calcitic ones, has been attributed to the lower solubility of dolomite, when compared with calcite, in salt solutions [23]. Oxidation processes can contribute to stains in limestone because of the action of salt solutions [71] and acid solutions [38], with this last publication also reporting the oxidation of iron-containing calcite. Physical agents can interact also with the characteristics of the minerals that are present in a rock. The presence of phyllosilicates has been considered to contribute to the susceptibility of arenaceous sedimentary rocks to salt weathering [50,56] and to wetting-drying [77], with these last authors proposing different impact for different clay minerals according to moisture content. 4.1. Minerals and Other Phase Constituents Biotite was found to be more susceptible to the development of fissures under stress conditions that promoted crack propagation in kersantite specimens [55]. Ultraviolet exposure tests have been reported as causing oxidation effects on sandstones exposed to the outdoors [12]. Alterations effects associated with thermal cycles have been indicated, namely in relation to calcite volumetric variations [78]. We can include in these considerations also a study that presented observations of slight bowing of magmatic rocks under thermal cycles [51]. There are also studies explaining mass loss in tuff and andesite as resulting from mineralogical changes associated with loss of interstitial water of layered minerals because of gas temperature under conditions simulating atmospheric pollution [64]. Chromatic changes resulting from heating have been reported for clay minerals in sandstones [40] and in limestone [27], and for biotite, amphiboles, garnet, alkaline feldspars, chlorite, and quartz in granitoids [68], and these authors also refer to the influence of the content in biotite and plagioclase on the rock physical damage by cracking. 4.2. Pore Network Features In a comparison Geosciences 2020, 10, 91 6 of 13 of limestone and granite, higher increase in porosity was found for limestone than for granite, porosity being lower in limestone [73]. On the other hand, there is at least one study explaining the slight impact of thermal shock on a limestone by the low porosity of this rock [18] Besides the total amount of pores, the dimensions of the pores have been considered. In freeze- thaw tests with diverse rock types (basalt, diabases, dolostones, gneiss, granite, limestones, and sandstone), susceptibility was higher for high porosity rocks but was also related to a parameter based on a volumetric fraction of the pore space [26]. The effects of salt weathering on granites have been found to be related to higher porosity but also to pore-size distribution [52]. Differences in the patterns of salt weathering of two limestone types were related to differences in pore size distribution with the most affected limestone being the most porous one and the one with smaller pore size [52]. A study with several tuffs reported that those with micropores dominance were particularly affected by salt weathering [47]. But bigger pores can favor limestone dissolution by acid attack [38] and according to Fogue-Djombou et al. [65], limestones with unimodal pore network dominated by micropores present higher resistance to freeze-thaw than limestone with bimodal pore system. On the other hand, a study with several rock types proposed that the rocks with greater variation in pore size (limestone and travertine) were more stable under freeze-thaw tests than the others (trachyandesite and tuff) [80]. The impact of salt solutions in tuff [20] and limestone [25] has been explained by crystallization pressures resulting from pore size distribution. It will be interesting to note that in a study of basalts, Dursun and Topal [62], found that the type with smaller pores (massive basalt) presented higher durability than the vesicular that presented higher porosity and water absorption as well as other physical characteristics (see below). Additionally, the interconnections of the pores can affect the action of decay agents. It has been found for trachytes tested with salt weathering that higher porosity did not necessarily imply low durability since poorly interconnected pores can limit the action of water-related agents [15]. 4.2. Pore Network Features Pores frequently favor the decay effects of diverse agents. In a study promoting biological colonization of limestones, microorganisms were detected inside pores, which was explained for pores being places with higher moisture [34]. In a limestone subjected to gaseous attack, the network of macropores allowed the penetration of gases and in-depth reactions [39] and it has been observed the enlargement by salt weathering of macropores and existing fissures in trachyte [15]. Higher porosity is often considered to promote stone susceptibility to alteration processes in the built environment and 10% porosity was implied as a kind of threshold for susceptibility to salt and ice weathering of the travertines and carbonate tufas studied by Benavente et al. [33], because of higher pore interconnection and fluid migration but this cannot be considered a universal rule, as the results of many other rocks have shown. Some studies have shown the higher susceptibility to salt weathering of more porous limestones [17,35,50], with similar results for granites [28] and for highly porous sandstones [53]. The same trend has been obtained in terms of the effects of acid solutions on limestones [38,44]. Similar trends have been observed in the comparison of different lithologies in salt weathering tests, with a more porous granite behaving worse than a limestone with lower porosity [73]. Higher biological colonization has also been observed on more porous types, with worse results for limestone than for marble [10] and for limestone than granite [59]. The penetration of soot was found [64] to be higher for the more porous lithologies (rhyolite tuff, travertine, granite and the more porous limestone) while deep penetration of particles was not observed by visual inspection on other rocks with more dense structure (andesite, marble, sandstone, and a less porous limestone). There is a report of higher susceptibility to sulfation of travertine than marble, being the porosity of the travertine higher [54]. Higher porosity, by promoting higher pollutants loads, can also furthermore contribute to other decay processes. According to the study by Thomachot-Schneider et al. [76], the thermal response of limestones that absorb more salts due to higher porosity contributed to the disaggregation of these stone types. However, there are references to the opposite for limestones, pointing that lower porosity promotes higher sensibility in the case of alteration because of thermal effects [17,22]. 4.2. Pore Network Features In a study of tuffs subjected to salt weathering tests [46], all types showed significant mass losses but lower resistance to salt weathering was observed for the types with higher water vapor diffusion, which was considered as an indicator of the transport of solutions. 4.3. Textural and Structural Features Rocks are generally multiphase aggregates and the impact of alteration agents can be affected by the interfaces between individual particles, as well as the orientation, geometry, and space distribution patterns of those individual particles (and their variations). The detachment and loosing of grains were observed in marbles subjected to heating-cooling and freeze-thaw tests [21]. There are also references to the action of salt and ice in interfaces between grains in sandstone [75] and in trachyandesite and tuff [80]. According to Murru et al. [45], marble (granoblastic texture) showed lower resistance to thermal shock than limestone with sparite and micrite and sparry cement has been reported as increasing durability of limestones under freeze-thaw tests [70]. The preferred orientation of calcite crystals in marbles has been considered as contributing to differential surface reactivity to pollutants of this kind of rock [69]. The action of pollutants was found to exploit finer crystals (higher specific surface) in limestones [14]. On the other hand, in heating tests of magmatic rocks, the presence of minerals with coarser size and different coefficients of thermal expansion corresponded to worse results [48]. Tuffs with different granularity have shown different decay features under tests of freeze-thaw and salt crystallization [67]. The presence of calcite and clay matrix in arenaceous sedimentary rocks seem to favor the propagation of cracks while more rigid minerals like quartz and feldspar are not affected [77]. The presence of oxides in vugs in laminated travertines promotes susceptibility to salt and ice, highlighting the effect of anisotropy in these rocks [33]. The presence of calcite cement in sandstone contributes to their susceptibility to acid attack [66] and has been related to the development of contour scaling under salt weathering [56]. Tuffs with Geosciences 2020, 10, 91 7 of 13 predominance of glassy groundmass and pumice clasts presented higher susceptibility to salt weathering [67]. predominance of glassy groundmass and pumice clasts presented higher susceptibility to salt weathering [67]. We found examples of the role played by heterogeneity features in alteration processes. In tests with acid attack to limestones, it was reported that ooids and fossils presented a lower resistance than the cement [38]. In a limestone subjected to acid attack, dissolution of ooids and cement did not present noteworthy differences and the voids in ooids that were present on the specimens before the test promoted sulphates and nitrates crystallization [39]. 4.3. Textural and Structural Features In freeze-thaw tests with limestones, growth of cracks at the interface between allochems and sparry cement and the detachment of peloids and ooids has been observed [27]. The cement between grains in sandstone was found to be affected by this kind of test [29] and also by wetting-drying cycles [60]. Salt weathering tests with volcanic rocks showed the effects of existing heterogeneities such as structures of preferred orientation and big pumice clasts in ignimbrites [43] and the higher susceptibility of groundmass in trachytes [15] and in tuffs [46,67]. Surface heterogeneities such as stylolites have been considered to increase the susceptibility of limestones to freeze-thaw [16,17,65,78], wet-dry cycles [31] and salt weathering [17], with cracks assumed to be presented before testing also promoting the effects of these decay agents [53]. In trachytes, salt weathering affects fronts with iron oxides and hydroxides [15]. But it has been proposed that sericite and clay minerals can have a sealing effect in granite cracks, limiting water movement and diminishing the impact of salt weathering [52]. g The effects of salt solutions on limestones appear to be potentiated along stratification [53] and the effects of bedding were found to be more marked for coarser portions in sandstones [53] and limestone [74]. 4.4. Multiple Factors This result was attributed 8 of 13 Geosciences 2020, 10, 91 by the authors to the lower dry/wet ratio of mechanical strength of the vesicular basalt, which, however, was also the more porous basalt type. Sato and Hattanj [49] presented a study with a tuff and two sandstones. Comparing the tuff and a sandstone with similar porosity and tensile strength, the sandstone with higher micropore volume and higher specific surface behave worse while the tuff had large pores associated with the alteration of pumice. The other sandstone with lower porosity and higher tensile strength showed also high resistance to salt weathering. In other studies, there was a concurrence of factors in the same direction. Lower durability in freeze-thaw tests of limestones [37] and salt weathering tests of ignimbrites [24] were related to higher porosity, higher capillarity coefficient, and lower mechanical strength. The higher resistance to acid solutions of dolomitic limestone, when compared with calcium carbonate sedimentary rocks, has been explained by coarser texture, lower porosity, and higher mechanical strength [57]. Explanations joining mechanical strength and bulk properties of the pore system, such as porosity, water absorption, and capillarity coefficient, with higher values of microporosity have been presented for higher susceptibility to salt crystallization of travertines [81] and pyroclastic rocks, with the variations in this last study being related to welding degree [43]. A comparison of rhyodacite and andesite found the former more susceptible than andesite because of the lower strength, higher porosity, and also higher microporosity [58]. Similar results were obtained in studies of freeze-thaw tests with travertines and limestones [41]. Higher porosity and water absorption, as well as bimodal pore space with important microporosity, were proposed to explain the lower durability of a tuff in relation to another tuff and an andesite in salt weathering tests [61]. In salt weathering studies with sandstones, highest durability was indicated for the type with lowest microporosity, better cementation, lowest anisotropy (albeit it is the type with highest thermal expansion) and that is the most homogeneous one, presenting mainly quartz and without swellable minerals, while the less durable type showed higher microporosity, the presence of phyllosilicates in significant amounts and marked thermal and hydric anisotropy [56]. The loss of gloss in serpentines under ultraviolet exposure tests presented positive correlation with water absorption and negative correlations with density and mechanical strength [72]. 4.4. Multiple Factors But this same study showed higher gloss loss in serpentinites where antigorite was dominant and that higher mineralogical diversity corresponded to lower gloss loss. Sometimes pore characteristics are associated with other textural features. For example, images of study by Török and Szemerey-Kiss [79], showed that a coarser limestone which was less porous and presented a higher percentage of fine pores presented higher erosion than a finer limestone that was more porous and had a higher percentage of the higher radii pores (in freeze-thaw tests with stone and mortars, where, hence the possibility of some salt contribution could be pondered). Bioturbation in limestones has been reported to be susceptible to salt weathering erosion because of the association with iron oxides and porosity [71]. In a study of two limestones and marble, the limestone with higher porosity and surface roughness showed higher darkening related to fixation of particulate matter and higher deposition of the soluble fraction [13]. In exposure tests, slabs of limestone showed higher deposition of sulphates than carbonate-rich sandstone and polished marble [32]. 4.4. Multiple Factors This section comprises cases where the authors of the considered papers proposed more than one factor for explaining a given trend, including other bulk physical properties of rocks that were not considered in previous sections of the present publication. Perhaps the most interesting result of those that were surveyed in the dataset studied here is the relation between mass loss in salt weathering tests and a petrographic index that includes both voids and mineralogical features, namely the relation between sound or primary minerals and secondary minerals formed by weathering [8], in a study that considered several magmatic and metamorphic silicate rocks with different weathering degree and that had a set of results that seem to comply with the necessary conditions for correlation. However, it is possible that this type of relation will not hold for rocks whose decay follow other petrographic models such as limestones and sandstones or for rocks with more chemically susceptible minerals but it must be highlighted that this is a very testable hypothesis that is particularly interesting for the geosciences since it involves petrographic criteria. Other majorly interesting publications have data that contribute to assess the role of different factors. In the study presented by Nasri et al. [71], comparing a carbonate tufa and a limestone under salt weathering tests, the tufa showed better durability, in spite of having much lower mechanical strength and much higher porosity and water capillary absorption, even after correcting for porosity differences, a result that the authors attribute to the presence of macropores in the carbonate tufa. In a study on tuffs under freeze-thaw and salt weathering tests [67], there were differences attributed to the pore size distribution, with smaller pores causing higher decay. However, according to the authors, this “can be considered only a secondary factor” in tuffs with lower porosity and higher tensile strength that present better results. In a study with acid solutions, a more porous but silica richer limestone showed lower mass loss than a limestone with lower porosity but richer in calcium carbonate [44]. The presence of clay minerals can promote an incipient lamination in a low porosity limestone that favors the action of freeze-thaw [18]. The study of Dursun and Topal [62] in basalts showed higher durability for the massive basalts than for a vesicular one, with the massive type presenting smaller pore size. 5. Final Considerations In the period surveyed (2017–2019), studies concerning ageing tests of stone materials showed a clear vitality, in general, averaging two publications by month. However, a marked disparity in terms of lithological types was observed. There are many more studies with sedimentary carbonate rocks than with metamorphic silicate rocks, and information for the latter is scarce. In relation to the types of ageing tests used, there is a wide diversity but salt weathering is clearly dominant, perhaps reflecting the recognized erosive impact of soluble salts on stone materials used in built structures. One can highlight, also, the low proportion of publications with information from tests promoting biological colonization (possibly reflecting the essentially chromatic effects of this kind of agent). Hence this survey seems to suggest clear trends in terms of objects and processes. The collected 9 of 13 Geosciences 2020, 10, 91 information regarding the effects of ageing agents ranges from responses of specific minerals to assessments of whole-rock behavior based on one or more factors. While the former is more limited in scope, the latter shows variations and even contradictions that might be related to a pervasive case- study way of thinking, where authors are in general concerned with some particular rock types, from specific places. The usual limitations in experimental studies in terms of the available techniques and situations with confounding conditions, where several factors could contribute to the same outcome, can also contribute to the observed dispersion. Hence, reviews like the present one are essential to assess the state of knowledge in relation not just to major trends but also to the reproducibility of specific claims; to recognize specific points that deserve and need further research. In relation to the study of alteration processes of stone materials in the built environment, one of the points that seem to deserve further attention concerns the role of pore size for alteration processes such as salt weathering and freezing-thaw, given the high number of references to this feature (pore size) and the results that have cast doubts on its real importance. There are also many results regarding the susceptibility of mineralogical, chemical, textural, and structural features of rocks. It seems clear that we are still far away from a unifying theory that can relate the alteration of stones to rock characteristics and the agents to which they are exposed in the built environment. 5. Final Considerations It is possible that this will only be achieved considering a suitable lithological taxonomy, based on the relevant petrological criteria, in a multivariate perspective. Petrographic criteria should be the starting base for explaining both physical characteristics of rocks and their alteration when used as stone materials. Perhaps the most interesting results showed the potential relation of alteration to a petrographic index based on the textural and mineralogical characteristics (voids, primary minerals, and weathering products). This approach seems very promising for magmatic and metamorphic rocks and might be suitable also for low porosity sedimentary and metamorphic carbonate rocks. But additional provisions need to be included for features such as chemical susceptibility, for example for carbonate rocks, for anisotropy, especially for some silicate metamorphic rocks, and for rocks with a granular framework, such as detrital rocks and diverse limestones. The presence of heterogeneities with an extension that it is not usually in the domain of thin sections is a further potential issue to be tackled. The incorporation of factors reflecting these diverse rock features, with several terms, e.g., applied at diverse scales and for different decay agents, could lead to the formulation of a universal petrographic index for the selection of stone to be used in a built environment according to the expected alteration agents. While we are not in a position to propose an expression for such an index, it is our opinion that the subject of stone alteration is not more complex than the characterization of the engineering behavior of rock masses, for which several indexes based predominantly on macroscopic field observations have been devised (many examples can be found in [82]). The relevant index could be expressed as additions and products of ratings based on the evaluation of pertinent features such as those collected in this review, and considering also the alteration agents that could affect the stone material in the built environment. Funding: The Lab2PT-Landscapes, Heritage and Territory laboratory-AUR/04509 is supported by the Portuguese FCT-“Fundação para a Ciência e a Tecnologia” (Portuguese funds and where applicable the FEDER co-financing, in the aim of the new partnership agreement PT2020 and COMPETE2020-POCI 010145 FEDER 007528). The authors also gratefully acknowledge the support of the CERENA (funded by a strategic project of the FCT-UID/ECI/04028/2019) and the LAMPIST of the Instituto Superior Técnico, University of Lisbon. 5. Final Considerations The University Institute of Geology of the University of A Coruña (Spain) receives support from the Xunta de Galicia from the programme “Consolidación y estructuración de unidades de investigación competitivas: Grupos de potencial de crecimiento” (ED431B 2018/47) and Redes de investigación (R2017/008). Acknowledgments: Many of the reflections presented were prompted by the Project PORENET (POCTI/CTA/44940/2002) funded by the FCT—Fundação para a Ciência e Tecnologia (Portugal). We also thank the anonymous reviewers for many contributions that contributed to the improvement of the present manuscript. Conflicts of Interest: The authors declare no conflict of interest. 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Consolidation effectiveness of modified Si-based nanocomposites applied to limestones. Mater. Struct. 2018, 51, 156. 43. Martínez-Martínez, J.; Pola, A.; García-Sánchez, L.; Reyes Agustin, G.; Osorio Ocampo, L.S.; Macías Vázquez, J.L.; Robles-Camacho, J. Building stones used in the architectural heritage of Morelia (México): Quarries location, rock durability and stone compatibility in the monument. Environ. Earth Sci. 2018, 77, 167. 44. Misra, A.; Franco Castillo, I.; Müller, D.P.; González, C.; Eyssautier-Chuine, S.; Ziegler, A.; de la Fuente, J.M.; Mitchell, S.G.; Streb, C. Polyoxometalate-ionic liquids (POM-ILs) as anticorrosion and antibacterial coatings for natural stones. Angew. Chem. Int. Ed. 2018, 57, 14926–14931. 45. Murru, A.; Freire-Lista, D.M.; Fort, R.; Varas-Muriel, M.J.; Meloni, P. Evaluation of post-thermal shock effects in carrara marble and santa caterina di pittinuri limestone. Constr. Build. Mater. 2018, 186, 1200–1211. 46. Pötzl, C.; Dohrmann, R.; Siegesmund, S. Clay swelling mechanism in tuff stones: An example of the Hilbersdorf Tuff from Chemnitz, Germany. Environ. Earth Sci. 2018, 77, 188. 47. Pötzl, C.; Siegesmund, S.; Dohrmann, R.; Koning, J.M.; Wedekind, W. Deterioration of volcanic tuff rocks from Armenia: Constraints on salt crystallization and hydric expansion. Environ. Earth Sci. 2018, 77, 660. 48. Rembiś, M.; Dubiniewicz, A. Zmiany mikrostrukturalne w płytach skał magmowych poddanych termicznej obróbce metodą płomieniowania. Przegląd Geol. 2018, 66, 450–456. 49. Sato, M.; Hattanji, T. A laboratory experiment on salt weathering by humidity change: Salt damage induced by deliquescence and hydration. Prog. Earth Planet. Sci. 2018, 5, 84. 50. References 2019, 38, 118–125. Geosciences 2020, 10, 91 13 of 13 13 of 13 64. Farkas, O.; Török, Á. Effect of exhaust gas on natural stone tablets, a laboratory experiment. Period. Polytech. Civil. Eng. 2019, 63, 115–120. 65. Fogue-Djombou, Y.I.; Corn, S.; Clerc, L.; Salze, D.; Garcia-Diaz, E. Freeze-thaw resistance of limestone roofing tiles assessed through impulse vibration monitoring and finite element modeling in relation to their microstructure. Constr. Build. Mater. 2019, 205, 656–667. 66. Geng, H.; Zhang, S.; Zhi, J.; Zhang, R.; Ren, J.; Ro, C.-U. Acid solution decreases the compressional wave velocity of sandstone from the Yungang Grottoes, Datong, China. Herit. Sci. 2019, 7, 4. 67. Germinario, L.; Török, Á. Variability of technical properties and durability in volcanic tuffs from the same quarry region—Examples from Northern Hungary. Eng. Geol. 2019, 262, 105319. 68. Korobiichuk, V.; Shlapak, V.; Kryvoruchko, A.; Sobolevskyi, R.; Zuievska, N. Analysis of change in the decorative properties of granites under thermal exposure. East. Eur. J. Adv. Technol. 2019, 2, 35–43. 69. Martínez-Martínez, J.; Benavente, D.; Pérez-Huerta, A.; Cueto, N.; García-del-Cura, M.A. Changes on the surface properties of foliated marbles at different cutting orientations. Constr. Build. 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An experimental investigation of the effects of grain size and pore network on the durability of Vicenza stone. Rock Mech. Rock Eng. 2019, 52, 2935–2948. 75. Sun, Q.; Dong, Z.; Jia, H. Decay of sandstone subjected to a combined action of repeated freezing–thawing and salt crystallization. Bull. Eng. Geol. Environ. 2019, 78, 5951–5964. 76. Thomachot-Schneider, C.; Vázquez, P.; Gommeaux, M.; Lelarge, N.; Conreux, A.; Drothière, X.; Mouhoubi, K.; Bodnar, J.-L. Thermal response of building stones contaminated with salts. © 2020 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 Constr. Build. Mater. 2019, 226, 331–344. 77. Tiennot, M.; Mertz, J.-D.; Bourgès, A. Influence of Clay Minerals nature on the hydromechanical and fracture behaviour of stones. Rock Mech. Rock Eng. 2019, 52, 1599–1611. 78. Torabi-Kaveh, M.; Heidari, M.; Mohseni, H.; Ménendez, B. Role of petrography in durability of limestone used in construction of Persepolis complex subjected to artificial accelerated ageing tests. Environ. Earth Sci. 2019, 78, 297. 79. Török, Á.; Szemerey-Kiss, B. Freeze-thaw durability of repair mortars and porous limestone: Compatibility issues. Prog. Earth Planet. Sci. 2019, 6, 42. 80. Uğur, İ.; Toklu, H.Ö. Effect of multi-cycle freeze-thaw tests on the physico-mechanical and thermal properties of some highly porous natural stones. Bull. Eng. Geol. Environ. 2019. 81. Zalooli, A.; Khamehchiyan, M.; Nikudel, M.R. Durability assessment of Gerdoi and red travertines from Azarshahr, East Azerbaijan province, Iran. Bull Eng Geol Environ 2019, 78, 1683–1695. 82. Singh, B.; Goel, R.K. Rock Mass Classification: A Practical Approach in Civil Engineering, 1st ed.; Elsevier: Amsterdam, The Netherlands; New York, NY, USA, 1999; ISBN 9780080430133. © 2020 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/). © 2020 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/W3106832369
https://link.springer.com/content/pdf/10.1007/s11948-021-00295-9.pdf
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Grant Review Feedback: Appropriateness and Usefulness
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* Stephen A. Gallo sgallo@aibs.org Grant Review Feedback: Appropriateness and Usefulness Received: 27 May 2020 / Accepted: 25 February 2021 / Published online: 17 March 2021 © The Author(s) 2021 2 Washington State University, Psychology, Vancouver, WA, USA Keywords  Peer review · Grant funding · Feedback · Race · Gender · Bias · Resubmission 1 Scientific Peer Advisory and Review Services, American Institute of Biological Sciences, Herndon, VA, USA 1 Scientific Peer Advisory and Review Services, American Institute of Biological Sciences, Herndon, VA, USA 2 Washington State University, Psychology, Vancouver, WA, USA Science and Engineering Ethics (2021) 27:18 https://doi.org/10.1007/s11948-021-00295-9 Science and Engineering Ethics (2021) 27:18 https://doi.org/10.1007/s11948-021-00295-9 ORIGINAL RESEARCH/SCHOLARSHIP Introduction Most scientific research funding agencies utilize a peer review system to evaluate submitted projects and select the most meritorious for funding. At the National Institutes of Health (NIH), after a grant application is peer reviewed, the scores and comments from the reviewers are sent back to the applicant (NIH 2018). If it is not funded, the applicant must address the reviewer comments if they are to resubmit an updated version of their application (NIH 2020; NIAID 2020). NIH reviewers evaluate the scientific and technical merit of each proposal and are required to justify their scores with comments on the proposal’s strengths and weaknesses. The comments “should be clear enough that an investigator has a sense of what needs to be done in order to craft a more competitive application if the current version is unfunded” (NIH CSR 2020). Thus, although not listed as a core value of the NIH peer review system, reviewer feedback to applicants for the purposes of improving investigator grantsmanship and the overall quality of applications is an important, if secondary, purpose of grant peer review (NIH 2019). Little empirical data exist that document whether grant review feedback is effective in informing applicants and improving applications. f Useful feedback is likely particularly important to help improve resubmitted applications, which are proportionally more likely to be funded than new appli- cations, although funding rates are low overall (Haggerty and Fenton 2018; Lauer 2016, 2017). The success of resubmitted applications depends on an appli- cant’s ability to address reviewer concerns in their resubmissions (NIAID 2020). Resources are available to guide scientists as to the best approaches (Boss and Eckert 2003; Sutcivni 2017). However, while reviewers tend to believe their feed- back is useful to move scientific fields forward (Irwin et al. 2013), it is unclear if applicants find the reviewer comments useful for resubmission. In 2015, NIH surveyed all stakeholders of their peer review process to learn about perceptions of the peer review process, including the value of reviewer feedback by applicants (NIH 2017). The results reveal only 53% of applicants “strongly agreed/agreed that the information in their summary statement helped them to focus on problem areas in the application” (NIH 2017, p. 4). Abstract The primary goal of the peer review of research grant proposals is to evaluate their quality for the funding agency. An important secondary goal is to provide construc- tive feedback to applicants for their resubmissions. However, little is known about whether review feedback achieves this goal. In this paper, we present a multi-meth- ods analysis of responses from grant applicants regarding their perceptions of the effectiveness and appropriateness of peer review feedback they received from grant submissions. Overall, 56–60% of applicants determined the feedback to be appro- priate (fair, well-written, and well-informed), although their judgments were more favorable if their recent application was funded. Importantly, independent of funding success, women found the feedback better written than men, and more white appli- cants found the feedback to be fair than non-white applicants. Also, perceptions of a variety of biases were specifically reported in respondents’ feedback. Less than 40% of applicants found the feedback to be very useful in informing their research and improving grantsmanship and future submissions. Further, negative perceptions of the appropriateness of review feedback were positively correlated with more nega- tive perceptions of feedback usefulness. Importantly, respondents suggested that highly competitive funding pay-lines and poor inter-panel reliability limited the use- fulness of review feedback. Overall, these results suggest that more effort is needed to ensure that appropriate and useful feedback is provided to all applicants, bolster- ing the equity of the review process and likely improving the quality of resubmitted proposals. Keywords  Peer review · Grant funding · Feedback · Race · Gender · Bias · Resubmission * Stephen A. Gallo sgallo@aibs.org 012341 456789) 3 18  Page 2 of 20 S. A. Gallo et al. 1 3 Introduction However, this result still does not indi- cate whether the feedback was specifically useful; we could define usefulness of feedback in terms of specifically improving resubmissions, and generally improv- ing applicant grantsmanship and informing future scientific endeavors. Impor- tantly, the responses to the NIH survey were greatly influenced by whether the applicants were recently funded, where “favorable responses were more prevalent among funded applicants than applicants whose applications were not funded” (NIH 2017, p. 17). The score an initial grant receives (including whether or not it was triaged) is a key predictor of whether the applicant decides to resubmit (Boyington et al. 2016; Lauer 2017), but it is not clear if applicant perception of the review feedback is also a significant predictor of resubmission. Recent studies have suggested that women applicants interpret peer review feedback more negatively than men, which was associated with reduced motivation to resubmit (Biernat et al. 2020). 1 3 1 3 Grant Review Feedback: Appropriateness and Usefulness Page 3 of 20 18 It is well documented that women submit fewer research applications than men (Hechtman et  al. 2018) and that under-represented minority (URM) women of color submit even fewer, have lower funding success compared to white women, and are less likely to resubmit unfunded applications (Ginther et al. 2016). Spe- cifically, African American scientists have been found to submit fewer new appli- cations, fewer resubmissions, and are funded at a lower rate than white scientists (Ginther et al. 2011; Mervis 2016). Thus, a negative interpretation of feedback by URM scientists compared to majority group scientists could reduce the rate of resubmissions, which may contribute to funding disparities. Despite this pos- sibility, little is known about how applicants view the usefulness of feedback in guiding their resubmissions. In addition, it is unknown whether applicants deem the feedback they receive to be appropriate, which we could define as being well-written, unbiased and based on expert perspective. Although the peer review process may be subject to a vari- ety of biases (Lee et al. 2013), it is unclear if applicants perceive these biases to be explicitly present in the review feedback. Some research has suggested that review feedback to women applicants contains different language than to men, particularly in the evaluation of the investigator’s leadership abilities (Pier et al. 2018). In the 2015 NIH survey, only 54% of applicants perceived the peer review process as fair. Introduction In addition, 91% of funded applicants and 53% of unfunded applicants “agreed that their application was evaluated by reviewers with the appropriate expertise,” sug- gesting that funding success influenced perceptions of the appropriateness of review feedback. However, little is known about the influence of applicant demographics on perceptions of the appropriateness of review feedback and if there is any associa- tion between perceived appropriateness and perceived usefulness of the feedback for resubmission. The objective evaluation of reviewer comments is made difficult by a lack of access to critiques of unfunded applications (Gropp et al. 2017; Gurwitz et al. 2014). Given the paucity of data surrounding grant review feedback, particularly from an applicant’s perspective, we created a survey for research scientists that asked appli- cant respondents to rate and comment on the review feedback they received on their most recent submission. Three publications have resulted from this survey (Gallo et al. 2018; Gallo et al. 2020a, b), but none of them focused on the questions related to the usefulness and appropriateness of peer review feedback; these questions are now addressed in the proceeding analysis. Survey Construction and Multi‑methods Approach To our knowledge, there are no reports in the peer-reviewed literature that have que- ried grant applicants about their perceptions of the peer review process. Therefore, the authors brainstormed questions to address the range of relevant content associ- ated with peer review feedback. These ideas were also informed by input from sci- entists, scientific review administrators and research funders, and the literature on 3 3 3 18  Page 4 of 20 S. A. Gallo et al. 18 peer review processes. A draft survey was examined by the authors and others expe- rienced in peer review for its clarity, face validity, and coverage of relevant content. The survey included questions on applicant perceptions of review feedback that yielded nominal and ordinal quantitative data and open text fields at the end of every section that yielded qualitative data. Our rationale for using this multi-meth- ods approach (Fig. 1) was to improve our analysis of applicant perceptions of the appropriateness and usefulness of review feedback. Text was associated with spe- cific questions with quantitative answer options, as described below, and then used to elaborate on respondents’ quantitative answers. Survey Data Collection The study was reviewed by the Washington State University Office of Research Assurances (Assurance# FWA00002946) and granted an exemption from IRB review consistent with 45 CFR 46.101(b)(2). Respondents were fully informed about the purpose, importance, intended use of the survey, and how we acquired their email address, and consented by their participation. The general survey description has been included in previous publications (Gallo et al. 2018); the survey contained 60 questions in 5 subsections, three of which were included in this analysis (Sect. 1: Demographics, Sect. 2: Grant submission and peer review experience, and Sect. 3: Investigator attitudes toward grant review). Specifically, in this analysis we exam- ined questions related to the usefulness and appropriateness of review feedback, from an applicant perspective. As suggested above, we define usefulness of feedback in terms of: improving future resubmissions; improving applicant grantsmanship; and informing future scientific endeavors. We define appropriateness of feedback as being: well-written, cohesive and balanced; fair and unbiased; and based on a rel- evant and expert perspective. Questions related to usefulness had Likert ordinal responses, questions related to appropriateness had nominal (yes/no) responses, and there was an open text field for respondent comments at the end of this survey section. Respondents could choose to 1 3 Fig. 1   Schematic of our multi-methods approach Fig. 1   Schematic of our multi-methods approach 1 3 Grant Review Feedback: Appropriateness and Usefulness Page 5 of 20 18 select no answer/prefer not to answer, and comments were not compulsory. The full survey is listed in other publications and is included as a supplement to this manu- script (Gallo et al. 2018, File S1). select no answer/prefer not to answer, and comments were not compulsory. The full survey is listed in other publications and is included as a supplement to this manu- script (Gallo et al. 2018, File S1). The survey was emailed in September 2016 to a total of 13,091 scientists in the American Institute for Biological Sciences’ database, which was developed for assisting in the recruitment of scientific expert reviewers to evaluate biomedical research applications for several funding organizations. Scientists recruited for this survey work in the biomedical area, ranging from clinical psychology to molecular biology. Of the individuals invited to participate in the survey, 74% had applied for research funding in the last 3 years. Reminder emails were sent out to non-respond- ers two weeks before the survey was closed. Data Summarization 1 3 18  Page 6 of 20 18  Page 6 of 20 S. A. Gallo et al. For the qualitative data, respondents’ comments from Sect. 3 of the survey (inves- tigator attitudes toward grant review) were extracted (N = 216). Comments were not mandatory, so the demographic characteristics of those who did and did not com- ment were compared. Comments were coded for content related to two groups of survey questions on the appropriateness (Q1-3) and usefulness (Q4-7) of the review feedback (Supplementary Table  1). These quotes were sorted into sub-categories by the presence of keywords that were related to the survey questions. Specifically, these keywords were “written” for Q1, “bias” for Q2, and “expertise” for Q3. In general, we chose these keywords for Q1-3 because they most directly addressed the survey questions and allowed for the most unambiguous and objective coding to specific questions. However, because several keywords in questions 4–7 appeared infrequently in the comments (namely “grantsmanship,” scientific endeavor” or “research area”), we used the keyword “useful” and its synonym “helpful” to iden- tify quotes related to Q4-7. Keyword searches utilized the simple word matching function in Excel and included all instances of the base words including suffix usage (e.g. usefulness) and different tenses (e.g. biased). Quotes could be sorted into mul- tiple groups if more than one keyword was present. A total of 79 quotes (37% of all quotes) was explicitly grouped in this way, with 19% of those quotes being rep- resented in more than one group (Supplementary Table 1). Although many of the ungrouped quotes had some relevance to the questions asked in the survey, only explicitly grouped quotes were included in the analysis below. Although the survey questions were worded positively, the associated com- ments could be of positive or negative valence. For example, both “reviewers had the expertise” and “reviews were unfair, biased, and lacked appropriate expertise” would be attributed to question Q3 (“Based on the reviewer feedback you received, do you feel that the reviewers had the appropriate expertise to evaluate your grant application?”) and reflected both positive and negative valence, respectively. Thus, each comment was also coded for valence: positive, negative, or both positive and negative (all of the coded comments had some positive or negative valence) (Sup- plementary Table 1). Data Summarization Two authors coded all comments for valence; there was agree- ment for 90% of comments and the 10% with disagreements were discussed until consensus was achieved. Data Summarization The survey was open for two months, with a reminder sent 2 weeks before the sur- vey closed. Responses were exported and Stat Plus software was used for the analy- sis. In this study, respondents were included if they completed the entire survey and answered three questions affirmatively (or greater than one): 2a (Have you submitted a grant for peer review in the last 3 years?), 2b (How many grant applications have you submitted in that time frame?), and 2c (Did you receive reviewer feedback on your last grant submission?). For the quantitative data, medians and percentages were calculated for the responses to the survey questions of interest, standard 95% confidence intervals were reported for the ordinal responses, and binomial proportion confidence inter- vals for the proportion data. To test the internal consistency of the survey’s quantita- tive items, we calculated Cronbach’s alpha for the four questions related to Useful- ness (Q4-7), which yielded an alpha of 0.87. The initial assessment of demographic factors related to responses was conducted through multiple binary logistic (for appropriateness responses) and ordinal logistic (for usefulness responses) regression for nominal and ordinal responses, respectively. Nominal responses were coded as Yes = 1, No = 0 and Likert responses were on a scale of 1 to 5 with 1 as the most useful and 5 as the least useful. Demographic data variables of applicant characteris- tics were categorical in nature, and were coded as 0 or 1; where there were unequal distributions between categories, the more frequently appearing category was coded as a 1. These variables included race (coded as 1 = white, 0 = non-white), gender (man = 1, 0 = woman), career stage (early/mid-career = 1, late-stage career/emeri- tus = 0), age (50 and over = 1, under 50 = 0), degree (PhD = 1, non-PhD = 0), and funding status (recently funded = 1, unfunded = 0). For the regression analyses, pre- dictors were entered together as a block. Chi square and Mann Whitney tests were used for post-hoc comparisons, using phi coefficient or the Z-score/√N, respec- tively, as the effect size. Differences between groups were determined to be signifi- cant if there was no overlap in confidence interval and tests for differences yielded p values < 0.01. Variance inflation factors were used to examine for potential multicol- linearity of the review feedback and demographic variables. Table 1   Demographics and success rates Response Rate and Demographics Of the 13,091 individuals contacted for this survey, 1231 responded, for a 9.4% response rate. Of the 1231 respondents, 634 answered questions 2a, 2b, and 2c in the affirmative, indicating they had submitted a proposal in the last 3 years and received review feedback. The remaining results focus on this sample of 634 participants. Over half of the responses were collected within a few hours of sending the emailed invitations to complete the survey. Another, smaller wave of responses was col- lected after a reminder email was sent. Comparisons of the quantitative answers to Grant Review Feedback: Appropriateness and Usefulness Page 7 of 20 18 questions for Usefulness and Appropriateness were nearly identical for these two groups (Supplementary Table 2). Sample demographics are listed in Table  1: the majority of respondents were men, Caucasian, academic PhDs in a late career stage. They had submitted a median of 5.0 ± 0.1 applications in the last 3 years. The overall funding success rate was 40%, which did not vary significantly by gender, race, age, career stage, degree, and organization (Table 1).f Some differences were evident in the demographics of respondents who made a comment versus non-commenting respondents (Supplementary Table  3). Non- whites represented only 17% (95%CI [12–22%]) of the commenting respondent pool compared to representing 29% (95%CI [26–34%]) of the non-commenting respondent pool (X2 [1] = 11.2, p = 0.0008, phi = 0.13). Additionally, respondents who made a comment were more likely to be older and in later career stages than non-respondents (Supplementary Table 3). Other demographic variables—degree, organization and gender—did not differ between commenting and non-commenting groups. However, it was also noted that 32% (N = 67; CI [26–38%]) of respondents who made a comment reported being recently funded compared to 44% (N = 183; 95%CI [39% to 49%]) of respondents who did not make a comment (X2 [1] = 8.9, p = 0.0029, phi = 0.12). Appropriateness of Feedback Overall, only 56% (95%CI [52–60%]) of respondents thought grant review feedback was well written, cohesive, and balanced. Respondents indicated issues related to the structure and length of the feedback (Supplementary Table 4; Q1.1) and that often reviewers do not support their score with comments (Supplementary Table 4; Q1.2). Additionally, 60% (95%CI [56–64%]) of respondents perceived grant reviewer feedback as fair and unbiased. Comments, however, identify various types of per- ceived biases toward specific application content, including bias against topic areas, bias against innovation, and methodology/model bias (Supplementary Table  4; Q2.1). Some comments also specifically mentioned biases against the applicants (Supplementary Table 4; Q2.2 and Q2.3). Some respondents suggested the impact biased reviews can have, particularly in an era of low funding success rates (Supple- mentary Table 4; Q2.4).i In terms of reviewer qualifications, 58% (95%CI [54–62%]) of respondents judged the reviewers to have appropriate expertise to evaluate their grant applica- tion, based on the reviewer feedback they received. In their comments, respondents identified a lack of reviewer expertise for interdisciplinary proposals, clinical pro- posals, statistical portions of the proposals, proposals with different animal models, and a lack of expertise in specific areas of science (Supplementary Table 4; Q3.1 and Q3.2). Response Rate and Demographics Factor (N = 634) Proportion (N) % Funding success Gender Men 63% (398) 41 Women 37% (236) 39 Age Under 50 29% (177) 37 50 and over 71% (436) 43 Race/ethnicity White 75% (478) 40 Non-white 25% (156) 41 Degree type Ph.d 83% (525) 40 Non-Ph.d 17% (109) 43 Organization Academia 88% (552) 39 Non-Academia 12% (72) 50 Career stage Early 4% (23) 30 Mid 31% (191) 39 Late/tenured 62% (385) 44 Emeritus 4% (27) 26 Table 1   Demographics and success rates Factor (N = 634) Proportion (N) % Funding success Gender Men 63% (398) 41 Women 37% (236) 39 Age Under 50 29% (177) 37 50 and over 71% (436) 43 Race/ethnicity White 75% (478) 40 Non-white 25% (156) 41 Degree type Ph.d 83% (525) 40 Non-Ph.d 17% (109) 43 Organization Academia 88% (552) 39 Non-Academia 12% (72) 50 Career stage Early 4% (23) 30 Mid 31% (191) 39 Late/tenured 62% (385) 44 Emeritus 4% (27) 26 18  Page 8 of 20 S. A. Gallo et al. Although the survey did not ask respondents to which funding agency they had applied, we did search the comments for mention of the two largest US funders, NIH and NSF. Of the comments that mentioned funding agency, 14% mentioned NSF and 86% mentioned NIH. Overview of Multi‑method Results of Respondent Comments and Ratings The sections below present the results of the qualitative analysis of the comments and the quantitative ratings of the associated survey questions Q1-7 (Supplementary Table 1). The 13 quotes listed in Supplementary Table 4 were specifically chosen as examples that captured a particular theme associated with the questions asked in the survey. It should be noted, though, that respondents’ comments often had a nega- tive valence and respondents with comments tended to be more negative even in the quantitative portions of the survey as compared to respondents without comments (Supplementary Table 5). We then examine how these results vary with applicant demographics, and the relationship between responses related to appropriateness and usefulness. Usefulness of Feedback Overall, only 38% (median of 3.0; 95%CI [2.9–3.1]) found the grant review feed- back they received on their last grant submission to be mostly useful or very useful. 1 3 1 3 Grant Review Feedback: Appropriateness and Usefulness Page 9 of 20 18 Further, only 30% (median of 3.0; 95%CI [2.9–3.1]) thought it was mostly useful or very useful in improving their grantsmanship; only 35% (median of 3.0; 95%CI [2.9–3.1]) found the review feedback was mostly useful or very useful in improving their future submissions; and only 26% (median value of 3.0; 95%CI [2.9–3.1]) felt the feedback was mostly or very useful in informing their future scientific endeavors in the proposed research area. Based on these data, the majority of applicants did not find the reviewer feedback to be highly useful.i Further, only 30% (median of 3.0; 95%CI [2.9–3.1]) thought it was mostly useful or very useful in improving their grantsmanship; only 35% (median of 3.0; 95%CI [2.9–3.1]) found the review feedback was mostly useful or very useful in improving their future submissions; and only 26% (median value of 3.0; 95%CI [2.9–3.1]) felt the feedback was mostly or very useful in informing their future scientific endeavors in the proposed research area. Based on these data, the majority of applicants did not find the reviewer feedback to be highly useful.i i Few comments specifically mentioned the usefulness of the feedback in terms of grantsmanship (Q5) or future scientific endeavors (Q7); more were related to the usefulness of the feedback in improving future submissions (Q6). Some remarked on how they received constructive criticism that helped improve their applications (Supplementary Table 4; Q4-7.1). However, some remarked that inconsistent feed- back from different sets of reviewers evaluating resubmissions reduces usefulness (Supplementary Table 4; Q4-7.2). Others commented that usefulness is hampered by a perceived lack of expertise (Supplementary Table  4; Q4-7.3). Several com- ments mentioned that the feedback format and lack of suggestions for improvement limit usefulness (Supplementary Table  4; Q4-7.4). Finally, some mentioned that usefulness of feedback was ultimately restricted by funding success rates (Supple- mentary Table 4; Q4-7.5). Perceptions of Feedback and Demographics We used multiple regression analysis to examine the effects of demographic vari- ables on perceived appropriateness and usefulness of feedback. As seen in Supple- mentary Table 6, the variance inflation factors between most of these demographic variables is low.i We first analyzed the relationships between demographic variables and the nomi- nal responses related to the appropriateness of review feedback using binary logistic regression. We found significant differences in terms of funding status for responses to all three questions related to appropriateness, as indicated by the reported odds ratios (Table 2). For example, for the Q1 regression, the factor of funding status had an odds ratio of 1.78 (95% CI 1.25–2.53). Thus, respondents who were funded were nearly twice as likely to indicate that the review feedback was well-written, cohesive, and balanced as compared to respondents who were not funded; indeed, 63% (95%CI, 57–69%) of funded respondents found the feedback to be well-written, cohesive and balanced compared to 51% (95%CI, 46% to 56%) of unfunded respondents (X2 [1] = 9.2, p = 0.0024, phi = 0.12). Similarly, funded respondents were more likely to find the feedback was fair and unbiased (Q2 Table 2): 71% (95%CI 65–77%) of funded respondents versus 53% (95%CI, 48% to 58%) of unfunded respondents (X2 [1] = 18.0, p < 0.0001, phi = 0.18). A greater number of funded respondents per- ceived the reviewers to have appropriate expertise to evaluate their proposal (Q3; Table 2): 68% (95%CI 62–74%) of funded respondents versus 51% (95%CI 46–56%) of unfunded respondents (X2 [1] = 17.0, p < 0.0001, phi = 0.17). 1 3 18  Page 10 of 20 S. A. Gallo et al. Table 2   Binary logistic regression of appropriateness of review feedback Factors Q1. Did you feel the reviewer feedback was well written, cohesive, and balanced? Q2. Did you feel the reviewer feedback was fair and unbiased? Q3. Based on the reviewer feedback you received, do you feel that the reviewers had the appropriate expertise to evaluate your grant application? Perceptions of Feedback and Demographics Beta ± SE (p value) Odds Ratio Beta ± SE (p value) Odds ratio Beta ± SE (p value) Odds ratio Intercept 0.85 – – 0.10 – –  − 0.59 – – Men − 0.56 ± 0.19 0.0026** 0.57 (0.40, 0.82) 0.24 ± 0.19 0.1925 1.28 (0.88, 1.84) 0.04 ± 0.19 0.8242 1.04 (0.72, 1.50) Age (50 and over) − 0.11 ± 0.22 0.6135 0.90 (0.58, 1.37) − 0.10 ± 0.22 0.6661 0.91 (0.59, 1.40) 0.16 ± 0.22 0.4788 1.17 (0.76, 1.82) White 0.32 ± 0.21 0.1321 1.37 (0.91, 2.07) 0.60 ± 0.21 0.0050** 1.82 (1.20, 2.76) 0.39 ± 0.21 0.0673 1.47 (0.97, 2.22) PhD − 0.02 ± 0.23 0.9233 0.97 (0.62, 1.54) 0.11 ± 0.24 0.6279 1.12 (0.71, 1.78) 0.32 ± 0.23 0.1679 1.38 (0.87, 2.17) Academia − 0.76 ± 0.30 0.0109 0.47 (0.26, 0.84) − 0.57 ± 0.29 0.0525 0.57 (0.32, 1.01) − 0.22 ± 0.28 0.4441 0.81 (0.46, 1.40) Early/mid-career 0.28 ± 0.21 0.1842 1.33 (0.87, 2.02) − 0.15 ± 0.22 0.4908 0.86 (0.57, 1.32) 0.48 ± 0.22 0.0297 1.62 (1.05, 2.49) Funded 0.58 ± 0.18 0.0014** 1.78 (1.25–2.53) 0.71 ± 0.19 0.0001** 2.03 (1.41–2.93) 0.76 ± 0.18  < 0.0001** 2.15 (1.50–3.08) Overall model evaluation X2[7] = 33.9, p < 0.0001** X2[7] = 30.2, p = 0.0001** X2[7] = 26.2, p = 0.0005** ** Indicates p < 0.01 1 Grant Review Feedback: Appropriateness and Usefulness Page 11 of 20 18 No differences were observed by career stage, age, organization or degree with respect to perceptions of appropriateness (Table 2). However, gender and race were found to predict perceptions of the appropriateness of review feedback (Table  2). Women were significantly more likely to rate the reviewer feedback as well written, cohesive, and balanced compared than men (64% [95%CI 58–70%] and 53% [95%CI 48–58%], respectively) (X2 [1] = 9.3, p = 0.0023, phi = 0.12). Whites were signifi- cantly more likely to rate the feedback as fair and unbiased than non-whites ((64%, 95% CI [60–68%]) and 49%, 95% CI [41–57%], respectively) (X2 [1] = 9.2, p = 0.0024, phi = 0.12). These differences were not due to funding success, as the rates were similar between groups (Table 1). In terms of reviewer expertise, responses to Q3 did not vary significantly by race or gender (Q3 Table 2). i Overall, for the responses related to the appropriateness of review feedback, no the- matic differences were found between the comments made by non-white versus white applicants. Similarly, no thematic differences were found between the comments made by women versus men. We then analyzed the relationships between demographic variables and the ordi- nal Likert responses (1–5 where 1 is most useful) related to the usefulness of review feedback using multiple ordinal logistic regression. None of the regression models for responses related to questions of general usefulness (Q4), usefulness in improving grantsmanship (Q5), usefulness in improving future submissions (Q6), and usefulness in informing future scientific endeavors (Q7) were found to explain significant propor- tions of the variance in the responses (Table 3). Moreover, none of the funding and demographic factors (including race, gender, career stage, age, degree, or organization) were found to be significant predictors of these responses. Appropriateness versus Usefulness of Feedback Perceived usefulness of review feedback may be associated with grant resubmission rates, but the associations of perceived appropriateness of feedback and applicant behavior are unclear. Based on our results that the majority of respondents did not find review feedback useful and a large minority of respondents did not find the feed- back appropriate, it is likely that applicants who don’t find the feedback appropriate also don’t find it useful. In fact, some comments in our survey suggested usefulness was limited by the lack of appropriate expertise. To test this assumption, we compared respondents who found the review feedback they received to be fair and unbiased (Q2) to respondents who did not. For these two groups, we examined their answers to the questions concerning the usefulness of the feedback (Q4–Q7). This comparison of use- fulness and appropriateness is listed in Table 4. The results revealed significantly more negative perceptions of the usefulness of the feedback for those who also felt the feed- back was biased compared to those who felt the feedback was unbiased. 1 3 18  Page 12 of 20 S. A. Gallo et al. 1 3 Table 3   Ordinal logistic regression of usefulness of review feedback Factors Q4. On a scale of 1–5 (1 most useful, 5 least useful), overall how useful was the reviewer feedback you received on your last grant submission? Q5. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your grantsmanship? Q6. If you were not funded, on a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your future submissions? Q7. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in informing your future scientific endeavors in the pro- posed research area? Appropriateness versus Usefulness of Feedback Beta ± SE p value Odds ratio Beta ± SE p value Odds Ratio Beta ± SE p value Odds ratio Beta ± SE p value Odds ratio Intercept 1|2 − 2.78 ± 0.40  < 0.0001** n.a − 2.40 ± 0.40  < 0.0001** n.a − 2.95 ± 0.43  < 0.0001** n.a − 2.82 ± 0.41  < 0.0001** n.a Intercept 2|3 − 0.64 ± 0.38 0.0903 n.a − 0.57 ± 0.37 0.1250 n.a − 1.21 ± 0.40 0.0026** n.a − 1.13 ± 0.39 0.0035** n.a Intercept 3|4 0.56 ± 0.38 0.1390 n.a 0.56 ± 0.37 0.1292 n.a − 0.15 ± 0.40 0.7042 n.a 0.14 ± 0.38 0.7141 n.a Intercept 4|5 1.97 ± 0.39  < 0.0001** n.a 1.58 ± 0.38  < 0.0001** n.a 1.15 ± 0.40 0.0042** n.a 1.16 ± 0.38 0.0025** n.a Men − 0.04 ± 0.16 0.8051 0.96 (0.71, 1.30) 0.07 ± 0.16 0.6718 1.07 (0.79, 1.45) − 0.26 ± 0.17 0.1262 0.77 (0.55, 1.08) 0.19 ± 0.16 0.2313 1.21 (0.89, 1.65) Age (50 and over) − 0.02 ± 0.19 0.9037 0.98 (0.68, 1.41) 0.17 ± 0.18 0.3605 1.18 (0.83, 1.68) 0.12 ± 0.19 0.5411 1.13 (0.77, 1.64) 0.08 ± 0.19 0.6477 1.09 (0.76, 1.57) White − 0.07 ± 0.18 0.7141 0.94 (0.66, 1.33) 0.26 ± 0.18 0.1411 1.30 (0.92, 1.85) − 0.07 ± 0.19 0.6982 0.93 (0.64, 1.34) 0.06 ± 0.18 0.7330 1.06 (0.75, 1.51) PhD − 0.13 ± 0.20 0.5124 0.88 (0.59, 1.30) 0.19 ± 0.20 0.3326 1.21 (0.82, 1.78) − 0.26 ± 0.22 0.2364 0.77 (0.51, 1.18) − 0.19 ± 0.20 0.3541 0.83 (0.56, 1.23) Aca- demia 0.28 ± 0.24 0.2495 1.32 (0.82, 2.11) − 0.07 ± 0.23 0.7501 0.93 (0.58, 1.47) − 0.10 ± 0.26 0.4031 0.90 (0.54, 1.49) − 0.03 ± 0.24 0.8947 0.97 (0.61, 1.55) Page 13 of 20  18 Grant Review Feedback: Appropriateness and Usefulness **Indicates p < 0.01 Table 3   (continued) Factors Q4. On a scale of 1–5 (1 most useful, 5 least useful), overall how useful was the reviewer feedback you received on your last grant submission? Q5. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your grantsmanship? Q6. If you were not funded, on a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your future submissions? Q7. Appropriateness versus Usefulness of Feedback On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in informing your future scientific endeavors in the pro- posed research area? Beta ± SE p value Odds ratio Beta ± SE p value Odds Ratio Beta ± SE p value Odds ratio Beta ± SE p value Odds ratio Early/ mid- career − 0.20 ± 0.18 0.2630 0.82 (0.57, 1.16) − 0.04 ± 0.18 0.8417 0.97 (0.68, 1.36) − 0.25 ± 0.19 0.1936 0.78 (0.54, 1.13) − 0.04 ± 0.18 0.8137 0.96 (0.67, 1.37) Funded − 0.30 ± 0.15 0.0473 0.73 (0.54, 1.00) − 0.28 ± 0.15 0.0619 0.75 (0.56, 1.01) − 0.14 ± 0.18 0.0042** 0.87 (0.61, 1.25) − 0.21 ± 0.16 0.1725 0.81 (0.60, 1.10) Overall model evalu- ation X2[7] = 6.9, p = 0.4361 X2[7] = 8.3, p = 0.3101 X2[7] = 7.0, p = 0.4268 X2[7] = 5.0, p = 0.6596 Table 3   (continued) Factors Q4. On a scale of 1–5 (1 most useful, 5 least useful), overall how useful was the reviewer feedback you received on your last grant submission? Q5. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your grantsmanship? Q6. If you were not funded, on a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your future submissions? Q7. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in informing your future scientific endeavors in the pro- posed research area? Beta ± SE p value Odds ratio Beta ± SE p value Odds Ratio Beta ± SE p value Odds ratio Beta ± SE p value Odds ratio Early/ mid- career − 0.20 ± 0.18 0.2630 0.82 (0.57, 1.16) − 0.04 ± 0.18 0.8417 0.97 (0.68, 1.36) − 0.25 ± 0.19 0.1936 0.78 (0.54, 1.13) − 0.04 ± 0.18 0.8137 0.96 (0.67, 1.37) Funded − 0.30 ± 0.15 0.0473 0.73 (0.54, 1.00) − 0.28 ± 0.15 0.0619 0.75 (0.56, 1.01) − 0.14 ± 0.18 0.0042** 0.87 (0.61, 1.25) − 0.21 ± 0.16 0.1725 0.81 (0.60, 1.10) Overall model evalu- ation X2[7] = 6.9, p = 0.4361 X2[7] = 8.3, p = 0.3101 X2[7] = 7.0, p = 0.4268 X2[7] = 5.0, p = 0.6596 1 3 18  Page 14 of 20 S. A. Gallo et al. Perceptions of Grant Review Feedback The results of our analysis suggest that while the majority of grant applicants in our survey deemed reviewer feedback to be appropriate across several dimen- sions—including how fair, well-written and well-informed the feedback was— there were sizable proportions (40–44%) who did not find it appropriate. Sim- ilar to the 2017 NIH survey, we found respondent perceptions were influenced significantly by funding success, where funded applicants found the feedback to be more appropriate. Admittedly, this variability by funding status highlights the subjectivity inherent in applicant perceptions. Nevertheless, respondent appli- cants noted a variety of specific types of perceived bias in the feedback, includ- ing bias against innovative ideas, methodology bias, and gender bias. In addi- tion, reliability concerns intersected with views on fairness; several respondents noted significantly different sets of issues identified in the feedback from panel to panel for resubmissions, revealing important inconsistencies in feedback that can be construed as inequitable to the applicant. Also, multiple respondents men- tioned the apparent lack of expertise of reviewers in areas of science related to the proposal, experience with animal models, and statistics. Applicants also indi- cated specific instances where the format, length and quality of the writing was insufficient; some commented that it appeared the reviewer had not fully read the proposal, as they penalized applicants for issues in the feedback that were specifi- cally addressed in the proposal. While this lack of attention or preparation may reflect the state of overburden experienced by many peer reviewers (Gallo et al. 2020b), it is clear that the lack of appropriate reviewer feedback is still an issue for many applicants. However, this interpretation could be slanted, as respondents with comments generally had more negative views of the appropriateness of feed- back as compared to non-commenting respondents. Importantly, respondent perception of appropriate feedback differed by race and gender. Non-white respondents found their feedback particularly unfair, sug- gest a potential perception of racial biases. This finding is in line with previous findings that suggest URM women are much less likely to resubmit an unfunded application compared to white women or men (Ginther et  al. 2016); racially biased feedback could be contributing to these low resubmission rates, which in turn could contribute to current funding gaps among underrepresented groups (Ginther et al. 2011). Appropriateness versus Usefulness of Feedback Table 4   Review feedback appropriateness versus usefulness Question Q2. Feedback was fair and unbiased (yes) Q2. Feedback was unfair and biased (no) Fair versus unfair Median ± 95%CI N Median ± 95%CI N Mann–Whitney Q4. On a scale of 1–5 (1 most useful, 5 least useful), overall how useful was the reviewer feedback you received on your last grant submission? 2.0 ± 0.10 356 4.0 ± 0.14 234 U[234, 356] = 61,212, p < 0.0001**, r = 0.40 Q5. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your grantsmanship? 3.0 ± 0.12 358 4.0 ± 0.15 233 U[233, 358] = 57,945, p < 0.0001**, r = 0.33 Q6. If you were not funded, on a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in improving your future submissions? 3.0 ± 0.13 271 4.0 ± 0.15 217 U[217, 271] = 42,715, p < 0.0001**, r = 0.39 Q7. On a scale of 1–5 (1 most useful, 5 least useful), how useful was the reviewer feedback in informing your future scientific endeavors in the proposed research area? 3.0 ± 0.12 342 4.0 ± 0.16 228 U[228, 342] = 50,536, p < 0.0001**, r = 0.25 1 3 Grant Review Feedback: Appropriateness and Usefulness Page 15 of 20  18 Perceptions of Grant Review Feedback These results could also suggest that there are significant perceived biases at play in the peer review process, which have also been sug- gested by scoring data (Tamblyn et al. 2018), and critique analysis (Pier et al. 2017). We also found that women were more likely to perceive their feedback as well written, cohesive, and balanced than men, but no gender difference was found for perceptions of usefulness of the feedback for preparing grant resubmis- sions. These results may differ from studies that found women to be more sensi- tive to peer feedback than men (Mayo 2016; Roberts and Nolen-Hoeksema 1989), to have inaccurate negative self-perceptions about the quality of their work (Beyer 1 3 18  Page 16 of 20 S. A. Gallo et al. 18 1998), and to have less motivation to resubmit unfunded applications (Biernat et al. 2020). A re-examination of racial and gender bias in the peer review process is needed as is the testing and application of valid mitigation strategies to reduce bias in review panels. Impartiality is needed to ensure the legitimacy of the peer review system, because the outcomes of such review panels are linked to funding and career trajectories and contribute to funding disparities currently seen among racial groups (Erosheva et  al. 2020). Thus, ensuring fair reviews should help improve diversity in the scientific community, which has been shown to promote innovation (Hofstra et al. 2020).i Our analysis also indicates that the majority of our respondents did not find review feedback very useful in improving grantsmanship, future submissions, or future areas of research. These results may hint at a breakdown in one of the sec- ondary functions of peer review––providing useful feedback to applicants; although funding agencies vary in their expectations for grant reviewers to provide such feed- back. Interestingly, perceptions of usefulness were quite negative independent of applicant funding status, and the demographics of the respondents did not appear to significantly affect perceptions. Some respondents listed the format of the feedback and the lack of constructive criticism as issues, although some felt comments were relevant and potentially useful. Many comments focused on the low funding success rates and the low reliability between reviewers, and between original reviews and those of resubmissions as important hurdles to the utility of feedback (e.g., one can address initial reviewer concerns, only to have a separate set of concerns appear in the review of the resubmission). Perceptions of Grant Review Feedback This reported lack of reliability may highlight some issues with the structure of the review process for resubmissions, which are exacer- bated by poor funding rates. Overall, more effort should be placed on ensuring that the process of providing feedback is strengthened to achieve all goals, primary and secondary, of the peer review of applications. Some respondents also mentioned how the appropriateness of feedback limits its usefulness for future submissions and our analysis confirms that negative per- ceptions of appropriateness are correlated with negative perceptions of usefulness. This relationship between appropriateness and usefulness is particularly concerning given the racial and gender differences found in the appropriateness ratings. While racial/gender factors do not seem to influence perceptions of the usefulness of feed- back directly in our study, respondents may perceive different reasons for the lack of utility, and the perception of persistent bias in the funding system may be a strong influence on scientists’ decisions to submit projects for funding, or even to continue on a research career track. These effects should be examined more rigorously by funding agencies (and the results made public and prominent) to ensure an equitable review process and a healthy, diverse set of applicants. 1 3 Generalizability Our results are limited by a relatively low response rate, although this response rate approximates the rate of similar surveys on peer review (Gallo et al. 2020a; Ware 2008). The majority of funding agency comments in our survey mentioned the NIH 1 3 Grant Review Feedback: Appropriateness and Usefulness Page 17 of 20 18 as a recent source of review feedback; the gender, race, and degrees of our sam- ple are similar to those reported from surveys and analyses of NIH applicants (NIH 2012a; Ginther et al. 2011, 2016). Our respondents tended to be older than NIH applicants (NIH 2012a) but comparable in age to funded NIH investigators (Daniels 2015), consistent with our sample’s high funding success rate. as a recent source of review feedback; the gender, race, and degrees of our sam- ple are similar to those reported from surveys and analyses of NIH applicants (NIH 2012a; Ginther et al. 2011, 2016). Our respondents tended to be older than NIH applicants (NIH 2012a) but comparable in age to funded NIH investigators (Daniels 2015), consistent with our sample’s high funding success rate. Despite the similarity of our overall sample to current applicant pools, white respondents were overrepresented among those who made comments. Future stud- ies should include larger samples of underrepresented minorities to better examine differences between racial/ethnic groups and the motivations for applying or not applying. These results should be also replicated for groups of investigators whose applications were reviewed on the same panel, such that differences across scien- tific topic areas and funding mechanisms are minimized, as these could be important confounding variables in what types of biases are perceived. Finally, an important limitation of this study is the potential effects of funding agency, as this variable was not assessed in our survey. While the majority of our respondents are likely referring to the NIH process based on their comments, some referred to NSF, which has a dif- ferent review process. Future studies should include this factor in their analysis. Conclusion In conclusion, our results suggest more emphasis should be placed on training reviewers to create constructive, useful, and appropriate feedback and enhancing procedures that detect strong biases and inappropriate comments early in the pro- cess, before they influence funding decisions and are communicated to applicants. These recommendations are in line with those from a 2012 report from the NIH Working Group on Diversity in the Biomedical Research Workforce, which was formed in response to reports of racial funding disparities (NIH 2012b). Our results also may suggest more progress on these recommendations is needed to “clarify the root causes for funding disparities” and to “significantly support the development and evaluation of programs that will increase diversity in the biomedical workforce”. Supplementary Information  The online version contains supplementary material available at https://​doi.​ org/​10.​1007/​s11948-​021-​00295-9. Authors’ contributions  SAG, KBS, LAT, and SRG had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. SAG, KBS, and LAT contributed to study concept and design; KBS prepared the Institutional Review Board application and was its point of contact; LAT implemented the survey data collection; SAG and LAT exported and pre- pared the data; all authors contributed to the analysis and interpretation of the data; SAG drafted the manuscript, KBS, LAT and SRG contributed to the critical revision of the manuscript; and SAG provided study supervision. All authors read and approved the final manuscript. Funding  The author(s) received no specific funding for this work. Availability of data and material  A full copy of the peer review survey is available in the S1 File in the Supporting Information. The raw, anonymized data are available on Figshare (https://​doi.​org/​10.​6084/​m9.​ figsh​are.​81324​53.​v1). 1 3 18  Page 18 of 20 S. A. Gallo et al. Consent for publication  Not applicable. 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 Com- mons 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/. Conflict of interest  The authors declare they have no competing interests. Conflict of interest  The authors declare they have no competing interests. Ethics approval  The study was reviewed by the Washington State University Office of Research Assur- ances (Assurance# FWA00002946) and granted an exemption from IRB review consistent with 45 CFR 46.101(b)(2). Consent to participate  Participants were free to choose whether or not to participate in the survey and consented by their participation. References f Race, ethnicity, and NIH research awards. Science, 333(6045), 1015–1019. Race, ethnicity, and NIH research awards. Science, 333(6045), 1015–1019. Gropp, R., Glisson, S., Gallo, S., & Thompson, L. (2017). Peer review: A system under stress. BioSci- ence, 67, 407–410. Gropp, R., Glisson, S., Gallo, S., & Thompson, L. (2017). Peer review: A system under stress. BioSci- ence, 67, 407–410. 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NIH peer review: Grants and cooperative agreements. https://​grants.​nih.​gov/​grants/​pee eview​22713​webv2.​pdf. Last accessed April 2020. p p NIH. (2020). Frequently asked questions. Applicant guidance: Next steps. https://​grants.​nih.​gov/​ faqs#/​next-​steps.​htm?​anchor=​quest​ion53​104. Last accessed April 2020. NIH CSR. (2020). CSR insider’s guide to NIH peer review for reviewers. https://​public.​csr.​nih.​g ForRe​viewe​rs/​Meeti​ngOve​rview/​Insid​ersGu​ideRe​viewe​rs. Last accessed October 2020 NIH CSR. (2020). CSR insider s guide to NIH peer review for reviewers. https://​public.​csr.​nih.​gov/ ForRe​viewe​rs/​Meeti​ngOve​rview/​Insid​ersGu​ideRe​viewe​rs. Last accessed October 2020 Pier, E. L., Raclaw, J., Kaatz, A., Brauer, M., Carnes, M., Nathan, M. J., & Ford, C. E. (2017). ‘Your comments are meaner than your score’: Score calibration talk influences intra-and inter-panel variability during scientific grant peer review. Research Evaluation, 26(1), 1–14. i Pier, E. 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References London, UK: Publishing Research Consortium. http://​cites​eerx.​ist.​psu.​edu/​viewd​oc/​downl​oad?​doi=​10.1.​1.​214.​9676&​ rep=​rep1&​type=​pdf. Last accessed April 2020. Publisher’s Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 1 3 1 3 1 3
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A data-driven approach to solving a 1D inverse scattering problem
arXiv (Cornell University)
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RESEARCH ARTICLE | JUNE 07 2023 A data-driven approach to solving a 1D inverse scattering problem Tristan van Leeuwen  ; Andreas Tataris AIP Advances 13, 065310 (2023) https://doi.org/10.1063/5.0154182   View Online CrossMark Export Citation Recent work in shape-based methods for diffusive inverse problems Rev Sci Instrum (March 2003) Source generation of the Davey-Stewartson equation J. Math. Phys. (January 2008) Inverse problems for the Schrödinger equations with time-dependent electromagnetic potentials and the Aharonov–Bohm effect J. Math. Phys. (February 2008) Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf Articles You May Be Interested In AIP Advances ARTICLE scitation.org/journal/adv A data-driven approach to solving a 1D inverse scattering problem Cite as: AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 Submitted: 13 April 2023 • Accepted: 12 May 2023 • Published Online: 7 June 2023 Tristan van Leeuwen1,2a) and Andreas Tataris2 AFFILIATIONS 2 Centrum Wiskunde and Informatica, Amsterdam, The Netherlands Utrecht University, Utrecht, The Netherlands a) Author to whom correspondence should be addressed: t.van.leeuwen@cwi.nl ABSTRACT In this paper, we extend a recently proposed approach for inverse scattering with Neumann boundary conditions [Druskin et al., Inverse Probl. 37, 075003 (2021)] to the 1D Schrödinger equation with impedance (Robin) boundary conditions. This method approaches inverse scattering in two steps: first, to extract a reduced order model (ROM) directly from the data and, subsequently, to extract the scattering potential from the ROM. We also propose a novel data-assimilation (DA) inversion method based on the ROM approach, thereby avoiding the need for a Lanczos-orthogonalization (LO) step. Furthermore, we present a detailed numerical study and A comparison of the accuracy and stability of the DA and LO methods. © 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). https://doi.org/10.1063/5.0154182 I. INTRODUCTION Inverse scattering appears in many applications, including medical imaging, non-destructive testing, and geophysical exploration.1 While acquisition setups differ at their core, all these inverse problems involve a wave equation and require an estimation of its variable coefficients from boundary data. Approaches to solving the resulting inverse problem can be classified as either direct or indirect methods. The direct methods originate in classical inverse scattering theory and rely on formulating a linear relation between scattering data and medium coefficients; see, e.g., Ref. 2. The indirect methods formulate a non-linear data-fitting problem that needs to be solved iteratively.3 The indirect methods have been extensively investigated in the past decades with major breakthroughs addressing the computational cost and the non-linearity of the data-fitting problem.4,5 Still, the non-linearity remains a major challenge for this approach. The direct methods have recently attracted renewed attention, as a means of addressing this non-linearity.6–8 A recent development is the use of data-driven reduced-order models (ROMs) for solving the inverse scattering problem.9 In this approach, a reduced-order model is computed directly from the data via an orthogonalization procedure, and from this, the underlying state is estimated. From the AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 estimated state, the corresponding coefficient is estimated by solving a Lippmann–Schwinger integral equation. Challenges for this approach include the sensitivity of the orthogonalization approach to noise in the measurements. The ROM-based approach has been applied in various settings, including time-domain wave propagation, see, e.g., Ref. 10, and frequency-domain diffusion processes, see Ref. 9. As a first step toward extending this procedure to frequency-domain wave problems, we extend the approach to a 1D Schrödinger equation with impedance boundary conditions. It turns out that both reflection and transmission measurements are needed to compute the ROM from the data. Furthermore, we propose an alternative approach to the orthogonalization-based state estimation approach described in Ref. 9. To study the accuracy and stability properties of the resulting methods, we present numerical experiments. This paper is organized as follows. First, we review the forward problem and present the relations between the boundary data and required ROM matrices. Then, we discuss the two-step approach to solve the inverse problem: state estimation and subsequent estimation of the coefficients from the state. We then present numerical experiments to illustrate the accuracy and stability of both methods on noisy data. We conclude this paper with a brief summary of the main findings and a discussion on further work. 13, 065310-1 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf 1 AIP Advances ARTICLE II. THE FORWARD PROBLEM Lemma 1. The ROM system matrices S, M [Eqs. (5) and (6)] are m−1 given in terms of the boundary data { fi }m−1 i=0 and {gi }i=0 [Eq. (3)] as Consider the 1D Schrödinger equation, − u′′ (x; k) + q(x)u(x; k) − k2 u(x; k) = 0, x ∈ (0, 1), ⎛ ki kj Bij k2j ki f j + k2i kj f i ⎞ , Sij = ı −2 ⎠ ⎝ ki − kj k2i − k2j (1) with boundary conditions, u′ (0; k) + ıku(0; k) = 2ık, u′ (1; k) − ıku(1; k) = 0, g(k) = u(1; k). i ≠ j, Sii = k2i (R( fi )I( f ′i ) − I( fi )R( f ′i ) + R(gi )I(gi′ ) (2) − I(gi )R(gi′ )) − I( f ′i ) − I( fi )/ki. which corresponds to an incoming plane wave from −∞. The scattering potential q is assumed to have compact support in (0,1). The measurements are given by f (k) = u(0; k), scitation.org/journal/adv Mij = ı( (3) i ≠ j, Mii = R( fi )I( f ′i ) − I( fi )R( f ′i ) + R(gi )I(gi′ ) − I(gi )R(gi′ ) − I( f ′i ) + I( fi )/ki. The proof of this lemma can be found in the Appendix. A. A reduced-order model The point of departure for the ROM-based approach is the weak formulation of (1) and (2), ⟨u′ , ϕ′ ⟩ + ⟨qu, ϕ⟩ − k2 ⟨u, ϕ⟩ − ık( f (k)ϕ(0) + g(k)ϕ(1)) = −2ıkϕ(0) ∀ ϕ, III. THE INVERSE PROBLEM (4) where ⟨⋅, ⋅⟩ denotes the standard inner product in L2 (0, 1) and ⋅ denotes the complex conjugation. Representing the solution as a linear combination of solutions m−1 {ui }i=0 with ui ≡ u(⋅; ki ), and using the same as test functions, the resulting system matrices are defined, correspondingly, Sij = ⟨u′j , u′i ⟩ + ⟨quj , ui ⟩, (5) Mij = ⟨uj , ui ⟩, (6) Bij = f j fi + g j gi , (7) bi = −2ıkfi. (8) and right-hand side, Correspondingly, the approximate solution is then given by m−1 ̃ u(x; k) = ∑ ci (k)ui (x), Remark 1. From the Proof of Lemma 1, we see that ci (kj ) = δij . Thus, we have ̃ u(ki ) = ui . (9) i=0 The inverse problem is now to retrieve the scattering potential, q, from boundary measurements at wave numbers {ki }m−1 i=0 , f = ( f (k0 ), f (k1 ), . . . , f (km−1 )) and g = (g(k0 ), g(k1 ), . . . , g(km−1 )). This is achieved in a two-step procedure. First, the states {ui }m−1 i=0 are estimated from the data, and subsequently, the scattering potential, q, is estimated from these approximated states {̃ ui }m−1 i=0 . A. Estimating the state As outlined in Sec. II, we can compute the coefficients in (9) directly from the data by solving (10) with S, M, B, b obtained from the boundary data as stated in Lemma 1. Since the basis {ui }m−1 i=0 needed to evaluate (9) is unknown, however, we need to use a dif(0) ferent basis. The basic idea is to use states {ui }m−1 i=0 corresponding (0) to a given q instead. It is tempting to directly replace ui in (9) by (0) ui corresponding to a reference scattering potential q(0) . However, (0) this will not work as it would yield ̃ u(x; ki ) = ui (x), see Remark 1. Below, we discuss two alternatives. with the coefficients obeying (S − k2 M − ıkB)c(k) = b(k). (10) We refer the reader to Refs. 12–15 for the discussion regarding the approximation error of such ROM approximations. The main feature making this approach useful for solving the inverse problem is that the system matrices can be computed from the data directly, as per the following lemma. AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 1. Lanczos orthogonalization The authors of Ref. 9 propose to use an orthogonalization procedure as follows. They first apply the M-orthogonal Lanczos procedure to M −1 S, which yields matrices Q ∈ Cm×r and T ∈ Cr×r , where r ≤ m, satisfying Q∗ SQ = T, Q∗ MQ = I. 13, 065310-2 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf Well-posedness of this forward problem has been well-established (at least when q is continuous) since the boundary value problem can be transformed to the Lippmann–Schwinger integral equation; see, e.g., Ref. 11. Bij ki f j + kj f i −2 2 ), ki − kj ki − k2j AIP Advances ARTICLE scitation.org/journal/adv ALGORITHM 1. Overview of the two-step inversion procedure to estimate the states and scattering potential from boundary data. Input: reference q(0) , data f , g at wavenumbers {ki }m−1 i=0 , regularisation parameters ((ϵ, α) or (ρ, α)) Output: reconstructed states {̃ ui }m−1 q. i=0 and scattering potential ̃ Step 1: state estimation Compute ROM-matrices M, S, B according to Lemma 1 (0) m−1 Compute reference states {ui }i=0 corresponding to q(0) . m−1 Compute approximate states {̃ ui }i=0 at wavenumbers {ki }m−1 i=0 according to the LO or DA procedures (outlined in sections 3.1.1, 3.1.2 resp.) Step 2: estimating the scattering potential Reconstruct the scattering potential ̃ q according to the procedure outlined in Sec. 3.1.3 in practice, we cannot form the orthogonal basis {vi }r−1 i=0 . Instead, we (0) , as replace it by {vi }r−1 i=0 m−1 The ROM approximation of the state (9) can then be expressed (0) vj as = ∑ Qij ui , (0) (0) i=0 m−1 ̃ u(x; k) = ∑ ciLO (k)vi (x), (11) i=0 with the coefficients cLO (k) satisfying (T − k2 I − ıkQ∗ BQ)cLO (k) = Q∗ b(k), and where r−1 {vi }i=0 (0) where the states ui are the solutions for a reference scattering potential q(0) and Q(0) is obtained by applying the Lanczos procedure to the corresponding system matrices. The resulting approximation of the state is then given by (12) m−1 (0) ̃ u LO (x; k) = ∑ ciLO (k)vi (x). defined by (13) i=0 m−1 vj = ∑ Qij ui , i=0 is an orthogonal (w.r.t. the regular L2 -inner product) basis for the m−1 span of {ui }m−1 i=0 . Because we do not have access to the states {ui }i=0 2. Data assimilation An alternative approach is inspired by Ref. 16 and sets up an overdetermined system of equations, which ensures that the resulting estimate of the internal solution closely matches the data. We FIG. 1. From left to right, the scattering potential q, the real (blue) and imaginary (red) part of the reflection data, f , and the real and imaginary part of the transmission data, g. AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 13, 065310-3 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf Remark 2. In practice, we replace M by M + ϵI for some ϵ > 0 to ensure it is invertible and to stabilize the Lanczos procedure. AIP Advances ARTICLE scitation.org/journal/adv where ρ > 0 is a penalty parameter controlling the trade-off between data-fit and model-fit. Note that we can readily setup this leastsquares problem for k ∈ {ki }m−1 i=0 since the required data f (ki ), g(ki ) for the right-hand-side is measured. If we want to evaluate this approximation for k ∉ {ki }m−1 i=0 , we need to interpolate the data first. (0) For ρ = 0, we will obtain ̃ u DA (x; ki ) = ui (x), and this will not yield any additional information on the true state. For ρ > 0, the additional terms aim to ensure that ̃ u DA (0; k) ≈ f (k) and ̃ u DA (1; k) ≈ g(k). This is a fundamental difference with the Lanczos-based approach, where data-fit is not enforced at all. B. Estimating the scattering potential directly define the approximated state in terms of the reference solutions, m−1 q i=0 where the coefficients cDA (k) are obtained by solving the following least-squares problem: © Author(s) 2023 (16) Remark 3. Note that replacing u by ̃ u in (15) induces an error in K. To explicitly account for this, a Total Least-Squares (TLS) formulation (see e.g., Ref. 17 for its use in inverse scattering) might be beneficial. (14) FIG. 3. Results using the reference state to reconstruct the scattering potential (i.e., the Born approximation). The top row shows the (reconstructed) states (solid) used in the subsequent step to estimate the scattering potential as well as the true states (dashed). In the second row, we see the reconstructed scattering potential (solid) and the corresponding data. The real part of the quantities is shown in blue, while the imaginary part is shown in red. AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 1 1 u(0) (x; k)u(x; k)(q(x) − q0 (x))dx. ∫ 2ık 0 (15) Representing q in terms of a suitable basis and enforcing the equation for wavenumbers {ki }m−1 i=0 yields a system of equations. In practice, we replace u by its approximation ̃ u and solve it in a least-squares sense to obtain an estimate of the scattering potential, f (k) − f (0) (k) = − min ∥Kq − (f − f(0) )∥22 + α∥q∥22. (0) ̃ u DA (x; k) = ∑ ciDA (k)ui (x), X X X X X ⎛S − k2 M − ıkB⎞ ⎛ b(k) ⎞X X X X X X X X X ⎟ ⎜ ⎜ ⎟ T X DA (0) X X ⎜ ⎟c − ⎜ρ f (k)⎟X X c (k) = arg min X , ρf X X ⎟ ⎜ ⎜ ⎟ X X X X ⎟ ⎜ ⎜ ⎟ c X X T X X (0) X X X ⎝ ⎠ ⎝ ρg(k) ⎠X ρg X X X X X X2 Using the weak formulation of the differential equation, we obtain a Lippmann–Schwinger-type equation for the scattering potential, IV. NUMERICAL RESULTS The inversion procedure consists of two steps: state estimation and estimation of the scattering potential from the states. For FIG. 4. Results using the LO approach on noiseless data. The top row shows the (reconstructed) states (solid) used in the subsequent step to estimate the scattering potential as well as the true states (dashed). In the second row, we see the reconstructed scattering potential (solid) and the corresponding data. The real part of the quantities is shown in blue, while the imaginary part is shown in red. 13, 065310-4 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf FIG. 2. Results using the true state to reconstruct the scattering potential. The top row shows the (reconstructed) states (solid) used in the subsequent step to estimate the scattering potential as well as the true states (dashed). In the second row, we see the reconstructed scattering potential (solid) and the corresponding data. The real part of the quantities is shown in blue, while the imaginary part is shown in red. AIP Advances ARTICLE scitation.org/journal/adv B. Benchmark results As a benchmark, we reconstruct the scattering potential using the approach described in Sec. III B using the true states (as the ideal setting) and the reference states for q(0) (x) = 0 (which corresponds to the Born approximation). The results are shown in Figs. 2 and 3. Even using the true states, we do not obtain a perfect reconstruction of the scattering potential due to the band-limited nature of the data. Furthermore, the inferior result obtained using the Born approximation underlines the need for non-linear inversion. C. Noiseless data FIG. 5. Results using the DA approach on noiseless data. The top row shows the (reconstructed) states (solid) used in the subsequent step to estimate the scattering potential as well as the true states (dashed). In the second row, we see the reconstructed scattering potential (solid) and the corresponding data. The real part of the quantities is shown in blue, while the imaginary part is shown in red. D. Noisy data the first step, we use either the Lanczos orthogonalization approach (LO) with parameter ϵ or the data-assimilation approach (DA) with parameter ρ. With the approximated states, the scattering potential is then estimated by solving the regularized Lippmann–Schwinger equation, with parameter α. This two-step algorithm is outlined in Algorithm 1. Implementation of the described method is fairly straightforward. The code used to produce these results is available at https://github.com/ucsi-consortium/1DInverseScatteringROM. A. Experimental settings To illustrate the methods, we use the scattering potential depicted in Fig. 1. The data are obtained by numerically solving the Schrödinger equation for m = 10 equispaced wave numbers in the interval (0,10). In this subsection, we compare the methods on noisy data. In particular, we add i.d.d. normally distributed noise to the data with mean zero and variance σ 2 . The parameters ϵ, ρ, α are chosen to yield the best approximation (as measured by the L2 error between the reconstructions and the ground truth, averaged over 100 realizations of the noise). The corresponding plots showing the dependence of the error on the parameters are included in the Appendix. In Table I, we summarize the results for varying σ. The corresponding plots are shown in Fig. 6. As expected, the noise influences the reconstruction of the state and consequently the reconstruction of the scattering potential. Overall, we see that the DA method gives superior estimates of the state. In terms of the scattering potential, there is no significant difference between both methods, however, for moderate noise levels, the DA method gives more stable results with a much smaller variance in the error. TABLE I. Comparison between the relative errors in reconstructed states and scattering potential for both methods. We report the average and standard deviation over 100 realizations of the noise. Method Parameters Error in u 10 −6 LO(ϵ, α) DA(ρ, α) (10 , 10 ) (10−2 , 10−4 ) 1.5 ⋅ 10 (1.6 ⋅ 10 ) 6.1 ⋅ 10−3 (1.4 ⋅ 10−5 ) 4.7 ⋅ 10−1 (3.2 ⋅ 10−3 ) 3.9 ⋅ 10−1 (2.3 ⋅ 10−3 ) 10−5 LO(ϵ, α) DA(ρ, α) (10−2 , 10−3 ) (10−1 , 10−3 ) 1.5 ⋅ 10−1 (5.3 ⋅ 10−4 ) 6.1 ⋅ 10−3 (3.0 ⋅ 10−5 ) 4.6 ⋅ 10−1 (2.3 ⋅ 10−3 ) 4.5 ⋅ 10−1 (2.8 ⋅ 10−3 ) 10−4 LO(ϵ, α) DA(ρ, α) (10−2 , 10−2 ) (10−1 , 10−2 ) 1.8 ⋅ 10−1 (1.5 ⋅ 10−1 ) 6.2 ⋅ 10−3 (3.4 ⋅ 10−4 ) 5.7 ⋅ 10−1 (1.4 ⋅ 10−1 ) 5.3 ⋅ 10−1 (3.2 ⋅ 10−3 ) 10−3 LO(ϵ, α) DA(ρ, α) (10−1 , 10−2 ) (100 , 10−2 ) 2.1 ⋅ 10−1 (1.2 ⋅ 10−1 ) 6.4 ⋅ 10−3 (7.0 ⋅ 10−4 ) 6.2 ⋅ 10−1 (1.3 ⋅ 10−1 ) 6.0 ⋅ 10−1 (5.9 ⋅ 10−2 ) 10−2 LO(ϵ, α) DA(ρ, α) (10−1 , 10−1 ) (101 , 10−1 ) 2.6 ⋅ 10−1 (7.1 ⋅ 10−1 ) 1.4 ⋅ 10−2 (4.4 ⋅ 10−3 ) 9.2 ⋅ 10−1 (9.4 ⋅ 10−2 ) 9.2 ⋅ 10−1 (9.0 ⋅ 10−2 ) σ AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 −3 −3 −1 Error in q −3 13, 065310-5 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf Next, we present the results yielded by the (LO) and (DA) methods for noise-free data in Figs. 4 and 5, respectively. We observe that the DA method gives slightly more accurate reconstructions of the states. The corresponding reconstructed scattering potentials are slightly different, but there seems to be little difference in the accuracy of the reconstructions. AIP Advances ARTICLE scitation.org/journal/adv Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf FIG. 6. Results for the LO (left) and DA (right) methods for varying noise levels (σ = 10−6 , 10−5 , 10−4 , 10−3 , respectively, from top to bottom). The subplots follow the same layout as the previous figures. Individual results for different realizations of the noise are superimposed to clearly show the variation. AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 13, 065310-6 AIP Advances ARTICLE scitation.org/journal/adv V. DISCUSSION AND CONCLUSION DATA AVAILABILITY We treat the inverse problem of retrieving the scattering potential in a 1D Schrödinger equation from boundary data. To do this, we propose a two-step approach inspired by a previously published ROM-based method. We extend this method, previously applied to 1D diffusion problems with Neumann boundary conditions, to the 1D Schrödinger equation with impedance boundary conditions. In particular, we presented explicit expressions for retrieving the ROM matrices from boundary data and proposed a novel approach for approximating the state from these matrices. This approach, based on ideas from data assimilation, is an alternative to the previously proposed method based on Lanczos orthogonalization. Given the estimates of the states, the scattering potential is obtained by solving an integral equation. We compared the two approaches numerically on a simulated example with varying noise levels. These experiments suggest that the data-assimilation approach for estimating the state is more accurate and stable and leads to a more stable estimate of the scattering potential for moderate noise levels. This work is the first step toward extending the ROMbased approach to frequency-domain wave-like problems (e.g., the Helmholtz equation) and 2D/3D. Our numerical experiments are idealized as we have allowed ourselves to compute the optimal values of the required regularization parameters. In practice, one would need to resort to one of the many available parameter estimation methods (e.g., the L-curve method, discrepancy principle, or cross validation). It is not clear if the observed benefits of the DA method remain if the parameters are not carefully tuned. Other open questions for further research include the approximation error, stability estimates, and more practical aspects such as an iterative approach where the reference potential is iteratively updated. Data sharing is not applicable to this article as no new data were created or analyzed in this study. This work was supported by the Utrecht Consortium for Subsurface Imaging (UCSI). AUTHOR DECLARATIONS Conflict of Interest The authors have no conflicts to disclose. Author Contributions Tristan van Leeuwen: Conceptualization (equal); Formal analysis (supporting); Funding acquisition (lead); Investigation (equal); Methodology (equal); Software (equal); Supervision (lead); Writing – original draft (equal); Writing – review & editing (equal). Andreas Tataris: Conceptualization (equal); Formal analysis (equal); Investigation (equal); Methodology (equal); Software (equal); Writing – original draft (equal); Writing – review & editing (equal). AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 Proof of Lemma 1. From the weak form, we find Sij − k2j Mij − ıkj Bij = −2ıkj f i and S ji − k2i Mji − ıki Bji = −2ıki f j , from which (by taking the conjugate transpose and using the fact that the matrices involved are Hermitian) Sij − k2i Mij + ıki Bij = 2ıki f j. Combining these yields (k2i − k2j )Mij − ı(ki + kj )Bij = −2ı(ki f j + kj f i ) and (k2i − k2j )Sij − ı(k2j ki + k2i kj )Bij = −2ı(k2j ki f j + k2i kj fi ), from which, we can compute M ij and Sij , Mij = ı( Sij = ı ki f j + kj f i Bij −2 2 ), ki − kj ki − k2j ⎛ ki kj Bij k2j ki f j + k2i kj f i ⎞ −2 . ⎝ ki − kj ⎠ k2i − k2j For the diagonal elements, we need to take a limit of the above two relations. We first compute the diagonal elements of M. We set λ = k2j and k2i = λ + h. We also define f (kj ) = ϕ(λ) = ϕ1 + ıϕ2 and ϕ(λ + h) = ϕh1 + ıϕh2 and, similarly, γ(λ) = g(kj ). Since I(Mjj ) = 0, we obtain √ h √ λϕ2 − λ + hϕ2 Mjj = lim {−2 h→0 h ⎫ h h ⎪ γ2 γ1 − γ1 γ2 + ϕ2 ϕh1 − ϕ1 ϕh2 ⎪ √ √ − ⎬ ⎪ λ+h− λ ⎪ ⎭ √ dϕ2 √ dγ1 1 −1/2 = −2( λ (λ) − λ ϕ2 (λ)) − γ2 (λ)2 λ (λ) dλ 2 dλ √ dγ2 (λ) √ dϕ1 + γ1 (λ)2 λ − ϕ2 (λ)2 λ (λ) dλ dλ √ dϕ2 (λ) + ϕ1 (λ)2 λ . (A1) dλ The product rule gives that γ. Combining gives dϕ dλ = df dk dk dk2 = f ′ (k)(2k)−1 similarly for 1 1 1 ′ I( f ) − I( f )) − I(g)2k R(g) + R(g)2k 2k 2k 2k 1 1 1 × I(g) − I( f )2k R( f ) + R( f )2k I( f )}∣ , 2k 2k 2k k=kj Mjj = {−2(k 13, 065310-7 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf ACKNOWLEDGMENTS APPENDIX A: PROOFS AIP Advances ARTICLE scitation.org/journal/adv AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 © Author(s) 2023 13, 065310-8 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf FIG. 7. Average error for both methods (LO, left and DA, right) for various noise levels (0, 10−6 , 10−5 , 10−4 , 10−3 , respectively, from top to bottom). AIP Advances ARTICLE 4 which gives Mjj = ′ ′ ′ R( f j )I( f j ) − I( f j )R( f j ) + R(g j )I(g j ) − I(g j )R(g ′j ) − I( f j′ ) + I( f j )/kj. We obtain similarly the relation for the diagonal of S. ◻ APPENDIX B: REGULARIZATION PARAMETER SELECTION REFERENCES 1 E. R. Pike and P. C. Sabatier, Scattering, Two-Volume Set: Scattering and Inverse Scattering in Pure and Applied Science (Elsevier, 2001). 2 J. A. Ware and K. Aki, “Continuous and discrete inverse-scattering problems in a stratified elastic medium. I. Plane waves at normal incidence,” J. Acoust. Soc. Am. 45, 911–921 (1969). 3 A. Tarantola, “Inversion of seismic reflection data in the acoustic approximation,” Geophysics 49, 1259–1266 (1984). AIP Advances 13, 065310 (2023); doi: 10.1063/5.0154182 J. Virieux and S. Operto, “An overview of full-waveform inversion in exploration geophysics,” Geophysics 74, WCC1–WCC26 (2009). 5 J. Virieux, A. Asnaashari, R. Brossier, L. Métivier, A. Ribodetti, and W. Zhou, “An introduction to full waveform inversion,” in Encyclopedia of Exploration Geophysics (Society of Exploration Geophysicists, 2017), p. R1–1. 6 F. Broggini and R. Snieder, “Connection of scattering principles: A visual and mathematical tour,” Eur. J. Phys. 33, 593–613 (2012). 7 A. Tataris and T. van Leeuwen, “A distributional Gelfand–Levitan–Marchenko equation for the Helmholtz scattering problem on the line,” J. Math. Phys. 63, 103507 (2022). 8 L. Diekmann, I. Vasconcelos, and T. van Leeuwen, “A note on Marchenkolinearised full waveform inversion for imaging,” Geophys. J. Int. 234, 228–242 (2023). 9 V. Druskin, S. Moskow, and M. Zaslavsky, “Lippmann–Schwinger–Lanczos algorithm for inverse scattering problems,” Inverse Probl. 37, 075003 (2021). 10 L. Borcea, J. Garnier, A. V. Mamonov, and J. T. Zimmerling, “Reduced order model approach for imaging with waves,” Inverse Probl. 38, 025004 (2021). 11 R. Kress, Linear Integral Equations (Springer, 2014), Vol. 82. 12 J. P. Fink and W. C. Rheinboldt, “On the error behavior of the reduced basis technique for nonlinear finite element approximations,” Z. Angew. Math. Mech. 63, 21–28 (1983). 13 Y. Maday, A. T. Patera, and G. Turinici, “A priori convergence theory for reduced-basis approximations of single-parameter elliptic partial differential equations,” J. Sci. Comput. 17, 437–446 (2002). 14 K. Veroy, C. Prud’Homme, D. Rovas, and A. Patera, “A posteriori error bounds for reduced-basis approximation of parametrized noncoercive and nonlinear elliptic partial differential equations,” in 16th AIAA Computational Fluid Dynamics Conference (AIAA, 2003), p. 3847. 15 S. Sen, K. Veroy, D. B. P. Huynh, S. Deparis, N. C. Nguyen, and A. T. Patera, “‘Natural norm’ a posteriori error estimators for reduced basis approximations,” J. Comput. Phys. 217, 37–62 (2006). 16 T. v. Leeuwen and F. J. Herrmann, “A penalty method for PDE-constrained optimization in inverse problems,” Inverse Probl. 32, 015007 (2015). 17 A. Tataris and T. van Leeuwen, “A regularised total least squares approach for 1D inverse scattering,” Mathematics 10, 216 (2022). 18 C. R. Vogel, Computational Methods for Inverse Problems (SIAM, 2002). 13, 065310-9 Downloaded from http://pubs.aip.org/aip/adv/article-pdf/doi/10.1063/5.0154182/17978355/065310_1_5.0154182.pdf The LO and DA methods both have two regularization parameters that regularize the problem. For the current experiments, these parameters are chosen to minimize the expected reconstruction error for the given noise level. We approximate the expected error by averaging the error over 100 realizations of the noise. The plots corresponding to the results presented in Table I and Figs. 4–6 are shown in Fig. 7. Obviously, this procedure can only be applied if the ground truth is known and is chosen here to provide a best-case comparison of the methods. In practice, one would result to datadriven or heuristic methods, such as the discrepancy principle, the L-curve method, or generalized cross validation,18 to select appropriate values for the parameters. © Author(s) 2023 scitation.org/journal/adv
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Corticotropin‐Releasing Hormone Neurons in the Paraventricular Nucleus Project to the External Zone of the Median Eminence: A Study Combining Retrograde Labeling with Immunocytochemistry
Journal of neuroendocrinology
1,993
public-domain
4,943
Abstract Corticotropin-releasing hormone (CRH) is the major regulator of the pituitary-adrenal axis. CRH-immunoreactive perikarya are widely distributed in the central nervous system; however, only those which participate directly in the regulation of adrenocorticotro- pin are connected to the portal circulation in the external zone of the median eminence. The present study describes the identification of these hypophysiotropic neurons using retrograde labeling and CRH immunocytochemistry. Fluoro-Gold was injected peripherally then, 5 days later, the animals were treated with colchicine. Twenty-four hours later the animals were sacrificed, and their brains were immunostained for CRH with the indirect immunofluorescence technique. The results indicate that the vast majority of the Fluoro-Gold-accumulating and CRH-immunopositive perikarya (hypophysiotropic neurons) are located in the medial parvicellular subdivision of the paraventricular nucleus (PVN). However, not each CRH-immunoreactive neuron contains Fluoro-Gold, i.e. a small portion of these neurons project to areas of the brain other than the median eminence. The anterior, lateral and periventricular subdivisions of the PVN also contain hypophysiotropic CRH-immunoreactive perikarya, however, their number is much less than in the medial parvicellular subdivision. Scattered double-labeled cells are also present in the medial preoptic area and the dorsal hypothalamus, just behind the PVN. These results support previous observations that the PVN, particularly the medial parvicellular subdivision, is the predominant source of the hypophysiotropic CRH neurons. Corticotropin-releasing hormone (CRH; also called corticotropin- releasing factor, CRF), a 41 amino-acid peptide (1, 2), is a member of the classic hypophysiotropic hormone family (3, 4). CRH-immunoreactive (CRH-i) neurons and nerve terminals are widely distributed, not only within the hypothalamus but, throughout the CNS (5-8), where CRH functions as a neuro- transmitter or neuromodulator. Within the hypothalamus, most of the immunoreactive perikarya are located in the parvicellular subdivisions of the paraventricular nucleus (PVN) and in the preoptic area. Fewer CRH-i perikarya are present in the dorsal hypothalamic area, the lateral hypothalamus, and the premammil- lary nuclei. Scattered CRH-i perikarya are located in the magno- cellular PVN and supraoptic nucleus. The hypophysiotropic CRH, after being synthesized by perikarya in the hypothalamus, is transported via rapid axonal transport to the median eminence (ME) where it is stored, and upon stimulation it is released from nerve terminals of the ME into the hypophysial portal circulation. Through this circulatory system CRH reaches the anterior pituit- ary where it stimulates the release of adrenocorticotropin (ACTH), /&endorphin and a-melanocyte-stimulating hormone (a-MSH) (2). Corticotropin-Releasing Hormone Neurons in the Paraventricular Nucleus Project to the External Zone of the Median Eminence: A Study Combining Retrograde Labeling with I m mu nocytochem istry David E. Lennard, William A. Eckert and lstvan Merchenthaler Functional Morphology Section, Laboratory of Molecular and Integrative Neuroscience, NIEHS, NIH, Research Triangle Park, North Carolina 27709. USA. Key words: corticotropin-releasing hormone, immunocytochemistry, retrograde labeling Journal of Neuroendocrinology, 1993, Vol. 5, 175-181 Journal of Neuroendocrinology, 1993, Vol. 5, 175-181 Correspondence to: I. Merchenthaler, MD C4-07, LMIN, NIEHS, NIH, Research Triangle Park, North Carolina 27709, USA. David E. Lennard, William A. Eckert and lstvan Merchenthaler Functional Morphology Section, Laboratory of Molecular and Integrative Neuroscience, NIEHS, NIH, Research Triangle Park, North Carolina 27709. USA. thaler, MD C4-07, LMIN, NIEHS, NIH, Research Triangle Park, North Carolina 27709, USA. Abstract CRH is also released into the vasculature of the organum vasculosum of the lamina terminalis (OVLT), the other circum- ventricular organ of the hypothalamus (the function of CRH released here is not known). Attempts to identify the hypophysiotropic CRH neurons, i.e. those which form nerve terminals on capillaries of the hypophysial portal circulatory system, and thereby, directly regulate ACTH, P-endorphin and c(-MSH secretion have included: 1) implantation of anterior pituitary fragments into different brain areas; 2) ablation or stimulation of selected brain regions and measurement of the subsequent changes in the concentration of ACTH and glucocorticoids in the peripheral blood; 3) surgical or electrical lesions of different brain areas containing CRH-i neurons followed by immunocytochemical detection of CRH in the ME; 4) use of hypophysectomized or adrenalectomized animals in which the negative feedback effect of ACTH and/or glucocorticoids has been disrupted; and 5) electron microscopic identification of degenerating CRH-i fibers and terminals in the ME following 176 CRH neurons projecting to the median eminence Location of CRH-i neurons lesion of their perikarya in the PVN (see review in 9). The results of these studies strongly suggested that the PVN is the major source of hypophysiotropic CRH neurons. However, because of their inherent limitations (e.g. their inability to discriminate between the location of hypophysiotropic neurons and fibers of passage and to distinguish between hypophysiotropic and non- hypophysiotropic CRH-i neurons), most of these techniques could not provide an unequivocal identification of the neuronal popula- tion that projects to the ME. Recently, a combinative effort of retrograde labeling from the ME and immunocytochemical detec- tion of endogenous CRH has also been introduced (10, 11). The present study was designed to clarify these observations by identifying the CRH neurons that project to the ME and the OVLT with a sensitive double labeling technique. Fluoro-Gold (FG), a retrograde tracer which does not penetrate the blood- brain barrier, was administered peripherally and those retro- gradely labeled perikarya that also contained CRH were identified by fluorescence immunocytochemistry in the same tissue section. In the hypothalamus, most of the C R H i perikarya were concen- trated in the parvicellular subnuclei of the PVN (14) (Fig. IA IB), the medial preoptic area, the dorsal and posterior hypothal- amic areas, the lateral hypothalamus, and the premammillary nuclei (see ref. 8 for details). Distribution of CRH-i and FG-accumulating perikarya: the hypophysiotropic CRH-i neuronal system Distribution of CRH-i and FG-accumulating perikarya: the hypophysiotropic CRH-i neuronal system The vast majority of CRH-i perikarya which retrogradely accumu- lated FG were seen in the parvicellular subdivisions of the PVN (Figs. lc, ID and 2A-2D). Only a few double-labeled cell bodies were observed in the medial preoptic and dorsal hypothalamic areas. Interestingly, not all CRH-i perikarya contained FG, and not every FG-accumulating cell in these regions was immunoreac- tive for CRH. Within the PVN, the vast majority of the retro- gradely labeled CRH-i perikarya were concentrated in the medial parvicellular subdivision. An average of 140 CRH-i perikarya were counted here and 70% of them contained FG. In the anterior and lateral parvicellular subdivisions, approximately 25% of CRH-i perikarya were retrogradely labeled. The horizontally located, large CRH-i cells above the medial parvicellular PVN and between the lateral edge of the PVN and the fornix did not concentrate FG. The distribution of CRM-i perikarya with access to fenestrated capillaries of the ME and OVLT is represented in Table 1 and Figs. 3 and 4. Location of FG-accumulaling neurons Location of FG-accumulaling neurons Location of FG-accumulaling neurons Within the hypothalamus, the majority of FG-containing neurons were concentrated in well defined nuclei, such as the PVN, the anterior periventricular, the supraoptic, arcuate and periventricu- lar preoptic nuclei, the medial preoptic area, and the diagonal band of Broca. Scattered FG-accumulating neurons were seen in the lateral hypothalamus, the accessory magnocellular nuclei and the posterior hypothalamic area. Within the PVN, the majority of the retrogradely labeled cells were located in the medial parvicellular subdivision. Somewhat less was seen in the anterior parvicellular subdivision. The lateral parvicellular subdivision contained only scattered FG-accumulating cells. In the arcuate nucleus, the retrogradely labeled perikarya occupied the dorsom- edial and ventrolateral subdivisions. The ventromedial subnucleus contained only a few FG-concentrating cells. FG-containing perikarya in the diagonal band of Broca and the lateral portion of the medial preoptic area showed a tent-like arrangement, similar to those immunoreactive for luteinizing hormone-releasing hormone (10). Another group of retrogradely labeled perikarya in the preoptic region occupied the periventricular preoptic nuc- leus. FG-accumulating cells in the anterior periventricular nucleus were densely packed and located close to the wall of the third ventricle (see refs. 1 2 and 13 for details). Abstract Within the PVN, the majority of the CRH-i perikarya (an average of 140 immunopositive cells in a 30 pm vibratome section) was present in the medial parvicellular subdivision. The anterior parvicellular subdivision contained less (an average of 30 immunoreactive perikarya per section) CRH-i cells. The periventricular and lateral parvicellular subdivision contained scattered cells (an average of 10 cells per section). The dorsal cap of the PVN contained only a few CRH-i perikarya. Within the hypothalamus, two circumventricular organs con- tained CRH-i nerve terminals: the ME and the OVLT. Discussion The present study describes the topographical location of CRH-i neurons projecting to the external zone of the ME and OVLT. Since only the CRH-i neurons that have access to fenestrated capillaries of the ME form the final common pathway regulating the function of the anterior pituitary, the identification of these hypophysiotropic neurons is of great importance. The hypophy- siotropic neurons, including the CRH-i neurons, even within a TABLE I. Relative Participation of Fluoro-Gold (FG)-Labeled CRH-i Perikarya in the Rat Brain. Vibratome sections Paraffin sections CRH-i cells FG-CRH-i cells YO 60.3 68.4 66.1 64.9 64.9 3.4 CRH-i cells FG-CRH-i cells Yo 282 ($1 209 74.1 308 (0) 212 68.8 240 (6) 187 77.9 346 (P) 259 74.9 1176 867 73.7 + 3.8 icipation of Fluoro-Gold (FG)-Labeled CRH-i Perikarya in the Rat Brain. TABLE I. Relative Participation of Fluoro-Gold (FG)-Labeled CRH-i Perikarya in the Rat Brain. CRH neurons projecting to the median eminence 177 RH neurons projecting to the median eminence 17 p j g . CRH-i perikarya (indicated by Texas red) in a 30 pm vibratome section from the medial parvicellular subdivision of the PVN (A and 6). The ventricle is represented by asterisks. CRH-i (c) and Fluoro-Gold (FG)-accumulating (D) perikarya in the periventricular subdivision of the PVN hin paraffin section. Those CRH-i perikarya that accumulate FG are indicated by arrows. The stars show identical blood vessels in (c) and (D). that each of the three CRH-i perikarya in (D) contains the retrograde tracer FG as shown in (c), but only three of the FG-containing perikarya ) are immunoreactive for CRH as shown in (B) (A) x 90; (B) x 200; (c and D) x 360. FIG. 1. CRH-i perikarya (indicated by Texas red) in a 30 pm vibratome section from the medial parvicellular subdivision of the PVN (A and 6). The third ventricle is represented by asterisks. CRH-i (c) and Fluoro-Gold (FG)-accumulating (D) perikarya in the periventricular subdivision of the PVN in a thin paraffin section. Those CRH-i perikarya that accumulate FG are indicated by arrows. The stars show identical blood vessels in (c) and (D). Note that each of the three CRH-i perikarya in (D) contains the retrograde tracer FG as shown in (c), but only three of the FG-containing perikarya in (c) are immunoreactive for CRH as shown in (B) (A) x 90; (B) x 200; (c and D) x 360. FIG. 1. Discussion CRH-i perikarya (indicated by Texas red) in a 30 pm vibratome section from the medial parvicellular subdivision of the PVN (A and 6). The third ventricle is represented by asterisks. CRH-i (c) and Fluoro-Gold (FG)-accumulating (D) perikarya in the periventricular subdivision of the PVN in a thin paraffin section. Those CRH-i perikarya that accumulate FG are indicated by arrows. The stars show identical blood vessels in (c) and (D). Note that each of the three CRH-i perikarya in (D) contains the retrograde tracer FG as shown in (c), but only three of the FG-containing perikarya in (c) are immunoreactive for CRH as shown in (B) (A) x 90; (B) x 200; (c and D) x 360. source of those CRH-i neurons that send their processes to the portal circulatory system. well circumscribed area or nucleus, are intermixed with non- hypophysiotropic neurons which also contain CRH but do not project to the ME. These neurons probably contact other neurons in the CNS where CRH functions as a neuromodulator or neurotransmitter. Our observations on the location of the hypophysiotropic CRH-i neurons are consistent with those obtained from studies using electrolytic lesion of the PVN (IS, 16). surgical isolation of the medial basal hypothalamus (1 7- 19), or adrenalectomy or hypophysectomy (20) followed by immunocytochemical detection of CRH in the ME. The results of these studies strongly suggested that the PVN was the major Recently, these observations have been further supported by studies using retrograde labeling from the ME in combination with CRH immunocytochemistry. In one of these recent studies, the lectin wheat germ agglutinin (WGA) was injected into the surgically isolated ME (10). The retrogradely labeled perikarya were visualized with the adjacent sections method by detecting the retrograde tracer and CRH in two adjacent sections. Identical cell bodies immunoreactive for WGA and CRH represented the hypophysiotropic CRH-i neurons (10). Although local injection 178 CRH neurons projecting to the median eminence 178 CRH neurons projecting to the median eminence FIG. 2. CRH-i perikarya (B and D) and Fluoro-Gold (FG)-containing perikarya (A and c) in two vibratome sections taken from two different levels of the medial parvicellular subdivisions of the PVN. Arrows in (A and (c) indicate FG-accumulating perikarya that are not immunoreactive for CRH, i.e. these cannot be seen in (B) and (D). Arrows in (B) and (D) indicate CRH-i perikarya that are not retrogradely labeled with FG, i.e. Discussion these cannot be seen in (A) and (c). Note that with the exception of a few perikarya, almost each CRH-i cell body in the medial parvicellular portion of the PVN contains FG. Stars in (A) and (B) show the same blood vessel. (A and B) x 200; (c and D) x 360. FIG. 2. CRH-i perikarya (B and D) and Fluoro-Gold (FG)-containing perikarya (A and c) in two vibratome sections taken from two different levels of the medial parvicellular subdivisions of the PVN. Arrows in (A and (c) indicate FG-accumulating perikarya that are not immunoreactive for CRH, i.e. these cannot be seen in (B) and (D). Arrows in (B) and (D) indicate CRH-i perikarya that are not retrogradely labeled with FG, i.e. these cannot be seen in (A) and (c). Note that with the exception of a few perikarya, almost each CRH-i cell body in the medial parvicellular portion of the PVN contains FG. Stars in (A) and (B) show the same blood vessel. (A and B) x 200; (c and D) x 360. directly into the ME through the third ventricle (1 1). The retro- gradely labeled CRH-i cells were identified in the same cryostat sections. Although the efficiency of this technique is superior to the adjacent section technique used by Kawano et ul. (lo), the precise location of the ME injection site could not be adequately controlled. In addition, since the ME is not a densely packed structure (rather, it is spongy) spread of the tracer into areas adjacent to the ME, including the arcuate nucleus, could not be ruled out (for technical details see ref. 12). of the retrograde tracer into the surgically isolated ME results in the most precisely controlled technique of administration to identify neurons that project to the ME, the technique is laborious and the amount of retrograde tracer necessary for optimal labeling cannot be precisely specified. In addition, when this technique is combined with the adjacent section technique (lo), many of the double-labeled perikarya are not counted due to the difficulties in identifying the same neurons in two adjacent sections. The advantage of the adjacent section technique, however, is that it provides data without cross-reactivity problems (21). A good estimation of the number of retrogradely labeled neurons can be achieved by the technique used in the present study. Discussion The use of FG as a retrograde tracer (22) is very convenient, Previously, hypophysiotropic CRH-i neurons have been identi- fied by using True Blue, a fluorescent retrograde tracer, injected CRH neurons projecting to the median eminence 179 the supramaximal dose ensures optimal labeling, and its detection can be combined with peptide immunocytochemistry in the same tissue section. The only disadvantage of using FG to identify the hypophysiotropic CRH-i perikarya is that it is also taken up from capillaries supplying the OVLT. However, the number of nerve terminals in the external zone of the ME is vastly greater than the number in the OVLT and, as we have shown in these studies, the number of FG-labeled CRH-i perikarya outside the PVN is low. These observations indicate that the primary source of CRH-i nerve terminals in the OVLT is the PVN. The findings that when the anterograde tracer, Phaseolus vulgaris, is injected into the medial parvicellular subdivision of the PVN, nerve terminals in the OVLT are labeled (23), indicate that some of the parvicellular neurons in the PVN, beside the ME, also project to capillaries of the OVLT. FG labeling provides a stable signal in retrogradely labeled neurons in both thin paraffin and thicker, vibratome sections. By simply changing appropriate filter com- binations of the microscope, both FG (metal gray fluorescence), and CRH-i (a fluorescent dye with a color different from that of FG, e.g. Texas red) can be detected. Although the detection of FG and CRH in thin paraffin sections may be less sensitive than in vibratome sections, the thin 5 to 7 pm sections providc cxcellent spatial resolution and, therefore, superior quantitative evaluation. The amount of FG in tangentially-sectioned perikarya may be below the detection limit and, therefore, the number of hypophysi- otropic neurons can be underestimated. In thicker (30 pm) vibratome sections overlapping of double-labeled cells cannot be ruled out; therefore, cell counting cannot be as precise as in thin paraffin sections (compare Figs. lc, I D with 2~-D). The thicker vibratome sections on the other hand, provide stronger signals both for FG and the endogenous CRH (compare Figs. 2A-D with Ic, 1 ~ ) . However, when densely packed nuclei are examined, such as the PVN, single- and double-labeled cells can overlap and be misinterpreted (for details see reference 10). Discussion A C 0 SP U E A 0 SP 0 0 The results of both techniques discussed above are in good agreement with our observations and indicate that the PVN is the predominate source of the hypophysiotropic CRH-i neurons. The few double-labeled cells seen in the posterior-dorsal hypothal- amus probably also project to the ME, and the few in the preoptic area, to the OVLT (see below). In the medial parvicellular subdivision of the PVN approximately 70% of the CRH-i neurons contain FG. The number of these hypophysiotropic neurons is less (approximately 25%) in the other subnuclei of the PVN. Interestingly, the periventricular subdivision of the PVN, which is known to project to the external zone of the ME (1 3, 24, 25) contained scattered CRH-i perikarya and only a few of them accumulated FG. The identification of the hypophysiotropic neurons is of great importance for understanding the regulation of these neurons, which form the final common pathway for the regulation of the anterior pituitary. FG labeling provides an C U C U FIG. 3. Schematic representation of CRH-i (dark circles), Fluoro-Gold (FG)-accumulating (small clear circles for the parvicellular and large clear circles for the magnocellular neurosecretory system), and double-labeled (asterisks) perikarya in a series of cross sections through the rat hypothal- amus. Note that the vast majority of the hypophysiotropic CRH-i cell bodies, i.e. those that accumulate the retrograde tracer FG, are located in the parvicellular subdivisions of the PVN. However, scattered hypophy- siotropic cells can be found in the medial preoptic area and the dorsal hypothalamus, just behind the PVN. am-nucleus amygdaloideus medialis; CA-commissura anterior; CAI-capsula interna; CC-crus cerebri; cm- nucleus magnocellularis caudalis; CO-chiasma opticum; F-fornix; FMT-fasciculus mammillothalamicus; gp-globus pallidus; LM-Iemniscus medialis; MFB-medial forebrain bundle; na-nucleus arcuatus; ndmd-nucleus dorsomedialis, pars dorsalis; ndmv-nucleus dorsomedialis, pars ventralis; nha-nucleus hypothalamicus anterior; nhp-nucleus hypothalamicus posterior; nist-nucleus interstitialis striae terminalis; nistv-nucleus interstitialis striae terminalis, pars ventralis; npe-nucleus periventricularis; npmd-nucleus premammillaris dorsalis; npmv-nucleus premammillaris ventralis; npvm-nucleus paraventricul- aris, pars magnocellularis; npvp-nucleus paraventricularis, pars parvicel- lularis; nsc-nucleus suprachiasmaticus; nso-nucleus supraopticus; nsor-nucleus supraopticus, retrochiasmatic part; nvm-nucleus ven- tromedialis; pol-nucleus preopticus lateralis; pom-nucleus preopticus medialis; pos-nucleus preopticus suprachiasmaticus; re-nucleus reun- iens thalami; rc-retrochiasmatic area; SM-stria medullaris; td-tractus diagonalis; TO-tractus opticus. Modified after Konig and Klippel (27). Discussion E 180 CRH neurons projecting to the median eminence 7 I BST I I I I I / / I A zi _ - , - - - _ _ _ , AHA FIG. 4. Schematic representation of CRH-i perikarya (dark circles) and CRH-i perikarya that are retrogradely labeled with Fluoro-Gold (asterisks) in the PVN of the hypothalamus. Each symbol represents three CRH-i perikarya. The vast majority of the hypophysiotropic CRH-i perikarya are located in the medial parvicellular subdivision (mp) of the PVN. Less are present in the anterior parvicellular (ap), the periventricular (pv), and the lateral parvicellular (Ip) subdivisions. The dorsal parvicellular subdivision (dp) contains only a few double-labeled perikarya. AHA-anterior hypothalamic area: am-anterior magnocellular subdivision of the PVN; BST-bed nucleus of the stria terminalis; fx-fornix; V3-third ventricle; pm-posterior magnocellular subdivision of the PVN. Modified after Sawchenko el al. (28). 180 CRH neurons projecting to the median eminence 7 I BST I I I I I / / I A A zi _ - , - - - _ _ _ , AHA FIG. 4. Schematic representation of CRH-i perikarya (dark circles) and CRH-i perikarya that are retrogradely labeled with Fluoro-Gold (asterisks) in the PVN of the hypothalamus. Each symbol represents three CRH-i perikarya. The vast majority of the hypophysiotropic CRH-i perikarya are located in the medial parvicellular subdivision (mp) of the PVN. Less are present in the anterior parvicellular (ap), the periventricular (pv), and the lateral parvicellular (Ip) subdivisions. The dorsal parvicellular subdivision (dp) contains only a few double-labeled perikarya. AHA-anterior hypothalamic area: am-anterior magnocellular subdivision of the PVN; BST-bed nucleus of the stria terminalis; fx-fornix; V3-third ventricle; pm-posterior magnocellular subdivision of the PVN. Modified after Sawchenko el al. (28). tribromoethanol (1 m1/100 g body wt of a 2.5% solution), and colchicine was administered into the lateral ventricle (5 pIjlO0 g body wt of a 20 mg/ ml solution). Twenty-four hours later the animals were anesthetized again with tribromoethanol and perfused through the ascending aorta with 1% paraformaldehyde in 0.05 M phosphate-buffered saline followed by 4% paraformaldehyde in the same buffer (10). Following overnight postfixa- tion, five hypothalami from both sexes were embedded in parafin and were sectioned at 8 pm. Seven hypothalami from both sexes were cut on a vibratome at 30pm. The antiserum against CRH (#569) was raised against rat-CRH in a rabbit and was used at a dilution of 1:4,000. Discussion Biotinylated goat anti-rabbit IgG and Texas-red-labeled avidin were purchased from Jackson ImmunoResearch (West Grove. PA, USA) and were used at dilutions of 1:500 and 1:1,000, respectively (see ref. 10 for technical details). Following completion of the immunocytochemical procedure, the sections were dehydrated in graded alcohols and cover- slipped from xylene with DePex (Fluka). excellent, simple, yet effective and, in most cases, specific, tech- nique for this purpose. In the future, this type of retrograde labeling should make it possible to characterize the true hypophy- siotropic neurons, i.e. their receptors, afferentations and the neuropeptides and neurotransmitters colocalized with hypophysi- otropic hormones, including CRH. In summary, although CRH-i perikarya are widely distributed within the hypothalamus, our studies, together with previous experiments, indicate that the vast majority of the hypophysi- otropic CRH-i neurons, i.e. those which directly regulate ACTH, @-endorphin and c(-MSH secretion from the anterior pituitary, is located in the medial parvicellular subdivision of the PVN. Hypophysiotropic and non-hypophysiotropic CRH-i neurons are intermixed in the PVN, indicating that CRH produced even in a classical hypophysiotropic nucleus like the PVN may function not only as a hypophysiotropic factor, but as a neuromodulator or neurotransmitter. All sections were examined with an Axiophot photomicroscope equipped with the necessary excitation and emission filters for immuno- fluorescence microscopy. Tmax 3200 black and white and P800/1600 color films (Eastman Kodak, Co., Rochester, NY, USA) werc used for photography. For quantitative analysis, two male and two female paraffin- embedded and two male and two female unembedded brains were used. Every tenth paraffin section and every fifth vibratome section was used for counting single-labeled (CRH-i) and double-labeled (CRH-i and FG- accumulating) perikarya. By changing appropriate filter combinations single- and double-labeled CRH-i perikarya were counted. The atlas of Paxinos and Watson (26) and Konig and Klippel (27) were used to determine the location in the rat hypothalamus of FG-accumulating and CRH-i neurons. References 1. Rivier J. Spiess J, Vale W. (1983). Characterization of rat hypothalamic corticotropin-releasing factor. Proc Natl Acad Sci USA. 80: 485 1-4855. 17. Anton] FA. Palkovits M, Makara GB, Linton EA, Lowry PJ, Kiss JZ. (1983). Immunoreactive corticotropin-releasing hormone in the hypothalamoinfundibular tract. Neuroendocrinology. 36: 41 5-423. 2. Vale W. Spiess J, Rivier C. (1981). Characterization of a 41-residue ovine hypothalamic peptide that stimulates the secretion of cortico- tropin and b-endorphin. Science. 213: 1394-1397. yp gy 18. Merchenthaler I, Hynes MA, Vigh S, Schally AV, Petrusz P. (1984). Corticotropin-releasing factor (CRF): origin and course of affezent pathways to the median eminence (ME) of the rat hypothalamus. Neuroendocrinology. 39: 296-306. p p 3. Palkovits M. (1986). Neuropeptides in the median eminence. Neuro- chem Int. 9: 131-139. 4. Merchenthaler I. (1991). Current status of brain hypophysiotropic factors. Morphologic aspects. Trends Endocrinol Metab. 2: 21 9-226. gy 19. Tilders FJ, Schipper HJ, Lowry PJ, Vermes 1. (1982). Effect of hypothalamus lesions on the presence of CRF-immunoreactive nerve terminals in the median eminence and on the pituitary-adrenal response to stress. Regul Pept. 5: 77-84. p g p 5. Olschowka JA, ODonohue TL, Mueller GP, Jacobowitz DM. (1982). Hypothalamic and extrahypothalamic distribution of CRF-like immu- noreactive neurons in the rat brain. Neuroendocrinology. 35: 305-308. 20. Merchenthaler I, Vigh S, Petrusz P, Schally AV. (1983). The paraven- triculo-infundibular corticotropin-releasing factor (CRF) pathway as revealed by immunocytochemistry in long-term hypophysectomized and adrenalectomized rats. Regul Pept. 5: 295-305. gy 6. Bloom FE, Battenberg ELF, Rivier J, Vale W. (1982). Corticotropin releasing factor (CRF): immunoreactive neurons and fibers in rat hypothalamus. Regul Pept. 4: 43-48. yp g p 7. Bugnon C. Fellmann D, Gouget A, Cardot J. (1982). Corticoliberin in rat brain: irnmunocytochemical identification and localization of a novel neuroglandular system. Neurosci Lett. 30: 25-30. g p 21. Hokfelt T, Tsuruo Y, Meister B, Melander T, Schalling M, Everitt B. (1987). Localization of neuroactive substances in the hypothalamus with special reference to coexistence of messenger molecules. Adv Exp Med Biol. 219: 21-45. g y 8. Merchenthaler I. Vigh S, Petrusz P, Schally AV. (1982). Immunocyto- chemical localization of corticotropin-releasing factor (CRF) in the rat brain. Am J Anat. 165: 385-396. 22. Schmeud LC. Fallon JH. (1986). Fluoro-Gold: a new fluorescent retrograde axonal tracer with numerous unique properties. Brain Res. 377: 147-154. 9. Petrusz P, Merchenthalcr I. (1992). The corticotropin-releasing factor system. In: Nemeroff CB, ed. Accepted 21 Octobcr 1992 Accepted 21 Octobcr 1992 16. Liposits Zs, Lengvari I, Vigh S, Schally AV, Flerko B. (1983). Immunohistological detection of degenerating CRF-immunoreactive nerve fibers in the median eminence after lesions of paraventricular nucleus of the rat. A light and electron microscopic study. Peptides. 4 941-953. Acknowledgements as demonstrated by retrograde fluorescence double-labeling method. J Comp Neurol. 194 555-570. The authors wish to thank Scott Trasti for his technical help and Drs Michael D. Culler and Francisco J. Lopez, and JoAnne Reid for critical reading of the manuscript. p 15. Bruhn TO, Plotsky PM, Vale WW. (1984). Effect of paravcntricular lesions on corticotropin releasing factor (CRF)-like immunoreactivity in the stalk-median cminence: studies on the adrenocorticotropin response to ether stress and exogenous CRF. Endocrinology. 114: 57-62. p response to ether stress and exogenous CRF. Endocrinology. 114: 57-62. Materials and Methods Twelve male rats and twelve female rats (sacrificed on the day of proestrus) were injected intraperitoneally with supramaximal doses of FG (I5 mg/kg body wt dissolved in 0.9% saline; Fluorochrome Inc., Engelwood, CO, USA) (12, 13, 22). Five days later the animals were anesthetized with References Comprehensive textbook of neuroendocrin- ology. 125-179. CRC Press, Boca Raton. 23. Larsen PJ, Moller M, Mikkelsen JD. (1991). Efferent projections from the periventricular and medial parvicellular subnuclei of the hypothalamic paraventricular nucleus to the circumventricular organs of the rat: a phaseolus vulgaris-leucoagglutinin (PHA-L) tracing study. gy 10. Kawano H, Daikoku S, Shibasaki T. (1988). CRF-containing neuron systems in the rat hypothalamus: retrograde tracing and immunohisto- chemical studies. J Comp Neurol. 272: 260-268. p g gg ( ) g J Comp Neurol. 307: 462-479. p g J Comp Neurol. 307: 462-479. p 11. Niimi M, Takahara J, Hashimoto K, Kawanishi K. (1988). Immuno- histochemical identification of corticotropin releasing factor-containing neurons projecting to the stalk-median eminence of the rat. Peptides. 9: 589-593. 24. Lechan RM, Nestler JL. Jacobson S, Rcichlin S. (1980). The hypothal- amic tuberoinfundibular system of the rat as demonstrated by horserad- ish peroxidase (HRP) microiontophoresis. Brain Res. 195: 13-27. 25. Wiegand SJ, Price JL. (1980). The cells of origin of the afferent fibers to the median eminence in the rat. J Comp Neurol. 192: 1-19. 12. Merchenthaler I. (1990). Retrograde labeling of hypophysiotropic neurons by local injection of wheat germ agglutinin (WGA) into the median eminence or peripheral administration of Fluoro-Gold. Mol Cell Neurosci. 1: 93-106. 26. Paxinos G, Watson C. (1986). The rat brain in stereotaxic coordinates, 2nd Ed. Academic Press, London. 27. Konig JFR, Klippel RA. (1963). The rat brain. A stereotaxic atlas of the forebrain and lower parts of the brain stem. Williams and Wilkins, Baltimore. 13. Merchenthaler I. (1991). Neurons having access to fenestrated capil- laries in the central nervous system of the rat: a retrograde tracing study with Fluoro-Gold. Neuroscience. 44: 655-662. 28. Sawchenko PE, Swanson LW, Vale W. (1984). Co-expression of corticotropin-releasing factor and vasopressin immunoreactivity in par- vicellular neurosecretory neurons of the adrenalectomized rat. Proc Natl Acad Sci USA. 81: 1883-1887. y 14. Swanson LW, Kuypers HGJM. (1980). The paraventricular nucleus of the hypothalamus: cytoarchitectonic subdivisions and organization of projections to the pituitary, dorsal vagal complex, and spinal cord
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Hadronic Higgs production through NLO $$+$$ + PS in the SM, the 2HDM and the MSSM
European physical journal. C, Particles and fields
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Hadronic Higgs production through NLO + PS in the SM, the 2HDM and the MSSM Hendrik Mantler1,a, Marius Wiesemann2,b 1 TH Division, Physics Department, CERN, 1211 Geneva 23, Switzerland 2 Physik-Institut, Universität Zürich, 8057 Zurich, Switzerland Received: 29 April 2015 / Accepted: 14 May 2015 / Published online: 10 June 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com Abstract The next-to-leading order (NLO) cross section of the gluon fusion process is matched to parton showers in the MC@NLO approach. We work in the framework of MadGraph5_aMC@NLO and document the inclusion of the full quark-mass dependence in the Standard Model (SM) as well as the state-of-the-art squark and gluino effects within the Minimal Supersymmetric SM embodied in the program SusHi. The combination of the two programs is realized by a script which is publicly available and whose usage is detailed. We discuss the input cards and the relevant parame- ter switches. One of our focuses is on the shower scale which isspecificallyimportantforgluon-inducedHiggsproduction, particularly in models with enhanced Higgs-bottom Yukawa coupling. (H) scalar, and a pseudo-scalar (A); as well as two charged Higgs particles (H±). Almost all 2HDM and MSSM scenar- ios that are in agreement with the experimental bounds fea- ture a light scalar which is SM-like in its couplings to vector bosons and fermions, while the other Higgs bosons are heav- ier and, therefore, escaped detection up to now. Indeed, the experimental search for other Higgs resonances is one of the major focuses regarding the discovery of physics beyond the SM (BSM) in the second run of the Large Hadron Collider (LHC). (H) scalar, and a pseudo-scalar (A); as well as two charged Higgs particles (H±). Almost all 2HDM and MSSM scenar- ios that are in agreement with the experimental bounds fea- ture a light scalar which is SM-like in its couplings to vector bosons and fermions, while the other Higgs bosons are heav- ier and, therefore, escaped detection up to now. Indeed, the experimental search for other Higgs resonances is one of the major focuses regarding the discovery of physics beyond the SM (BSM) in the second run of the Large Hadron Collider (LHC). Higgs production through gluon fusion is mediated by a colored particle. In the SM, the top quark gives the domi- nant contribution to the cross section [6–8]. While also the bottom quark gives a sizable contribution, the effects due to other quarks are small and therefore usually neglected. 2 Note that in theories with an enhanced bottom Yukawa the associated Higgs production with bottom quarks becomes relevant; see Refs. [9– 17] and references therein. Eur. Phys. J. C (2015) 75:257 DOI 10.1140/epjc/s10052-015-3462-1 Regular Article - Theoretical Physics Regular Article - Theoretical Physics Hadronic Higgs production through NLO + PS in the SM, the 2HDM and the MSSM In the 2HDM and the MSSM the Higgs-bottom Yukawa cou- pling can be enhanced with respect to the one of the top quark and the bottom loop may even constitute the domi- nant contribution to the cross section. In those models it is stringently required to include the bottom-quark contribu- tion.2 The gluon fusion cross section is known at the next-to- leading order (NLO) in the SM including top- and bottom- mass effects [18,19], in the 2HDM and in the MSSM includ- ing contributions from squarks and gluinos [20–34]. For the top quark, an effective field theory approach can be applied in which the top quark is considered to be infinitely heavy and can be integrated out from the full theory. In this approx- imation, Higgs production has been calculated up to the next-to-NLO (NNLO) inclusively [35–37] as well as fully differential [38–40]. Electro-weak contributions and effects beyond NNLO in the heavy-top approximation have been studied in Refs. [41–50] for example, while there was a large effort [51,52] to push the accuracy to next-to-NNLO ( N3LO) 1 Introduction Higgs production proceeds predominantly through gluon fusion in a large number of theories, including the Stan- dard Model (SM). The recently discovered resonance [1,2] in searches for a Higgs boson is fully consistent with the SM picture,1 so far. Still, the measured Higgs boson may be embedded in an enlarged Higgs sector with respect to the one of the SM which predicts only a single physical par- ticle breaking the electro-weak symmetry. Two-Higgs dou- blet models (2HDM’s) such as the Minimal Supersymmet- ric SM (MSSM) are among the most popular theories with enlarged Higgs sectors. Such theories inevitably require the existence of further physical Higgs particles. A 2HDM pre- dicts three neutral Higgs bosons: a light (h) and a heavy 1 See Refs. [3–5] for a theoretical overview. a e-mail: hmantler@cern.ch b e-mail: mariusw@physik.uzh.ch 12 3 257 Page 2 of 14 257 Page 2 of 14 257 Page 2 o 257 Eur. Phys. J. C (2015) 75 :257 The relevant NLO matrix elements are taken from Ref. [74], which include both SM-like contributions and sbottom, stop and gluino effects. Examples of corresponding Feynman diagrams are illustrated in Fig. 1. They are combined and matched to a parton shower by the well-known MC@NLO- method. The matched cross section in the MC@NLO frame- work can be written symbolically as which has been succeeded very recently [53]. Finite top-mass effects have been shown to be small for both the inclusive cross section at the NNLO [54–59] and differential quan- tities [60,61] as long as no kinematical scale (such as the transverse momentum of a particle) that is not integrated out exceeds the top-mass threshold. The full dependence of the top- and the bottom-mass at the NLO has been included so far in a POWHEG- type [62] matching to parton showers (PSs) [33], the analytically resummed transverse momentum spectrum of the Higgs boson at NLO + NLL [63], a MC@NLO- type [64] matching to the Herwig Monte Carlos [65– 67], the NNLO + NNLL jet-vetoed [68] and the fully dif- ferential NNLO [69] cross section; and in some approxi- mated form recently also in the NNLOPS approach [70, 71]. Furthermore, the 2HDM as well as supersymmetric effects from squarks and gluinos within the MSSM [20– 34] have been implemented in the first two approaches from that list [33,72]. 3 aMCSusHi can be downloaded under https://cp3.irmp.ucl.ac.be/ projects/madgraph/wiki/aMCSushi. 4 SusHi has recently been extended to include NMSSM Higgs pro- duction [75], which may be made available in aMCSusHi in the future. 1 Introduction In this manuscript, we report on a new implementation of NLO QCD corrections in the SM, 2HDM and MSSM applying the MC@NLO-type match- ing to both Herwig and Pythia showers. We work in the framework of MadGraph5_aMC@NLO [73] and combine its capabilities with the corresponding ampli- tudes provided by SusHi [74]. The linking of SusHi to MadGraph5_aMC@NLOisrealizedbyascript3 aMCSusHi. Its usage as well as the application of the combined code to obtain cross section predictions in the SM, the 2HDM and the MSSM is detailed in this paper.4  dσ dO  MC@NLO =  dn  Bn+Vn+  d MC 1 K MC n+1  I MC n (O) +   dn+1Rn+1 −d MC n+1K MC n+1  I MC n+1(O) , (1) where Bn determines the Born-level cross section, Vn the virtual (including mass factorization) and Rn+1 the real cor- rections; K MC n+1 is the Monte Carlo subtraction term, with the same IR poles as Rn+1, the Monte Carlo phase space dMC n+1 tends to dn+1 in the IR limits, and dMC 1 = dMC n+1/dn. The quantity IMC n (O) is the shower spectrum for observable O, as obtained by running the shower starting from an n-body configuration. The cross section at Born level is derived from the LO dia- grams for gg →φ where φ ∈{h, H, A}; see e.g. Fig. 1a–c. The NLO virtual and real corrections are governed by dia- grams like the ones shown in Fig. 1d–g and h, i, respectively, and similar ones with quark loops replaced by squark loops. Equation (1) is implemented for all standard parton show- ers [76–81] in the fully automated framework MadGraph5_aMC@NLO. This code determines NLO QCD corrections to arbitrary scattering processes at the LHC. On the basis of UFO models [82], the code even allows one to carry out computations in any theory beyond the SM in a general manner as soon as the renormalization is known and implemented in a UFO model; see Refs. [73,83–85] for further information. However, the Higgs pro- duction mode through gluon fusion is special, being loop- induced already at the LO. Such processes cannot be han- dled in a fully automated manner by any code to date, since it requires the automation of two-loop amplitudes which is beyond current technology. 1 Introduction Therefore, we have treated Higgs production through gluon fusion in the SM, 2HDM and MSSM as a special case, by linking the relevant ampli- tudes from SusHi. Furthermore, as far as the MSSM is concerned SusHi requires a link to FeynHiggs [86–96] which evaluates the corresponding Higgs masses and cou- plings in user defined scenarios. Setting up the SusHi ampli- tudes in MadGraph5_aMC@NLO is handled by a publicly available script called aMCSusHi, which is automated to create the gg →φ process folder; download SusHi and FeynHiggs; compile, install and link them; and replace the relevant amplitudes in the process folder. In the upcoming section, we describe the application of the script and explain the necessary steps to obtain phenomenological results. The manuscript is organized as follows: In Sect. 2 we present a brief overview of the elements of the computation at hand. Section 3 is dedicated to introduce aMCSusHi and is separated in three parts which cover: how to use the script (Sect. 3.1), how to run the resulting code (Sect. 3.2) and how to treat the shower scale (Sect. 3.3). We will show a brief application of the code to phenomenological results in Sect. 4 and conclude in Sect. 5. Eur. Phys. J. C (2015) 75 :257 Eur. Phys. J. C (2015) 75 :257 Fig. 1 A sample of Feynman diagrams for gg →φ contributing to the NLO cross section; a–c LO, d–g virtual, and h, i real corrections. The graphical notation for the lines is: solid straight = quark; spiraled = gluon; dashed = scalar (squark or Higgs); spiraled with line = gluino φ φ φ φ φ φ φ φ φ (a) (b) (c) (d) (e) (f) (g) (h) (i) 3 aMCSusHi script This code is based on MadGraph5_aMC@NLO and SusHi. > ./set up ggH MSSM script.pl <ggH-folder> [<FeynHiggs-folder> [<SusHi-folder>]] φ (a) φ φ φ φ φ φ (b) (c) (e) (f) (h) (i) > ./set up ggH MSSM script.pl <ggH-folder> [<FeynHiggs-folder> [<SusHi-folder>]] φ (b) φ (c) φ φ (b) (e) (b) (c) (a) φ (c) (f) φ (e) (f) (d) (e) φ (g) φ (h) φ (i) (h) (i) (g) > ./set up ggH MSSM script.pl <ggH-folder> [<FeynHiggs-folder> [<SusHi-folder>]] 3 aMCSusHi script 3 aMCSusHi script This code is based on MadGraph5_aMC@NLO and SusHi. For further information on theses codes we refer the reader to corresponding publications [73,74]. After using the script to set up the code, we will focus on the rel- evant user inputs to obtain phenomenological predictions for Higgs cross sections in the SM, the 2HDM and the MSSM. The first argument is mandatory and determines the path to the process folder for gg →φ that is generated by the script. The only requirement is that this folder has to be definedasasub-folderoftheMadGraph5_aMC@NLOdirec- tory. The second and third arguments are optional. If there are compiled versions of FeynHiggs and SusHi avail- able on your computer you can give the names of the fold- ers that contain the files libFH.a and libsushi.a, respectively. When executed with two (one) argument(s) the script will ask whether it should automatically download and install SusHi (and FeynHiggs). The script will always download the latest versions of these codes. While running, the script requires some user inputs: It asks whether or not SusHi (and FeynHiggs) should be downloaded, in which folder they should be installed (default is inside the ⟨ggH-folder⟩) or where to find SusHi (and FeynHiggs) if already installed. The user is simply required to follow these on-screen instructions. 5 See the README file how this can easily be obtained with the MadGraph5_aMC@NLO script. Eur. Phys. J. C (2015) 75 :257 Furthermore, the script creates log-files in the working directory for the download (“XX_curl.log”), the configure command (“XX_conf.log”) and the compilation (“XX_make.log”), where XX = FH for FeynHiggs and XX = SusHi for SusHi. These files are supposed to give complementary information for any kind of troubleshoot- 2 Outline of the calculation The goal of this paper is to present a tool which allows for the computation of arbitrary infra-red safe differential observ- ables at both the parton and the hadron level for the produc- tion of neutral Higgs bosons via gluon fusion in the SM, the 2HDM and the MSSM by matching the NLO cross section to a shower. 12 3 Page 3 of 14 257 Page 3 of 14 257 3.1 Usage of the script The aMCSusHi script is available for download from the website https://cp3.irmp.ucl.ac.be/projects/madgraph/wiki/ aMCSushi. It is fully automatic in setting up the gg → φ process folder which includes downloading, installing and linking FeynHiggs and SusHi. At first, a dummy HEFT process folder for gg → h in the five-flavor scheme at NLO (without the virtuals) is created;5 then the HEFT amplitudes in MadGraph5_aMC@NLO are consis- tently replaced by the ones from SusHi (including the virtuals). The setup requires only a single call of the aMCSusHi script: 12 3 3 Eur. Phys. J. C (2015) 75 :257 257 Page 4 of 14 ing.6 Further information about the aMCSusHi script pro- vides the README file. ing.6 Further information about the aMCSusHi script pro- vides the README file. choice is reasonable, since it respects effects from hard radi- ation and corresponds to a value of mφ/2 in the soft/collinear limit which is the current recommendation for the total inclu- sive gg →φ cross section [3,5]. choice is reasonable, since it respects effects from hard radi- ation and corresponds to a value of mφ/2 in the soft/collinear limit which is the current recommendation for the total inclu- sive gg →φ cross section [3,5]. 6 Please note that even in cases where the compilation of FeynHiggs or SusHi fails, the linking may still work fine as long as the files libFH.a and libsushi.a have been created in the corresponding library folders. > ./bin/generate events and following the usual steps in MadGraph5_aMC@NLO to choose the run-modes (order, shower or fixed-order, mad- spin). Before running the code, one may want to mod- ify the input settings. In the following we will discuss the differences between aMCSusHi and the ordinary MadGraph5_aMC@NLO code regarding the input files. The param_card.dat, on the other hand, receives some significant changes by the aMCSusHi script. The new version basically combines the orignial parameter card from MadGraph5_aMC@NLO with the input file from SusHi which are both written in the SUSY Les Houches accord (SLHA) format [97] and, therefore, easily con- nectable. We will address the different options in the param_card.dat in more detail, since there are a number of changes and some of the original parameters lose their functionality. In the SLHA format inputs are organized in blocks which have different entries that are characterized by a number. For simplicity, we introduce the following short- hand notation: Block example[i] corresponds to entry i in Block example. E.g., entry 25 of Block mass (Block mass[25]) in the SLHA format is devoted to the Higgs mass in the SM, which is required as an input in the param_card.dat. A typical parameter card of aMCSusHi in the SM is shown below: The input cards can be found under ⟨ggH-folder⟩/Cards/, where the param_card.dat, run_card.dat and shower_card.dat contain all the essential information. The run card con- trols the usual parameters, e.g. the renormalization (μR) and factorization scale (μF). Note that by default the flags fixed_ren_scale and fixed_fac_scale are set to false, so that these two scales are chosen on an event-wise basis. Their values are specified in the last routine of ⟨ggH- folder⟩/SubProcesses/setscales.f which, due to the default option dynamical_scale_choice = −1 in the run card, sets μR = μF = HT /2 ≡1/2 i(m2 i + p2 T (i))1/2, where i runs over all final state particles and mi and pT (i) are their mass and transverse momentum, respectively. This 6 Please note that even in cases where the compilation of FeynHiggs or SusHi fails, the linking may still work fine as long as the files libFH.a and libsushi.a have been created in the corresponding library folders. 12 3 3.2 Running the code Also the shower card in aMCSusHi contains no new information and has the usual functionality. Since MadGraph5_aMC@NLO supports all standard parton show- ers, for the first time Pythia6 and Pythia8 can be applied at NLO + PS to SM Higgs production in the full theory in the MC@NLO framework. In general, it is advisable to apply the most recent versions of the showers for meaningful physics runs. Once the gg →φ process folder has been set up by the script, the run can be started directly from the ⟨ggH-folder⟩ by typing 3 C (2015) 75 :257 ################################### ## INFORMATION FOR MASS ################################### Block mass 15 1.777000e+00 # MTA 23 9.118800e+01 # MZ 25 1.250000e+02 # MH -- only effective if FEYNHIGGS Block is absent [...] ################################### ## INFORMATION FOR SMINPUTS ################################### Block sminputs 1 1.325070e+02 # aEWM1 2 1.166390e -05 # Gf 3 1.180000e -01 # aS # additional information needed for SusHi 4 9.118800e+01 # m_Z(pole) 5 0.416000e+01 # m_b(m_b) -- only used if m_b is not on -shell 6 1.730000e+02 # m_t(pole) -- top mass is set here ################################### ## INFORMATION FOR YUKAWA ################################### Block yukawa 15 1.777000e+00 # ymtau ################################### ## INFORMATION FOR DECAY ################################### DECAY 6 1.491500e+00 # WT DECAY 23 2.441404e+00 # WZ DECAY 24 2.047600e+00 # WW DECAY 25 6.382339e -03 # WH DECAY 9000006 6.382339e -03 # WH1 [...] ################################### ## INFORMATION FOR SUSHI ################################### Block sushi 1 0 # model: 0 = SM , 1 = MSSM , 2 = 2HDM 2 0 # 0 = light Higgs (h), 1 = pseudoscalar (A), 2 = heavy Higgs (H) Block renormbot # Renormalization of the bottom sector 1 0 # m_b used for bottom Yukawa: 0 = OS , 1 = MSbar(m_b), 2 = MSbar(muR) 4 4.75 d0 # mbOS fixed -- used if m_b is on -shell (default) Block factors 1 0.d0 # factor for yukawa -couplings: c 2 1.d0 # t 3 1.d0 # b ################################### ## INFORMATION FOR MASS ################################### Block mass 15 1.777000e+00 # MTA 23 9.118800e+01 # MZ 25 1.250000e+02 # MH -- only effective if FEYNHIGGS Block is absent [...] ################################### ## INFORMATION FOR SMINPUTS ################################### Block sminputs 1 1.325070e+02 # aEWM1 2 1.166390e -05 # Gf 3 1.180000e -01 # aS # additional information needed for SusHi 4 9.118800e+01 # m_Z(pole) 5 0.416000e+01 # m_b(m_b) -- only used if m_b is not on -shell 6 1.730000e+02 # m_t(pole) -- top mass is set here ################################### ## INFORMATION FOR YUKAWA ################################### Block yukawa 15 1.777000e+00 # ymtau ################################### ## INFORMATION FOR DECAY ################################### DECAY 6 1.491500e+00 # WT DECAY 23 2.441404e+00 # WZ DECAY 24 2.047600e+00 # WW DECAY 25 6.382339e -03 # WH DECAY 9000006 6.382339e -03 # WH1 [...] ################################### ## INFORMATION FOR SUSHI ################################### Block sushi 1 0 # model: 0 = SM , 1 = MSSM , 2 = 2HDM 2 0 # 0 = light Higgs (h), 1 = pseudoscalar (A), 2 = heavy Higgs (H) Block renormbot # Renormalization of the bottom sector 1 0 # m_b used for bottom Yukawa: 0 = OS , 1 = MSbar(m_b), 2 = MSbar(muR) 4 4.75 d0 # mbOS fixed -- used if m_b is on -shell (default) Block factors 1 0.d0 # factor for yukawa -couplings: c 2 1.d0 # t 3 1.d0 # b Most of the inputs are self-explanatory due to the com- ments initiated by the hash symbol # after the entries. 7 Note that only in the on-shell scheme the automatic MadGraph5_aMC@NLO reweighting for μR is functionable. 3 Page 5 of 14 257 Eur. Phys. J. 3 At this point we shall remark that the particle identification number in the generated event files is always 25 regardless of the Higgs boson under consideration.8 This is irrelevant for the production (which is correctly computed through the SusHi amplitudes), but it plays a role for the decay where the shower will consider particle 25 to be the light Higgs, which is indeed fine for any scalar Higgs, but a problem for pseudo-scalar ones. Therefore, decays of a pseudo-scalar Higgs are currently not supported in the official version of aMCSusHi. A user interested in decaying the pseudo-scalar Higgs is strongly encouraged to contact us. Additionally to the inputs which we defined already for the SM the following parameters have to be set in the 2HDM: Block renormbot[2] specifies whether or not a resum- mation10 of terms enhanced by tan(β) is applied through reweighting of the bottom Yukawa coupling as described in Ref. [74]; Block 2hdm determines which type of the 2HDM is used; the value of tan(β) is set through Block minpar[3]; and the mixing angle α corresponds to the entry in Block alpha. y The computation of MSSM Higgs cross sections requires Block extpar, Block feynhiggs and Block renormsbot in addition, which fix the parame- ters of the third family of quarks and squarks, determine the FeynHiggs inputs and yield information on the renor- malization of the sbottom section, respectively. We will not provide any further information on these blocks, instead, we refer to the SusHi manual [106] and the FeynHiggs man pages [107]. Moreover, Block alpha can be omitted in the MSSM and the Higgs masses in Block mass have no effect, since they are determined by FeynHiggs, once Block feynhiggs is present. The MSSM Higgs mass that has been computed and applied in the run is provided to the user in Block mass[25] of the parameter card, which will be overwritten by the mass of the respective Higgs boson at the beginning of each MSSM run. The other parameters are relevant to SusHi. Block sushi[1] chooses the model with the three options SM(Block sushi[1]= 0),MSSM(Block sushi[1] = 1) and 2HDM (Block sushi[1] = 2). The sec- ond entry of Block sushi determines the Higgs boson: light Higgs (Block sushi[2] = 11 or 0), pseudo-scalar Higgs (Block sushi[2] = 21 or 1) and heavy Higgs (Block sushi[2] = 12 or 2). 10 See Refs. [100–105] for further information. 3 Fur- thermore,thestandardSLHAblocksmatchtheuniversalcon- vention of Ref. [97]. Some of the inputs, though, require fur- ther comments. In the Block mass all parameters have the expected function, except for the top and the bottom mass, Block mass[6] and Block mass[5], respec- tively. While the former only affects and is required for the shower, the latter can be omitted completely. Instead, due to the link to SusHi the top mass that is used for the top loop and the top Yukawa is set in Block sminputs[6] and is expected to be on-shell. For the bottom mass, on the other hand, SusHi allows for three different choices: on-shell scheme or MS scheme with mb(mb) or mb(μR), which can be switched in Block renormbot[1] by a value between 1 and 3.7 Also here the recommendation is to use the on-shell scheme which according to Refs. [18,98] ensures the cancelation of large logarithms ln(mh/mb) at NLO QCD, while the MS scheme does not, due to an incom- plete resummation of these terms. The on-shell mb value is determined by Block renormbot[4], while when the MS scheme is chosen the corresponding input of mb(mb) is set in Block sminputs[5]. The other entries of Block sminputs again have the same impact as in the usual MadGraph5_aMC@NLO code. The same is true for Block yukawa. For the decay of light and heavy Higgs bosons one may specify a finite width of the Higgs boson in the 12 12 3 3 257 Page 6 of 14 257 Page 257 Eur. Phys. J. C (2015) 75 :257 respective BSM scenario by using Decay 25 irrespective of whether the light or the heavy Higgs boson is considered. At this point we shall remark that the particle identification number in the generated event files is always 25 regardless of the Higgs boson under consideration.8 This is irrelevant for the production (which is correctly computed through the SusHi amplitudes), but it plays a role for the decay where the shower will consider particle 25 to be the light Higgs, which is indeed fine for any scalar Higgs, but a problem for pseudo-scalar ones. Therefore, decays of a pseudo-scalar Higgs are currently not supported in the official version of aMCSusHi. A user interested in decaying the pseudo-scalar Higgs is strongly encouraged to contact us. respective BSM scenario by using Decay 25 irrespective of whether the light or the heavy Higgs boson is considered. 3.3 Choosing different shower scales 3.3 Choosing different shower scales The choice of the shower scale is a very peculiar one in the gluon fusion process. In presence of the bottom-quark loop, factorization of soft and collinear radiation maybe spoiled at scales significantly smaller than the Higgs boson mass. This was pointed out by Ref. [69] in the context of analytic transverse momentum resummation. On the other hand, these terms might well be treated as a finite remainder as long as their impact remains moderate [68]. σ(Qt, Qb) = σt(Qt) + σt+b(Qb) −σt(Qb). (2) (2) To obtain all three contributions of different Yukawa origin with different scales that allows for a model independent treatment, on the other hand, MadGraph5_aMC@NLO has to be run five times: σ(Qt, Qb, Qtb) = σt(Qt) + σb(Qb) + σt+b(Qtb) −σt(Qtb) −σb(Qtb). (3) (3) Due to their additive matching of the resummed low- pT region with the fixed-order distribution valid at large transverse momenta, analytic pT -resummation and the MC@NLO-method are quite similar. In both cases there is a scale associated with that matching, the resummation scale Qres and the shower scale Qsh, respectively. These scales can be interpreted as transition scales that separate the soft/collinear from the hard physics, very similar to the factorization scale of the PDFs. In other words, they define the range where resummation, and therefore the shower in MC@NLO, takes effect. Their value has to be chosen of the order of the typical scale of the problem. The scales Qt, Qb, and Qtb determine the scale for top, the bottom and their interference, respectively. As indicated before, the individual contributions can be separated using the Block factors in the parameter card. The shower scale in MadGraph5_aMC@NLO cannot sim- ply be accessed through the input cards, since it requires an advanced user to be familiar with its specific treatment in the code. MadGraph5_aMC@NLO does not use a simple fixed scale for Qsh, instead, it statistically extracts the shower scale from a distribution peaked at a specific value. The user can only change the range of the interval of the distribution which of course also affects the peak. Therefore, we identify Qt, Qb, and Qtb in Eqs. (2) and (3) with the peak of the respective shower scale distributions. In gluon fusion, the typical scale depends on the quark considered in the loop. 3 The choice of the masses of the relevant Higgs bosons depends on the model. As stated before, Block mass[25] sets the Higgs mass in the SM. In the 2HDM, this entry corresponds to the mass of the light Higgs boson, while Block mass[35] and Block mass[36] specify the input for the heavy and the pseudo- scalar Higgs, respectively. All other 2HDM inputs are set in the information for SusHi. For reference, we give an example of the corresponding inputs for a heavy Higgs in the 2HDM below9: So far we did not comment on the Block factors. It allows one to turn on and off individual contributions in all models. In fact, it even provides the possibility to rescale the respective Yukawa couplings by choosing val- [...] ################################### ## INFORMATION FOR SUSHI ################################### Block sushi 1 2 # model: 0 = SM , 1 = MSSM , 2 = 2HDM 2 2 # 0 = light Higgs (h), 1 = pseudoscalar (A), 2 = heavy Higgs (H) Block renormbot # Renormalization of the bottom sector 1 0 # m_b used for bottom Yukawa: 0 = OS , 1 = MSbar(m_b), 2 = MSbar(muR) 2 2 # tan(beta)-res. of Y_b: 0 = no , 1 = naive , 2 = full (for OS only) 4 4.75 d0 # mbOS fixed Block 2hdm # 2HDM version according to arXiv :1106.0034 2 # (1=I ,2= II ,3=III ,4=IV) Block minpar 3 50d0 # tanb Block alpha 0.0247 d0 # mixing in Higgs sector Block factors 1 0d0 # factor for yukawa -couplings: c 2 1d0 # t 3 1d0 # b ues different from 0 and 1. With Block factors[1] one can include the charm quark in the computation. This 8 Bear in mind that this has to be taken into account to identify the Higgs in the analysis of the showered events. 9 A link to 2HDMC [99] with the corresponding input convention is currently not supported. 12 3 Eur. Phys. J. C (2015) 75 :257 Page 7 of 14 257 [72] it was further proposed to separate three contributions according to their Yukawa couplings: the square of the top and the bottom, and their interference; and choose separate shower/resummation scales for all of them. 3 This splitting allows for a model independent treatment of the problem by a rescaling of the individual contributions with the respec- tive top and bottom Yukawas of a specific scenario in the 2HDM as well as the MSSM when neglecting squark effects. In the literature, two pragmatic approaches with physical motivation have been presented [72,108] to determine sepa- rate scales for the three contributions. Their comparison will be studied elsewhere [109]. When studying phenomenolog- ical results in Sect. 4 we will apply the scales from Ref. [72] (referred to as “HMW” in what follows). requires one to specify its MS mass mc(mc) in Block sminputs[8] which is then translated to its on-shell mass. Furthermore, Block factors[2] and Block factors[3] multiply the top and the bottom Yukawa, respectively. In the MSSM, the stop Yukawa is rescaled by Block factors[4] and the sbottom one by Block factors[5]. For further information on the input cards we refer the reader to Ref. [73] of MadGraph5_aMC@NLO, the manual of SusHi [106] and the man pages of FeynHiggs [107]. Three example parameter cards are provided in the folder ⟨ggH-folder⟩/Cards; one for the SM (param_card.dat_SM), the 2HDM (param_card.dat_2HDM_scenB) and the MSSM (param_card.dat_MSSM_mhmodp). They match the scenarios that we study in the result section of this paper. The separation of the bottom contribution (including the interference) from the top one with different shower scales (Qb and Qt, respectively) requires three runs in MadGraph5_aMC@NLO, which have to be combined as fol- lows: 11 For further information we refer the reader to Sect. 2.4.4 of Ref. [73]. 3.3 Choosing different shower scales The corresponding Qsh distribution is peaked around where s0 is the Born-level partonic center of mass energy squared. Evidently, scaleMClow and scaleMCdelta only take effect if the interval obtained through frac_low and frac_upp does not meet the corresponding restric- tions. The corresponding Qsh distribution is peaked around 3.3 Choosing different shower scales Since mt ∼mφ, there exist only two relevant scales for the top-quark loop (mφ and pT ) and the shower scale can be chosen of the order of the Higgs mass. Whenconsideringthebottomloop,ontheotherhand,weface a three-scale problem (mφ, mb, and pT ) which has not been solved to date. However, it has been suggested [69] to apply a lower transition scale to the bottom contribution, which, in particular, respects the fact that soft/collinear factorization is valid only up to smaller scales for the bottom loop. In Ref. The so-called shape parameters define the interval of the distribution from which the shower scale is picked on an event-wise basis. They can be specified in the include file ⟨ggH-folder⟩/SubProcesses/madfks_mcatnlo.inc, where the relevant part is given by (MadGraph5_aMC@NLO default values): 12 123 257 Page 8 of 14 257 Page 8 of 14 Eur. Phys. J. C (2015) 75 :257 [...] c Define lower and upper veto range (see MC subtraction terms) double precision frac_low ,frac_upp parameter (frac_low =0.1 d0) parameter (frac_upp =1.0 d0) c Other control switches on veto (see MC subtraction terms) double precision scaleMClow , scaleMCdelta parameter (scaleMClow =10. d0) parameter ( scaleMCdelta =20. d0) [...] [...] ction terms) on terms) ph5_aMC@NLO has to b by typing make clean ⟨ggH-folder⟩, which for un of the code. . 4 we show some appli tudy the effect of differe c Define lower and upper veto range (see MC subtraction terms) double precision frac_low ,frac_upp parameter (frac_low =0.1 d0) parameter (frac_upp =1.0 d0) c Other control switches on veto (see MC subtraction terms) double precision scaleMClow , scaleMCdelta parameter (scaleMClow =10. d0) parameter ( scaleMCdelta =20. d0) The parameters frac_low and frac_upp are used to compute the upper and lower bounds of the Qsh distribu- tion, which will be explained in more detail below, while scaleMClow allows one to set an absolute value of the lower bound on Qsh and scaleMCdelta is used to apply a minimal value to the size of the distribution interval. In formulas the interval is defined by11 Qmin ≤Qsh ≤Qmax, with Qmin = max(frac_low · √s0, scaleMClow) and (4) Qmax = max(frac_upp · √s0, Qmin+scaleMCdelta), where s0 is the Born-level partonic center of mass energy squared. Evidently, scaleMClow and scaleMCdelta only take effect if the interval obtained through frac_low and frac_upp does not meet the corresponding restric- tions. 4 Results: brief application We shall note at this point that sim- ply due to their inclusion in the default analysis we were able to produce a large number of further observables at no additional computing cost. and Herwig6 (yellow, solid with filled boxes). We apply the MSTW2008 68 % CL NLO PDF set [112] with the corre- sponding value of the strong coupling constant. The shower scale has been chosen as Qsh = mh/2 in all cases, while for μF and μR we use the defaults specified in Sect. 3.2. Clearly, the mass effects are hardly dependent on the specific Monte Carlo, which is particularly evident at small (pT ≲50GeV) and large (pT ≳150GeV) transverse momenta. Neverthe- less, there are some visible differences in the intermediate region which consistently discriminate the Herwig from the Pythia showers. Overall, they are at most 5 % though and therefore still moderate. To demonstrate the range of applicability of aMCSusHi, we consider two realistic BSM scenarios in Figs. 4 and 5: the heavy Higgs boson in Scenario B of Ref. [113] (a bottom dominated 2HDM scenario); and the pseudo-scalar Higgs boson in the mmod+ h (800, 40) MSSM scenario [114] defined in Table 2 of Ref. [72]. The corresponding input files can be found in the folder ⟨ggH-folder⟩/Cards. Figure 3 shows the effects of quark masses with respect to the heavy-top approximation as well, but for different choices of the associated shower scales. In all cases, the denomi- nator and therefore the distribution in the heavy-top limit is computed with the respective scale of the top contribu- tion Qsh = Qt. As we observed before the Monte Carlo dependence is quite small; therefore, we only consider the Pythia8 shower. For reference the black solid curve is the same as in Fig. 2 with Qsh = mh/2 for all contributions. We compare it to the scales choices proposed in Ref. [69], which imply setting the shower scale of the bottom contri- bution (including the interference) to the bottom mass fol- lowing Eq. (2) (red dotted curve). For the blue dashed curve with points we chose the HMW scales determined in Ref. [72] which can be found in Table 1 of that paper, applying a three-scale approach according to Eq. (3) (Qt = 49GeV, Qtb = 34GeV and Qb = 23GeV). 4 Results: brief application The gg →φ process folder created by the aMCSusHi script preserves all the highly convenient features that come with MadGraph5_aMC@NLO. Besides many others, this entails an interface to the most common showers, the fully automatic determination of scale and PDF variations without any extra- costs of computing time [110], the creation of any number of observables with a single run and analysis routines available for the most important processes including the gluon fusion Higgs production mode. Qpeak ∼(frac_low + frac_upp) 2 ⟨s0⟩. (5) (5) For a 2 →1 process like gluon fusion this relation is an identity and √s0 equals the mass of the final state particle, i.e., the Higgs mass in the case of gluon fusion. To change the peak-value to its half, e.g., for shower scale variations, one can simply divide frac_low and frac_upp by a factor of two. In this sense, it is convenient to keep the ratio between frac_low and frac_upp a constant, which in the default setup of MadGraph5_aMC@NLO is a factor of ten. Under this prerequisite, in order to choose a specific shower scale Qsh for gg →φ we simply have to determine aMCSusHi allows one to compute gluon-induced Higgs production including the complete dependence on the quark masses in the SM for the first time in a MC@NLO-type matching applying all versions of Pythia and Herwig Monte Carlos. While previous computations did only fea- turetheHerwigshowers[65–67],phenomenologicalresults exist to our knowledge only for Herwig6 [111]. As a first application we therefore study the impact of different show- ers on the top- and bottom-mass effects with respect to the heavy-top approximation at the 13TeV LHC. For this purpose, Fig. 2 shows the ratio of the NLO + PS com- putation including mass effects and the corresponding cross section in the heavy-top limit as a function of the transverse momentum of the Higgs for different Monte Carlos: Pythia8 (black, solid), Herwig++ (red, dot- ted), Pythia6 pT -ordered (blue, dashed with points), Pythia6 Q-ordered (green, dash-dotted with open boxes) frac_upp= 2 1.1 · Qsh mφ and frac_low= frac_upp 10 . (6) (6) Here and in what follows, we associate Qpeak with the shower scale Qsh and vice versa unless stated otherwise. After modifying the corresponding include file accordingly, 123 Eur. Phys. J. C (2015) 75 :257 Page 9 of 14 257 Page 9 of 14 257 Fig. 4 Results: brief application 2 Transverse momentum distribution of a SM Higgs at NLO + PS in the full theory normalized to the one in the heavy top effec- tive field theory for different Monte Carlos: Pythia8 (black solid), Herwig++ (red, dotted), Pythia6 pT -ordered (blue, dashed with points), Pythia6 Q-ordered (green, dash-dotted with open boxes) and Herwig6 (yellow, solid with filled boxes) For the pT distribution in Fig. 3a, the change of the scale of the bottom contribution to Qb = mb has a significant impact on the mass effects at small and intermediate trans- verse momenta. It develops an extremely steep drop at small transverse momenta which due to unitarity affects also the intermediate pT -range in the opposite direction. The ben- efit of the usage of such a low scale is clearly disputable. While the Herwig6 curve agrees rather well with previ- ous result of Ref. [111] becoming flat for pT ≲5GeV, the Pythia8 curve develops a steep increase in this region. This signals a significant Monte Carlo dependence at very small pT which is not observed for larger Qb scales. Further- more, the rigorously low value also poses a technical prob- lem in the code regarding the fact that the default shower scale choice in MadGraph5_aMC@NLO, as explained in Sect. 3.3, is a distribution. In order to solve this problem, we had to use a fixed value of Qsh = Qb by setting frac_low = frac_upp = Qb/mh and scaleMClow = scaleMCdelta = 0. Fig. 2 Transverse momentum distribution of a SM Higgs at NLO + PS in the full theory normalized to the one in the heavy top effec- tive field theory for different Monte Carlos: Pythia8 (black solid), Herwig++ (red, dotted), Pythia6 pT -ordered (blue, dashed with points), Pythia6 Q-ordered (green, dash-dotted with open boxes) and Herwig6 (yellow, solid with filled boxes) Considering the HMW scales, the scale of the bottom con- tribution is not chosen at such low values. We find that the mass effects in this case (blue dashed line with points) are rather similar to the ones where all scales are set to mh/2 (black solid line), although the individual HMW scales being quite different from this value. Looking at the rapidity distri- bution in Fig. 3b, on the other hand, we observe the expected feature of being essentially insensitive to any choice of the respective shower scales. 4 Results: brief application The green dash-dotted curve with open boxes serves mostly for comparison with previous Herwig6 results [111] which were computed with the scales of Ref. [69] as well. In Fig. 4 we study the transverse momentum distributions of the Higgs and the hardest jet, while Fig. 5 depicts their rapiditydistributions.InbothcasesweapplytheHMWscales of Ref. [72]. At low transverse momenta the pT distributions have similar shapes comparing the red dotted (LO + PS) to the black solid curves (NLO + PS). This can easily be inferred from the first inset where all curves are normal- ized to the black solid line in the main frame. However, it is well known that at the LO + PS pT distributions yield unphysicalresultsfortransversemomentabeyondtheshower scales indicated by a steep drop. Note that both curves are normalized to the same (the NLO) cross section. Continu- ing the comparison at hand, we observe a significant reduc- tion of the scale uncertainties shown in the lower inset, where the bands are obtained by dividing the upper and 12 3 257 Page 10 of 14 257 Page 10 of 14 Eur. Phys. J. C (2015) 75 :257 (a) (b) Fig. 3 a Same as Fig. 2, but for different choices of the shower scales; see text for details. b Corresponding plot for the rapidity distribution of the Higgs (b) Fig. 3 a Same as Fig. 2, but for different choices of the shower scales; see text for details. b Corresponding plot fo Higgs Fig. 3 a Same as Fig. 2, but for different choices of the shower scales; see text for details. b Corresponding plot for the rapidity distribution of the Higgs (a) (b) Fig. 4 Transverse momentum distribution of a the heavy Higgs boson and b the associated hardest jet computed in a bottom dominated sce- nario of the 2HDM (see text for details). The graphical notation is the following: the black solid curve shows Pythia8 at NLO + PS, the red dotted curve is the same at LO + PS (normalized the NLO) and the blue dashed one with points corresponds to the fixed-order curve at NLO (b) (a) (b) following: the black solid curve shows Pythia8 at NLO + PS, the red dotted curve is the same at LO + PS (normalized the NLO) and the blue dashed one with points corresponds to the fixed-order curve at NLO (b) (a) Fig. 12 Note that the Higgs reaches its kinematical limit slightly before |y(φ)| ∼3 already. 4 Results: brief application In this region the cross section will receive large effects of collinear radiation which renders the shower to yield the more reliable description. in the central region |y( j1)| ≲3, but it features a significant enhancement when the hardest jet is more forward. In this region the cross section will receive large effects of collinear radiation which renders the shower to yield the more reliable description. Acknowledgments We are indebted to Emanuele Bagnaschi, Stefano Frixione, Robert Harlander, Paolo Torrielli and Alessandro Vicini for several fruitful discussions and comments on the manuscript. We would like to thank Marco Zaro and Rikkert Frederix for their help on tech- nical issues concerning MadGraph5_aMC@NLO, and Stefan Liebler for providing the diagrams in Fig. 1. HM was supported by a Marie Curie Early Initial Training Network Fellowship of the European Com- munity’s Seventh Framework Programme under Contract No. (PITN- GA-2012-315877-MCnetITN). This research was supported in part by the Swiss National Science Foundation (SNF) under Contract 200020- 141360. 5 Conclusions In this article we presented the new tool aMCSusHi which is a link between MadGraph5_aMC@NLO and SusHi for the computation of Higgs cross sections in gluon fusion at hadron colliders. The code gives NLO + PS accurate results in the SM, 2HDM and MSSM. The inputs in the MSSM are conveniently controlled through a link to FeynHiggs. We discussed the specific treatment of the shower scale in MadGraph5_aMC@NLO and pointed out its special role in the context of gluon-induced Higgs production. In the phe- nomenological part we study the impact of different shower scale choices on the mass effects in the SM. Furthermore, we studied results for 2HDM and MSSM Higgs produc- tion as an application of aMCSusHi. The aMCSusHi script can be downloaded from https://cp3.irmp.ucl.ac.be/projects/ madgraph/wiki/aMCSushi. 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. 3 4 Results: brief application 4 Transverse momentum distribution of a the heavy Higgs boson and b the associated hardest jet computed in a bottom dominated sce- nario of the 2HDM (see text for details). The graphical notation is the following: the black solid curve shows Pythia8 at NLO + PS, the red dotted curve is the same at LO + PS (normalized the NLO) and the blue dashed one with points corresponds to the fixed-order curve at NLO 1. We see that for the Higgs rapidity in Fig. 5a all curves agree extremely well in terms of shape up to the forward region in which, nevertheless, the deviations are still well within the respective uncertainty bands.12 For the rapidity distribution of the hardest jet the same is true for the two showered results, while the fNLO distribution, on the other hand, agrees only lower bound of the respective cross section by the same central cross section as in the first inset. The uncertainties correspond to the independent variation of all unphysical scales (μR, μF, Qt, Qb, Qtb) by a factor of two. Comparing NLO + PS to the NLO fixed-order result denoted by fNLO, we observe the expected matching toward large transverse momenta. In order to compare shapes, the rapidity distributions in Fig. 5 are normalized in a way that the sum of their bins yields 123 123 Page 11 of 14 257 Eur. Phys. J. C (2015) 75 :257 (a) (b) Fig. 5 Rapidity distribution of a the pseudo-scalar Higgs boson and b the associated hardest jet computed in the mmod+ h scenario [114] of the MSSM with MA = 800GeV und tan β = 40. The graphical notation is the same as in Fig. 4. All curves are normalized so that their bins add up to 1 (b) (a) (b) (a) Fig. 5 Rapidity distribution of a the pseudo-scalar Higgs boson and b the associated hardest jet computed in the mmod+ h scenario [114] of the MSSM with MA = 800GeV und tan β = 40. The graphical notation is the same as in Fig. 4. All curves are normalized so that their bins add up to 1 tive field theory. This is certainly beyond the scope of the present paper and is left for a future publication. in the central region |y( j1)| ≲3, but it features a significant enhancement when the hardest jet is more forward. 2. CMS Collaboration, S. Chatrchyan et al., Observation of a new boson at a mass of 125 GeV with the CMS experiment at the LHC. Phys. Lett. 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The effectiveness of Promoting Alternative Thinking Strategies program: A meta-analysis
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The effectiveness of Promoting Alternative Thinking Strategies program: A meta-analysis Jieping Shi, Alan C. K. Cheung* and Aohua Ni Department of Educational Administration and Policy, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China OPEN ACCESS EDITED BY Gary Wong, The University of Hong Kong, Hong Kong SAR, China REVIEWED BY Xiaoyan Lai, The University of Hong Kong, Hong Kong SAR, China Dominick Fantacone, SUNY Cortland, United States Tony Chase, Indiana University, United States *CORRESPONDENCE Alan C. K. Cheung alancheung@cuhk.edu.hk SPECIALTY SECTION This article was submitted to Educational Psychology, a section of the journal Frontiers in Psychology RECEIVED 29 August 2022 ACCEPTED 25 November 2022 PUBLISHED 09 December 2022 CITATION Shi J, Cheung ACK and Ni A (2022) The effectiveness of Promoting Alternative Thinking Strategies Jieping Shi, Alan C. K. Cheung* and Aohua Ni Promoting Alternative Thinking Strategies (PATHS) is a widely-used social emotional learning program for preschool and elementary school students. The purpose of this review is to examine its effects, and explore the moderation effects of methodological and implementation features on intervention effectiveness. Using stringent inclusion criteria, 20 qualified studies and 177 effect sizes involving 30,454 participants were included. Results showed that the overall effect size of PATHS was 0.11. In particular, the effect size of PATHS on social emotional skills (ES = 0.16) was the largest compared with other outcome domains, including attitude or relations (ES = 0.08), emotional well-being (ES = 0.02), prosocial behaviors (ES = 0.04), conduct problems (ES = 0.06), and academic performance (ES = 0.05). PATHS had no different impact whether it was implemented in the universal or target contexts. Research design, sample size, and intervention dosage could moderate the effectiveness of PATHS significantly, and dosage was the predominant factor in determining the effects of PATHS. Policy and practical implications were discussed. CITATION Shi J, Cheung ACK and Ni A (2022) The effectiveness of Promoting Alternative Thinking Strategies program: A meta-analysis. Front. Psychol. 13:1030572. doi: 10.3389/fpsyg.2022.1030572 COPYRIGHT © 2022 Shi, Cheung and Ni. 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. TYPE Systematic Review PUBLISHED 09 December 2022 DOI 10.3389/fpsyg.2022.1030572 TYPE Systematic Review PUBLISHED 09 December 2022 DOI 10.3389/fpsyg.2022.1030572 Promoting Alternative Thinking Strategies, social emotional learning, meta-analysis, systematic review, program effectiveness Introduction Though several previous reviews (e.g., Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016) have estimated the effects of social emotional learning intervention programs for young children, few have done so separately by one specific program using rigorous inclusion criteria. Crean and Johnson, 2013; Novak et al., 2017; Seyhan et al., 2019; Upshur et al., 2019). Though several previous reviews (e.g., Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016) have estimated the effects of social emotional learning intervention programs for young children, few have done so separately by one specific program using rigorous inclusion criteria. The purpose of this review is to examine the effects of Promoting Alternative Thinking Strategies (PATHS) on preK- 6 students. PATHS is one of the most widely-used social emotional learning programs for preschool and elementary school children. It was first designed by Greenberg and Kusche to improve social and emotional development for deaf children in 1982 (Greenberg and Kusché, 1993). It was later adapted and conducted as a universal social emotional intervention in mainstream classrooms. Since then, the objectives and content have continued to be expanded. All versions of PATHS emphasize common core components in the curriculum like self-control, emotional understanding and interpersonal problem solving (Greenberg et al., 2004). The primary focus is to reduce behavioral and emotional problems, improve academic performance and facilitate emotional process through promoting children’s social emotional development (Kusché and Greenberg, 2020). So far, PATHS has been translated into multiple versions in different languages and implemented for decades in different countries, such as Canada, the UK, Netherlands, Australia, Turkey, Croatia, Switzerland (Kusché and Greenberg, 2020). g The reasons for selecting PATHS are threefold: (1) wide reach of use. It was implemented in more than 20 countries and thousands of schools. For instance, over 250 schools delivered PATHS in the UK (The Paths Programme for Schools (Uk Version), n.d.); (2) high quality. It was identified as a “SELect” or high quality social emotional learning program by Collaborative for Academic Social Emotional Learning [CASEL] (2013, 2015) and Jones et al. (2017). It was rated as one of the 15 “Model Programs” among over 1,400 programs by Blueprints for Healthy Youth Development (The Paths Program, n.d.); (3) largest number of experimental studies. The What Works Clearinghouse (WWC) identified 35 PATHS studies, and we found over 50 experimental studies, which was the largest compared to other SEL programs. Introduction Therefore, the current review will choose PATHS to conduct an in-depth review and explore which features could moderate its effects. Moreover, there are three additional theories related to the PATHS program. First, ecological theory provides another perspective from which to understand and facilitate the development of students. It explains that the child interacts with parents, teachers, peers, and others in different ecological settings and these settings affect each other (Bronfenbrenner, 1979). Particularly, teachers act as role models and have great influence on children’s social and emotional development during school years. Under this circumstance, PATHS is no longer restricted to the courses that teach children skills. It also emphasizes the creation of a positive and supportive class environment and school environment, and provides opportunities for students to apply the social emotional skills they have learned (Greenberg et al., 2004). Second, the ABCD model of PATHS, like any other psychological model, must be consistent with the developmental neurobiology. There are two important mechanisms of brain organization, “vertical” control and “horizontal” control. “Vertical” communication and control involves the higher-order processing of emotions and actions in which the limbic system transfers the information from sensory-motor areas to the neocortical areas and then Frontiers in Psychology Introduction There is an increasing consensus on the crucial role of social emotional learning in student development among parents, teachers, and policy makers (Miyamoto et al., 2015). Social emotional learning refers to the processes through which “children and adults acquire and effectively apply the knowledge, attitudes, and skills necessary to understand and manage emotions, set and achieve positive goals, feel and show empathy for others, establish and maintain positive relationships, and make responsible decisions” (Collaborative for Academic Social Emotional Learning [CASEL], 2015, p. 5). Social emotional learning has been broadly implemented for decades from kindergarten to high school globally, and its effectiveness has been supported by a large number of randomized controlled trials and quasi-experimental studies (e.g., Jones et al., 2011; Frontiers in Psychology 01 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 and cognitions. It is generated from multiple psychological theories, including developmental social cognition, cognitive development theory, and attachment theory (Greenberg and Kusché, 1993). The premise of this model declares that “the child’s coping, as reflected in his or her behavior and internal regulation, is a function of emotional awareness, affective-cognitive control, and social-cognitive understanding” (Greenberg and Kusché, 1993). In addition, the ABCD model believes that different phases of development have different defenses from infancy to adolescence, and there are substantial changes from the previous phase to the next phase. From this development of defense mechanisms, it can be inferred that affective development occurs in advance of other modes of development in the process of individual growth (Greenberg et al., 2004). In other words, affective development should be paid attention to in the early stages of child growth due to its pioneering role. The ABCD model also highlights the crucial role of language development in personality development, indicating that it can incorporate with affective development and then process the previous emotional forms into linguistic forms (Greenberg and Kusché, 1993). This verbal mediation of affect should be cultivated in the lower grades of elementary school. Additionally, language development can also contribute to emotional management and behavioral control. In short, the ABCD model provides a general holistic and dynamic mechanism of individual maturation in terms of affects, behaviors, and cognitions, and illustrates the critical development stages of each function, which lays a solid foundation for the design and implementation of the PATHS curriculum. Crean and Johnson, 2013; Novak et al., 2017; Seyhan et al., 2019; Upshur et al., 2019). Previous relevant reviews To the best of our knowledge, there is only one review focusing on the effects of the PATHS program. That review synthesized the published studies on PATHS in preschool settings, and found that preschool PATHS had a positive mild to moderate effect on children’s social emotional competence and little effect on problem behaviors (Stanley, 2019). Since there were only five studies included, the review looked at the effects of each study separately, instead of performing a meta- analysis. Two of the included studies did not have control groups (i.e., Gibson et al., 2015; Mihic et al., 2016), and one study had a control group of less than thirty participants (i.e., Hughes and Cline, 2015). Therefore, the findings of the effects of preschool PATHS in this review should be interpreted with much caution. Third, psychoanalytic education is highly related to the development of PATHS, which makes PATHS different from many other social emotional learning programs (Kusché and Greenberg, 2012). It highlights “positive teacher-student relationships, internalization of prosocial values, use of creativity, optimal educational and cognitive integration, appropriate expression (rather than repression) of affect, and learning as a process of joyful discovery” (Kusché and Greenberg, 2012). Children are no longer required to comply with external expectations, but are encouraged to actively participate and interact in the learning process (Greenberg et al., 2004). From this perspective, PATHS is enjoyable for both teachers and students to teach and learn (Kusché, 2002). In addition to this preschool PATHS review, two other reviews of Second Step may be of some relevance to the current review because both programs consist of similar social emotional components. Moy and Hazen (2018) analyzed 24 studies in which Second Step was implemented as a Tier 1 intervention, and found its effects on knowledge of program content, prosocial outcomes and antisocial outcomes in independent group design studies were 0.77, 0.06, and −0.11, respectively. However, it employed a set of rather loose inclusion criteria, which might hinder the accuracy of the findings of the overall effects. For instance, 10 of the 24 included studies used a single-group repeated measures design, which might overestimate the effect sizes. The other review also conducted by Moy et al. (2018) synthesized 27 randomized controlled or quasi-experimental studies of Second Step from 1984 to 2016, indicating a large effect of 1.08 on program knowledge and two small effects of 0.19 and 0.22 on prosocial and antisocial behaviors. Theory of PATHS The PATHS program is based on the Affective-Behavioral- Cognitive-Dynamic (ABCD) theoretical model, which underlines the developmental integration of affects, behaviors, 02 Frontiers in Psychology frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 technical support and consultation during the procedure of teaching courses. the neocortical areas modify impulses and send messages back to the limbic system. “Horizontal” control involves the interaction processing of the left hemisphere and the right hemisphere (Greenberg et al., 2004). If a child fails to achieve neocortical control by around the age of seven, “behavioral problems” will occur (Greenberg and Kusché, 1993). Therefore, based on these two kinds of communication and control, the PATHS program offers multiple strategies and materials to help a child manage emotions and control behaviors, like self-talk, feeling face cards, etc. (Greenberg et al., 2004). the neocortical areas modify impulses and send messages back to the limbic system. “Horizontal” control involves the interaction processing of the left hemisphere and the right hemisphere (Greenberg et al., 2004). If a child fails to achieve neocortical control by around the age of seven, “behavioral problems” will occur (Greenberg and Kusché, 1993). Therefore, based on these two kinds of communication and control, the PATHS program offers multiple strategies and materials to help a child manage emotions and control behaviors, like self-talk, feeling face cards, etc. (Greenberg et al., 2004). Previous relevant reviews It also examined five factors which could moderate the effects of Second Step, but the corresponding analysis was limited. In short, these two reviews summarized the effects of another social emotional learning program Second Step, which supported the feasibility of examining a particular social emotional learning program in depth. Implementation of PATHS The PATHS curriculum is a series of school-based comprehensive lessons which aims to improve social emotional skills, prevent emotional and behavioral problems, enhance academic performance, and reinforce a positive atmosphere in classrooms and schools. In general, it consists of five aspects, self-control, emotional understanding, positive self-esteem, relationships, and interpersonal problem- solving skills (Kusché and Greenberg, 2020). There are approximately 40 lessons in each grade from Pre-K to grade 6, involving the aforementioned domains with different levels of difficulty. It can be taught by teachers to regular classes as well as self-contained special education classes with the dosage of two to three times per week. It provided students with a variety of classroom activities, such as story, discussion, role-play, drawing, music, and painting. Moreover, it is important for teachers to encourage students to generalize the corresponding social emotional skills into real-life situations. For instance, students can integrate them into other academic subjects, or play games or communicate with their parents to strengthen the concepts and skills in the PATHS curriculum. In addition, teachers are required to participate in a short-term training workshop before starting the course, and can get additional Finally, there are several reviews synthesizing the effects of multiple school-based social emotional learning programs (Payton et al., 2008; Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016; Blewitt et al., 2018; Corcoran et al., 2018; Yang et al., 2019; Murano et al., 2020). Compared to the reviews targeting one program, they involve diverse social emotional learning programs in terms of objectives, participants, durations, courses, assessments, etc., which could lead to a high heterogeneity of included studies. For instance, Frontiers in Psychology 03 frontiersin.org frontiersin.org 10.3389/fpsyg.2022.1030572 Shi et al. one widely-cited review by Durlak et al. (2011) summarized the effects of 213 school-based social emotional learning studies on Pre-K-12 students from 1955 to 2007. They found that social emotional learning could significantly promote social emotional skills (ES = 0.57, k = 68), attitudes toward self and others (ES = 0.23, k = 106), positive social behavior (ES = 0.24, k = 86), academic performance (ES = 0.27, k = 35) and reduce conduct problems (ES = 0.22, k = 112) and emotional distress (ES = 0.24, k = 49). In addition, four recommended practices of developing students’ skills (SAFE, including Sequenced, Active, Focused, Explicit) and program implementation could moderate the effectiveness of social emotional learning. Implementation of PATHS (2016) also examined the effects of 89 universal school-based social emotional learning studies, and found small to medium effects on social emotional competence (ES = 0.53, k = 24), attitudes towards self (ES = 17, k = 9), prosocial behavior (ES = 0.33, k = 39), conduct problems (ES = 0.28, k = 40), emotional distress (ES = 0.19, k = 32), academic achievement (ES = 0.28, k = 15) and emotional competence (ES = 0.27, k = 14). Taylor et al. (2017) explored the follow-up effects of social emotional learning and found seven small positive effect sizes on social emotional skills, attitudes, positive social behavior, academic performance, conduct problems, emotional distress and drug use. In short, these four comprehensive reviews synthesized the effects of social emotional learning on multiple outcome domains at post-test and follow-up, and the classification of outcomes was almost the same. However, they failed to find any meaningful moderation effects for social emotional learning implementation, owing to the high heterogeneity of the included studies. In sum, there is a general consensus that social emotional learning has positively small to medium effects on multiple outcomes, including social emotional skills, attitudes, prosocial behavior, conduct problems, emotional distress, and academic performance. But these reviews did not reach a general consensus of the moderating effects of implementation features. Therefore, it is advisable to conduct an in-depth review of the effects of one particular social emotional program PATHS to explore which implementation factors works. First, this review will employ a set of rigorous criteria, which can result in a more convincing conclusion of PATHS. Second, both universal PATHS and targeted PATHS studies will be included in the current review, which provides the ability to compare the effects of PATHS in different contexts. Third, it will extract and identify multiple methodological features and implementation features of studies, and then examine their moderation effects. Particularly, the moderation effects in this review will be more convincing than other reviews of social emotional learning, since the treatments in the present corpus of studies are highly homogeneous, which can minimize the impacts of the intervention itself. Finally, it will update and enrich the results of previous reviews on PATHS or other related social emotional learning programs. Implementation of PATHS In particular, SAFE criteria were too loose that most studies could achieve, hindering their further implications for policy and practice. Implementation problems significantly decreased social emotional learning outcomes, but the authors did not specify what those implementation problems were. Consequently, there was no meaningful suggestions for implementation, even though two moderators were effective. Sklad et al. (2012) analyzed 75 published studies about social emotional or behavioral programs from 1995 to 2008, and concluded that this kind of intervention could improve social emotional skills (ES = 0.70, k = 31), academic performance (ES = 0.46, k = 10), positive self- image (ES = 0.46, k = 8), prosocial behavior (ES = 0.39, k = 6), and decrease antisocial behavior (ES = 0.43, k = 39), mental disorders (ES = 0.19, k = 13) and substance abuse (ES = 0.09, k = 10). It also showed that the effect size of studies with 20 sessions or more on social skills were 0.24, whereas the effect size of studies with less than 20 sessions were 0.80, which seemed to be counterintuitive. Wigelsworth et al. (2016) also examined the effects of 89 universal school-based social emotional learning studies, and found small to medium effects on social emotional competence (ES = 0.53, k = 24), attitudes towards self (ES = 17, k = 9), prosocial behavior (ES = 0.33, k = 39), conduct problems (ES = 0.28, k = 40), emotional distress (ES = 0.19, k = 32), academic achievement (ES = 0.28, k = 15) and emotional competence (ES = 0.27, k = 14). Taylor et al. (2017) explored the follow-up effects of social emotional learning and found seven small positive effect sizes on social emotional skills, attitudes, positive social behavior, academic performance, conduct problems, emotional distress and drug use. In short, these four comprehensive reviews synthesized the effects of social emotional learning on multiple outcome domains at post-test and follow-up, and the classification of outcomes was almost the same. However, they failed to find any meaningful moderation effects for social emotional learning implementation, owing to the high heterogeneity of the included studies. from the above four reviews. Frontiers in Psychology Implementation of PATHS The first one analyzed 63 studies involving children aged 2 to 6 years and pointed out that social emotional learning had positive effects on social competence, emotional competence, problem behaviors and emotions, self-regulation, and early learning outcomes, of which the effect sizes ranged from 0.18 to 0.54 (Blewitt et al., 2018). The second review summarized 29 studies for low-income children aged 3-5 years and obtained a small positive effect size of 0.24 on social emotional competence (Yang et al., 2019). The third one estimated the effects of universal and targeted social emotional learning programs in preschool. This review found that both universal and targeted social emotional learning could improve social emotional skills and reduce problem behaviors, with effect sizes of 0.34, 0.32, 0.44, and 0.50, respectively (Murano et al., 2020). The last one involved 11 preschool social emotional learning studies, but their effects and quality varied largely (Sabey et al., 2017). In addition, another review of social emotional learning may be also relevant. It concentrated on the effects of social emotional learning on academic performance, and found that social emotional learning could improve scores on reading, math and science with effect sizes of 0.25, 0.26, and 0.19 (Corcoran et al., 2018). Consequently, the results of these reviews were quite consistent, showing positive effects of social emotional learning on multiple outcomes. from the above four reviews. The first one analyzed 63 studies involving children aged 2 to 6 years and pointed out that social emotional learning had positive effects on social competence, emotional competence, problem behaviors and emotions, self-regulation, and early learning outcomes, of which the effect sizes ranged from 0.18 to 0.54 (Blewitt et al., 2018). The second review summarized 29 studies for low-income children aged 3-5 years and obtained a small positive effect size of 0.24 on social emotional competence (Yang et al., 2019). The third one estimated the effects of universal and targeted social emotional learning programs in preschool. This review found that both universal and targeted social emotional learning could improve social emotional skills and reduce problem behaviors, with effect sizes of 0.34, 0.32, 0.44, and 0.50, respectively (Murano et al., 2020). The last one involved 11 preschool social emotional learning studies, but their effects and quality varied largely (Sabey et al., 2017). In addition, another review of social emotional learning may be also relevant. (1) What is the overall effect of PATHS on students? Implementation of PATHS It concentrated on the effects of social emotional learning on academic performance, and found that social emotional learning could improve scores on reading, math and science with effect sizes of 0.25, 0.26, and 0.19 (Corcoran et al., 2018). Consequently, the results of these reviews were quite consistent, showing positive effects of social emotional learning on multiple outcomes. one widely-cited review by Durlak et al. (2011) summarized the effects of 213 school-based social emotional learning studies on Pre-K-12 students from 1955 to 2007. They found that social emotional learning could significantly promote social emotional skills (ES = 0.57, k = 68), attitudes toward self and others (ES = 0.23, k = 106), positive social behavior (ES = 0.24, k = 86), academic performance (ES = 0.27, k = 35) and reduce conduct problems (ES = 0.22, k = 112) and emotional distress (ES = 0.24, k = 49). In addition, four recommended practices of developing students’ skills (SAFE, including Sequenced, Active, Focused, Explicit) and program implementation could moderate the effectiveness of social emotional learning. In particular, SAFE criteria were too loose that most studies could achieve, hindering their further implications for policy and practice. Implementation problems significantly decreased social emotional learning outcomes, but the authors did not specify what those implementation problems were. Consequently, there was no meaningful suggestions for implementation, even though two moderators were effective. Sklad et al. (2012) analyzed 75 published studies about social emotional or behavioral programs from 1995 to 2008, and concluded that this kind of intervention could improve social emotional skills (ES = 0.70, k = 31), academic performance (ES = 0.46, k = 10), positive self- image (ES = 0.46, k = 8), prosocial behavior (ES = 0.39, k = 6), and decrease antisocial behavior (ES = 0.43, k = 39), mental disorders (ES = 0.19, k = 13) and substance abuse (ES = 0.09, k = 10). It also showed that the effect size of studies with 20 sessions or more on social skills were 0.24, whereas the effect size of studies with less than 20 sessions were 0.80, which seemed to be counterintuitive. Wigelsworth et al. Coding Study coding mainly contained two parts. First, research features were coded as categorical moderators, namely: (1) research design, studies were coded as quasi-experiment or randomized controlled trial; (2) sample size, the numbers of participants in each study were coded as large (N > 1,000) or small; (3) grade level, studies were coded as Pre-K or elementary; (4) social economic status, studies were coded as low, middle, mixed or unknown according to the predominant social economic status of participants; (5) duration, the studies were coded as one year or more than one year; (6) dosage, studies were coded as standard if the interventions were implemented two or three times per week as recommended by the program. If the studies did not reach the standard dosage, they were coded as low; (7) intervention types, studies were coded as universal if the program was delivered for all students and as targeted if the program was offered to some specific students who needed additional support. Second, the outcomes of each study were categorized into six domains, namely social emotional skills, attitudes or relations, emotional well-being, prosocial behaviors, conduct problems, and academic performance. This classification approach is consistent with several previous reviews of social emotional learning (Payton et al., 2008; Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016). Two researchers coded the studies separately, and their coding reliability was 96%. Any disagreements about coding were solved through discussion. Searching procedures (8) It must have enough quantitative statistics to calculate effect sizes. In order to find all possible articles about the effects of PATHS, we employed the following three searching strategies. First, we used the term “Promoting Alternative Thinking Strategies” or “PATHS” and “impact” or “effect” or “effectiveness” or “evaluation” or “assessment” as Abstract to search the academic databases, including Web of Science, Proquest, ERIC, PsycINFO. Second, we searched the references in previous related reviews of PATHS or social emotional learning, which might provide additional studies. Third, we searched the relevant websites of PATHS to reduce publication bias, and found some empirical articles and reports about PATHS. In this way, some unpublished gray studies could be obtained as a supplement. In sum, there were 22 studies in the final sample, but only 20 of them had effect sizes at post-tests. Even though 30 articles were eligible, eight articles were partially duplicated because they used the same samples as other studies (i.e. Bierman et al., 1999a, 2002, 2007; Malti et al., 2011; Sheard et al., 2013; Humphrey et al., 2015, 2016; Panayiotou et al., 2020). The flow chart shows the specific searching procedures step by step (Figure 1). Criteria for inclusion and exclusion The criteria used to select eligible studies are set out below. Implementation of PATHS Moreover, there were another four reviews that only focused on the effects of preschool social emotional learning programs, and their categorization of outcomes was different This review has three research questions. (1) What is the overall effect of PATHS on students? 04 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 10.3389/fpsyg.2022.1030572 (7) It must be of initial equivalence at pre-tests in terms of outcome measurements. In other words, the baseline difference between treatment group and control group must be less than 0.25 standard deviation, which is suggested by What Works Clearinghouse. If a study didn’t have equivalent baseline scores or didn’t report whether baseline scores were equivalent, it was excluded (e.g. Kam et al., 2003; Curtis and Norgate, 2007; Saltali and Deniz, 2010; Arda and Ocak, 2012; Fishbein et al., 2016). (2) Are there any differential effects of PATHS on particular subgroups of students? (2) Are there any differential effects of PATHS on particular subgroups of students? (7) It must be of initial equivalence at pre-tests in terms of outcome measurements. In other words, the baseline difference between treatment group and control group must be less than 0.25 standard deviation, which is suggested by What Works Clearinghouse. If a study didn’t have equivalent baseline scores or didn’t report whether baseline scores were equivalent, it was excluded (e.g. Kam et al., 2003; Curtis and Norgate, 2007; Saltali and Deniz, 2010; Arda and Ocak, 2012; Fishbein et al., 2016). (7) It must be of initial equivalence at pre-tests in terms of outcome measurements. In other words, the baseline difference between treatment group and control group must be less than 0.25 standard deviation, which is suggested by What Works Clearinghouse. If a study didn’t have equivalent baseline scores or didn’t report whether baseline scores were equivalent, it was excluded (e.g. Kam et al., 2003; Curtis and Norgate, 2007; Saltali and Deniz, 2010; Arda and Ocak, 2012; Fishbein et al., 2016). (3) What features of included studies can moderate the effectiveness of PATHS? (3) What features of included studies can moderate the effectiveness of PATHS? The criteria used to select eligible studies are set out below. The criteria used to select eligible studies are set out below. (1) It must be written in English. (1) It must be written in English. (2) It was published before December 31, 2020. (2) It was published before December 31, 2020. (3) It must focus on the effects on students. Studies only focused on the effects of PATHS on teachers were excluded (e.g. Bierman et al., 2013; Pas et al., 2015; Domitrovich et al., 2016; Berg et al., 2017). (4) Only PATHS must be implemented for the treatment group. If the treatment group combined PATHS and other programs, the study was excluded (e.g. Ialongo et al., 2019; Bradshaw et al., 2020; Hart et al., 2021). (5) It must have a control group. Studies without control group was excluded (e.g. Kelly et al., 2004; Kam et al., 2011; Raynor, 2011; Faria et al., 2013; Gibson et al., 2015; Mihic et al., 2016; Wilson, 2016; Humphrey et al., 2018). Further, if the control group had other social emotional learning components, the study was excluded (e.g. Schonfeld et al., 2012). (6) At least two teachers and 30 students were required in each of treatment groups and control groups to reduce the potential interference of teachers’ effectiveness. Studies without enough participants were excluded (e.g. Greenberg and Kusche, 1998; Bardon et al., 2008; Howe, 2013; Hughes and Cline, 2015; McDaniel et al., 2021). (6) At least two teachers and 30 students were required in each of treatment groups and control groups to reduce the potential interference of teachers’ effectiveness. Studies without enough participants were excluded (e.g. Greenberg and Kusche, 1998; Bardon et al., 2008; Howe, 2013; Hughes and Cline, 2015; McDaniel et al., 2021). 05 Frontiers in Psychology frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 FIGURE 1 Flow chart of searching procedures. Flow chart of searching procedures. Results In the current review, standardized mean difference was used to explain the effects of PATHS on multiple outcomes for the included studies. Furthermore, all scores were transformed into the same direction, positive scores represented that the treatment group had better performance than the control group regardless of the outcome domains. For the studies with more than one effect sizes on different outcomes, we followed the suggestions of Borenstein et al. (2011) to calculate the synthetic effect size for each included study. As to the statistical analysis of the body of included studies, Hedge’s g was employed to attenuate the impacts of sample size, and the effect sizes of each study were weighted based on the inverse variance (Borenstein et al., 2011). Subgroup analysis and meta-regression were conducted to examine the effects of methodological factors and implementation features. Finally, the software Comprehensive Meta-Analysis version 3 was used in the current review. Frontiers in Psychology Overall effects A total of 22 studies met the inclusion criteria. However, two of these studies only reported effect sizes at follow-up rather than post-tests (i.e. Kam et al., 2004; Malti et al., 2011; Averdijk et al., 2016). Therefore, this review consisted of 20 qualified studies with 177 effect sizes, involving 30,454 participants (15,743 from treatment group, 14,711 from control group) from preschools to elementary schools. A brief description of the 20 included studies was shown in Table 1 and Figure 2. The result of the random model showed that the overall effect size of PATHS was 0.11 (k = 20), indicating a significantly positive effect. Moreover, the effect sizes of primary studies were of moderately high heterogeneity (Q = 60.61, df = 19, p < 0.05; I2 = 68.65%), which showed that the impacts of multiple PATHS programs were somewhat similar. Compared to the Frontiers in Psychology 06 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 TABLE 1 A brief description of included studies about PATHS. Overall effects References Type Design Sample Grade SES Duration Dosage Country Overall ES Bierman et al., 1999a, 2002, 2004, 2007 Pub Rct Small Ele Mid More Standard USA 0.163 Bierman et al., 1999b Pub Rct Large Ele Low 1 year Standard USA 0.090 Bierman et al., 2008 Pub Rct Small Pre Mixed 1year Low USA 0.191 Bierman et al., 2010 Pub Rct Large Ele Low More Standard USA 0.120 Berry et al., 2016 Pub Rct Large Ele Mixed More Low Other −0.045 Crean and Johnson, 2013 Pub Rct Small Ele Low More Low USA 0.140 Domitrovich et al., 2007 Pub Qed Small Pre Low 1 year Low USA 0.170 Greenberg et al., 1991 Un Qed Small Ele NA 1 year Standard USA 0.300 Greenberg et al., 1995 Pub Qed Small Ele Mid 1 year Standard USA 0.211 Goossens et al., 2012 Pub Qed Large Ele NA More Low Other 0.015 Hamre et al., 2012 Pub Rct Small Pre Low 1 year Low USA 0.170 Hennessey and Humphrey, 2020 Pub Rct Large Ele Mid More Low Other −0.028 Hsueh et al., 2014 Un Rct Small Pre NA 1 year NA USA 0.096 Humphrey et al., 2016, 2018 Un Rct Large Ele Mid More Low Other 0.008 Johannes, 2003 Un Qed Small Ele NA 1 year Low USA 0.120 Novak et al., 2017 Pub Rct Small Ele NA more Standard Other 0.101 Riggs et al., 2006 Pub Qed Small Ele NA 1 year Standard USA 0.310 Seyhan et al., 2019 Pub Qed Small Pre Mid 1 year Standard Other 0.355 Sheard et al., 2012, 2013 Pub Qed Large Ele Mid More NA Other 0.181 Social Character Development Research Consortium [SACD], 2010 Un Rct Small Ele Low More Low USA 0.003 Pub represents published studies, un represents unpublished studies; Rct represents randomized controlled trial, Qed represents quasi-experimental design; Pre represents preschool, Ele represents elementary school; 1 year represents one year or less, More represents more than one year. Type Design Sample Grade SES Duration Dosage Country Overall ES Pub represents published studies, un represents unpublished studies; Rct represents randomized controlled trial, Qed represents quasi-experimental design; Pre represents preschool, Ele represents elementary school; 1 year represents one year or less, More represents more than one year. Overall effects comprehensive reviews with 75% or higher I2, the heterogeneity of the current review was relatively low, indicating that restraining the various social emotional learning interventions to PATHS was an effective approach to reduce heterogeneity. Additionally, in order to examine whether there were any outliers that may bias the results, a “one study removed” operation was performed. After removing each study in turn, the effect sizes of the remaining studies ranged from 0.09 to 0.12, which lay in the 95% confidence interval from 0.06 to 0.16. In other words, the overall effect size was convincing because it would not change even if any one study was deleted. than those of the other outcomes. Therefore, the main outcome of PATHS was to promote social emotional skills, whereas the effects on reducing problem behaviors, improving academic performance, etc., were trivial. As to the follow-up effect sizes, there were only 5 studies and 58 effect sizes. The follow-up periods ranged from one to seven years. Results showed that the effect size of PATHS at follow- up was 0.10, which was marginally significant (p = 0.07). In other words, the PATHS program had a small and marginally significant long-term effect size, which might be a function of the small number of included studies. Note that the following analyses only focused on the post-test effect sizes owing to the limited number of follow-up studies. Moreover, if the outcomes were categorized into six domains according to the classification in previous reviews, the effects varied (Table 2). Note that these outcomes were interrelated (Corcoran et al., 2020). In particular, PATHS had a small but significant positive effect on social emotional skills (ES = 0.16, k = 16), which was higher than the overall effect size. Nevertheless, the effects on other aspects were nearly negligible, including attitude or relations (ES = 0.08, k = 7), emotional well- being (ES = 0.02, k = 4), prosocial behaviors (ES = 0.04, k = 6), conduct problems (ES = 0.06, k = 14) and academic performance (ES = 0.05, k = 12). Moreover, the differences of effects among multiple domains were consistent with previous reviews (Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016), in which the effects on social emotional skills were substantially larger Moderators sizes between published and unpublished studies were also examined. The results of the subgroup analysis showed that there was no difference between these two kinds of studies (p = 0.43 > 0.05; Table 3), which also partially supported the absence of publication bias. The funnel plot was shown in Figure 3. Even though the heterogeneity of the included studies was not too high, the methodological features and implementation features of the studies were still examined as moderators in order to explore the factors which may have had an influence on the intervention effectiveness. Six features, namely research design, sample size, grade level, social economic status, duration, and dosage, were extracted and examined separately and simultaneously. Since the number of included studies was small, especially when the outcomes were classified into six domains, subgroup analyses and meta-regression were conducted on all outcomes instead of each domain. Subgroup analysis Subgroup analysis was conducted to explore whether the PATHS program had differential impacts when it was delivered to different student groups. The intervention effects were classified as universal or targeted based on the characteristics of the participants. Since four studies included both universal and targeted effects, the subgroup analysis here was based on subgroup level instead of study level. Results showed that the effect size of targeted participants was slightly larger than that of universal participants, but it was not significant (p > 0.05). Hence there was not sufficient evidence to support that the PATHS program had significantly higher effects on targeted participants. One possible reason is that the number of effect sizes on targeted participants was too small, and another is that the characteristics of targeted participants were rather diverse. Publication bias The publication bias was examined by multiple approaches. First of all, the result of the Classic fail-safe N test showed that 247 missing studies were needed to make the p-value become insignificant and the true effect become zero (Z = 7.16, p < 0.05). Second, the result of Orwin’s fail-safe N test explained that 115 missing studies were required if the trivial value was set to the 0.01 level. Both results showed that there was no publication bias because the number of missing studies was too large to be achieved. Additionally, the differences in effect 07 Frontiers in Psychology frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 FIGURE 2 Forest plots of included studies. TABLE 2 The overall effect sizes of PATHS. Domain Number of ES (n) Number of studies (k) ES Standard error Lower limit Upper limit Overall 177 20 0.11 0.02 0.06 0.16 Follow-up 58 5 0.10 0.06 −0.01 0.21 Social emotional skills 57 16 0.16 0.05 0.07 0.25 Attitude or relations 15 7 0.08 0.04 0.00 0.16 Emotional well-being 8 4 0.02 0.04 −0.07 0.11 Prosocial behaviors 11 6 0.04 0.02 0.01 0.08 Conduct problems 50 14 0.06 0.02 0.01 0.11 Academic performance 36 12 0.05 0.02 0.01 0.09 TABLE 2 The overall effect sizes of PATHS. TABLE 2 The overall effect sizes of PATHS. Domain Number of ES (n) Number of studies (k) ES Standard error Lower limit Upper limit Overall 177 20 0.11 0.02 0.06 0.16 Follow-up 58 5 0.10 0.06 −0.01 0.21 Social emotional skills 57 16 0.16 0.05 0.07 0.25 Attitude or relations 15 7 0.08 0.04 0.00 0.16 Emotional well-being 8 4 0.02 0.04 −0.07 0.11 Prosocial behaviors 11 6 0.04 0.02 0.01 0.08 Conduct problems 50 14 0.06 0.02 0.01 0.11 Academic performance 36 12 0.05 0.02 0.01 0.09 ES (n) Number of studies (k) ES Standard error Lower limit Upper limit Frontiers in Psychology Research design Research design is an important factor that may affect the effect sizes of studies. In general, quasi-experimental studies have higher effect sizes than randomized controlled ones (Cheung and Slavin, 2016). In this review, the effect size of quasi-experimental studies (ES = 0.20, k = 8) was approximately three times that of randomized controlled studies (ES = 0.07, k = 12) and the difference between them was statistically significant (p < 0.05). Therefore, this result was consistent with Frontiers in Psychology 08 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 Effect size and 95% confidence interval Study features Effect size and 95% confidence interval Test of heterogeneity Number of studies Point estimate Standard error Lower limit Upper limit Q-value df (Q) P-value Overall effect size Random 20 0.11 0.02 0.06 0.16 60.64 19 0.00 By publication Published 15 0.12 0.03 0.06 0.17 Unpublished 5 0.07 0.05 −0.03 0.17 Total between 20 0.62 1 0.43 By type Universal 19 0.10 0.03 0.06 0.15 Targeted 5 0.17 0.10 −0.02 0.36 Total between 24 0.44 1 0.51 By study design QED 8 0.20 0.05 0.10 0.30 RCT 12 0.07 0.02 0.02 0.12 Total between 20 5.46 1 0.02 By sample size Small (≤1000) 13 0.17 0.03 0.12 0.23 Large (>1000) 7 0.05 0.03 −0.01 0.10 Total between 20 10.66 1 0.00 By grade level Preschool 5 0.20 0.05 0.11 0.29 Elementary 15 0.08 0.03 0.03 0.13 Total between 20 5.23 1 0.02 By socioeconomic status Low 6 0.10 0.02 0.07 0.14 Middle 6 0.13 0.05 0.02 0.23 Mixed 2 0.05 0.12 −0.18 0.28 Unknown 6 0.13 0.05 0.03 0.24 Total between 20 0.63 3 0.89 By duration One year 10 0.19 0.04 0.11 0.26 More than one year 10 0.06 0.03 0.00 0.11 Total between 20 7.50 1 0.01 By dosage Standard 8 0.17 0.03 0.10 0.24 Low 10 0.03 0.03 −0.02 0.08 NA 2 0.16 0.05 0.07 0.25 Total between 20 12.78 2 0.00 previous studies, in which the research design could moderate the intervention effectiveness. Sample size Sample size is another factor which may moderate the effectiveness. Generally, studies with large sample sizes tend to have lower effect sizes (Slavin and Smith, 2009; Cheung and Slavin, 2016). Sample size Sample size is another factor which may moderate the effectiveness. Generally, studies with large sample sizes tend to have lower effect sizes (Slavin and Smith, 2009; Cheung and Slavin, 2016). In this review, the effect size of small studies (ES = 0.17, k = 13) was nearly four times that of large studies (ES = 0.05, k = 7), which was also significant (p < 0.05). Research design In this review, the effect size of small studies (ES = 0.17, k = 13) was nearly four times that of large studies (ES = 0 05 k = 7) which was also significant (p < 0 05) In particular, the effect size of studies with more than 1,000 participants was only 0.05, which was not significantly different from zero (p > 0.05). Therefore, the large studies had almost negligible effect sizes, while the small studies had substantially positive effect sizes. Grade level As to the grade level, it may also moderate the effects of social emotional interventions (Sklad et al., 2012; Corcoran et al 2018) The primary studies in this review were classified Test of heterogeneity Number of studies Point estimate Standard error Lower limit Upper limit Q-value df (Q) P-val previous studies, in which the research design could moderate the intervention effectiveness. previous studies, in which the research design could moderate the intervention effectiveness. In particular, the effect size of studies with more than 1,000 participants was only 0.05, which was not significantly different from zero (p > 0.05). Therefore, the large studies had almost negligible effect sizes, while the small studies had substantially positive effect sizes. Frontiers in Psychology frontiersin.org Frontiers in Psychology Grade level As to the grade level, it may also moderate the effects of social emotional interventions (Sklad et al., 2012; Corcoran et al., 2018). The primary studies in this review were classified 09 Frontiers in Psychology frontiersin.org frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 FIGURE 3 Funnel plot. as preschool or elementary studies. Results explained that preschool studies (ES = 0.20, k = 5) did have higher effect sizes than elementary ones (ES = 0.08, k = 15), which was statistically significant (p < 0.05). is required to be taught two to three sessions per week in each grade, studies that took less than two sessions per week were marked as low dosage. Otherwise, they were marked as standard dosage. Results showed that the effect size of studies with standard dosage (ES = 0.17, k = 8) was approximately five times that of studies with low dosage (ES = 0.03, k = 10), which was statistically significant (p < 0.05). Specifically, the effect size of studies with low dosage was not significantly different from zero, indicating that low dosage would make the outcomes negligible, even though they used the same curriculum. Meta-regression Overall, only the social economic status of the six moderators was not significantly related to intervention effectiveness. Consequently, the other five moderators, namely research design, sample size, grade level, duration, and dosage, were those involved in the meta-regression. The aim of conducting meta-regression was to examine the effects of each factor simultaneously, since they could significantly moderate the intervention effects independently. The results of the random-effects model showed that three of the six covariates were statistically significant (Table 4). The variable of research design was statistically significant after controlling for other covariates (Coefficient = −0.09, CI = [−0.16 - −0.01], p < 0.05), indicating that the effect size of quasi-experimental studies was 0.09 higher than the effect size of randomized controlled studies. The variable of sample size was also significant (Coefficient = 0.08, CI = [0.00-0.15], p < 0.05), which illustrated that the studies with small sample size had a higher effect size of Duration The duration of intervention was tested as an indicator of effect sizes. The duration of the included studies was classified either as one year and more than one year. Results indicated that there was significant difference between these two categories (p < 0.05). Particularly, the effect size of studies which were implemented one year or less (ES = 0.19, k = 10) was about three times that of studies which were implemented for more than one year (ES = 0.06, k = 10). Social economic status The predominant social economic status of participants may also have an influence on the intervention effects. In this review, the primary studies were coded as low, middle, mixed and unknown. The results showed that there was no significant difference among these four categories (p > 0.05). For instance, the effect size of studies with low socioeconomic background samples and the effect size of studies with middle socioeconomic background samples were both around 0.10. The difference between them was minimal. Dosage The relationship between dosage and intervention effectiveness was also examined. Since the PATHS curriculum 10 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 TABLE 4 Meta-regression for overall effects. g Random effects Coefficient Standard error 95% lower 95% upper Z-value P-value Intercept 0.181*** 0.042 0.100 0.262 4.36 0.000 Design (RCT) −0.088* 0.038 −0.162 −0.014 −2.33 0.020 Sample size (Small) 0.077* 0.038 0.003 0.151 2.04 0.041 Grade (Pre-kindergarten) 0.082 0.066 −0.048 0.211 1.23 0.218 Duration (more than one year) 0.010 0.037 −0.063 0.083 0.27 0.788 Dosage (low) −0.122*** 0.033 −0.187 −0.057 −3.68 0.000 Dosage (NA) −0.045 0.061 −0.165 0.075 −0.73 0.465 In meta-regression, the number of studies was 20, and the number of effect size was 177. *p < 0.05, **p < 0.01, ***p < 0.001. In meta-regression, the number of studies was 20, and the number of effect size was 177. *p < 0.05, **p < 0.01, ***p < 0.001. the effect size of this review was only about 0.11. One possible reason for these differences could be due to the inclusion criteria. The inclusion criteria in the current review were more rigorous than those in previous reviews, especially in terms of research design, sample size and initial equivalence. For instance, more than 20 experimental studies involving PATHS were excluded in the current review since they did not meet our stringent inclusion criteria. These studies were more likely to overestimate the effects since they had small sample sizes or did not have control groups, contributing to the less positive results. Second, the distribution of effects on multiple outcome domains in this review was roughly consistent with the previous ones. Previous reviews showed that the effect sizes of social emotional learning on social emotional skills were substantially larger than those on other outcome domains, including attitude or relations, emotional well-being, prosocial behaviors, conduct problems and academic performance (Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016). In this review, the effect size of PATHS on social emotional skills was also higher than those on other aspects. Consequently, the core output of PATHS or other social emotional learning programs was to reinforce students’ social emotional skills. Other outcomes, such as promoting prosocial behaviors, reducing problem behaviors, improving academic performance, etc., were all secondary. 0.08 than the large ones. Conclusion and discussion The objective of the current review was to examine the effects of PATHS program on students and investigate the moderation effects of methodological and implementation features. Collectively, 20 studies involving 30,454 participants from preschool to elementary school were included, indicating a significant, small and positive effect of PATHS on students at post-tests (ES = 0.11). As to the follow-up effects ranging from one year to seven years, only 5 studies were eligible, indicating a small positive effect (ES = 0.10). In particular, the effect on social emotional skills was largest (ES = 0.16), whereas the effects on other domains, including attitude or relations (ES = 0.08), emotional well-being (ES = 0.02), prosocial behaviors (ES = 0.04), conduct problems (ES = 0.06) and academic performance (ES = 0.05), were nearly negligible. Regarding the interpretation of effect size, we adopted Kraft’s benchmarks for causal studies of Pre-K-12 education interventions, which supposed that less than 0.05 was small, 0.05 to less than 0.20 was medium, and 0.20 or greater was large (Kraft, 2020). The current overall effect size of 0.11 was medium, and the effect sizes for multiple outcomes was small to medium. Regarding the methodological factors and implementation features that may moderate the effectiveness, the results of univariate subgroup analysis and meta-regression differed slightly. In the current review, six factors were extracted to explain the heterogeneity of PATHS studies, namely research design, sample size, grade level, social economic status, duration and dosage. The results of univariate subgroup analysis showed that five of them could moderate the intervention effectiveness significantly with the exception of social economic status. However, only three factors were still statistically significant when the five factors were included in the meta-regression simultaneously. In other words, when controlling for the covariables of grade level and duration, the variables of research design, sample size, and dosage could still significantly moderate the intervention effectiveness. In particular, the quasi- experimental studies had a higher effect size of 0.09 than the randomized controlled studies, the studies with less than 1,000 participants had a higher effect size of 0.08 than the larger ones, Two points should be highlighted and further explained for these findings. First, the overall effect size obtained in this review was substantially smaller than previous ones. Dosage The variable of dosage was statistically significant (Coefficient = −0.12, CI = [−0.19 - −0.06], p < 0.05), in which studies with low dosage had 0.12 lower effect sizes compared to studies with standard dosage. The variables of grade and duration were no longer statistically significant in the meta-regression. In particular, the coefficient of dosage was the largest among the three significant covariates, indicating that dosage was the strongest factor that could moderate the effects of the PATHS program. In addition, adding dosage alone to the regression could explain 54% of the variance, indicating that dosage was a predominant predictor of PATHS effects. Frontiers in Psychology Conclusion and discussion In particular, the overall effect sizes of previous reviews mainly ranged from 0.20 to 0.70 (Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016; Taylor et al., 2017; Blewitt et al., 2018; Corcoran et al., 2018; Yang et al., 2019; Murano et al., 2020), whereas 11 frontiersin.org frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 differed in the levels of dosage irrespective of fidelity, quality, responsiveness and reach. Therefore, dosage is an excellent distinguishing feature of implementation, and its moderation effect on the outcomes of PATHS is supported in the current review. As mentioned above, dosage had a predominant influence on the effectiveness of PATHS among all moderators. If the PATHS curriculum was taught with the designed dosage of two to three times per week, the overall effect size was expected to be 0.17. However, if this dosage was not achieved, the overall effect size would drop to 0.03, which was not significantly different from zero. This positive relation between dosage and PATHS outcomes was consistent with the findings of some experimental studies (Faria et al., 2013; Schonfeld et al., 2015). In short, insufficient dosage would make an otherwise effective project ineffective. and the studies that implemented two to three PATHS sessions per week had a higher effect size of 0.12 than the studies with lower dosage. The impacts of research design and sample size were consistent with previous findings (Slavin and Smith, 2009; Cheung and Slavin, 2016). Furthermore, the impact of dosage on intervention effectiveness was the largest, indicating that dosage was the predominant factor in determining the overall practical effects of the PATHS curriculum. It is worth noting that, to our best knowledge, this is the first time that the variable of dosage has been introduced in a meta-analysis of social emotional learning and its significant effect has been supported. As to the differential effects for particular subgroups, there was no significant difference between targeted groups and universal groups. In the current review, targeted groups referred to students in special education classes, low social economic background students or students with more serious problem behaviors. Even though the effect for targeted participants was slightly larger than that for universal participants, the difference did not reach a statistically significant level. Two previous reviews about social emotional learning also exhibited similar findings. For instance, Payton et al. (2008) and Murano et al. Conclusion and discussion (2020) highlighted that the targeted social emotional interventions had higher effects than the universal ones for at-risk preschool students or students aged 5 to 13 years, separately. There are three reasons that may account for the insignificant difference of PATHS on different groups. First, the number of targeted effects was too small to reach a statistically significant level. Second, the characteristics of targeted participants varied substantially, making it difficult to draw a general conclusion. Third, the interventions in different targeted studies were not the same. Some studies only implemented PATHS curriculum and examined the effects of some particular subgroups separately, whereas some studies carried out extra individual or small group consultation for targeted subgroups beyond the common PATHS curriculum. Consequently, the difference in effects between targeted students and universal students was not significant, even if there seemed to be a higher effect for targeted subgroups. This finding has potential policy and practical implications. In recent decades, social emotional learning programs have been increasingly carried out, but there is no doubt that academic performance still dominates in schools. Social emotional learning is often considered to be supplementary in schools (e.g., Murray et al., 2014; Gaspar et al., 2018; Seabra-Santos et al., 2018). Even if some schools do conduct curriculum-based social emotional learning programs, it is difficult to guarantee the dosage of courses (Bierman et al., 2008; Hamre et al., 2012; Berry et al., 2016; Humphrey et al., 2016; Hennessey and Humphrey, 2020). However, social emotional skills are at least as important as cognitive skills in predicting personal achievement in the future (Heckman et al., 2006). Social emotional learning, including PATHS, could not only cultivate social emotional skills but also indirectly improve students’ academic performance more or less (Durlak et al., 2011; Sklad et al., 2012; Wigelsworth et al., 2016). Therefore, the importance of social emotional learning should arouse more attention from policy makers, teachers and parents. One review about social emotional learning recommended that it should be conducted as regular curriculum rather than supplementary activities (Shi et al., unpublished1). The current review further suggests that the social emotional learning curriculum should be implemented with sufficient dosage to maintain effectiveness. After all, if the dosage does not achieve the recommended level, the overall effect size would become negligible even for a well-designed and high-quality program like PATHS. 1 Shi, J., Cheung, A. C. K., and Ni, A. (2022). Effective school-based social emotional learning programs in Pre-K-12 classrooms: A meta- analysis. Unpublished manuscript. Frontiers in Psychology Conclusion and discussion Note that the recommended dosage by PATHS might not be suitable for other social emotional learning programs, which should be taken seriously. One key contribution of the current review was the findings on the predominant moderation effect of dosage on the impacts of PATHS. The reason for choosing dosage as one implementation feature was that most primary studies reported the frequency of conducting the curriculum and it had a good distinguishing feature among studies. If a study conducted 2 to 3 lessons per week as recommended by PATHS manual, it was considered as standard dosage. Conversely, if it failed to reach the dosage of two times per week, it was regarded as low dosage. This operational definition was very concise and easily accessible, and clearly divided primary studies into two categories, except for two studies that did not report relevant information. In contrast, other implementation features, such as quality, were difficult to extract due to limited information in most experimental studies. This distinguishing feature of dosage was partially supported by Hennessey and Humphrey (2020), who explained that distinct implementation profiles mainly Some limitations in the current review need to be mentioned. First, since the number of studies involving subgroup effects (e.g., gender, race, etc.) was too small, we were not able to examine the differential effects of PATHS on these variables. Further experimental studies are expected to pay more attention to the differential effects of subgroups with 12 frontiersin.org Shi et al. 10.3389/fpsyg.2022.1030572 contributed to the revised version and the final version of the manuscript. All authors contributed to the article and approved the submitted version. special characteristics. Second, there were multiple informants for different measurement tools, including teachers, students, parents, and task observers. The informant might affect the effect sizes, but it was not included as a moderator, because one study might have more than one informant, which made it difficult to be analyzed on the study level. Since the number of included studies was limited, too many moderators may not be appropriate. Hence, we only selected some core moderators in the current review, which may omit other important moderators and bias our results. Finally, the effects of dosage on other social emotional learning programs need further exploration. The substantial effects of dosage should be interpreted with caution due to the limited number of studies. References Arda, T. B., and Ocak, S. (2012). Social competence and promoting alternative thinking strategies–PATHS preschool curriculum. 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Overall, the current review chose PATHS as a representative of social emotional learning, and found that dosage was a predominant predictor to the effectiveness of PATHS curriculum. 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. 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. Author contributions The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/ fpsyg.2022.1030572/full#supplementary-material JS and AC performed the searching procedure, analytic calculations, and the final version of the manuscript. AN Data availability statement The original contributions presented in this study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author. References T., Kusche, C. A., Cook, E. T., and Quamma, J. P. (1995). Promoting emotional competence in school-aged children: The effects of the PATHS curriculum. Dev. Psychopathol. 7, 117–136. doi: 10.1017/ S0954579400006374 Bradshaw, C. P., Shukla, K. D., Pas, E. T., Berg, J. K., and Ialongo, N. S. (2020). Using Complier Average causal effect estimation to examine student outcomes of the pax good behavior game when integrated with the paths curriculum. Admin. Policy Ment. Health Ment. Health Serv. 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References Can early childhood curriculum enhance social-emotional competence in low-income children? a meta-analysis of the educational effects. Early Educ. Dev. 30, 36–59. doi: 10.1080/10409289.2018.1539557 Raynor, E. (2011). The effect of the promoting alternative thinking strategies curriculum on internalizing symptoms in both a maltreated and non-maltreated sample. Ph.D thesis. Rochester, NY: Rochester Institute of Technology. Frontiers in Psychology 15 frontiersin.org
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The Complexation of Iron by Marine Humic Acid
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The Complexation of Iron by Marine Humic Acid The Complexation of Iron by Marine Humic Acid Gerald L. Picard University of Rhode Island Follow this and additional works at: https://digitalcommons.uri.edu/theses Terms of Use All rights reserved under copyright. Recommended Citation Recommended Citation Recommended Citation Recommended Citation Picard, Gerald L., "The Complexation of Iron by Marine Humic Acid" (1974). Open Access Master's Theses. Paper 2111. https://digitalcommons.uri.edu/theses/2111 Recommended Citation Recommended Citation Picard, Gerald L., "The Complexation of Iron by Marine Humic Acid" (1974). Open Access Master's Theses. Paper 2111. https://digitalcommons.uri.edu/theses/2111 This Thesis is brought to you by the University of Rhode Island. It has been accepted for inclusion in Open Access Master's Theses by an authorized administrator of DigitalCommons@URI. For more information, please contact digitalcommons-group@uri.edu. For permission to reuse copyrighted content, contact the author directly. BY GERALD L. PICARD A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE . REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE FOOD AND RESOURCE CliEMISTRY ABSTRAC Cation exchange capacity measurements, performed before and after removal of the humic acid fraction from various Narragansett Bay sediments, indicate that low concentrations cf these organic substances strongly influence the abi 1 i ty of the sediment to react \>Jith meta 1 ions. Atomic absorption and spectrophotometric methods have been developed which allm·J quantitat·ive determinations of the extent of reactions between a naturally occurring hurnic acid a~d iron 1n artificial sea- water. The results indicate that different humic acid-iron complexes are formed with varying solubilities depending on the hum-ic acid-iron ratio used -in the experiment. This study suggests that humic acid is a transport substance for trace metais in Narragansett Bay. ACKNOWLEDG The progress and completion of my Master's research \\las made possible by the encouragement and guidance of Dr. George T. Felbeck, Jr. I would like to thank him for his efforts. I am also grateful to Dr. Terry Bidleman, Dr. Charles E .. Olne_y, Dr. Richard H. Pierce, Jr., and Dr. Jerry M. Serra, Jr., for their ideas and suggestions during the formulation of the thesis problem and through to its completion. I would like to thank Mr. Roland Gilbert for his technical assistance and suggestions throughout the course of the analytical work and Gayle Osborne for her help with preparing the thesis and the manuscript for publication. Also, I am grateful to Dr. Luke Albert, Dr. James Quinn, and Dr. Milton Salomon for their review of this work. Finally, I thank my wife, Scharma, for her support and patience throughout the course of this work. This investigation was supported by the National Sea Grant Program. iii TABLE OF CONTENT PAGE LIST OF TABLES . LIST OF FIGURES. • • • • i V MANUSCRIPT ... THE COMPLEXATION OF IRON BY MARINE HUMIC ACID ABSTRACT. INTRODUCTION. METHODS AND MATERIALS RESULTS AND DISCUSSION. TABLES AND FIGURES. REFERENCES ..... . V l 2 3 8 13 27 APPENDIX A. APPENDIX B. APPENDIX C. APPENDIX D. LITERATURE REVIEW. . . . . . . . ......... 29 METHOD OF ISOLATION AND PURIFICATION OF HUMIC ACID . 37 THE ARTIFICIAL SEAWATER MEDIUM. . . . ... 39 BIBLIOGRAPHY OF THE COMPLETE THESIS. . 41 PAGE LIST OF TABLES . LIST OF FIGURES. • • • • i V V APPENDIX A. APPENDIX B. APPENDIX C. APPENDIX D. LITERATURE REVIEW. . . . . . . . ......... 29 METHOD OF ISOLATION AND PURIFICATION OF HUMIC ACID . 37 THE ARTIFICIAL SEAWATER MEDIUM. . . . ... 39 BIBLIOGRAPHY OF THE COMPLETE THESIS. . 41 iv LIST OF TABLE TABLE PAGE l. Effect of Humic Substances on Cation Exchange Capacity of Some Narragansett Bay Sediments . 2. Effect of Added Humic Acid on Soluble Humate in the 'Soluble' Fraction of the Complexation Experiments . 3. Percent Saturation of the Available Exchange Sites on the 13 14 Humic Colloids with Fe(OH);l . . . . . 15 4. Stability Data on Soluble Iron-Humates 16 TABL TABL V LIST OF FIGURE FIGURE PAGE l. Row Diagram of the Analytical Procedure Used in the H.A. Complexation Studies ...... . 2. Effect of Hurnic Acid on Iron Solubility in the Complexation Experiments ... 3. Effect of Added Humic Acid on Precipitated Humate in the Complexation Experiments. 4. Schematic Representation of the Interaction of Iron with i8 20 22 Humic Acid with Increasing Hurnic Acid to Iron Ratios. . . . 24 5. Effect of Added Iron on Percent Materials in the Soluble Phase in the Complexation Experiments .. 26 PREFAC PREFAC This thesis has been prepared according to the manuscript thesis plan. The manuscript is in the format of the journal,. Geochimica et Cosmochimica Acta. MANUSCR MANUSCR THE COMPLEXATION OF IRON BY MARINE HUMIC ACID THE COMPLEXATION OF IRON BY MARINE HUMIC ACID G. L. Picard and G. T. Felbeck, Jr. Department of Food and Resource Chemistry University of Rhode Is1and Kingston, Rhode Island 02881 G. L. Picard and G. T. Felbeck, Jr. Department of Food and Resource Chemistry University of Rhode Is1and Kingston, Rhode Island 02881 ABSTRA Cation exchange capacity measurements, performed before and after removal of the humic acid fraction from various Narragansett Bay sediments, indicate that low concentrations of these organic substances strongly influence the ability of the sediment to react with metal ions. Atomic absorption and spectrophotometric methods have been developed which allow quantitative determinations of the extent of reactions between a naturally occurring humic acid and iron in artificial seawater. The results indicate that different humic acid-iron complexes are formed with varying solubilities depending on the humic acid-iron ratio used in the experiment. This study suggests that humic acid is a transport substance for trace metals in Narragansett Bay. METHODS AND Mi\TERI .l\LS METHODS AND Mi\TERI .l\LS INTRODUCTI· The nature of iron in seawater has been the subject of considerable specui ation in recent years (Siegel, 1971). Part of the discrepancy between the high concentrations of 'soluble' iron found in near shore waters and the concentrations predicted on the basis of the solubility product of iron hydroxide has been attributed to the presence of natural organic chelators (Duursma and Sevenhuysen, 1966). Scant data are available on the complexing ability of the organic materials present in seawater (Rashid, 1971, 1972; Rashid and Leonard, 1973). Studies have indicated that these materials resemble humic substances found in soils and fresh water (Hair and Bassett, 1973; Schnidler, et al., 1972). The simi'larity of these hurnic substances found in a'l1 natural systems, their abundance, ond their ability to form complexes with metals (Schnitzer and Khan, 1972) make marine humic materials of prime concern in the transport, availability, and accumula- tion of iron and other trace elements in marine environments. We have investigated the iron complexing properties of a marine humic acid (H.A.) iso1at~d from a Narragansett Bay sediment. A model has been developed which yields some insight into the role of this organic chelator in the transport and accumulation of iron in sedimen- tary deposits. A. Isolation and Purification of Humic Acid The hurnic acid isolated for use in the iron complexation experi- ments was extracted from sediment samples obtained with an Eckman Dredge from a location in Narragansett Bay, R.I., designated station F.P. by Farrington and Quinn (1973). This location is about 100 yards down- stream from the municipal sewage outfall for the city of Providence, R.I. The sediment was kept frozen until use, at which time it was air dried, ground to pass a 2 mm sieve, and oven dried at 100°C for 24 hours. The method of extraction and purification of the humic acid from the sediment samples is a modification of the procedure commonly used by humic acid chemists and has been described in detail by Pierce and Felbeck (1974). The method consists of 0.5 N NaOH extractions of the sediment samples with subsequent precipitation of the humic acid from the sodium hydroxide solution by addition of 6 N HCl to pH 2.0, followed by centrifugation. The humic acid is then redissolved in 0.5 N NaOH, the alkaline solution of humic acid is dialyzed for 5 days against distilled water, and the resulting humic acid solution is centrifuged at 20,000 X g for 30 min to remove clays and other impurities. This humic acid solution is used in the complexation experiments. The ammonium acetate method (Peech, et al., 1947) was used to determine cation exchange capacities (C.E.C.) of the sediment samples from stations F.P., D, E-2 and B before and after removal of the humic substances \'Jith O. 5 N NaOH. Cati on exchange capacity measurements were performed on the station F.P. humic acid using the barium acetate method of Chandler (1939). Organic carbon analyses of the sediment 4 4 samples were performed using an F and M Model 185 Carbon, Nitrogen, Hydrogen Analyzer. B. Complexation Studies The complexation studies were performed in the following manner. Ten ml of a concentrated artificial seawater solution containing 175 ppt NaCl, 2.0 ppt Ca, and 6.0 ppt Mg were added from a buret to 100 ml beakers containing various amounts of the humic acid stock solution, ranging from O µg to 7500 µg of humic acid. Fifty µg of iron as ferric chloride from Baker Dilut-It Standards were added slowly, drop-wise from a separate buret. The mixture was constantly readjusted to pH 8.0 with NaOH and stirred using a Teflon-coated magnetic stirring bar during the addition of iron. The volume of the mixture at this point was about 40 ml. Time studies indicated that 18 hours was sufficient time for equilibrium to be attained. The mixture was then readjusted to pH 8.0 and diluted to 50 ml in volumetric flasks. At this point, the mixture contained the following concentrations of materials: 35 ppt NaCl, 400 ppm Ca, 1200 ppm Mg, l ppm Fe and con- centrations of humic acid ranging from O ppm to 150 ppm. The 50 ml of solution was centrifuged at 40,000 X gin poly- carbonate centrifuge tubes for 30 minutes and the supernatant solution was decanted from the precipitate. Four to seven replicates were performed for each experimental point corresponding to a particular ratio of humic acid to iron in these experiments. A flow diagram describing the analytical procedures used in the complexation experi- ments is presented in Figure 1. 5 D. Analysis of the Precipitate The precipitate was dissolved in 4 ml of a 0.026 N EDTA solution (pH= 12). This solution was diluted to 10 ml or 25 ml depending on the nature of the particular experiment performed. The humic acid and iron were analyzed using the instrumentation already discussed. Standards were prepared from the same EDTA solution used to prepare the samples. Standards for iron analysis contained a fixed amount of humic acid and varying amounts of iron in the EDTA medium. Standards for humic acid analysis contained the same concen~ration of iron as the samples for that particular set of experiments and varying amounts of humic acid. C. Analysis of the Soluble Fraction The concentration of humic acid in the supernatant solutions was determined a.t 350 nm using a Beckman DU Spectrophotometer equipped with l cm glass cuvettes. Standards were prepared from the same artificial seawater solution and from the humic acid stock solution which were used to prepare the samples. with 0.05 N NaOH. The standards were adjusted to pH 8.0 I A possible source of error in this measurement was that the humic acid-iron complexes could have different absorption properties than the uncomplexed humic acid in the standards. This possible source of error was investigated by preparing a standard humic acid solution at exactly the same concentration of the humic acid in the sample solutions measured by the described technique, and comparing these two solutions on a double beam spectrophotometer. This experiment yielded a straight base line relationship from 600 nm to 320 nm indicating no detectable differential absorption of light by the humic acid-iron complexes in the sample compared to the uncomplexed humic acid in the standards. Iron in the supernatant solutions was analyzed using a Perkin Elmer Model 303 Atomic Absorption Spectrophotometer equipped with a three-slot burner head, a manual readout system and an air-acetylene flame. The standards for the iron analysis were prepared from the same seawater solution as the samples but contained no humic acid. There are two possible corrections that need to be made in this iron measurement. One correction involved the presence of residual iron remaining after isolation and purification of the humic acid; this residual iron in the humic acid was taken into consideration in the 6 6 mass balance calcuiations performed on the system. The second source of error was the possibility of an enhancement of the iron signals due to the presence of humic acid in the samples. This enhancement has been reported by Yuan and Breland (1969) to be on the order of 10%. We were unable to detect the enhancement effect in our system and therefore included no factor for enhancement in our mass balance calculations for i ran. E. Blanks The blanks for the iron analyses consisted of the humic acid in the artificial seawater medium and were treated in the same manner as the samples except for the addition of iron. The iron in the blanks was never mare than 10 percent of the iron ir1 the samples. This iron in the blanks was most likely due to the residual iron in.the humic acid remaining after purification and, as already mentioned, was taken 7 into consideration in the mass balance calculations. The blanks for the humic acid analysis consisted of iron in the artificial seawater medium and were treated in the same manner as the samples except for the addition of humic acid. The absorption of light at 350 nm by these blanks was essentially zero. F. Sta ti sti cs All results are reported as an average of replicates with its uncertainty calculated at the 90 percent confidence limit using the. t-test based on range developed by Snedecor and Cochran (1968). RESULTS AND DISCUSSIO Cation exchange capacity meas:.1rements performed before and after removal of the humic fraction from various Narragansett Bay sediments indicated that extraction of the humic fraction significantly lowered the cation exchange capacity of the sediment (Table 1). There i.; a positive corre 1 ati on between cation exchange capacity and percent organic carbon. The removal of the humic fraction decreased the cation exchange capacity by as much as 55% (sediment E-2). This indicated that the humic fraction strongiy influences the ability of the sediment to interact with metal ions. This capacity of the humic fraction to complex metal ions was investigated in our model complexation experiments. The humic acid used in these experiments was obtained from the sodium hydroxide extract of sediment from station F.P. The results of the iron analyses in the complexation experiments are presented in Figure 2. As the amount of humic acid used in the experiment was increased from O mg to 7.50 mg, the amount of iron 1solubilized 1 increased and the quantity of iron found in the precipitate decreased. The mass balance for each set of experimental conditions is also presented (Figure 2). The results of these comp"lexation experiments indicate that humic acid could be involved in the transport and accumulation of iron in Narragansett Bay. This conc1usion is in agreement v1ith the findings of Rashid (1971, 1972), and Koshy, et al., (1969) in their work on the so1ub·ilization of metai salts by marine humic substances. Moreover, iron could be one of the trace metals responsible for the precipitation 9 of humic acid in estuaries, thus implicating these reactions as mechanisms for the accumulation of iron-rich organic matter deposits common in near-shore sed·iments (Swanson and f-laiacas, 1965). of humic acid in estuaries, thus implicating these reactions as mechanisms for the accumulation of iron-rich organic matter deposits common in near-shore sed·iments (Swanson and f-laiacas, 1965). The humic acid-iron ratios used in our model experiments regulated the solubilization and precipitation equilibria. High humic acid-iron ratios increase the solubility of iron in the medium. The results of the humic acid analyses in the model experiments are presented in Table 2. As the amount of total humic acid used is increased, the amount and the percent of soluble humic acid are also increased. Above the humic acid-iron ratio of 50/1 w/w, the amount of humic acid found in the precipitate decreases (Figure 3). RESULTS AND DISCUSSIO This increase in the solubility of humic acid-iron complexes is due to a different distribution of the limited quantity of iron on the humic colloids, thus making them less susceptible to precipitation by the iron. The mass balance for each humic acid analysis is also included in Figure 3. The results of these experiments can be visualized if one considers that humic acid consists of fragments ranging in molecular weight from a few hundred to several million (Schnitzer and Khan, 1972). Rashid (1971) has demonstrated that the lower molecular weight fragments of marine humic acid are more efficient in solubilizing iron than the higher molecular weight fragments. Since the higher molecular weight fragments are less efficient in solubilizing iron due to a smaller charge to mass ratio, these will be precipitated out upon reaction with a given number of ferric ions (x), while the lower molecular weight fragments will solubilize the x ferric ions (Figure 4). As the humic acid-iron ratio is experimentally increased, the iron becomes limiting 10 and each humic acid fragment becomes associated with fewer than x atoms of ferric iron. Hence, the negative charge on each fragment is main- tained and as a consequence some of the higher molecular weight fragments, present as a gradation of molecular weight sizes, are more efficiently hydrated and are thus more soluble (Ong and Bisque, 1968). Increasing the humic acid-iron ratio further will lead to the solubiliza- tion of a11 the iron and humic acid used in experiment. This rationale attempts to explain the increase in the iron and humic acid in the soluble phase as the humic acid-iron ratio is experimentally increased. It also accounts for the increase in humic acid as precipitate for humic acid-iron ratios up to 50/1 w/w, and the subsequent decrease in precipitate as the humic acid-iron ratio is ·j ncrea.sed. Other observations lending plausibility to this model are summarized in Figure 5. A decrease in the percentage of 'soluble' iron and soluble humic acid results when increasing quantities of iron are added to a constant amount of humic acid. We would predict from our model that the humic acid fragments eventually would become so saturated with iron that all the complexes would become insoluble, due to charge reduction on the polymers, regardless of the size of the humic acid fragment. An additioral line cf evidence to substantiate this concept is presented in Table 3. RESULTS AND DISCUSSIO By calculating the cation exchange sites avail- able on the humic acid in tath phases of the system and using the equivalent weight of iron along with the assumptions listed below, we were ab1e to ca1cult\te the percent of saturation of the humic acid in 11 each phase of the system at the various experimental points. The cation exchange capacity measurements were performed on the humi c acid using y the Ba(Ac)2 method of Chandler (1939). This yielded a cation exchange of 141 ~ 42 meq/100 g of humic acid. This figure, along with the measured quantity of humic acid found in each phase at each experimental point, was used to calculate the sites available for reaction on the humic acid. The amount of iron found in each phase along with its equivalent weight was used to calculate the sites occupied by iron on the humic acid fragments. The three assumptions we made in making this calculation were: 1. The primary inorganic iron species reacting with the humic acid in the medium was Fe(OH);1. Thermodynamic calculations ·indicate this to be the main form of iron at the pH and ionic strength used in these experiments (Kester and Byrne, 1972). Also, Schnitzer and Khan (1972) present data suggesting that at pH 8 humic acid forms iron hydroxy complexes. 2. Iron is preferentially chelated over calcium, magnesium and sodium. 3. The precipitated humic acid in our complexation experiments has the same cation exchange capacity as the humic acid measured as a whole. This assumption may not be entirely valid because the exchange capacity of the precipitated humi c acid may be 10\1/er than the exchange capacity of the bulk humic acid. The results of these calculations are presented in Table 3. The data indicate that more of the available sites are occupied by Fe(OH);1 on the precipitated humic acid than on the soluble humic acid. Al- though there are great variations in the percent saturation of the 12 humic acid, particularly in the precipitate, this calculation does illustrate that the negative sites on the humic acid in the precipitate exhibit a saturation effect and hence are insoluble in the medium as defined by our centrifugation technique. The results of an experiment indicating the stability of these 1scluble 1 iron humates are presented in Table 4. RESULTS AND DISCUSSIO After centrifugation and analysis, the soluble phase of a comp1exaticn experiment was refrigerated and reanalyzed after 60 days. At-test performed at the 10% level indicates that there is no significant difference between the means of the two populations in the iron or humic acid data. This indicates that the 'soluble' iron humates are capable of resisting hydrolysis to the insoluble iron hydroxide. These reactions between iron and humic acid may be important in the solubilization and precipitation of these materials in natural water systems, particularly in areas where municipal and domestic sewage dumping promote high organic matter and trace metal concentrations. The formation and transport of soluble metal complexes from these areas, with subsequent deposition as the complexes become more saturated with iron and other metals or clays, may be an important mechanism in the accumulation of iron-organic matter complexes in sedimentary deposits. The possibility also exists that these soluble and insoluble complexes are capable of undergoing ion exchange or adsorption reactions with toxic metal ions, thus implicating this mechanism in the scavenging of trace metals from natural waters and accumulating these metals in the organic fraction of sedimentary deposits and into the food web via deposit and filter feeders. MEN E N O XT. TY OF SOME NARRAGANSETT BAY SEDIM % DECREASIN Meq./lOOg C. E. C. DUE T 5 N NaOH EXT. 0. 5 N NaOH E 6 + 0.5 29% 9 + 0.7 16% 4 + 0.1 55% 4 + 0.1 54% 14 TABLE 2. EFFECT OF ADDED HUMIC ACID ON SOLUBLE HUM/.\TE IN THE SOLUBLE FRACTION OF THE COMPLEXATION EXPERIMENTS H.A. ADDED H.A. TO EXPERIMENT H.A. SOLUBLE % SOLUBLE 0 119 750 400 + 31 µg 53% 1250 873 + 30 70% 1750 1175 + 47 67% 2500 1738 + 53 70% 5000 4514 + 105 90% 7500 7150 + 66 95% TATE HANGE SITES ON THE HUMIC COLLOIDS WITH Fe(OH) UPIED TION % OF AVAILABLE SITES OCCUPIED ON H.A. IN PRECIPI 148 + 50 % 127 + 38 80 + 25 56 + 18 62 + 20 100 + 43 HANGE SITES ON THE HUMIC COLLO UPIED TION % OF AV OCCUPIED ON H 14 12 8 5 6 10 16 TABLE 4. STABILITY DATA ON SOLUBLE IRON-HUM/HES 2500 µ2 H.A. USED IN EXPERIMENT TIME (DAYS) 0 60 SOLUBLE IRON 24 ::_ 4. µg 19 ~ 3 µg 50 µg IRON ADDED SOLUBLE HUMIC ACID 1750 ::_ 50 µg 1950 + 100 µa - ::, Fig. l. Flow diagram of the analytical procedure used in the H.A. com1exation studies. 19 Fig. 2. Effect of humic acid on iron solubility in the complexation exper-iments. (constant amount of iron added= 50 ug) Fig. 2. Effect of humic acid on iron solubility in the complexation exper-iments. (constant amount of iron added= 50 ug) 103±4 % IRON RECOVERED l0l-t 3 99±1 / IRON IN PRECIPITATE OLUBLE PHASE --------- 4 I S I ~ I 7 I mg H.A. USED IN EXPERIMENT -- SED IN LUB LUB 21 Ftg, 3. Effect of added hurnic acid on precipitated humate in the complexation experiments. (constant amount of iron added= 50 ug) Ftg, 3. Effect of added hurnic acid on precipitated humate in the complexation experiments. (constant amount of iron added= 50 ug) Cl w 0:: w > 0 U. w 0:: . c::( ::c ~ r- +• I.O 0-, N +1 r--.. 0) .- u w 0:: Cl... z ...... c::( ::c 01 ::l -:l LC) I-z w ::E: ...... 0:: w Cl... X w z <:j- ...... Cl L,J (./) ::::, . c::( :::c 01 ('0 E N . 23 Fig. 4. Schematic representation of the interaction of iron with humic with increasing humic acid to iron ratios. 24 0 LLJ 0 0 c::r: . c::r: ::c C.!J z ....... V) c::r: LLJ a:::: u z ....... I FRAGMENTS ASSOCIATED WITH IRON - 'INSOLUBLE' Fe Fe Fe 0 (x)Fe FeQ Fe Fe (-)0 (-)0 (x)Fe Fe (x)Fe (-) 0 (x)Fe (-) ( -) ( -) 0 (-)0 (x)Fe (x)Fe - - - .... ' - ' / I J_-)_ ((-) 0 (-) C) \ (x)Fe \ (x) Fe ' ' ,.!:. .... - ·-- -- LOW MOLECULAR WEIGHT I FRAGMENTS ASSOCIATED WITH IRON - I SOLUBLE I Fe Fe Fe 0 Fe 0 ( x) Fe (x)Fe (-) 0 (-) u (x)Fe (x)Fe Fe (-) 0 (x)Fe 0 (-) (-) ( -) 0 (x)Fe (x)Fe ' \ (-) ( -) • I I (-) 0 0 I ( -) I I I I ( x) Fe (x)Fe I - - - - - ➔ Fe Fe 0 ( x) Fe Fe FeQ Fe Fe 0 (x)Fe Fe Fe 0 (x)Fe (-) 0 (x)Fe (-) u (x)Fe . I (-) ( -) 0 (x)Fe J_-)_ (-) C) (x)Fe ( -) (-)0 (x)Fe - - - .... ' - ' / I ((-) 0 \ \ (x) Fe ' ' ,.!:. .... - ·-- -- 0 (-) (x)Fe ' \ (-) I I (-) 0 I I I I I ( x) Fe I - - - - - ➔ (-) ( -) 0 (x)Fe 0 (-) (x)Fe (-) (-)0 (x)Fe ( -) • 0 ( -) (x)Fe ( -) • 0 ( -) (x)Fe (x)Fe 25 25 Fig. 5. Effect of added iron on percent materials in the soluble phase of the complexation experiments. (constant amount of humic acid added= 2500 ug) Fig. 5. Effect of added iron on percent materials in the soluble phase of the complexation experiments. (constant amount of humic acid added= 2500 ug) w _J OJ ::::, _J 0 (/) L1.J :c i-- z ..... . < ::1: ~ L1.J _J o:::i ::::, _J 0 (/) N 0 <:j- N I- 0 z 0 L1.J N :a: ..... 0:: L1.J Cl... X L1.J z ..... 0 Cl I.O w r- (/) ::::, z 0 0:: I-< 0) ::, 0 N r- 0 co REFERENC Chandler, R. F. (1939) Cation exchange capacity and exchangeable hydrogen. Journal of Agr. Res., Vol. 59, p. 491. Duursma, E. K. and Sevenhuysen, W. (1966) Note on chelation and solubility of certain metals in seawater at different pH valu solubility of certain metals in seawater at different pH values. lubility of certain metals in seawater at different pH values. Netherlands Journal of Sea Research, Vol. 3, No. l, p. 95. Farrington, J. W. and Quinn,. J. G. (1973) Biogeochemistry of fatty acids in recent sediments from Narragansett Bay, Rhode Island. Geochim. Cosmochim. Acta, Vol. 37, p. 259. Hair, M. E. and Bassett, C. R. (1973) Dissolved and particulate humic acids in an East Coast estuary. Estuarine and Coastal Marine Science, Vol. 1, p. 107. Kester, D. R. and Byrne, R.H., Jr. (1972) Chemical forms of iron in seawater. in FERROMANGANESE DEPOSITS ON THE OCEAN FLOOR, David R. Horn, Palisades, New York, p. 107. Koshy, E., Desai, M. and Ganguly, A. (1969) Studies on organic-metallic interactions in the marine environment. Part I, Interaction of some metallic ions with dissolved organic substances in seawater. Current Science, Vol. 38, No. 23, p. 558. Ong, H. L. and Bisque, R. E. (1968) Coagulation of humic colloids by metal ions. Soil Sci., Vol. 106, p. 220. Peech, M., Alexander, L. T., Dean, L.A., Reed, J. F. (1947) Methods of soil analysis for soil fertility investigations. USDA Circ. No. 757, p. 25. Pierce, R. H., Jr. and Felbeck, G. T., Jr. (1974) A comparison of three methods of extracting organic matter from soils and marine sediments. Proc. Netherlands Limnological (in press). 28 Rashid, R. (1971) Role of humic acids of marine origin and their different molecular weight fractions in complexing di- and tri- valent metals. Soil Sci., Vol. III, No. 5~ p. 298. Rashid, R. (1972) Role of quinone groups in solubility and complexing of metals in sediments and soils. Chem. Geology, No. 9, p. 241. Rashid, R. and Leonard, J. D. (1973) Modification in the solubility and· precipitation behavior of various metals as a result of their interaction vJith sedimentary humic acid. Chem. Geology, Vol. 2, No. 2, p. 89. Schnidler, F., Alberts, J. J. and Hornick, K. C. (1972) A preliminary investigation of organic-inorganic associations in a stagnating system. Limnology and Oceanography, Vol. 17, p. 952. Schnitzer, M. and Khan, S. V. (1972) .i!!_ HUMIC SUBSTANCES IN THE ENVIRONMENT, Marcel Dekker, Inc., New York, Chapter 1, p. 1. Siegel, A. (1971) Metal-organic interactions in the marine environment . .i!!_ ORGANIC COMPOUNDS IN AQUATIC ENVIRONMENTS, Maree l Dekker, Inc., New York, Chapter 12, p. 265. Snedecor, G. W. and Cochran, W. G. (1968) Short cut and non-parametric methods. 1!!_ STATISTICAL METHODS, The Iowa State University Press, 6th Ed., Ames, Iowa, Chapter 5, p. 120. Swanson, V. E. and Palacas, J. G. (1965) Humate in coastal sands of northwest Florida. U.S. Geol. Survey Bull., 12148, p. Bl. Yuan, J. L. and Breland, H. L. (1969) Evaluation of atomic absorption methods for determinations of Al, Fe and Si in clay and soil extracts. Soil Sci. Soc. Am. Proc., Vol. 33, No. 6, p. 851. APPENDIX A LITERATURE REVIEW LITERATURE REVIEW 30 Introduction to the Nature and Complexation of Introduction to the Nature and Complexation of Iron in Seawater Iron in Seawater The nature of iron in seawater has been the subject of consider- able speculation in recent years (Siegel, 1971). Part of the discrepancy between the high concentrations of 1soluble 1 iron found in seawater and the concentrations predicted on the basis of the solubility product of iron hydroxide has been attributed to the presence of natural organic chelators (Duursma and Sevenhuysen, 1966). These chelators can change the solubility characteristics and the properties of iron in aqueous systems (Corcoran, 1967). Iron, like many other metallic ions in seawater, becomes coordinated with water molecules. These water molecules may·be replaced or displaced to varying extents by other groups, including hydroxyl ions. Chelation resembles coordination except that the molecular linkage is a ring structure (Johnston, 1964). Experiments conducted by Laevastu and Thompson (1957) demonstrated that up to 75% of the 1soluble 1 iron present in coastal seawater was present in the form of iron organic complexes. They concluded that these organic chelators play an important role in regulating the concen- trations of 'soluble' iron in seawater. Corcoran (1967) found iron to exist in two principal forms in tropical seawater, namely particulate and as a soluble organic complex. He states that while runoff controls the supply of iron to the sea, the content in seawater is regulated by water movements, solubility, biological ·activity and the ability of iron to form organic complexes. 31 Soil Humic Substances and_ Iron Complexation Soil Humic Substances and_ Iron Complexation Scant data are available on natural organic substances in seawater (Rashid, 1971). However, studies indicate that these organics resemble humic substances found in soils and fresh water (Schnidler, et al., 1972). Although the actual structure of soil humic substances is poorly understood, much ·is known about the ability of these soil organics to chelate metal ions. The formal distinction between complex and chelate is often arbitrary for meta 1 humates and ful vates. It is diffi cuH to differen- ·tiate bet\,1een the tvm, especially when the same kind of donor groups en the organic molecules are involved (Schnitzer and Khan, 1972). Hence, these terms will be used interchangeably in referring to metal organic compounds in the course of this discussion. Humic substances are a group of amorphous, dark-colored, poly- meric materials operationally defined as an acid soluble, base soluble fulvic acid and a base soluble, acid insoluble humic acid. The molecular weights of these substances have been reported to range from a few hundred to several millions and are probably the most widely distributed natural products on the earth's surface, occurring in lakes, soils, rivers and the sea (Schnitzer and Khan, 1972). The great variation in molecular weights of these substances could effect the solubilities of the metal complexes formed (Rashid, 1971). Superimposed on this solubility relationship, due to the size of the molecular weight fraction in these complexation reactions, is the fact that more than one type of complex can be formed between metal ion and complexing agent. Schnitzer and Skinner (1963) demonstrated that 32 soil humic acid is capable of forming i range of molar complexes with iron and aluminum ranging from 1:1 to 6:1 metal to humic acid complexes and becoming increasingly water insoluble as more metal is ·complexed. The Fuess theory can be used to understand the coagulation of humic acid by metal ions (Ong and Bisque~ 1968). In the presence of cations, the charge on the humic acid is reduced. This reduction of the charge decreases the amount of water of hydration that can be held by the colloids. Consequently, the macromolecule takes on the properties of a hydrophobic sol and precipitates out of solution. Soil Humic Substances and_ Iron Complexation Ong and Bisque (1968) investigated the coagulation of soil humic acid with metal ions and concluded that the greater the charge on the metal ion, the less metal required to precipitate the humic acid, in agreement with the Schultz Hardy Rule. Also, for monovalent or diva·!ent metal ions, the coagulation po~ver increases as the radius of the hydrated ion decreases. Schnitzer and Skinner (1965, 1966) have been able to identify the functional groups of soil humic acids involved in the solubilization and precipitation of metal ions. Using methylation and acetylation techniques, they concluded that two types of reactions must be involved in the retention of iron and other metallic ions by humic acid: one involving simultaneously both acidic carboxyl and phenolic hydroxyl groups and a minor reaction in which only carboxyl groups participate. In another study by Schnitzer and Skinner (1964), infrared spectra of iron humic acid complexes indicated the formation of electrovalent metal carboxylate bonds. Other investigators have demonstrated that iron can react chemically with humic acid. Van Dijk (1971) showed iron to be firmly bound to the soil humic acid molecules, judging from the magnitude of 33 the pH decrease on addition of the inorganic iron salt. Pqtentiometric titrations of soil humic acid in the presence of iron III indicated the formation of metal humic acid complexes (Khan, 1969). Drozdova (1968) has even suggested that iron can act as a catalyst in the formation of humic acid polymers. Ha 11 and Packham ( 1965) performed coagulation experiments on soil fulvic acid with iron and followed the precipitation of fulvic acid spectrophotometrically. The fact that maximum removal of the humic acid occurs at or near the pH corresponding to the maximum zeta potential suggests the formation of basic salts rather than occlusions of humic acid in iron hydroxide sols. Aquatic Humic Substances and Iron Transport The ability of humic acids to form complexes with metal ions and their widespread distribution in the environment has led investigators to consider these materials as a means of transport of otherwise in- soluble metal ions in aquatic systems. Studies of organic color from fresh water lakes indicate that the nature of these substances and their possible reactions with iron are similar to those of soil humic sub- stances (Christman, 1968). Shapiro (1964) investigated the phenomena of solubilization of iron by yellow organic acids isolated from lake water. He found increased iron holding capacity of the yellow organic acids under alkaline conditions. Shapiro proposed that the solubiliza- tion of iron is due to chelation and dispersion of iron hydroxide coated with organic acids. He ascribed the iron holding capacity of these acids to carboxyl and phenolic hydroxy groups. The results 34 34 suggest the large quantities of iron held in apparent solution in highly colored lake waters may be in the form of a protected colloid. Although there is some evidence for chelation, it seems to play a minor role unless there is a high organic matter to iron ratio. Christman (1968) has separated concentrates of organic color isolated from lake water on Sephadex and found iron to be associated with all size molecular \veight fractions. A strong chelating agent was not able to remove all the iron from the colored macromolecules and was least efficient in removing iron from the largest size molecular weight fractions. Martin, Doig and Pierce (1971) have suggested that there is a linear correlation between humic acid and soluble iron in west coast Florida streams. Swanson and Palacas (1965) analyzed the metal content of natural humates isolated from river water and found high iron and aluminum concentrations and varying amounts of trace metals. They suggest that trace metals can be adsorbed during floculation of the iron or aluminum humate. They implicate this as a possible mechanism for concentrating trace elements in organic deposits. Marine Humic Substances and the Solubilization of Iron A few studies have been conducted which demonstrate the ability of marine humic substances to effect the migration and accumulation of various metals. Rashid ( 1971) determined the ability of humi c acids of marine origin (sediments) to solubilize metal ions. He found low molecular weight fractions of humic acid to be considerably more 35 -effective in solubilizing various metals, including iron, than high molecular weight fractions. Rashid (1972) has demonstrated the impor- tance of quinone groups in complexing studies with marine humic acids isolated from sediment samples and the ability of these humic acids to solubilize metal carbonates. Koshy, Desai and Ganguly (1969), using radioactive tracer techniques, demonstrated that the dissolved organic matter form a sediment extract was capable of solubilizing iron. Significance of Iron Complexation in Natural Waters The phenomena of chelation and the availability of iron to organisms in aqu~tic systems has been discussed by many investigators. Saunders (1957) states that organic compounds present in sewater may effectively keep iron in a soluble state in the photic zone thus keeping this essential element available to organisms. Johnston (1964) con- cludes that in seawater there is a very small margin of safety in the supply of iron to algae and that there is reason for concern over the mechanism of sustaining this supply. He states that the chelation of iron in seawater increases the concentration of soluble iron, presents exchangeable iron to the cell membrane and affects the oxidation- reduction equilibrium of the trace metals. Johnston's experiments with mixed cultures confirms the importance of chelation by demonstrating that there was an optimum level of chelation for growth and that in unfiltered sea water no addition of metals need be supplied as enough are already present in colloidal or particulate form. He concludes that the solubilization of trace metals ·is a very important aspect of seav~ater ferti 1 ity in the presence of adequate nutrients. 36 Schelske 1s (1962) experiments on a Marl lake water indicated that nutrients did not increase primary productivity of phytoplankton greatly unless chelated iron was also added. Prakash and Rashid (1968) have demonstrated that humic substances exert stimulatory effect on marine dinoflagellates that is reflected in increased y·ield~ growth rate and carbon-14 uptake. However, they con- cluded that the positive effect of humic substances pn phytoplankton growth cannot be attributed entirely to chelation processes. Burk (1931) concluded that natural humic acid increases growth primarily, if not entirely, by virtue or the iron it contains. Barsdate and Matson (1966) state that an excess of a strong com- plexing agent like humic aci? would certainly alter the cycling of trace metals in aquatic systems. They also conclude that the avail- ability of the metals involved would be governed largely by ability of the organisms to assimilate the complex. Schnidler, et al. (1972), have stated that studies of naturally occurring organics in aquatic systems have not kept pace with their counterparts in soils and drawing parallels between the behavior of soil humics and aquatic humics is questionable. Significance of Iron Complexation in Natural Waters They conclude that more information on the chemical composition and behavior of this organic material, as well as the metal complexes, must be obtained for an understanding of the role of organic material in the metal transport process. APPENDIX B METHOD OF ISOLATION AND PURIFICATION OF HUMIC ACID 38 Method af Isolation and Purification of Humic Acid The method of extraction and purification used to obtain the stock solution of humic acid was one commonly used by hurnic acid chemists. The method consists of twenty-four hour exhaustive extl"actior:s of 100 g of sed'irnent \'lith O. 5 N NaOH and centri fugations at 800 X grav-ity for 20 min until the supernatant liquid obtained was colorless. The com- bined supernatant solutions are acidifted with concentrated hydrochloric acid to pH 2 and centrifuged at 800 X gravity for 20 rnin. The super- natant fulvic acid V✓as discarded and the precipitated humic acid re- dissolved in 0.5 N NaOH and reprecipitated with concentrated hydro- chloric acid at pH l. The solid humic acid was then redissolved in a minimum of 0.5 N NaOH. centrifuged at 20,000 X gravity in a Sorvall Superspeed RC 2-B for twenty minutes to remove clays and other inipurities and then dialyzed against distilled water for five days. The resulting soluble humic acid was centrifuged again at 20,000 X gravity and the humic acid concentration of the solution determined by drying aliquots of the solution at 100°C for 24 hrs in platinum crucibles. The remain- ing solution was diluted to a volume which was calculated from the humic acid· determinations to yield a 250 ppm humic acid stock solution. APPENDIX C THE ARTIFICIAL SEAWATER MEDIU 40 The Artificial Seawater Medium The artificial seawater solution was made by adding a sufficient amount of concentrated hydrochloric acid to dissolve 12.3 grams of magnesium metal and 10.l grams of calcium carbonate. Three hundred and fifty grams of A.C.S. Certified sodium chloride was added and the solution was adjusted to pH 8.0 with NaOH. The iron impurities in the reagents, now in the form of iron hydroxide, were removed by repeatedly filtering through a double layer of Whatman #42 filter paper in a porcelain Buchner funnel under suction and the filtrate was diluted to two liters with distilled water. This was used as the concentrated seawater solution in all the complexation experiments. BIBLIOGRAPHY OF THE COMPLETE THESIS BIBLIOGRAPH Barsdate, R. J. and Matsont W. R. (1966) Trace metals in Arctic and sub- Arctic lakes with reference to the organic ccmp]exes of metals. in RADIOECOLOGICAL CONCENTRATION PROCESSES, B. Alberg and F. Hungate, p. 711. Burk, D., Lineweaver~ H., Horner, C. K. and Allison, F. E. (1931) The relation between iron, humic acids and organic matter in the nutrition and stimulation of plant growth. Science, Vol. 74, p. 522. Chandler, R. F. (1939) Cation exchange capacity and exchangeable hydrogen. Journal of Agr. Res., Vol. 59, p. 491. Christman, R. F. (1968) Chemical structures of color producing organic substances in water. Symposium on Organic Matter in Natural Waters, College, Alaska, p. 181. Corcoran, E. F. (1967) Distribution of copper and iron in tropical sea- water. Proceedings of the International Conference on Tropical Oceanography, Vol. 5, p. 290. Drozdova, T. V. (1968) Role of humic acids in concentrating rare elements in soils. Soviet Soil Sci., Vol. 10, p. 1393. Duursma, ~- K. and Sevenhuysen, W. (1966) Note on chelation and solub:lity of certain metals in seavrnter at different pH values. Netherlands Journal of Sea Research, Vol. 3, No. 1 s p. 95. Farrington, J. vJ. and Quinn, J. G. (1973) Biogeochemistry of fatty acids in recent sediments from Narragansett Bay, Rhode Island. Geochim. Cosmochim. Acta, Vol. 37, p. 259. Hair, M. E. and Bassett, C. R. (1973) Dissolved and particulate humic acids in an East Coast estuary. Estuarine and Coastal Marine Science, Vol. l, p. 107. 4?. ,v Hall, E. S. and Pijckham, R. P. (1965) Coagulation of organic color with hydrolyzing coagulants. J. Am. W. W. Assn., Vol. 57, p. 1149. Johnston, R. (1964) Seawater, the natural medium of phytoplankton, II. The Artificial Seawater Medium Trace metals and chelation and general discussion. J. Mar. Biol. Assn U K Vol 44 p 87 Trace metals and chelation and general discussion. J. Mar. Biol. Assn., U.K., Vol. 44, p. 87. Kester, D. R. and Byrne, R.H., Jr. (1972) Chemical forms of iron in seawater. j..!}_ FERROMANGANESE DEPOSITS ON THE OCEAN FLOOR, David R. Horn, Palisades, New York, p. 107. Khan, S. U. (1969) Interaction between the humic acid fraction of soils and certain metallic cations. Soil Sci. Soc. Am. Proc., Vol. 33, No. 6, p. 851. Koshy, E., Desai, M. and Ganguly, A. (1969) Studies on organic-metallic interactions in the marine environment. Part I, Interaction of some metallic ions with dissolved organic substances in seawater. Current Science, Vol. 38, No. 23, p. 558. Laevastu, T. and Thompson, T. (1957) Soluble iron in coastal waters. J. of Mar. Res., Vol. 16, p. 192. J. of Mar. Res., Vol. 16, p. 192. Martin, D., Doig, M. T. and Pierce, R. H., Jr. (1971) Distribution of naturally occurring chelators (humic acid) and selected trace metals in some west coast Florida streams. University of South Florida Prof. Paper Series #12, p. 39. Ong, H. L. and Bisque, R. E. (1968) Coagulation of humic colloids by metal ions. Soil Sci., Vol. 106, p. 220. Peech, M., Alexander, L. T., Dear., L. A., Reed, J. F. (1947) Methods of soil analysis for soil fertility investigations. USDA Circ. No. 757, p. 25. 44 Pierce, R. H., Jr. and Felbeck, G. T., Jr. (1974) A comparison of three methods of extracting organic matter from soils and marine sediments. Proc. Netherlands Limnological Institute (in press). Prakash, A. and Rashid, M.A. (1968) Influence of humic substances on the growth of marine phytoplankton: dinoflagellates. Limnology and Oceanography, Vol. 13, p. 598. Rashid, R. (1971) Role of humic acids of marine origin and their different molecular weight fractions in complexing di- and tri- valent metals. Soil Sci., Vol. III, No. 5, p. 298. Rashid, R. (1972) Role of quinone groups in solubility and complexing of metals in sediments and soils. Chem. Geology, No. 9, p. 241. Rashid, R. and Leonard, J. D. (1973) Modification in the solubility and precipitation behavior of various metals as a result of their interaction with sedimentary humic acid. Chern. Geology, Vol. 2, No. 2, p. 89. Saunders, G. W. (1957) Interrelationships of dissolved organic matter and phytoplankton. Botanical Review, Vol. 23, p. 389. The Artificial Seawater Medium Schelske, C. L. (1962) Iron, organic matter and other factors limiting primary productivity in a Marl lake. Science, Vol. 136, p. 45. Schnidler F Alberts J J and Hornick K C (1972) A preliminary Schelske, C. L. (1962) Iron, organic matter and other factors limiting primary productivity in a Marl lake. Science, Vol. 136, p. 45. Schnidler, F., Alberts, J. J. and Hornick, K. C. (1972) A preliminary investigation of organic-inorganic associations in a stagnating system Limnologyand Oceanography Vol 17 p 952 primary productivity in a Marl lake. Science, Vol. 136, p. 45. Schnidler, F., Alberts, J. J. and Hornick, K. C. (1972) A preliminary investigation of organic-inorganic associations in a stagnating system. Limnology and Oceanography, Vol. 17, p. 952. Schnitzer, M. and Skinner, S.I.M. (1963) Organo-metallic interactions in soils: 1. Reactions between a number of metal ions and the organic matter of a podzol Bh horizon. Soil Sci., Vol. 96, No. 2, p. 86. Schnitzer, M. and Skinner, S.I.M. (1964) Organo-metallic interactions in Schnitzer, M. and Skinner, S.I.M. (1963) Organo-metallic interactions in soils: 1. Reactions between a number of metal ions and the organic matter of a podzol Bh horizon. Soil Sci., Vol. 96, No. 2, p. 86. Schnitzer, M. and Skinner, S.I.M. (1964) Organo-metallic interactions in 45 soils: 3. Properties of iron a.nd a1uminum-orga.nic matter complexes prepared in the laboratory and extracted from a soil. Soil Sci., Vol. 98, No. 3, p. 197. Schnitzer, M. and Skinner, S.I.M. (1965) Organo-metallic interactions in soi_.ls: 4. Carboxyl and hydroxyl groups in organic matter and meta·1 retention. Soil Sci., Voi. 99, No. 4, o. 278. --- ' Schnitzer, M. and Skinner, S.I.M. (1966) Organo-metallic interactions in soils: 5. Stability constants of Cu+2, Fe+2, and Zn+2 - fulvic acid complexes. Soil Sci., Vol. 102, No. 6, p. 361. Schnitzer, M. and Khan, S. V. (1972) .i!l HUMIC SUBSTANCES IN THE ENVIRON MENT, Marcel Dekker, Inc., New York, Chapter l, p. 1. Shapiro, J. (1964) Effect of yellow organic acids on iron and other metals in \l✓ater. J. Am. W.W. Assn., Vol. 56, p. 1062. Siegel, A. (1971) Metal-organic interactions in the marine environment . .i!l ORGANIC COMPOUNDS IN AQUATIC ENVIRONMENTS, Marcel Dekker: Inc.~ New York, Chapter 12, p. 265. Snedecor, G. W. and Cochran, W. G. (1968) Shortcut and non-parametric methods. ii}_ STATISTICAL METHODS, The Iowa State University Press, 6th ed., Ames, Iowa, Chapter 5, p. 120. Swanson, V. E. The Artificial Seawater Medium and Palacas, J. G. (1965) Humate in coastal sands of northwest Florida. U.S. Geol. Survey Bull., 1214B, p. Bl. Van Dijk, H. (1971) Cation binding of humic acids. Geoderma, Vol. 5, p. 53. Yuan, J. L. and Breland, H. L. (1969) Evaluation of atomic absorption methods fer determinations of Al, Fe and Si in clay and soil extracts. Soil Sci. Soc. Am. Proc., Vol. 33, No. 6, p. 851.
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Commentary on: “A Multi-Institutional Experience in Pediatric High Grade Glioma”
Frontiers in oncology
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Reviewed by: y Jason Fangusaro, Ann & Robert H. Lurie Children’s Hospital of Chicago and Feinberg School of Medicine, USA Mariko D. DeWire, Cincinnati Children’s Hospital Medical Center, USA Keywords: pediatric high-grade glioma, chemotherapy, pediatric cancer, radiotherapy, molecular target therapy chemotherapy, TMZ, has shown syner- gistic activity (7). Phase I or II stud- ies of small molecules that target spe- cific pathways or proteins in the cancer cells such as gefitinib (8), imatinib (9), cloretazine (10), tipifarnib (11), erlotinib (12), and nimotuzumab (13) disclosed no efficacy, despite occasional remarks of stable disease (1). Recently, fractionated schedules of drug administration using smaller doses than the maximum tolerated dose (metronomic schedules) have been reported that might enhance the antian- giogenic activity of some chemotherapeu- tic agents (14). Metronomic chemother- apy shows potential advantages in pediatric brain tumors treatment, including pri- mary effect on the host cells of the tumor microenvironment, the possibility of greater long-term efficacy and toler- ability than conventional cytotoxic ther- apy (14). dose of 54 Gy or the same radiotherapy with a combination of concomitant and maintenance chemotherapy. Patients ran- domized to receive chemotherapy were given weekly vincristine during radiation followed by eight maintenance chemother- apy cycles consisting of prednisone,lomus- tine, and vincristine (PCV) each given approximately 6 weeks apart (3). This important study showed that treatment with chemotherapy prolonged the survival and event-free survival. The Children’s Cancer Group (CCG) study-945 showed that children with HGG who underwent a surgical resection of 90% or greater had a PFS of 35 ± 7% as compared to a 5-year PFS of 17 ± 4% in patients who did not (4). The authors did not refer any benefit to the treatment of high- grade astrocytomas in children with eight- drugs in 1-day chemotherapy compared with CCNU, vincristine, and prednisone. Extent of tumor resection and histopatho- logic diagnosis were significant prognos- tic variables (4). The CCG-945 trial also looked at a variety of molecular and cytogenetic markers in an effort to bet- ter define prognostic variables in pedi- atric HGG. A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 Thismulti-institutionalretrospectivestudy evaluates the association of clinical, patho- logical, and treatment characteristics with their outcomes. Their results show total resection and receiving chemotherapy adjuvant to radiation or chemoradiation are most strongly related with improved progression-free survival (PFS) and over- all survival. For higher risk incom- pletely resected patients, temozolomide (TMZ) use and treatment intensification with concurrent chemoradiation, adjuvant chemotherapy, and higher radiation dose were associated with improved outcomes. It is a well written and conducted paper about a remarkable challenge to neuro- surgeon and pediatric oncologists. Little progress has been made in the outcome of these tumors in the last four decades. Outcome remains dismal with <20% of patients surviving (1). The degree of sur- gical resection is one of the most impor- tant clinical prognostic factors known in children with supratentorial high-grade gliomas (HGGs), independent of location, histology, and age as the authors show (2). In recent years, important advances in the comprehension of the molecular characteristics of HGG in pediatric age have been made. Initial genomic stud- ies of pediatric HGG disclosed signifi- cant differences compared to tumors from adult patients suggesting the existence of molecularly diverse subsets within pedi- atric cohorts. Data about the interactions between genetic alterations and changes in DNA methylation, histone modifications, chromatin remodeling, and gene expres- sion contribute to explain pathogenesis of malignant gliomas. Adult HGG are char- acterized by IDH1, PTEN, and/or EGFR aberrations; whereas pediatric HGG often harbors PDGFR amplification. PDGFR amplification or overexpression represents the most common abnormality of HGG Currently, the efficacy of chemothera- peutic compounds against pediatric brain tumors is unsatisfactory. Efficacy of TMZ has generally been found to be non- superior to other chemotherapeutic agents in pediatric HGG, and various stud- ies in children have shown no benefit over conventional treatment (5). Cilen- gitide was well tolerated in pediatric HGG, yet had modest anti-tumor activ- ity as a single agent (6). However, cilen- gitide in combination with radiation and Chemotherapy was first introduced into the treatment schema for children with newly diagnosed HGG in 1970s. Maria Caffo* Department of Neuroscience, School of Medicine, University of Messina, Messina, Italy *Correspondence: mcaffo@unime.it Edited by: André O. Von Bueren, University Medical Center Göttingen, Germany A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 IDH1 muta- tions at codon 132 strongly differentiate adult secondary from primary glioblas- toma, with frequencies of 85% compared with 5%. Paugh et al. sequenced IDH1 exon 4, containing codon 132, from 78 pediatric HGGs and 11 pediatric low-grade gliomas, and no codon 132 mutations were detected (15). 3. Sposto R, Ertel IJ, Jenkin RD, Boesel CP, Venes JL, Ortega JA, et al. The effectiveness of chemother- apy for treatment of high grade astrocytoma in children: results of a randomized trial. A report from the childrens cancer study Group. J Neuroon- col (1989) 7:165–77. doi:10.1007/BF00165101 concurrently with radiotherapy for children, ado- lescents,and young adults with high-grade glioma. Clin Cancer Res (2009) 15:701–7. doi:10.1158/ 1078-0432.CCR-08-1923 13. Cabanas R, Saurez G, Rios M, Alert J, Reyes A, Valdes J. Treatment of children with high grade glioma with nimotuzumab: a 5-year institutional experience. MAbs (2013) 5(2):202–7.doi:10.4161/ mabs.22970 4. Finlay JL, Boyett JM, Yates AJ, Wisoff JH, Milstein JM, Geyer JR, et al. Randomized phase III trial in childhood high-grade astrocytoma compar- ing vincristine, lomustine, and prednisone with the eight-drugs-in-1-day regimen. Childrens cancer group. J Clin Oncol (1995) 13(1):112–23. 14. Robison NJ, Campigotto F, Chi SN, Manley PE, Turner CD, Zimmerman MA, et al. A phase II trial of a multi-agentoral antiangiogenic (metronomic) regimen in children with recurrent or progressive cancer. Pediatr Blood Cancer (2014) 61:636–42. doi:10.1002/pbc.24794 5. Nicholson HS, Kretschmar CS, Krailo M, Bern- stein M, Kadota R, Fort D, et al. Phase 2 study of temozolomide in children and adolescents with recurrent central nervous system tumors: a report from the children’s oncology group. Cancer (2007) 110:1542–50. doi:10.1002/cncr.22961 15. Paugh BS, Qu C, Jones C, Liu Z, Adamowicz-Brice M,Zhang J,et al. Integrated molecular genetic pro- filing of pediatric high-grade gliomas reveals key differences with the adult disease. J Clin Oncol (2010) 28(18):3061–8. doi:10.1200/JCO.2009.26. 7252 6. MacDonald TJ, Vezina G, Stewart CF, Turner D, Pierson CR, Chen L, et al. Phase II study of cilen- gitide in the treatment of refractory or relapsed high-grade gliomas in children: a report from the children’s oncology group. Neuro Oncol (2013) 15(10):1438–44. doi:10.1093/neuonc/not058 16. Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature (2012) 482(7384):226–31. doi:10.1038/nature10833 7. Nabors LB, Mikkelsen T, Hegi ME, Ye X, Batch- elor T, Lesser G, et al. A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 One the first randomized study was CCG-943 trial, in which children with newly diag- nosed HGG were randomized to receive either focal radiation therapy alone to a April 2015 | Volume 5 | Article 88 | 1 www.frontiersin.org www.frontiersin.org Pediatric high grade gliomas Caffo in pediatric patients (15). BRAF and CDKN2A mutations have been reported to characterize HGG in a subset of pediatric patients, although BRAF abnormalities are not as frequently as described in childhood low-grade glioma (15). Schwartzentruber et al. reported in a large cohort of gliomas of various grades and histologies H3F3A mutations to be prevalent in children and young adults affected by malignant gliomas (16). Mutations of genes H3F3A and HIST1H3B are epigenetic and play a role in chromatin remodeling (17). Muta- tions in IDH1 or IDH2 are exceptional in pediatric patients but occur in the major- ity of adult patients with HGG. A study of pediatric primary HGG from the Chil- dren’s Oncology Group observed IDH1 mutations in 7 of 43 tumors. Remarkably, all of these IDH1 mutations occurred in children ≥14 years old, with none occur- ring in younger children. No IDH2 muta- tions were observed (18). IDH1 muta- tions at codon 132 strongly differentiate adult secondary from primary glioblas- toma, with frequencies of 85% compared with 5%. Paugh et al. sequenced IDH1 exon 4, containing codon 132, from 78 pediatric HGGs and 11 pediatric low-grade gliomas, and no codon 132 mutations were detected (15). in pediatric patients (15). BRAF and CDKN2A mutations have been reported to characterize HGG in a subset of pediatric patients, although BRAF abnormalities are not as frequently as described in childhood low-grade glioma (15). Schwartzentruber et al. reported in a large cohort of gliomas of various grades and histologies H3F3A mutations to be prevalent in children and young adults affected by malignant gliomas (16). Mutations of genes H3F3A and HIST1H3B are epigenetic and play a role in chromatin remodeling (17). Muta- tions in IDH1 or IDH2 are exceptional in pediatric patients but occur in the major- ity of adult patients with HGG. A study of pediatric primary HGG from the Chil- dren’s Oncology Group observed IDH1 mutations in 7 of 43 tumors. Remarkably, all of these IDH1 mutations occurred in children ≥14 years old, with none occur- ring in younger children. No IDH2 muta- tions were observed (18). A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 Citation: Caffo M (2015) Commentary on: “A multi- institutional experience in pediatric high grade glioma”. Front. Oncol. 5:88. doi: 10.3389/fonc.2015.00088 11. Fouladi M, Nicholson HS, Zhou T, Laningham F, Helton KJ, Holmes E, et al. A phase II study of the farnesyl transferase inhibitor, tipifarnib, in children with recurrent or progressive high-grade glioma,medulloblastoma/primitive neuroectoder- maltumor,orbrainstemglioma:achildren’soncol- ogy group study. Cancer (2007) 110:2535–41. doi: 10.1002/cncr.23078 This article was submitted to Neuro-Oncology, a section of the journal Frontiers in Oncology. A multi-institutional experience in pedi- atric high-grade glioma by Walston S, Hamstra DA, Oh K, Woods G, Guiou M, Olshefski RS, et al. Front Oncol (2015) 5:28. doi: 10.3389/fonc.2015.00028 A safety run-in and ran- domized phase 2 study of cilengitide combined with chemoradiation for newly diagnosed glioblas- toma (NABTT 0306). Cancer (2012) 118:5601–7. doi:10.1002/cncr.27585 17. Sturm D, Bender S, Jones DT, Lichter P, Grill J, Becher O, et al. Paediatric and adult glioblas- toma: multiform (epi)genomic culprits emerge. Nat Rev Cancer (2014) 14(2):92–107. doi:10.1038/ nrc3655 18. Pollack IF, Hamilton RL, Sobol RW, Nikiforova MN, Lyons-Weiler MA, LaFramboise WA, et al. IDH1 mutations are common in malignant gliomas arising in adolescents: a report from the children’s oncology group. Childs Nerv Syst (2011) 27:87–94. doi:10.1007/s00381-010-1264-1 8. Geyer JR, Stewart CF, Kocak M, Broniscer A, Phillips P, Douglas JG, et al. A phase I and biol- ogy study of gefitinib and radiation in children with newly diagnosed brain stem gliomas or supra- tentorial malignant gliomas. Eur J Cancer (2010) 46:3287–93. doi:10.1016/j.ejca.2010.07.005 j j 9. Pollack IF, Jakacki RI, Blaney SM, Hancock ML, Kieran MW, Phillips P, et al. Phase I trial of ima- tinib in children with newly diagnosed brain- stem and recurrent malignant gliomas: a pediatric brain tumor consortium report. Neuro Oncol (2007) 9:145–60. doi:10.1215/15228517-2006-031 10. Gururangan S, Turner CD, Stewart CF, O’Shaughnessy M, Kocak M. Phase I trial of VNP40101M (cloretazine) in children with recur- rent brain tumors: a pediatric brain tumor consor- tium study. Clin Cancer Res (2008) 14(4):1124–30. doi:10.1158/1078-0432.CCR-07-4242 9. Pollack IF, Jakacki RI, Blaney SM, Hancock ML, Kieran MW, Phillips P, et al. Phase I trial of ima- tinib in children with newly diagnosed brain- stem and recurrent malignant gliomas: a pediatric brain tumor consortium report. Neuro Oncol (2007) 9:145–60. doi:10.1215/15228517-2006-031 The recent genomic groundbreaking work added tremendously to our under- standing of the mutational landscape of pediatric HGG, bringing to light new, potentially targetable pathways, and promise of more effective therapies. In light of these observations, new trials and emerging data about pediatric HGG could improve the outcome of HGG in children and young adults. Conflict of Interest Statement: The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 10. Gururangan S, Turner CD, Stewart CF, O’Shaughnessy M, Kocak M. Phase I trial of VNP40101M (cloretazine) in children with recur- rent brain tumors: a pediatric brain tumor consor- tium study. Clin Cancer Res (2008) 14(4):1124–30. doi:10.1158/1078-0432.CCR-07-4242 Received: 05 February 2015; accepted: 24 March 2015; published online: 08 April 2015. Received: 05 February 2015; accepted: 24 March 2015; published online: 08 April 2015. Citation: Caffo M (2015) Commentary on: “A multi- institutional experience in pediatric high grade glioma”. Front. Oncol. 5:88. doi: 10.3389/fonc.2015.00088 This article was submitted to Neuro-Oncology, a section of the journal Frontiers in Oncology. Copyright © 2015 Caffo. 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. Copyright © 2015 Caffo. 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. REFERENCES Copyright © 2015 Caffo. 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. 1. MacDonald TJ, Aguilera D, Kramm CM. Treat- ment of high-grade glioma in children and ado- lescents. Neuro Oncol (2011) 13:1049–58. doi:10. 1093/neuonc/nor092 2. Adamski J, Tabori U, Bouffet E. Advances in the management of paediatric high-grade glioma. Curr Oncol Rep (2014) 16:414. doi:10.1007/ s11912-014-0414-0 12. Broniscer A, Baker SJ, Stewart CF, Merchant TE, Laningham FH, Schaiquevich P, et al. Phase I and pharmacokinetic studies of erlotinib administered April 2015 | Volume 5 | Article 88 | 2 Frontiers in Oncology | Neuro-Oncology
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Deployment of a Distributed Multi-Agent Architecture for Transformable Assembly
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To cite this version: Jack C. Chaplin, Svetan Ratchev. Deployment of a Distributed Multi-Agent Architecture for Trans- formable Assembly. 8th International Precision Assembly Seminar (IPAS), Jan 2018, Chamonix, France. pp.15-28, ￿10.1007/978-3-030-05931-6_2￿. ￿hal-02115843￿ Deployment of a Distributed Multi-Agent Architecture for Transformable Assembly Jack C. Chaplin, Svetan Ratchev To cite this version: Jack C. Chaplin, Svetan Ratchev. Deployment of a Distributed Multi-Agent Architecture for Trans- formable Assembly. 8th International Precision Assembly Seminar (IPAS), Jan 2018, Chamonix, France. pp.15-28, ￿10.1007/978-3-030-05931-6_2￿. ￿hal-02115843￿ Jack C. Chaplin, Svetan Ratchev. Deployment of a Distributed Multi-Agent Architecture for Trans- formable Assembly. 8th International Precision Assembly Seminar (IPAS), Jan 2018, Chamonix, France. pp.15-28, ￿10.1007/978-3-030-05931-6_2￿. ￿hal-02115843￿ Distributed under a Creative Commons Attribution 4.0 International License Deployment of a Distributed Multi-Agent Architecture for Transformable Assembly Jack C Chaplin1[0000-0003-3282-2386] and Svetan Ratchev1[0000-0001-9955-2806] 1 Institute for Advanced Manufacturing, Advanced Manufacturing Building, Jubilee Campus, University of Nottingham, UK, NG7 2GX. jack.chaplin@nottingham.ac.uk Abstract. Industry 4.0 represents a new philosophy in manufacturing systems, based on networked, intelligent, and cooperative resources. This revolution is necessary to make the cost-effective production of batch-size-of-one customised items in high-value manufacturing domains such as aerospace a reality. However, there exist large numbers of legacy production cells which generate value for enterprises which would ideally become part of a future manufacturing system, but which lack the necessary computational or networking capabilities. This is especially important in the case of small to medium enterprises, where Industry 4.0 is perceived as an expensive endeavour out of reach due to cost. There is a requirement for Industry 4.0 to be brought to existing legacy production cells in a cost effective and standards-compliant manner. This paper describes the tech- nical implementation of an Evolvable Assembly Systems deployment onto an existing legacy manufacturing cell, describing the concepts and technical specif- ics of how to interface a software-based multi-agent system with real manufac- turing hardware, and demonstrates how it is possible to make a transformable manufacturing cell which is compliant to the Industry 4.0 ideals in a cost-effec- tive and expedient manner. Keywords: Industry 4.0, Evolvable Assembly Systems, Smart Manufacturing Keywords: Industry 4.0, Evolvable Assembly Systems, Smart Manufacturing HAL Id: hal-02115843 https://inria.hal.science/hal-02115843v1 Submitted on 30 Apr 2019 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 1 Introduction Higher product complexity in terms of physically complex designs and assemblies with stringent tolerance requirements, demand for customer-unique customisation, and increasingly smart products with bespoke software installed at assembly-time is a sig- nificant challenge for modern and future manufacturing. Exacerbating this situation, products are changing to meet customer demands increasingly quickly, reducing the time available to develop an assembly process for a product [1]. There are numerous national and international initiatives to address the challenges of managing the data generated by such complex manufacturing processes, so more effective decisions can be made quicker. These include Industry 4.0 [2] and the Industry 4.0 reference architecture RAMI4.0 [3], and the Industrial Internet Consortium and their Industrial Internet Reference Architecture (IIRA) [4]. 2 There is a need for distributed intelligent control that can mitigate the exponential rise in the number of communication interconnections between increasing numbers of networked manufacturing resources and sensors, which would enable production lines to be agile in response to new product variants and robust to system failure. In addition, with individually customised products becoming increasingly important in the manufacturing economies of high-technology, high-wage cost regions, there is a requirement to track and log data associated with every single product created, to ensure full traceability when a product has been assembled with a unique assembly strategy. This is particularly important in highly regulated domains such as aerospace, pharma- ceuticals, and construction. Many modern production systems utilise Programmable Logic Controllers (PLCs) to control manufacturing resources, and which possess the ability to exchange and pro- cess information. However, these can often only communicate via vendor-specific pro- tocols, and program execution may be constrained to IEC 61131-3 programming lan- guages [5], limiting the opportunity for more complex algorithms. In addition, many legacy production resources still provide value to their operators, but these may lack any computational capacity or utilise obsolete communication methods if they possess any communication methods at all. It is important that the fourth industrial revolution does not pass over small to medium enterprises (SMEs), who may have higher propor- tions of legacy equipment because they cannot afford to purchase expensive new re- sources or controllers, or lack the time and expertise to invest in manufacturing digiti- sation [6]. Hence, a solution must be found to include legacy resources in any smart manufacturing system in a homogeneous, simple, and low-cost way. 2 Scenario and Current Limitations To demonstrate the approach described in this paper, we present a scenario using aerospace components on a robotic assembly cell. The cell forms part of a larger as- sembly line – the Future Automated Aerospace Assembly Demonstrator (FA3D) – and prepares rib components for inclusion in a wing or fuselage assembly by applying seal- ant and/or scanning the part with a line scanner to check part accuracy and the quality of the sealant application. This cell has two primary challenges that must be met for which the current control method is inadequate. The first challenge is that the FA3D assembles batch-size-of-one products, where every item being assembled is unique and must be treated differently. The larger assembly line is required to produce aircraft components for high-complex- ity, highly-customisable, and low-volume airframes while keeping costs low, and as such each assembled airframe can be considered to be unique. Additionally, the high precisions required of the final assembly require every part to be analysed for deviations from specification, and the assembly process altered to compensate. As a result, seem- ingly identical components being handled in the cell must be identifiable and able to be treated differently as the quality of supply varies. y y y The second primary challenge for the cell is the logging of data. In highly regulated industries such as aerospace, pharmaceuticals, or construction, logging data is essential for tracing the root causes of problems, analysing data to identify problems before they occur, and providing accountability for failures. This is especially important for batch- size-of-one manufacturing, where every product is assembled in a unique manner which may be determined automatically by intelligent manufacturing systems. The data must be interrogable to understand why decisions were made in the event of failure, and to understand the behaviour of the system over time. The demonstration cell operates on rib components for aerospace assemblies. The ribs are placed in pallets, which can then be moved around the cell. The cell utilises two ABB IRB6700-150-320 robotic arms to perform operations on the rib components. The robots are set-up in a master-slave configuration, with a single Siemens S7 1513- 1 PN PLC controlling both. Each robot has a separate tool changing rack. The master robot has access to a proxy sealant applicator (to facilitate testing), and a Micro Epsilon scanCONTROL compact 2900-50/BL laser line scanner. 1 Introduction This requirement for an open, accessible, and low-cost solution to the digitalisation of manufacturing processes would enable the implementation of system-wide intelli- gence, and a strategy for sharing system-generated data to allow companies to partici- pate in the fourth industrial revolution. The system must facilitate the dynamic checking of the manufacturability of new products to ensure the system can keep up with the increasing pace of product change, and facilitate transformable manufacturing cells able to evolve to match changing product requirements. Information on the manufac- turing process must be logged to ensure traceability of product data. There are existing architectures for distributed system-wide intelligence that tackle the above problems based on multi-agent systems [7-9]. These include the Product- Resource-Order-Staff Architecture (PROSA) [10], the Adaptive Holonic Control Ar- chitecture for Distributed Manufacturing Systems (ADACOR) [11], and Evolvable As- sembly Systems (EAS) [12]. However, how these software architectures are actually deployed on to existing legacy manufacturing lines remains an open challenge. This paper details the implementation of a technical solution for deploying a distrib- uted multi-agent manufacturing intelligence architecture (specifically Evolvable As- sembly Systems) on to an existing legacy robotic manufacturing cell which lacks in- herent Industry 4.0 features. It does this in a standards-compliant, low-cost way which would be applicable to SMEs which want to take advantage of Industry 4.0 principles, but cannot risk the high expenditure required to replace existing production cells. 3 2 Scenario and Current Limitations The slave robot has access to a bespoke pallet gripper and a bespoke rib gripper, allowing it to pick up pallets or pick ribs out of pallets. To one side is a storage rack, where pallets with or without ribs can be stored and retrieved. The cell has a loading / unloading area for loading pallets and ribs onto a conveyor system. Loaded pallets move into the slave robot’s working area, allowing the pallet or rib to be picked up. The conveyor system is to be expanded to allow complete ribs in pallets to be dispatched to the second cell to be assembled in a larger aerospace assem- bly. The conveyor system is controlled by a Siemens SIMATIC ET 200SP Open Con- troller with software-based PLC functionality. 4 Fig. 1. (Top) Schematic layout of the demonstrator cell. (Bottom) View of the cell from in front of the storage rack, showing the two robots. Fig. 1. (Top) Schematic layout of the demonstrator cell. (Bottom) View of the cell from in front of the storage rack, showing the two robots. The cell in its current state has several technical limitations. With the expansion to the conveyor system planned to link the cell to the wider FA3D production line, these limitations must be overcome if the cell is able to contribute to high-precision, batch- size-of-one products. The first limitation is that the demonstration cell has no networking between its com- ponents; the PLCs for the robots and for the conveyor system are not connected, and instead rely on user interfaces with which a worker can execute several pre-specified actions manually. The second limitation is that it does not have any system-wide control that allows for automated production of parts. For batch-size-of-one products, this approach is in- sufficient as the worker must understand the production plan for a potentially complex 5 part sufficiently to correctly pick the order of operations, as well as to know when to perform any manual operations such as loading / unloading parts. Additionally, with no networking, the system cannot communicate with the wider production line, which is a significant problem if this cell is to be integrated with the FA3D. The third limitation is that data collected by the system is transitory and not stored, which does not allow for retrospective analysis of cell performance or identification of errors. 2 Scenario and Current Limitations Additionally, data generated by the laser line scanner is saved as a file, which must then be manually transferred to the FA3D via USB drive. To remove this manual step, it would be preferable for data to be transferred automatically to the appropriate resources. The fourth limitation is that the actions which can be performed by the robots and the conveyor system are fixed. The commissioning of the cell included programming the PLCs and specifying the actions performable by the robots, and changing these risks violating the safety certification of the cell necessary to have the cell open for manual worker access. 3 Enabling Technologies for Low-Cost Industry 4.0 Implementation To address these limitations and upgrade the cell, we propose the use of technologies which directly tackle the issues of networking, system-wide intelligence, and data log- ging, and also mitigate the issue of fixed actions which are inherent to including legacy production cells into Industry 4.0-compliant manufacturing lines. These technologies and approaches are discussed here. 3.1 Data Distribution Services Increasing the number of devices within manufacturing production lines, combined with a requirement for devices to talk to other devices in the line requires an exponential number of interconnects. Though service-orientated architectures are an improvement on existing point-to-point solutions, this still requires a client / server relationship. In- stead, the approach taken by the Industrial Internet Consortium [4] to decouple indus- trial manufacturing as much as possible is the use of Data Distribution Services (DDS) [13], which is a standard administered by the Object Management Group (OMG). DDS is a networking middleware designed to decouple the origins and consumers of data within a specified domain. Nodes in the DDS that produce data are called pub- lishers, and publish pieces of information (called samples) to topics. A publisher can publish data without needing to know what (if any) nodes will consume this data. Nodes which consume data are called subscribers, and subscribe to topics to receive samples published there. Similarly, a subscriber can subscribe to topics without needing to know the origin node of the data. The result is a data-driven communication system, where the most important element – the data – drives the operation of the manufacturing system. Nodes in the system do 6 6 not communicate directly, but instead form a shared system context where a single ca- nonical view of the state of the system is distributed between the nodes, and from which nodes can selectively subscribe to information relevant to them. The lack of a communication broker, or direct interconnects between resources in the system serves two important roles in the context of a manufacturing system. Firstly, there is no single point of failure and data is replicated by the middleware between nodes (in most DDS implementations), leaving a robust system that can continue exe- cution even if nodes fail. Secondly, with no explicit network structure, the system can be reconfigured and nodes added or removed without having to alter the networking configuration. Additionally, if the networking uses wireless methods (as with this demonstration), there is no requirement to alter the physical networking infrastructure either. 3.2 Embedded Computers With a data-driven approach, there is no direct communication between resources in the manufacturing system. As a result, there is no single orchestrator that instructs each resource as to what to do and when to do it, in contrast to traditional monolithic archi- tecture. Instead, each resource must be smart enough to analyse the state of the system in the shared system context and make decisions as to what to do. For this, every re- source in the system requires a degree of computing power, which is not something that can be assumed for legacy systems. Neither can it be assumed that resources with com- puting abilities (such as those with Programmable Logic Controllers) are provided as open by their vendors and hence capable of running the necessary decision making algorithms or DDS implementation. To solve this problem, the approach given here uses embedded computers to handle decision making and communication, as this allows for the execution of general-pur- pose code and use of communication standards which might not otherwise by available. This approach removes vendor-specific implementation considerations at the earliest possible stage, and transforms all control and information into homogeneous and open methods. This does require an interface between the embedded computer and the re- source controller, which may be a modern PLC with interface APIs, a legacy controller with no consideration for external interfacing, or a human worker which will require a smart or wearable device to communicate information. Embedded computers also provide local data storage capacity, and the ability to con- nect to larger capacity database, enabling the storage of large quantities of operational data that would otherwise be lost, which could be pre-processed and analysed at the edges of the system to extract events and filter out unneeded data. Combined with the data distribution services, the use of embedded computer solves the challenges of networking and lost data. However, the challenges of system-level intelligence and fixed actions remain. To solve this limitation, we utilise intelligent agents. 7 3.3 Intelligent Agents Each module in an Industry 4.0 enabled cell requires localised intelligence to make decisions, be context aware, and share information with the rest of the production line. These intelligences represent the production resources which carry out operations on parts in line with their capabilities. To implement localised intelligence, we utilise Belief-Desire-Intention (BDI) [14, 15] intelligent agents (or simply ‘agents’) [7-9] which are independent, self-contained software entities which use the BDI model of planning, allowing a decoupling of the agent’s perceptions of the world, the selection of plans, and the execution of plans. These agents execute on the embedded computers, and are the interface with the wider production line, publishing and subscribing to the shared system context, and making decisions based on the state of the cell as to when to execute capabilities. Upon these agents, we implement the Evolvable Assembly Systems architecture. 4 Technical Implementation of Evolvable Assembly Systems The three key technologies of DDS, embedded computers, and intelligent agents can be used together to create an implementation of a smart Industry 4.0-compatible man- ufacturing system. Combined with the data distribution services, the use of embedded computers solves the challenges of networking and lost data. However, the challenge of system-wide intelligence remains despite the use of intelligent agents – agents are a general purpose solution and not tailored to manufacturing cells. To solve this chal- lenge, we employ Evolvable Assembly Systems. g y y y Evolvable Assembly Systems [7, 8] is a manufacturing paradigm defining transform- able, responsive production lines for effectively producing low-volume products. It fo- cuses on the use of multiple independent and modular components to allow for rapidly reconfigurable and transformable production cells. The use of intelligent agents to ex- ecute the Evolvable Assembly System paradigm to make decisions as to what actions to perform based on the state of the system as per the shared system context satisfies the requirement for system-wide intelligence, as this enables batch-size-of-one produc- tion where each step in manufacturing is defined in a recipe. Our software implemen- tation of EAS is detailed in [12, 16], and utilises agents to implement distributed intel- ligence in manufacturing systems, the automated checking of the manufacturability of submitted batch-size-of-one product recipes against the capabilities of a production cell or line, and allocation of requirements to manufacturing resources. However, the tech- nical challenges remain of how the agents are deployed, and how the determined re- quirements are automatically executed on manufacturing resources. This is solved with the approach detailed in this section, resulting in a functional demonstrator of an Evolv- able Assembly systems deployment. 4.1 Embedded Computers and Smart Devices To implement our approach, we used embedded computers. A wide variety of em- bedded computers are available, ranging from the basic Raspberry Pi Zero W [17], to 8 more fully featured products such as the Siemens SIMATIC IOT2000 Intelligent Gate- way series [18]. The exact model used will depend on the interface requirements with the resource controller. As our implementation is hardware agnostic, a mixture of em- bedded computer models could be used. In our case, the Siemens SIMATIC S7 1513-1 PN PLC and SIMATIC ET 200SP Open Controller offer interfacing via Ethernet connections, so any embedded computer would require an Ethernet port. Our code, including BDI agents, networking middle- ware, and manufacturability analysis implementation described in [16], is implemented in Java so any model chosen must support this. Communication via the data-centric shared system context between nodes is also required. As the demonstrator used in this example is not physically reconfigurable, wireless networking has less merit than in other more modular reconfigurable demonstrators such as those presented in [12, 16]. However, wireless communication is important when a human worker is involved in the process as with this demonstrator, as the human will be mobile and utilising a smart device to interface with the system. Additionally, there are few models of embedded computer with two Ethernet ports (as one is required to connect to the PLC), and so wireless networking was determined as preferential over wired technologies. To satisfy these requirements, we selected one of the most widely available single- board computers to use as our standard model of embedded computer – the Raspberry Pi 3 Model B [19]. The Raspberry Pi is globally available, low cost, open, and flexible, and features all the connectivity we require, including in-built wireless connectivity. It is powered via a micro-USB 2.5A power source. Though more computationally powerful or more fully featured single board comput- ers exist, the Raspberry Pi is useful as a baseline for demonstrating this approach, as a successful implementation on a Raspberry Pi would also function on other more pow- erful and more expensive models. These embedded computers enable the execution of intelligent agents which communicate and cooperate, giving the demonstration cell sys- tem-wide intelligence and context awareness as required. Human workers in the production line also require interfacing to the wider system intelligence. This is achieved through the use of mobile smart devices. 4.2 Interfaces with Resources The intelligent agents executing on the embedded computers and smart devices re- quire interfaces with the resources (or human workers), enabling the requesting of ca- pability instantiation and collection of data. This approach suggests use of service-orientated architecture such as OPC Unified Architecture [20] where the resource advertises services (i.e. the instantiation of capa- bilities) and the embedded computer acts as the client to select these. However, retro- fitting these capabilities into existing production lines (such as this demonstration cell) does not necessarily allow for such idealised solutions. PLC code may have been tested and proven correct for years prior to the decision being made to include Industry 4.0 technologies, and stakeholders may not want to risk sweeping changes to PLC execu- tion. Additionally, some legacy resources may not be able to execute OPC UA (or sim- ilar) at all. An alternative solution must be found. As the demonstration cell was designed to be used manually, the PLCs to control the robots and to control the conveyor system both have user interfaces by which a worker can instantiate capabilities by pressing virtual buttons on a touch screen interface. Though not designed with service-orientation in mind, a user interface essentially al- lows the resource to advertise capabilities in the form of buttons or other UI elements, and to receive requests from a client in the form of button presses. To leverage this indirect service orientation, the embedded computers must be able to simulate a button press on the user interface, which enables automated execution of PLC code without modifying the PLC code itself. The precise manner in which this is achieved will necessarily vary depending on the user interface and vendor in question. Presented here is the method used for both the Siemens SIMATIC S7 1513-1 PN PLC and SIMATIC ET 200SP Open Controller used for the robots and conveyor system respectively. User interfaces for Siemens PLCs are created using SIMATIC WinCC [21]. This executes on the PLC, but in a separate memory space to the main PLC code. Buttons are created and have actions associated with them when the button is pressed; the gen- eral pattern is for a bit in memory to be set when the button is depressed and reset when the button is released. Code in the PLC checks the state of the bit associated with the button and performs actions if the bit is set. 4.1 Embedded Computers and Smart Devices For now, we utilise Lenovo X260 Ultrabooks, though future work will include the deployment of the interfaces to low-cost tablet computers. Fig. 2. A legacy production resource can be considered to be advertising its capabilities via a user interface. A smart manufacturing system such as an Evolvable Assembly System wishes to instantiate these capabilities. But how can the intelligent agents actually interface with the re- source? Fig. 2. A legacy production resource can be considered to be advertising its capabilities via a user interface. A smart manufacturing system such as an Evolvable Assembly System wishes to instantiate these capabilities. But how can the intelligent agents actually interface with the re- source? 9 4.2 Interfaces with Resources Despite both the S7 and Open Controller PLCs having different internal architectures, they both follow this pattern (with minor deviations as both were commissioned by different organisations). S7Connector is an open source Java library for interfacing with S7 PLCs via Ethernet [22]. As the ET 200SP is based on an S7-1500 CPU, both PLCs are compatible with this approach. It allows for reading and writing values to the memory of the PLC via a Java program executing on a connected device. This permits the connected device to alter the bit that is set by pressing a button on the user interface, simulating a button press. One limitation of this approach is that it requires knowledge of the memory location of the bit connected to the button on the user interface, which in turn means access to the original project files for the PLC. Interfacing with a user interface via an embedded computer without access to the source for the PLC program would be challenging, and 10 other solutions may be required, such as having the resource embedded computer using its own interface on a smart device to instruct a worker to press the required button. With the same approach, any data made available to the user interface (resource sta- tus or data generated by the line scanner for example) can be retrieved in the same manner by reading the variable which controls the UI element display. This allows the embedded computer to know what the attached resource is doing, and read (and option- ally publish) data it generates. Human workers are also perceived in Evolvable Assembly Systems as manufactur- ing resources, and hence require an interface between the smart device on which code executes and the worker themselves. This takes the form of a user interface, instructing the operator what tasks to perform at a given time, and offering the user the ability to specify the completion of work. Fig. 3. The communication stack for an agent to execute a capability on a resource, using the example of the master/slave robots. Fig. 3. The communication stack for an agent to execute a capability on a resource, using the example of the master/slave robots. Fig. 4. (Left) A Raspberry Pi 3 Model B is networked to the conveyor PLC. (Right) A worker is instructed to load a pallet onto the conveyor system by the worker resource interface. Fig. 4. 4.2 Interfaces with Resources (Left) A Raspberry Pi 3 Model B is networked to the conveyor PLC. (Right) A worker is instructed to load a pallet onto the conveyor system by the worker resource interface. 4.3 Networking and Data Collection Networking resources in the production cell allows for data to be published and sub- scribed to via DDS and the shared system context. As the Raspberry Pi 3 Model Bs and 11 Lenovo X260s feature built-in Wi-Fi, and as the Raspberry Pi Ethernet ports are used to interface with the PLCs, a wireless network was created using a TP-LINK TD- W8970 router. The wireless networking allows for the mobility of the human workers with laptops (and later, tablets or other smart devices), and simplifies system reconfig- uration. To operate using a data-centric model, we use DDS. For this implementation, we use RTI’s Connext DDS Professional [23], which is a fully featured and compliant implementation of the OMG DDS standard [13]. It has Java libraries and native support for Raspberry Pi single board computers. With advances in data storage and data-centric manufacturing systems, it’s now pos- sible to store all data on a product being assembled, including a digital ‘black box’ of why decisions were made, to facilitate the tracing of errors and verification of system behaviour. We call this ProductDNA, and it includes all data generated by the involved resources, any metrology data produced including environmental data, tolerances and deviations, and system decisions made and the reasons why. To achieve this, an additional ProductDNA agent is added to the manufacturing cell, executing on a Dell Precision 7510 laptop. This agent, like other agents in an Evolvable Assembly System, can subscribe to topics to receive data. To gather all pos- sible data, it subscribes to all topics available using Connext DDS’ discovery service, and saves every sample to file (organised by topic) for future analysis. Fig. 5. Use of data in the solution. The agent (on the embedded computer) is able to retrieve in- formation about the resource provided that information is presented on the resource user inter- face. This is shared (with optional pre-processing) to the shared system context, where other agents in the system can select what information they require to make optimum decisions. All data is stored by the ProductDNA agent. Fig. 5. Use of data in the solution. The agent (on the embedded computer) is able to retrieve in- formation about the resource provided that information is presented on the resource user inter- face. 4.3 Networking and Data Collection This is shared (with optional pre-processing) to the shared system context, where other agents in the system can select what information they require to make optimum decisions. All data is stored by the ProductDNA agent. 12 4.4 Agents Each resource in the system is controlled by an intelligent agent running on the em- bedded computer or smart device. We programmed agents in Java using the Java Agent Development Framework (JADE) [24, 25] which is an open source and flexible agent framework. On top of this, a BDI framework [15] was developed by which the agents reason about the demonstration cell. The use of BDI agents has several advantages in this context. Firstly, there are strong synergies between the concept of beliefs and the use of a belief set in the BDI model, and of the use of data-centric communication, as the belief set of an agent is a subset of the shared system context representing the entire system, and the beliefs can be updated as the shared system context changes. Secondly, the BDI model decouples the storage of beliefs and the development of plans, from the execution of plans. As each agent may have a unique interface with its resource (or it may be a user interface in the case of a human worker), this simplifies the insertion of bespoke code whilst the rest of the code base remains homogenous. The method by which the agents analyse recipes and determine how to execute ca- pabilities to create a unique batch-size-of-one product is detailed in [16]. Users are able to submit recipes to the production line via an interface also running on the Dell laptop, which submits the recipe to the shared system context where the agents will check man- ufacturability and assign tasks. 5 Conclusions This paper has presented a technical method for implementing Industry 4.0 and Evolvable Assembly Systems concepts on pre-existing legacy manufacturing cells, uti- lising data-centric communication, and intelligent agents executing on embedded com- puters which interface with their respective manufacturing resources. This method al- lows for a cost-effective manner in which smart manufacturing could be achieved by SMEs looking to include their production cells in the fourth industrial revolution. One limitation of this approach is in not solving the issue of fixed actions. The use of capability topologies [10] helps mitigate the restriction of fixed actions, though does not solve the problem. The issue is inherent to the design of manufacturing cells, and in particular those not designed with maximum flexibility in mind. Moving forwards, we aim to implement the user interfaces for human workers on smart devices such as tablet computers or smart watches, to make receiving and auc- tioning instructions, as well as relaying information back to the shared system context simpler. The entire demonstration cell will be integrated with the wider FA3D cell, during which the implementation will be extended to include the entire manufacturing cell, including challenges relating to interfacing with the more complex control system of the FA3D. We will also use additional models of embedded computer, including the Siemens IOT2000 [18] to experiment with system heterogeneity. 13 6 Acknowledgements The reported research has been funded by the EPSRC grant EP/K018205/1, the sup- port of which is gratefully acknowledged. We would also like to thank RTI for provid- ing a license for Connext DDS Professional as part of their University Program. 7 References 1. Rhodes, C., Manufacturing: statistics and policy. House of Commons Library, 2014. 13. 2. Kagermann, H., et al., Recommendations for Implementing the strategic initiative INDUSTRIE 4.0: securing the future of German manufacturing industry; final report of the Industrie 4.0 working group. 2013: Forschungsunion. 3. Adolphs, P., et al., Reference architecture model industrie 4.0 (rami4. 0). VDI/VDE Society Measurement and Automatic Control (GMA), 2015. 4. Shi-Wan Lin, B.M., Jacques Durand, Graham Bleakley, Amine Chigani, Robert Martin), Brett Murphy, and Mark Crawford, The Industrial Internet of Things Volume G1: Reference Architecture. 2017, Industrial Internet Consortium. 5. International Electrotechnical Commission, IEC 61131-3:2013 in Programmable controllers - Part 3: Programming languages. 2013. 6. 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IFAC-PapersOnLine, 2015. 48(3): p. 2065-2070. 13. Object Management Group Inc. Data Distribution Service (DDS) Version 1.4. 2015 [cited 12th November 2017]; Available from: http://www.omg.org/spec/DDS/1.4/. 14. Faccin, J. and I. Nunes. Modelling and Reasoning about Remediation Actions in BDI Agents. in Proceedings of the 16th Conference on Autonomous Agents and MultiAgent Systems. 2017. International Foundation for Autonomous Agents and Multiagent Systems. 15 Rao A S and M P Georgeff BDI agents: From theory to practice in ICMAS 1995 1. Rhodes, C., Manufacturing: statistics and policy. House of Commons Library, 2014. 13. 2. Kagermann, H., et al., Recommendations for Implementing the strategic initiative INDUSTRIE 4.0: securing the future of German manufacturing industry; final report of the Industrie 4.0 working group. 2013: Forschungsunion. the Industrie 4.0 working group. 2013: Forschungsunion. 3. Adolphs, P., et al., Reference architecture model industrie 4.0 (rami4. 0). VDI/VDE Society Measurement and Automatic Control (GMA), 2015. 4. 15. Rao, A.S. and M.P. Georgeff. BDI agents: From theory to practice. in ICMAS. 1995. 7 References Shi-Wan Lin, B.M., Jacques Durand, Graham Bleakley, Amine Chigani, Robert Martin), Brett Murphy, and Mark Crawford, The Industrial Internet of Things Volume G1: Reference Architecture. 2017, Industrial Internet Consortium. 5. International Electrotechnical Commission, IEC 61131-3:2013 in Programmable controllers - Part 3: Programming languages. 2013. 6. Sommer, L., Industrial revolution-industry 4.0: Are German manufacturing SMEs the first victims of this revolution? Journal of Industrial Engineering and Management, 2015. 8(5): p. 1512. 7. Jennings, N.R., On agent-based software engineering. Artificial intelligence, 2000. 117(2): p. 277-296. 8. Weiss, G., Multiagent systems: a modern approach to distributed artificial intelligence. 1999: MIT press. 9. Wooldridge, M. and N.R. Jennings, Intelligent agents: Theory and practice. The knowledge engineering review, 1995. 10(2): p. 115-152. 10. Van Brussel, H., et al., Reference architecture for holonic manufacturing systems: PROSA. Computers in industry, 1998. 37(3): p. 255-274. 11. Barbosa, J., et al., Dynamic self-organization in holonic multi-agent manufacturing systems: The ADACOR evolution. Computers in Industry, 2015. 66: p. 99-111. 12. Chaplin, J., et al., Evolvable assembly systems: a distributed architecture for intelligent manufacturing. IFAC-PapersOnLine, 2015. 48(3): p. 2065-2070. f g p , ( ) p 13. Object Management Group Inc. Data Distribution Service (DDS) Version 1.4. 2015 [cited 12th November 2017]; Available from: http://www.omg.org/spec/DDS/1.4/. Object Management Group Inc. Data Distribution Service (DDS) Version 1.4. 2015 13. Object Management Group Inc. Data Distribution Service (DDS) Version 1.4. 2015 [ i d 12 h N b 2017] A il bl f h // / /DDS/1 4/ 13. Object Management Group Inc. Data Distribution Service (DDS) Version 1.4. 2015 [cited 12th November 2017]; Available from: http://www.omg.org/spec/DDS/1.4/. [cited 12th November 2017]; Available from: http://www.omg.org/spec/DDS/1.4/. 14. Faccin, J. and I. Nunes. Modelling and Reasoning about Remediation Actions in BDI Agents. in Proceedings of the 16th Conference on Autonomous Agents and MultiAgent Systems. 2017. International Foundation for Autonomous Agents and Multiagent Systems. 15. Rao, A.S. and M.P. Georgeff. BDI agents: From theory to practice. in ICMAS. 1995. 14 16. de Silva, L., et al., Realisability of production recipes, in 22nd European Conference in Artificial Intelligence (ECAI 2016). 2016: The Hague, Netherlands. 17. Raspberry Pi Foundation. Raspberry Pi Zero W. 2017 [cited 2017 6th December]; Available from: https://www.raspberrypi.org/products/raspberry-pi-zero-w/. 18. Siemens AG. The intelligent gateway for industrial IoT solutions: SIMATIC IOT2000. 2017 [cited 6th December 2017]; Available from: http://w3.siemens.com/mcms/pc- based-automation/en/industrial-iot/pages/default.aspx. 19. Raspberry Pi Foundation. Raspberry Pi 3 Model B. 2017 [cited 7th December 2017]; Available from: https://www.raspberrypi.org/products/raspberry-pi-3-model-b/. 20. 7 References OPC Foundation. Unified Architecture. 2016 [cited 5th December 2017]; Available from: https://opcfoundation.org/about/opc-technologies/opc-ua/. 21. Siemens AG. SIMATIC WinCC V7 - maximum plant transparency and productivity. 2017 [cited 2017 7th December]; Available from: http://w3.siemens.com/mcms/human-machine-interface/en/visualization- software/scada/simatic-wincc/pages/default.aspx. 22. S7Connector Members. S7Connector: Java library for S7 PLCs. 2016 [cited 7th December 2017]; Available from: https://s7connector.github.io/s7connector/. 23. Real-Time Innovations. RTI connext DDS professional. 2017 [cited 6th December 2017; Available from: https://www.rti.com/products/dds. 24. Bellifemine, F., et al., JADE—a java agent development framework, in Multi-Agent Programming. 2005, Springer. p. 125-147. 25. Bellifemine, F., A. Poggi, and G. Rimassa. JADE–A FIPA-compliant agent framework. in Proceedings of PAAM. 1999. London. 16. de Silva, L., et al., Realisability of production recipes, in 22nd European Conference in Artificial Intelligence (ECAI 2016). 2016: The Hague, Netherlands. 17. Raspberry Pi Foundation. Raspberry Pi Zero W. 2017 [cited 2017 6th December]; Available from: https://www.raspberrypi.org/products/raspberry-pi-zero-w/. 18. Siemens AG. The intelligent gateway for industrial IoT solutions: SIMATIC IOT2000. 2017 [cited 6th December 2017]; Available from: http://w3.siemens.com/mcms/pc- based-automation/en/industrial-iot/pages/default.aspx. 19. Raspberry Pi Foundation. Raspberry Pi 3 Model B. 2017 [cited 7th December 2017]; 19. Raspberry Pi Foundation. Raspberry Pi 3 Model B. 2017 [cited 7th December 2017]; Available from: https://www.raspberrypi.org/products/raspberry-pi-3-model-b/. Available from: https://www.raspberrypi.org/products/raspberry pi 3 model b/. 20. OPC Foundation. Unified Architecture. 2016 [cited 5th December 2017]; Available from: https://opcfoundation.org/about/opc-technologies/opc-ua/. 21. Siemens AG. SIMATIC WinCC V7 - maximum plant transparency and productivity. 2017 [cited 2017 7th December]; Available from: http://w3.siemens.com/mcms/human-machine-interface/en/visualization- software/scada/simatic-wincc/pages/default.aspx. 22. S7Connector Members. S7Connector: Java library for S7 PLCs. 2016 [cited 7th December 2017]; Available from: https://s7connector.github.io/s7connector/. 23. Real-Time Innovations. RTI connext DDS professional. 2017 [cited 6th December 2017; Available from: https://www.rti.com/products/dds. 24. Bellifemine, F., et al., JADE—a java agent development framework, in Multi-Agent Programming. 2005, Springer. p. 125-147. Bellifemine, F., et al., JADE—a java agent development framework, in Multi-Agent Programming. 2005, Springer. p. 125-147. 25. Bellifemine, F., A. Poggi, and G. Rimassa. JADE–A FIPA-compliant agent framework. in Proceedings of PAAM. 1999. London.
https://openalex.org/W3098413970
https://link.springer.com/content/pdf/10.1007/JHEP10(2019)098.pdf
English
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Localization of gauge bosons and the Higgs mechanism on topological solitons in higher dimensions
˜The œJournal of high energy physics/˜The œjournal of high energy physics
2,019
cc-by
20,521
Published for SISSA by Springer Received: July 30, 2019 Accepted: September 19, 2019 Published: October 8, 2019 Open Access, c⃝The Authors. Article funded by SCOAP3. Keywords: Field Theories in Higher Dimensions, Solitons Monopoles and Instantons, Spontaneous Symmetry Breaking Localization of gauge bosons and the Higgs mechanism on topological solitons in higher dimensions https://doi.org/10.1007/JHEP10(2019)098 Contents 1 Introduction 2 Localization by a neutral stabilizer in D = 5 2.1 The model 2.2 An illustrative example 2.3 Generic models 3 Neutral stabilizers in higher dimensions 3.1 Useful formulae 3.2 The quadratic Lagrangian 3.2.1 The scalar part 3.2.2 The four dimensional component Aµ 3.2.3 The extra dimensional component Aa 4 Localization by a charged stabilizer in D = 5 5 Localization by a charged stabilizer in D ≥5 6 Several examples in D = 6 6.1 Intersection of domain walls 6.1.1 Neutral stablizer 6.1.2 Charged stabilizer 6.2 Axially symmetric case 6.2.1 Neutral stablizer 6.2.2 Charged stablizer 7 Conclusion Contents JHEP10(2019)098 Contents 1 Introduction 1 2 Localization by a neutral stabilizer in D = 5 3 2.1 The model 3 2.2 An illustrative example 4 2.3 Generic models 8 3 Neutral stabilizers in higher dimensions 11 3.1 Useful formulae 12 3.2 The quadratic Lagrangian 14 3.2.1 The scalar part 15 3.2.2 The four dimensional component Aµ 15 3.2.3 The extra dimensional component Aa 16 4 Localization by a charged stabilizer in D = 5 20 5 Localization by a charged stabilizer in D ≥5 25 6 Several examples in D = 6 30 6.1 Intersection of domain walls 30 6.1.1 Neutral stablizer 32 6.1.2 Charged stabilizer 33 6.2 Axially symmetric case 34 6.2.1 Neutral stablizer 34 6.2.2 Charged stablizer 35 7 Conclusion 35 1 Introduction 1 Introduction 2 Localization by a neutral stabilizer in D = 5 2 Localization by a neutral stabilizer in D = 5 2.1 The model 2.2 An illustrative example 2.3 Generic models JHEP10(2019)098 4 Localization by a charged stabilizer in D = 5 5 Localization by a charged stabilizer in D ≥5 6 Several examples in D = 6 6.1 Intersection of domain walls 6.1.1 Neutral stablizer 6.1.2 Charged stabilizer 6.2 Axially symmetric case 6.2.1 Neutral stablizer 6.2.2 Charged stablizer 7 Conclusion 35 7 Conclusion 35 Localization of gauge bosons and the Higgs mechanism on topological solitons in higher dimensions JHEP10(2019)098 Minoru Etoa,b and Masaki Kawaguchia aDepartment of Physics, Yamagata University, Kojirakawa-machi 1-4-12, Yamagata, Yamagata 990-8560, Japan bResearch and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Yokohama, Kanagawa 223-8521, Japan E-mail: meto@sci.kj.yamagata-u.ac.jp, ddwbb.daigaku@gmail.com Minoru Etoa,b and Masaki Kawaguchia aDepartment of Physics, Yamagata University, Kojirakawa-machi 1-4-12, Yamagata, Yamagata 990-8560, Japan bResearch and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Yokohama, Kanagawa 223-8521, Japan E-mail: meto@sci.kj.yamagata-u.ac.jp, ddwbb.daigaku@gmail.com Minoru Etoa,b and Masaki Kawaguchia aDepartment of Physics, Yamagata University, Kojirakawa-machi 1-4-12, Yamagata, Yamagata 990-8560, Japan bResearch and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Yokohama, Kanagawa 223-8521, Japan E-mail: meto@sci.kj.yamagata-u.ac.jp, ddwbb.daigaku@gmail.com aDepartment of Physics, Yamagata University, Kojirakawa-machi 1-4-12, Yamagata, Yamagata 990-8560, Japan bResearch and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Yokohama, Kanagawa 223-8521, Japan E-mail: meto@sci.kj.yamagata-u.ac.jp, ddwbb.daigaku@gmail.com Abstract: We provide complete and self-contained formulas about localization of mass- less/massive Abelian gauge fields on topological solitons in generic D dimensions via a field dependent gauge kinetic term. The localization takes place when a stabilizer (a scalar field) is condensed in the topological soliton. We show that the localized gauge bosons are massless when the stabilizer is neutral. On the other hand, they become massive for the charged stabilizer as a consequence of interplay between the localization mechanism and the Higgs mechanism. For concreteness, we give two examples in six dimensions. The one is domain wall intersections and the other is an axially symmetric soliton background. Keywords: Field Theories in Higher Dimensions, Solitons Monopoles and Instanton Spontaneous Symmetry Breaking Keywords: Field Theories in Higher Dimensions, Solitons Monopoles and Instantons, Spontaneous Symmetry Breaking ArXiv ePrint: 1907.04573 Open Access, c⃝The Authors. Article funded by SCOAP3. 1 Introduction The idea that our world is a four-dimensional hyper surface (a 3-brane) in higher- dimensional spacetime has been widely studied for decades. Such models are called brane- world models. By utilizing geometry of the extra dimensions, the brane-world models can solve many unsatisfactory problems of the Standard Model (SM), as provided by the seminal works [1–4]. A conventional setup of the brane-world models is that extra dimensions are prepared as a compact manifold/orbifold. Namely, our four-dimensional spacetime is treated dif- ferently from the extra dimensions. Furthermore, 3-branes are introduced by hand as – 1 – non-dynamical objects which are infinitely thin. In order to make the models more natu- ral, we can harness topology of extra dimensions. The idea is quite simple [5]: Dynamical compactification of the extra dimensions and dynamical creation of 3-branes originate in a spontaneous symmetry breaking in a vacuum. Namely, it gives rise to a topologically stable soliton/defect of a finite width. The topology ensures not only stability of the brane but also the presence of chiral matters localized on the brane [5, 6]. In addition, graviton can be trapped [7–12]. In contrast, localizing massless gauge bosons, especially non-Abelian gauge bosons, is quite difficult. There were many works so far [13–36]. However, each of these has some advantages/disadvantages and there seems to be only little universal understanding. Then a new mechanism utilizing a field dependent gauge kinetic term (field dependent perme- ability) JHEP10(2019)098 −β(φi)2FMNF MN, (M, N = 0, 1, 2, 3, 4, · · · , D −1), (1.1) (1.1) came out in ref. [37] where φi are scalar fields which we call stabilizer throughout this paper. This is a semi-classical realization of the confining phase [1, 38–43]. Recently, one of the author and the collaborators have tried to improve the brane-world models with topological solitons by using (1.1) [44–52]. Brief highlights of the results are the following: Ref. [48] provided the geometric Higgs mechanism which is the conventional Higgs mech- anism driven by the positions of multiple domain walls in an extra dimension, similarly to D-branes in superstring theories. Then the geometric Higgs mechanism was applied to SU(5) Grand Unified Theory in ref. [49]. However, in these early works, treatment of gauge fixing was partially unsatisfactory. In order to resolve this point, we have developed anal- ysis by extending the Rξ gauge under spatially modulated backgrounds in any spacetime dimensions D [50]. 1 Introduction Then, we gave a new attempt in ref. [51] that the SM Higgs field plays a role of the stabilizer φi in a D = 5 model. The latest development along this direction is that the same localization mechanism can be applied not only on vector fields but also scalars and tensors in ref. [52]. Another group also recently studied the SM in a similar model with β2 taken as a given background in D = 5 [53–55]. The purpose of this paper is to provide complete and self-contained formula about localization of massless/massive Abelian gauge fields on topological solitons in generic D dimensions via the field dependent gauge kinetic term (1.1). The basic template is a domain wall in a D = 5 model with stabilizers φi which are neutral to the would-be localized gauge fields. Such models have been studied in refs. [37, 44–49]. We firstly reanalyze it with the extended Rξ gauge to provide more complete arguments in section 2. Then, there are two directions for extending the basic template. The one is to go to higher dimensions D ≥6, and the other is to make the neutral stabilizers φi charged to the would-be localized gauge fields. The former direction has been investigated in ref. [50] which we will give a review with several improvements especially on divergence-free parts of extra-dimensional components of the gauge fields in section 3. The latter extension that localization of gauge fields by charged stabilizers was applied to the SM in D = 5 dimensions [51]. In ref. [51], the charged stabilizer is nothing but the SM Higgs field. Therefore, the Higgs field plays three roles: breaking of the electroweak symmetry, generating fermion masses, and localizing – 2 – the electroweak gauge bosons on the domain wall. Since details on gauge field localization by the charged stabilizer were not given in ref. [51], in this work we will give a complete formula in details for accounting localization mechanism which occurs together with the Higgs mechanism in section 4. Finally, we proceed to unify the two directions into the most generic models in D ≥6 with charged stabilizers. In general, fluctuations are mixed each other under a soliton background, so that it is not easy to distinguish which field is physical or unphysical. 1 Introduction To overcome this difficulty, we will carefully analyze the small fluctuations in the extended Rξ gauge in section 5, and succeed in cleaning up related Lagrangian up to quadratic order of the fluctuations, and providing a simple and compact formula. With the formula at hand, it becomes easy for us to obtain physical mass spectra appearing in a low energy effective theory on topological solitons for generic models. To be concrete, we give examples in section 6. The first example is an intersection of two normal domain walls in D = 6 dimensions. We will find an extremely good approximation which allow us to compute analytically mass spectra localized on an intersecting point. In the second example, we take an axially symmetric background on the assumption that the topological soliton is a vortex-type soliton in D = 6. JHEP10(2019)098 For both cases that the stabilizer is neutral and/or charged, our formula provides us a transparent road to obtain the physical mass spectra, and to specify the lightest degrees of freedom in the low energy effective theory. We will figure out that the lightest fields are massless four-dimensional gauge bosons and Nambu-Goldstone fields for the neutral stabilizer. There are infinite tower of Kaluza-Klein (KK) modes but there is a large mass gap (of order inverse soliton width) between the low-lying mode and the higher KK modes. Once we replace the neutral stabilizer by charged one, the Higgs mechanism occurs together with localization of the gauge fields. As a result, the lowest mass mode becomes the massive four-dimensional gauge field, and the heavy KK modes follow with the large mass gap. We should stress that the scalar fields originated from the extra-dimensional components of the gauge fields are always above the large mass gap, so that they do not supply any low-lying physical degrees of freedom. The organization on the paper is the following. The basic template of the localization mechanism with neutral stabilizers in D = 5 is given in section 2. The extension of section 2 with the neutral stabilizers in higher dimensions D ≥5 is explained in section 3. Section 4 is devoted to explain the other generalization of section 2 with charged stabilizers in D = 5. Then, the most generic models with charged stabilizers in higher dimensions D ≥6 is studied in section 5. 1 Introduction Several concrete examples in D = 6 are given in section 6, and concluding remarks are given in section 7. 2.1 The model We consider the following Lagrangian in non-compact five dimensions, (2.1) (2.2) L(H, T, AM) = Lg(H, AM) + Ls(H, T), (2.1) Lg(H, AM) = −β(H)2FMNFMN, (2.2) (2.2) – 3 – where M, N = 0, 1, 2, 3, 4, and H is a complex scalar field, T is a real scalar field, and AM is a U(1) gauge field. The field strength is given by where M, N = 0, 1, 2, 3, 4, and H is a complex scalar field, T is a real scalar field, and AM is a U(1) gauge field. The field strength is given by FMN = ∂MAN −∂NAM. (2.3) (2.3) For L to be real, β should be a real functional of H. The scalar Lagrangian Ls(H, T) depends on H and T as (2.4) Ls(H, T) = ∂MH∂MH∗+ ∂MT∂MT −V (H, T). (2.4) JHEP10(2019)098 As we will see below, T is responsible for generating a non-trivial soliton background configuration, and H plays an important role for localizing gauge fields on the soliton. We will refer to H as a stabilizer. In this section, we will also assume that both H and T are neutral under the gauge transformation associated with the gauge field AM; Namely, they do not interact with the gauge field AM through conventional covariant derivatives. Nevertheless, the neutral stabilizer H can couple to AM through the factor β2 in front of the F2 term. Clearly, if β is a constant, the Lagrangian reduces to a conventional minimal one. Note that β2 can be interpreted as an extension of inverse square of a gauge coupling constant which can be a function of the stabilizer H. The Euler-Lagrange equations of the model read The Euler-Lagrange equations of the model read ∂M∂MH + ∂V ∂H∗= −2β ∂β ∂H∗FMNFMN, (2.5) ∂M∂MT + ∂V ∂T = 0, (2.6) ∂M β2FMN = 0. (2.7) (2.5) (2.7) Clearly, AM = 0 solves the last equation. Then, we are left with the first two equations with zeros at the right hand sides. Hereafter, we will assume that H and T take a nontrivial background configuration depending only on the extra-dimensional coordinate y = x4. Such configurations generically appear as a topological soliton when a discrete symmetry is spontaneously broken. 2.2 An illustrative example Before describing a generic model, let us make a pause for illustrating relevant phenomena through one of the simplest example in D = 5. Let us consider the scalar potential V = Ω2|H|2 + λ2 T 2 + |H|2 −v22 . (2.8) (2.8) The model has the U(1) global symmetry H →eiαH, and the Z2 symmetry T →−T. When Ω2 > 0, there are two discrete vacua (H, T) = (0, ±v). Thus, the Z2 symmetry is spontaneously broken, which gives rise to a topologically stable domain wall: It is straight- forward to verify that the analytic domain wall solution is given by (2.9) T0 = v tanh Ω(y −y0), H0 = eiα0vH sech Ω(y −y0), (Ω< λv) , (2.9) – 4 – where y0 and α0 are real moduli parameters, and we defined vH ≡ q v2 −Ω2 λ2 . The Z2 symmetry is recovered at the center of domain wall y = y0, whereas the unbroken symme- tries at the vacua, namely the translational symmetry and the U(1) global symmetry, are spontaneously broken only near the domain wall. This locally broken symmetries are re- sponsible for the presence of the moduli parameters under the Nambu-Goldstone theorem. Another domain wall solution is known for Ω≥λv as T0 = v tanh λv(y −y0), H0 = 0, (Ω≥λv) . (2.10) (2.10) Here, the global U(1) symmetry is unbroken everywhere. Thus, there is only the transla- tional moduli parameter y0. JHEP10(2019)098 Either the translational symmetry or the global U(1) symmetry is broken in the vicinity of the domain wall whereas they are not broken at the vacua. Therefore, we expect the corresponding zero modes are localized on the domain wall. This can easily be verified by perturbing the background solution as T = T0(y) + τ(xµ, y), H = ( h1 + ih2 for Ω≥λv eiϑ(xµ,y) {H0(y) + h(xµ, y)} for Ω< λv (2.11) (2.11) where τ, h1,2, h and ϑ are real. In the following, we will set y0 = α0 = 0 just for ease of the notation. 2.2 An illustrative example Plugging these into the Lagrangian Ls(T, H) and taking the terms quadratic in the fluctuations (we will shortly take fluctuations of the gauge fields into account below), we find L(2) s = ( −⃗ξ † ∂µ∂µ + M2 ⃗ξ for Ω≥λv −⃗ξ T ∂µ∂µ + M2 ⃗ξ −H2 0 ϑ ∂µ∂µ −H−2 0 ∂yH2 0∂y  ϑ for Ω< λv , (2.12) (2.12) where we defined where we defined ⃗ξ = τ h1 + ih2 ! for Ω≥λv, ⃗ξ = τ h ! for Ω< λv, (2.13) (2.13) and M2 = −∂2 y + 2λ2 3T 2 0 + H2 0 −v2 4λ2T0H0 4λ2T0H0 −∂2 y + 2λ2 T 2 0 + 3H2 0 −v2 + Ω2 ! . (2.14) (2.14) The KK mass spectra for ⃗ξ can be obtained by expanding ⃗ξ by eigenstate of M2 as ⃗ξ(xµ, y) = ∞ X n=0 ⃗Ξ(n)(y)ξ(n)(xµ), M2 ⃗Ξ(n) = m2 ξ,n ⃗Ξ(n). (2.15) (2.15) (2.15) Now, it is clear that there always exists the translational zero mode: Now, it is clear that there always exists the translational zero mode: M2⃗Ξ (0) = 0, ⃗Ξ (0) = ∂y T0(y) H0(y) ! . 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Flows of mass eigenvalues of the localized states on the domain wall. ⃗Ξ(0) and θ(0) correspond to the translational and U(1) NG modes, respectively. JHEP10(2019)098 Figure 1. Flows of mass eigenvalues of the localized states on the domain wall. ⃗Ξ(0) and θ(0) correspond to the translational and U(1) NG modes, respectively. As expected, this is localized around the domain wall, which can easily be verified by looking at |⃗Ξ(0)|2 = T ′ 0 2 + H′ 0 2. Note that the translational zero mode exists regardless of values of the parameters Ω, v, λ. We can also derive several exact results for massive modes. Analysis for λv ≤Ωis easy since M2 is diagonal. 1The negative mass square m2 h,1 implies that H0 = 0 is unstable for λv > Ω. Indeed, H0 ̸= 0 for the solution in eq. (2.9). 2.2 An illustrative example – 6 – the mass eigenvalues are calculated as m2 τ,1 Ω≲λv ≃ Z ∞ −∞ dy ⃗Ξ(1)T τ M2⃗Ξ(1) τ = 3Ω2 + 4Ω2 5 ϵ2, (2.20) m2 h,1 Ω≲λv ≃ Z ∞ −∞ dy ⃗Ξ(1)T h M2⃗Ξ(1) h = 4Ω2ϵ2. (2.21) (2.20) (2.21) Thus, the both eigenvalues grow up as λv/Ωincreasing, see the yellow band in figure 1. ⃗(1) Thus, the both eigenvalues grow up as λv/Ωincreasing, see the yellow band in figure 1. ⃗(1) Thus, the both eigenvalues grow up as λv/Ωincreasing, see the yellow band in figure 1. On the other hand, a linear combination of ⃗Ξ(1) h1,2 remains massless, and transforms to the U(1) NG mode. Indeed, H0 ∝sech Ωy never vanishes at finite y for Ω< λv, so that ϑ has the non minimal kinetic term To make the lower Lagrangian of eq (2 12) be On the other hand, a linear combination of ⃗Ξ(1) h1,2 remains massless, and transforms to the U(1) NG mode. Indeed, H0 ∝sech Ωy never vanishes at finite y for Ω< λv, so that ϑ has the non minimal kinetic term. To make the lower Lagrangian of eq. (2.12) be canonical, let us redefine ϑ by θ JHEP10(2019)098 ϑ = θ √ 2 H0 . (2.22) (2.22) Then, the quadratic Lagrangian can be rewritten as L(2) s = −⃗ξ T ∂µ∂µ + M2 ⃗ξ −1 2θ  ∂µ∂µ + Q† yQy  θ, (2.23) (2.23) with with Qy ≡−∂y + ∂yH0 H0 , Q† y ≡∂y + ∂yH0 H0 . (2.24) (2.24) The mass spectrum corresponds to the eigenvalues of the Hermitian operator Q† yQy as Q† yQyq(n) = m2 Q,nq(n). (2.25) (2.25) Since Q† yQy is positive semidefinite, the eigenvalues are m2 Q,n ≥0. The normalizable zero mode is uniquely given by mQ,0 = 0, q(0) = H0(y). (2.26) (2.26) There are no other localized modes. All the excited states are continuum modes and given by mQ(k) = p Ω2 + k2 , q(y; k) = eiky mQ(k) (k + iΩtanh Ωy) . (2.27) (2.27) Thus, the mass gap between the zero mode (the U(1) NG mode q(0)) and the continuum scattering modes is Ω. The final piece of the fluctuation analysis is on the gauge fields. Since the background gauge fields are zeros, let AM itself be fluctuations. 2.2 An illustrative example There are two orthogonal low lying mass eigenstates m2 τ,1 = 3λ2v2, ⃗Ξ(1) τ = r 3λv 2 sech λvy tanh λvy 0 ! , (2.17) m2 hi,1 = Ω2 −λ2v2, ⃗Ξ(1) hi = r λv 2 0 sech λvy ! , (i = 1, 2). (2.18) (2.17) (2.18) m2 τ,1Ω−2 is monotonically increasing function of λv/Ωwhereas the degenerate masses m2 hi,1Ω−2 are monotonically decreasing function. The two masses cross at λv/Ω= 1/2, see figure 1. The thresholds (the dotted lines in figure 1) between localized discrete modes and scattering continuum modes are 2λv and Ωfor τ and hi, respectively. At the critical point λv = Ω, ⃗Ξ(1) hi becomes exactly massless, whereas ⃗Ξ(1) τ becomes heavy whose mass is of order Ω. There, the quadratic Lagrangian switches from the upper to the lower one in eq. (2.12). It is not easy to analytically compute mass eigenvalues for λv > Ω,1 since M2 is no longer diagonal. However, due to the continuity at λv = Ω, ⃗Ξ(1) τ and ⃗Ξ(1) hi should continuously be connected to corresponding degrees of freedom for Ω> λv. Let us estimate the eigenvalues by treating H0 as a small perturbation. To the first order of ϵ2 defined by m2 τ,1Ω−2 is monotonically increasing function of λv/Ωwhereas the degenerate masses m2 hi,1Ω−2 are monotonically decreasing function. The two masses cross at λv/Ω= 1/2, see figure 1. The thresholds (the dotted lines in figure 1) between localized discrete modes and scattering continuum modes are 2λv and Ωfor τ and hi, respectively. At the critical point λv = Ω, ⃗Ξ(1) hi becomes exactly massless, whereas ⃗Ξ(1) τ becomes heavy whose mass is of order Ω. There, the quadratic Lagrangian switches from the upper to the lower one in eq. (2.12). It is not easy to analytically compute mass eigenvalues for λv > Ω,1 since M2 is no longer diagonal. However, due to the continuity at λv = Ω, ⃗Ξ(1) τ and ⃗Ξ(1) hi should continuously be connected to corresponding degrees of freedom for Ω> λv. Let us estimate the eigenvalues by treating H0 as a small perturbation. To the first order of ϵ2 defined by ϵ2 ≡λ2v2 Ω2 −1, (2.19) (2.19) 1The negative mass square m2 h,1 implies that H0 = 0 is unstable for λv > Ω. Indeed, H0 ̸= 0 for the solution in eq. (2.9). 2.2 An illustrative example A relevant part to quadratic order in the fluctuation AM is L(2) g = −β2 0 (∂MAN −∂NAM)2 , β0(y) ≡β(H0(y)). (2.28) (2.28) To illustrate essence, let us take one of the simplest example β(H) = |H| 2µ → β0(y) = vH 2µ sech Ωy, (2.29) (2.29) where µ is a constant for λv > Ω. Since nothing interests happen for λv ≤Ω, we will investigate the parameter region λv > Ωin what follows. To figure out mass spectrum of – 7 – the gauge field, we first need to fix the U(1) gauge symmetry. To this end, we add the following to the quadratic Lagrangian the gauge field, we first need to fix the U(1) gauge symmetry. To this end, we add the following to the quadratic Lagrangian Lξ = −2β2 ξ  ∂µAµ −ξ 1 β2 ∂y β2Ay 2 . (2.30) (2.30) Here, ξ is a gauge fixing parameter. If β is a constant, it reduces to a conventional covariant gauge Lξ = −2β2 ξ (∂MAM)2. We call eq. (2.30) the extended Rξ gauge [50–55]. In terms of the canonically normalized gauge field defined by AM ≡2β0AM, (2.31) (2.31) JHEP10(2019)098 the quadratic Lagrangian reads (Lg + Lξ) quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνQ† yQy  Aν −1 2Ay  □+ ξQyQ† y  Ay . (2.32) Thanks to the gauge fixing term in eq. (2.30), Aµ and Ay are not mixed. Hence, the KK mass spectra of Aµ and Ay correspond to eigenvalues of Q† yQy and ξQyQ† y, respectively. It is coincident for the particular choice of β in eq. (2.29) that the Schr¨odinger operators for θ and Aµ are identical (As we will see below, they are different in generic models.). Therefore, the KK mass spectrum of Aµ consists of mQ,0 = 0 for the localized mode and mQ(k) = √ Ω2 + k2 for the continuum scattering states with the momentum k. Fortunately, no further computations are needed for Ay, since Q† yQy and QyQ† y operators have the same mass eigenvalues except for a zero eigenvalue. Therefore, the mass square for Ay is given by ξmQ(k)2 = ξ Ω2 + k2 . It is peculiar that they depend on the gauge fixing parameter ξ. Since any observable should not depend on gauge, we conclude that Ay do not include any unphysical degrees of freedom. 2.2 An illustrative example As we will show below, one can understand they are eaten by Aµ to give longitudinal modes of the massive KK modes of A(KK) µ . 2.3 Generic models So far, we have argued over the specific model with the scalar potential (2.8) and β linear in H given in eq. (2.29). For a generic scalar potential, the matrix M2 given in eq. (2.14) is modified as  2 2  M2 =  −∂2 y + ∂2V (T0,H0) ∂T 2 0 ∂2V (T0,H0) ∂T0∂H0 ∂2V (T0,H0) ∂T0∂H0 −∂2 y + ∂2V (T0,H0) ∂H2 0  . (2.33) (2.33) Accordingly, the detail mass spectrum of the scalar fields are different from those for the simplest model considered above. However, the presence of the translational NG mode is intact, and indeed the mode function ⃗Ξ(0) given in eq. (2.16) formally remains correct. Fur- thermore, the quadratic Lagrangian of the scalar sector given in eq. (2.23) is also formally valid for the generic model. Therefore, we again have the following for H0 ̸= 0 Accordingly, the detail mass spectrum of the scalar fields are different from those for the simplest model considered above. However, the presence of the translational NG mode is intact, and indeed the mode function ⃗Ξ(0) given in eq. (2.16) formally remains correct. Fur- thermore, the quadratic Lagrangian of the scalar sector given in eq. (2.23) is also formally valid for the generic model. Therefore, we again have the following for H0 ̸= 0 L(2) s = −⃗ξ T ∂µ∂µ + M2 ⃗ξ −1 2θ  ∂µ∂µ + Q† yQy  θ. (2.34) (2.34) – 8 – Here, although the profile H0 itself is different from eq. (2.9) in general, but the definition of the operators Qy and Q† y are same as eq. (2.24). Here, although the profile H0 itself is different from eq. (2.9) in general, but the definition of the operators Qy and Q† y are same as eq. (2.24). On the other hand, the gauge sector given in eq. (2.32) gets modified when we generalize the linear function β(H) ∝H to a generic function β(H). After a little computations, we get (Lg + Lξ) quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνD† yDy  Aν −1 2Ay  □+ ξDyD† y  Ay . (2.35) (2.35) JHEP10(2019)098 JHEP10(2019)098 Compared to eq. (2.32), Qy and Q† y are replaced by Dy and D† y which are defined by Compared to eq. 2.3 Generic models (2.32), Qy and Q† y are replaced by Dy and D† y which are defined by Dy = −∂y + ∂yβ0 β0 , D† y = ∂y + ∂yβ0 β0 . (2.36) (2.36) Note that Dy = Qy and D† y = Q† y hold when β is linear in H. Note that Dy = Qy and D† y = Q† y hold when β is linear in H. Note that Dy = Qy and D† y = Q† y hold when β is linear in H. † To complete the analysis, let us expand Aµ and Ay by eigenfunctions of D† yDy and DyD† y, respectively. To this end, let us introduce the eigenfunctions D† yDyd(n)(y) = m2 D,nd(n)(y). (2.37) (2.37) Similarly to Q† yQy, D† yDy is positive semidefinite, so that m2 D,n ≥0. The normalizable zero mode, if it exists, is unique. It is given by Similarly to Q† yQy, D† yDy is positive semidefinite, so that m2 D,n ≥0. The normalizable zero mode, if it exists, is unique. It is given by mD,0 = 0, d(0)(y) = β0(y). (2.38) (2.38) Hereafter, we assume that β0(y) = β(H0(y)) is non zero and square integrable 0 < Z ∞ −∞ dy β0(y)2 < ∞. (2.39) (2.39) We expand Aµ in terms of d(n) as Aµ(x, y) = ∞ X n=0 A(n) µ (x)d(n)(y). (2.40) (2.40) Thus, we conclude that Aµ always has the unique normalizable massless mode A(0) µ . Similarly, we expand Ay by the eigenfunctions of DyD† y DyD† y ˜d(n)(y) = ˜m2 D,n ˜d(n)(y). (2.41) (2.41) As m2 D,n, ˜m2 D,n ≥0 holds. The massless eigenfunction is given by ˜d(0)(y) = β0(y)−1. (2.42) (2.42) However, this is non normalizable since we always impose the square integrability condi- tion (2.39). As is well-known, for the massive modes with n > 0, we have the following re- lations ( ) However, this is non normalizable since we always impose the square integrability condi- tion (2.39). As is well-known, for the massive modes with n > 0, we have the following re- lations ( ) ˜d(n)(y) = Dyd(n)(y) mD,n , mD,n = ˜mD,n. (2.43) (2.43) – 9 – – 9 – Thus, Ay is expanded as Thus, Ay is expanded as Ay(x, y) = ∞ X n̸=0 a(n)(x) ˜d(n)(y) = ∞ X n̸=0 a(n)(x)Dyd(n)(y) mD,n . (2.44) (2.44) Plugging these into eq. 2.3 Generic models (2.35) and integrating it over y, we find the quadratic La- grangian for the low energy effective theory Plugging these into eq. (2.35) and integrating it over y, we find the quadratic La- grangian for the low energy effective theory Z dy (Lg + Lξ) quad = ∞ X n=0 L(n) g , (2.45) (2.45) JHEP10(2019)098 with L(0) g = 1 2A(0) µ  ηµν□−  1−1 ξ  ∂µ∂ν  A(0) ν , (2.46) L(n>0) g = 1 2A(n) µ  ηµν□−  1−1 ξ  ∂µ∂ν+ηµνm2 D,n  A(n) ν −1 2a(n) □+ξm2 D,n  a(n) . (2.47) (2.46) (2.47) Clearly, L(0) g is a usual Lagrangian in the Rξ gauge (covariant gauge) for the massless Abelian gauge field A(0) µ in four dimensions. Similarly, L(n>0) g is identical to a conventional Lagrangian in the Rξ gauge for the Abelian gauge field A(n>0) µ which gets the mass mD,n as a result of the Higgs mechanism by absorbing the scalar field a(n>0). Thus, Ay does not provide any physical degrees of freedom to the low energy effective action but is converted into longitudinal degrees of freedom to A(n>0) µ . Before closing this section, for later convenience, let us describe the above results from a slightly different view point. We decompose Ay into a divergence part and a divergence- free part as Ay = Ad y + Adf y , (2.48) (2.48) where the separation is done by the following projection operator P = Dy  D† yDy −1 D† y, Ad y = PAy, Adf y = (1 −P)Ay. (2.49) (2.49) Then, it holds D† yAdf y = 0. (2.50) (2.50) Furthermore, we can easily show D† yAy is orthogonal to the zero mode d(0) of D† yDy as Z dy d(0)D† yAy = Z dy (Dyd(0))Ay = 0. (2.51) (2.51) This ensures that the projection operator P is well-defined. Now, we can rewrite the quadratic Lagrangian of the gauge sector given in eq. (2.35) as (Lg + Lξ) quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνD† yDy  Aν (Lg + Lξ) quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνD† yDy  Aν −1 2Adf y □Adf y −1 2Ad y  □+ ξDyD† y  Ad y . 2.3 Generic models (2.52) −1 2Adf y □Adf y −1 2Ad y  □+ ξDyD† y  Ad y . (2.52) (2.52) – 10 – – 10 – Note that the divergence-free condition (2.50) implies Note that the divergence-free condition (2.50) implies Adf y = ηβ−1 0 , (2.53) (2.53) with η being a constant in y. Indeed, this corresponds to the non-normalizable zero mode ˜d(0) of DyD† y given in eq. (2.42). Therefore, eliminating ˜d(0) from Ay in eq. (2.44) is nothing but getting rid of the divergence-free part Adf y form Ay. Thus, eliminating the unphysical Adf y , the quadratic Lagrangian reduces to with η being a constant in y. Indeed, this corresponds to the non-normalizable zero mode ˜d(0) of DyD† y given in eq. (2.42). Therefore, eliminating ˜d(0) from Ay in eq. (2.44) is nothing but getting rid of the divergence-free part Adf y form Ay. Thus, eliminating the unphysical Adf y , the quadratic Lagrangian reduces to (Lg + Lξ) quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνD† yDy  Aν −1 2a  □+ ξD† yDy  a , (2.54) ere we defined a = 1 q D† yDy D† yAy = 1 q D† yDy D† yAd y. (2.55) JHEP10(2019)098 (2.54) where we defined where we defined (2.55) Now, we run into a direct correspondence between the mass square operators D† yDy for Aµ and ξD† yDy for a. This implies a is the one which is eaten by A(n>0) µ . Thus, our statement becomes more solid than before: The divergence-free part of Ay is unphysical because it diverges at the spatial infinity. The divergence part of Ay is also unphysical because it is absorbed by A(n>0) µ . µ Since D† yAy is orthogonal to d(0), a is also orthogonal to d(0). Thus, we can expand a by the eigenfunction d(n) of D† yDy as a(x, y) = ∞ X n>0 a(n)(x)d(n)(y). (2.56) (2.56) This is perfectly consistent with eqs. (2.44) and (2.55). Comparing this with the decom- position of Aµ in eq. (2.40), it is quite natural that the absorbing state A(n>0) µ and the absorbed state a(n>0) have the same wave function d(n>0). We briefly summarize the gauge sector with figure 2. 2.3 Generic models There are only two massless states in the low energy effective theory in four dimensions: the one is the gauge field A(0) µ and the other is the U(1) NG field θ(0). There are infinite KK towers of A(KK) µ (eating a(KK)), and θ(KK). Several lower KK discrete modes would be localized on the domain wall, followed by the infinite KK bulk modes. These spectra are dependent of the details of the model. However, it is always true that the massless states are gapped from the KK towers by the order of inverse of the domain wall width. 3 Neutral stabilizers in higher dimensions For example, a domain wall in D = 5, a vortex in D = 6, a monopole in D = 7, and so on.2 Furthermore, we will assume that the neutral stabilizer H locally condenses about the topological soliton as H →H0(y) = ( non-zero · · · around the topological soliton zero · · · far from the topological soliton . (3.1) (3.1) Hereafter, we will use y to express the extra dimensional coordinates y = {x4,x5,··· ,xD−1}. Thus, the coefficient β(H) in the gauge kinetic term (2.2) becomes a nontrivial function of the extra dimensional coordinates as Hereafter, we will use y to express the extra dimensional coordinates y = {x4,x5,··· ,xD−1}. Thus, the coefficient β(H) in the gauge kinetic term (2.2) becomes a nontrivial function of the extra dimensional coordinates as β0(y) = β(H0(y)). (3.2) (3.2) As a natural extension of eq. (2.39), it will turn out that the sufficient condition to β0 for a massless 4D gauge field to be localized on the topological soliton is the square integrability of β0 As a natural extension of eq. (2.39), it will turn out that the sufficient condition to β0 for a massless 4D gauge field to be localized on the topological soliton is the square integrability of β0 0 < Z dD−4y β2 0 < ∞. (3.3) (3.3) This implies that β is non-zero and quickly approaches to zero at the extra-dimensional spatial infinity. This implies that β is non-zero and quickly approaches to zero at the extra-dimensional spatial infinity. 3 Neutral stabilizers in higher dimensions Let us next extend the previous 5D models to generic D dimensional models. We study the Lagrangians which are formally same as those given in eqs. (2.1) and (2.2), by reinterpreting the spacetime indices M, N = 0, 1, · · · , D −1. In the following arguments, we will not specify a concrete model for the scalar part Ls(H, T), as we did in section 2.3. Instead, – 11 – Aµ <latexit sha1_base64="XSV3qU0cknvS+cOgQL/l9pzqeAE=">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</latexit><latexit 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sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">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</latexit><latexit sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">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</latexit><latexit sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">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</latexit><latexit sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">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</latexit> θ(0) <latexit sha1_base64="WTkBQ9OMXelNsaFWzkT7YziDUQ=">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</latexit><latexit sha1_base64="WTkBQ9OMXelNsaFWzkT7YziDUQ=">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</latexit><latexit sha1_base64="WTkBQ9OMXelNsaFWzkT7YziDUQ=">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</latexit><latexit sha1_base64="WTkBQ9OMXelNsaFWzkT7YziDUQ=">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</latexit> Adf y = ηβ−1 0 <latexit sha1_base64="BXay0namR2PL5eaCvyfYxwhTkVk=">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</latexit><latexit sha1_base64="BXay0namR2PL5eaCvyfYxwhTkVk=">AChXichVFNSxtBGH6ytU1MPxLbi+BlabB4MbxbpC1CadSLR7+igtFld53Exf1idxJIl1w9+Ac8eFIQEb3aP9CLf8CDP6F4tODFQ9sFkSD9h1m5pln3uedZ2bMwLEjSXSVUV4MvHyVzQ3mX795+65QHq/HPnN0BJVy3f8cNU0IuHYnqhKWzpiNQiF4ZqOWDG3Z7r7Ky0RrbvLcl2INZdo+HZdsyJFN6UZ3S2xtxLXTVzXpH/a7WhDTUmsmjThvxuNbRiyUqUxJqP9BSUEIac37xGDVswoeFJlwIeJCMHRiIuK1BAyFgbh0xcyEjO9kX6CDP2iZnCc4wmN3mscGrtZT1eN2tGSVqi09xuIesVDFKl3RCN3RBp/SH7p6sFSc1ul7aPJs9rQj0wu7w4u1/VS7PElv3qmc9S9TxLfFqs/cgYbq3sHr61s+9m8XJhdH4Ex3SNfs/oCv6zTfwWn+to3mxsI8f4D2+Ln7wfLnsZ4fqJUmU6/IocRfMQYv/dXVDCLOVT53B2c4Ry/lKwyrkwoX3qpSibVfMCDUH78A6XMlOo=</latexit><latexit sha1_base64="BXay0namR2PL5eaCvyfYxwhTkVk=">AChXichVFNSxtBGH6ytU1MPxLbi+BlabB4MbxbpC1CadSLR7+igtFld53Exf1idxJIl1w9+Ac8eFIQEb3aP9CLf8CDP6F4tODFQ9sFkSD9h1m5pln3uedZ2bMwLEjSXSVUV4MvHyVzQ3mX795+65QHq/HPnN0BJVy3f8cNU0IuHYnqhKWzpiNQiF4ZqOWDG3Z7r7Ky0RrbvLcl2INZdo+HZdsyJFN6UZ3S2xtxLXTVzXpH/a7WhDTUmsmjThvxuNbRiyUqUxJqP9BSUEIac37xGDVswoeFJlwIeJCMHRiIuK1BAyFgbh0xcyEjO9kX6CDP2iZnCc4wmN3mscGrtZT1eN2tGSVqi09xuIesVDFKl3RCN3RBp/SH7p6sFSc1ul7aPJs9rQj0wu7w4u1/VS7PElv3qmc9S9TxLfFqs/cgYbq3sHr61s+9m8XJhdH4Ex3SNfs/oCv6zTfwWn+to3mxsI8f4D2+Ln7wfLnsZ4fqJUmU6/IocRfMQYv/dXVDCLOVT53B2c4Ry/lKwyrkwoX3qpSibVfMCDUH78A6XMlOo=</latexit><latexit sha1_base64="BXay0namR2PL5eaCvyfYxwhTkVk=">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</latexit> ! <latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">ACanichVG7SgNBFD1ZXzG+YmwUGzFGrMJEBMUqaGMZE2MCSQi762Qdsi92NwEN+QE7K8FUCiLiZ9j4AxZ+gminYGPhzWZBNKh3mJkzZ+65c2ZGsXheow9hqSBwaHhkfBoZGx8YnIqOh3bd62Go/K8aumWU1Rkl+vC5HlPeDov2g6XDUXnBaW+3d0vNLnjCsvc845sXjFkzRQ1ocoeUYWyIjSt3K5G4yzJ/FjoB6kAxBFExopeo4wDWFDRgAEOEx5hHTJcaiWkwGATV0GLOIeQ8Pc52oiQtkFZnDJkYus0arQqBaxJ625N1erdIpO3SHlAhLsgd2wV3bPbtkT+/i1Vsuv0fVyRLPS03K7OnUym3v/V2XQ7OHwS/WnZw81bPheBXm3faZ7C7Wnbx6fveY2s4nWMrtkz+T/gj2yO7qB2XxTr3Z5toMIfUDq53P3g/3VZIrw7lo8vRV8RjzWMQKvfc60thBnf3SnO0Qm9SDFpTprvpUqhQDODbyEtfQKLG4yK</latexit><latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">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</latexit><latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">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</latexit><latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">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</latexit> massless vector massive vector unphysical massless NG massive NG d(0) = β0 <latexit 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sha1_base64="H0GKair8Idz8EsDhAuK8O/T6wTs=">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</latexit> d(KK) <latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit> q(KK) <latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit> q(0) = H0 <latexit sha1_base64="ouyWNOAIUBMYogGN0B0Ab3rqwhU=">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</latexit><latexit sha1_base64="ouyWNOAIUBMYogGN0B0Ab3rqwhU=">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</latexit><latexit 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A brief summary of the effective fields localized on the domain wall by a neutral stabilizer H in five-dimensional models. 4D JHEP10(2019)098 Figure 2. A brief summary of the effective fields localized on the domain wall by a neutral stabilizer H in five-dimensional models. we will assume that the Lagrangian Ls(H, T) allows for the scalar field T to give rise to a topological soliton whose world-volume dimensions are four (codimension is D −4). For example, a domain wall in D = 5, a vortex in D = 6, a monopole in D = 7, and so on.2 Furthermore, we will assume that the neutral stabilizer H locally condenses about the topological soliton as we will assume that the Lagrangian Ls(H, T) allows for the scalar field T to give rise to a topological soliton whose world-volume dimensions are four (codimension is D −4). 3.1 Useful formulae For later convenience, let us first correct some useful equations. Let us introduce a differ- ential operator Da and its adjoint operator D† a by Da = −β0∂a 1 β0 , D† a = 1 β0 ∂aβ0, (a = 4, 5, · · · , D −1). (3.4) (3.4) 2Here, T symbolically stands for multiple scalar fields which are needed to form a topological soliton. 2Here, T symbolically stands for multiple scalar fields which are needed to form a topological soliton – 12 – Clearly, these are natural extensions of Dy and D† y given in eq. (2.36). They satisfies the following algebra Clearly, these are natural extensions of Dy and D† y given in eq. (2.36). They satisfies the following algebra h Da, D† b i = −2 (∂a∂b log β0) , [Da, Db] = h D† a, D† b i = 0. (3.5) (3.5) We will frequently encounter a self-adjoint operator defined by We will frequently encounter a self-adjoint operator defined by D† aDa = −∂2 a + (∂2 aβ0) β0 , (3.6) (3.6) where the sum on a is implicitly taken. We will also use the following vector notation where the sum on a is implicitly taken. We will also use the following vector notation JHEP10(2019)098 JHEP10(2019)098 ⃗D =    D4 ... DD−1   , ⃗D† =  D† 4, · · · , D† D−1  . (3.7) (3.7) Clearly, ⃗D† ⃗D = D† aDa is positive semidefinite. Let d(n) be eigenstates of ⃗D† ⃗D as ⃗D† ⃗Dd(n) = m2 D,nd(n). (3.8) (3.8) Suppose d(0) be a normalizable eigenfunction. Then, we have 0 = Z dD−4y d(0) ⃗D† ⃗D d(0) = Z dD−4y  Dad(0)2 . (3.9) (3.9) Therefore, d(0) must be annihilated by all Da’s as Dad(0) = 0, (a = 4, 5, · · · ). (3.10) (3.10) There is a unique solution up to a normalization constant to these equations d(0) = β0. (3.11) (3.11) We now understand the square integrability condition (3.3) is nothing but ensuring the normalizablity for the zero mode of ⃗D† ⃗D. Namely, we here proved the existence and uniqueness of the normalizable zero eigenfunction d(0) of ⃗D† ⃗D. Note that the previous work [50] also studied the zero mode d(0), where the uniqueness was only proved for a radially symmetric background solution β0 which is a function of r = p (xa)2. 3.1 Useful formulae Another self-adjoint operator will also take part in the following arguments, DaD† a = −∂2 a + ∂2 aβ−1 0  β−1 0 . (3.12) (3.12) Similarly to ⃗D† ⃗D, this operator is positive semidefinite. An obvious zero eigenstate ˜d(0) is given by 1 ˜d(0) = 1 β0 , (3.13) (3.13) up to a constant. However, this is non-normalizable under the condition (3.3). Thus, we conclude that there are no normalizable eigenstates for zero eigenvalue of DaD† a. up to a constant. However, this is non-normalizable under the condition (3.3). Thus, we conclude that there are no normalizable eigenstates for zero eigenvalue of DaD† a. – 13 – There is a useful corollary. Let {Ba(y)} be a set of D −4 non-singular and finite functions. Then we find that DaBa is orthonormal to d(0). This can be shown as follows: Z dD−4y d(0)D† aBa = Z dD−4y  Dad(0) Ba = 0, (3.14) (3.14) where we have used eq. (3.10). where we have used eq. (3.10). Finally, let us mention about ⃗D ⃗D† which is “super-partner” of ⃗D† ⃗D = D† aDa. Note that ⃗D ⃗D† is a (D −4) × (D −4) matrix operator and it is different form the one by one operator DaD† a. Zero eigenstates of ⃗D ⃗D† are given by ⃗˜d(0) = ⃗aβ−1 0 , (3.15) JHEP10(2019)098 (3.15) with ⃗a being a constant D −1 vector. This is non-normalizable under the condition (3.3). It is easy to show that non-zero eigenvalues of ⃗D† ⃗D and ⃗D ⃗D† coincide as with ⃗a being a constant D −1 vector. This is non-normalizable under the condition (3.3). It is easy to show that non-zero eigenvalues of ⃗D† ⃗D and ⃗D ⃗D† coincide as ⃗D ⃗D†( ⃗Dd(n)) = ⃗D( ⃗D† ⃗Dd(n)) = m2 D,n ⃗Dd(n). (3.16) (3.16) 3.2 The quadratic Lagrangian With these preparations at hand, we are now ready to study mass spectra of the small fluctuations about the soliton background. We use the same notations for the scalar fluc- tuations τ(xµ, y), ϑ(xµ, y) and h(xµ, y) as eq. (2.11). Of course, here, we understand y to represent the extradimensional coordinates y = {xa}. As in the five dimensional case, AM = 0 for the soliton background, and we again use AM(x, y) itself for the small fluctu- ations. First thing we have to do is to fix the U(1) gauge symmetry. To this end, similarly to the 5D case, we add the following gauge fixing term Lξ = −2β2 ξ  ∂µAµ + ξ 1 β2 ∂a β2Aa 2 . (3.17) (3.17) As before, we use canonically normalized fields AM ≡2βAM. Then, we find that the quadratic Lagrangian consists of two independent parts: The scalar part and the gauge part as L(2) = L(2) s + (Lg + Lξ) quad. (3.18) (3.18) The gauge part is given by (Lg + Lξ) quad = 1 2AµΓµνAν + 1 2AaΓabAb, (3.19) (3.19) with with Γµν = ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν ⃗D† ⃗D, (3.20) Γab = −  □δab + Hab + ξDaD† b  . (3.21) (3.20) (3.21) We defined Hab ≡δab ⃗D† ⃗D −D† bDa, (3.22) We defined We defined Hab ≡δab ⃗D† ⃗D −D† bDa, (3.22) Hab ≡δab ⃗D† ⃗D −D† bDa, (3.22) – 14 – which satisfies the following identity which satisfies the following identity which satisfies the following identity HabDb = 0. (3.23) HabDb = 0. (3.2 HabDb = 0. (3.23) The scalar part for H0 ̸= 0 is given by The scalar part for H0 ̸= 0 is given by The scalar part for H0 ̸= 0 is given by t for H0 ̸= 0 is given by L(2) s = −⃗ξ T □+ M2 ⃗ξ −h2 0 ϑ □−H−2 0 ∂aH2 0∂a  ϑ , (3.24) L(2) s = −⃗ξ T □+ M2 ⃗ξ −h2 0 ϑ □−H−2 0 ∂aH2 0∂a  ϑ , (3.24) (3.24) with ⃗ξ = τ h ! , M2 =  −∂2 a + ∂2V (T0,H0) ∂T 2 0 ∂2V (T0,H0) ∂T0∂H0 ∂2V (T0,H0) ∂T0∂H0 −∂2 a + ∂2V (T0,H0) ∂H2 0  . (3.25) (3.25) JHEP10(2019)098 JHEP10(2019)098 3.2.1 The scalar part We can further rewrite the above scalar quadratic Lagrangian with respect to the canoni- cally normalized field θ defined in eq. (2.22) as We can further rewrite the above scalar quadratic Lagrangian with respect to the canoni- cally normalized field θ defined in eq. (2.22) as L(2) s = −⃗ξ T □+ M2 ⃗ξ −1 2θ  □+ Q† aQa  θ, (3.26) (3.26) where we defined the differential operators which are natural extension of Qy and Q† y by where we defined the differential operators which are natural extension of Qy and Q† y by Qa ≡−∂a + ∂aH0 H0 , Q† a ≡∂a + ∂aH0 H0 . (3.27) (3.27) As in the five dimensional model, Qa and Da coincide if β0 ∝H0. It is obvious that Q† aQa has a unique zero eigenstate (0) As in the five dimensional model, Qa and Da coincide if β0 ∝H0. It is obvious that Q† aQa has a unique zero eigenstate ( ) q(0) = H0. (3.28) (3.28) Thus we conclude that θ has the physical zero mode (U(1) NG mode) and expanded as Thus we conclude that θ has the physical zero mode (U(1) NG mode) and expanded as θ(x, y) = H0θ(0)(x) + ∞ X n>0 q(n)(y)θ(n)(x). (3.29) (3.29) 3.2.2 The four dimensional component Aµ 3.2.3 The extra dimensional component Aa Let us next turn to the extra dimensional components Aa which provide additional scalar fields to the low energy effective theory in four dimensions. The multiple scalars Aa make the quadratic Lagrangian more complicated compared to the one in five dimensions. To make the matter clear, let us first decompose Aa into a divergence part Ad a and divergence- free parts Adf a as Ad a = PabAb, Adf a = (δab −Pab)Ab, (3.33) (3.33) with a projection operator with a projection operator JHEP10(2019)098 JHEP10(2019)098 Pab = Da  ⃗D† ⃗D −1 D† b. (3.34) (3.34) It satisfies the following equations It satisfies the following equations It satisfies the following equations PabPbc = Pac, D† aPab = D† b, PabDb = Da. (3.35) (3.35) With these at hand, it is straightforward to verify the divergence free condition should be satisfied D† aAdf a = 0. (3.36) (3.36) One immediately finds that Adf a includes a component proportional to β−1 0 as One immediately finds that Adf a includes a component proportional to β−1 0 as ⃗Adf = β−1 0 ⃗η + ⃗A bdf, (3.37) (3.37) with ⃗η being an arbitrary but constant N vector, and ⃗A bdf standing for rest component orthogonal to β−1 0 ⃗η. However, we should remove β−1 0 ⃗η since it diverges at the spatial infinity. This is an extension of eq. (2.53) in the D = 5 case. In contrast to the D = 5 case, there still exist physical degrees of freedom in ⃗A bdf in the higher dimensions. From the definition of Ad a given in eq. (3.33) and the identity (3.23), it also follows HabAd b = 0. (3.38) (3.38) Since the projection operator includes the inverse of ⃗D† ⃗D, one might worry whether it is well defined or not. However, it is always well defined because D† aAa is orthonormal to the zero mode d(0) of ⃗D† ⃗D, see the corollary in eq. (3.14). Now, by using eqs. (3.36) and (3.38), we can rewrite the quadratic Lagrangian as 1 2AaΓabAb = −1 2A bdf a (δab□+ Hab) A bdf b −1 2Ad a  δab□+ ξDaD† b  Ad b. (3.39) (3.39) The divergence and the divergence-free parts are decoupled. The divergence part Let us first examine the divergence part. The divergence part Ad a essentially include only one independent degree of freedom. 3.2.2 The four dimensional component Aµ The quadratic Lagrangian for Aµ The quadratic Lagrangian for Aµ 1 2AµΓµνAν = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν ⃗D† ⃗D  Aν (3.30) (3.30) is a natural extension of eq. (2.35) by exchanging D† yDy by ⃗D† ⃗D. We naturally expand the four dimensional components Aµ by the eigenfunctions of ⃗D† ⃗D as Aµ(x, y) = ∞ X n=0 A(n) µ (x)d(n)(y). (3.31) (3.31) As was proved in eq. (3.11), the ground state is unique d(0) ∝β0 with m0 = 0, and there is a finite mass gap (about inverse of the background soliton width) between the ground state and excited states. Plugging this into the Lagrangian and integrating it in the extra dimensional coordinate y, we find the four dimensional effective Lagrangian for A(n) µ as As was proved in eq. (3.11), the ground state is unique d(0) ∝β0 with m0 = 0, and there is a finite mass gap (about inverse of the background soliton width) between the ground state and excited states. Plugging this into the Lagrangian and integrating it in the extra dimensional coordinate y, we find the four dimensional effective Lagrangian for A(n) µ as Z dD−4y 1 2AµΓµνAν = ∞ X n=0 1 2A(n) µ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνm2 n  A(n) ν . (3.32) (3.32) – 15 – – 15 – 3.2.3 The extra dimensional component Aa Similarly to the five dimen- sional case in eq. (2.55), let us define a scalar field as a = 1 p ⃗D† ⃗D D† aAa. (3.40) (3.40) – 16 – – 16 – Then, the divergence part of eq. (3.39) can be written as Then, the divergence part of eq. (3.39) can be written as Then, the divergence part of eq. (3.39) can be written as −1 2Ad a  δab□+ ξDaD† b  Ad b = −1 2a  □+ ξ ⃗D† ⃗D  a. (3.41) (3.41) Since D† aAa is orthogonal to the zero mode d(0) of ⃗D† ⃗D, a is also independent of d(0). Hence, a is expanded by the eigenstates d(n) of ⃗D† ⃗D as a = ∞ X n>0 d(n)(y)a(n)(x). (3.42) (3.42) Then contributions to the low energy effective action from the divergence part is JHEP10(2019)098 Z dD−4y −1 2Ad a  δab□+ ξDaD† b  Ad b = ∞ X n>0 −1 2a(n) □+ ξm2 n  a(n). (3.43) (3.43) This together with eq. (3.32) for the four dimensional component Aµ, we confirm that the massless gauge boson A(0) µ robustly exists even in higher dimensional case, and all the KK modes A(n>0) µ become heavy by eating a(n). This together with eq. (3.32) for the four dimensional component Aµ, we confirm that the massless gauge boson A(0) µ robustly exists even in higher dimensional case, and all the KK modes A(n>0) µ become heavy by eating a(n). The divergence-free parts Our last task in this subsection is clarifying mass spectra for the divergence-free part A bdf a , which are new degrees of freedom appearing only for D ≥6. To this end, let us first note that the operator Hab can be expressed in the following form 1 Hab = 1 (N −2)!εi1i2···iN−2adεi1i2···iN−2bcD† dDc , (3.44) (3.44) where εi1···iN is an N = D −4 dimensional completely anti-symmetric tensor. We can rewrite this as a product of a N 2  × N matrix D and its adjoint D† as where εi1···iN is an N = D −4 dimensional completely anti-symmetric tensor. We can rewrite this as a product of a N 2  × N matrix D and its adjoint D† as H = D†D . 3.2.3 The extra dimensional component Aa (3.45) (3.45) One can easily imagine the components of D from the first several examples One can easily imagine the components of D from the first several examples D N=2 = (D5, −D4) , (3.46) D N=3 =  0 D6 −D5 −D6 0 D4 D5 −D4 0  , (3.47) D N=4 =    0 0 D7 −D6 0 −D7 0 D5 0 D6 −D5 0 D7 0 0 −D4 −D6 0 D4 0 D5 −D4 0 0   . (3.48) We can construct D N+1 from D N as We can construct D N+1 from D N as D N+1 =               0 ... D N(a →a + 1) 0 (−1)N−1DN+4 (−1)ND4 (−1)N−2DN+3 (−1)N−1D4 ... ... D5 −D4               , (3.49) (3.49) – 17 – where D N(a →a + 1) means D N whose indices are all shifted by 1 as a →a + 1. Obviously, the decomposition is not unique under a unitary transformation D →UD with U ∈U N 2  . However, this ambiguity does not yields any physical consequences. So we fix the ambiguity by choosing a specific D. We are primally interested in existence of a massless state since its presence would be critical in the low energy effective theory on the host topological soliton. Since H in eq. (3.45) is semi-positive definite, the zero eigenstate is unique and satisfies D⃗α(0) = 0, ⃗α(0) =   α(0) 4 ... α(0) D−1  . (3.50) (3.50) JHEP10(2019)098 For example, this condition in the D = 6, 7, 8 cases read For example, this condition in the D = 6, 7, 8 cases read For example, this condition in the D = 6, 7, 8 cases read D = 6 : D5α(0) 4 −D4α(0) 5 = 0, (3.51) D = 7 :   D6α(0) 5 −D5α(0) 6 D4α(0) 6 −D6α(0) 4 D5α(0) 4 −D4α(0) 5  = 0, (3.52) D = 8 :        D7α(0) 6 −D6α(0) 7 D5α(0) 7 −D7α(0) 5 D6α(0) 5 −D5α(0) 6 D7α(0) 4 −D4α(0) 7 D4α(0) 6 −D6α(0) 4 D5α(0) 4 −D4α(0) 5        = 0. 3We should mention about the result of the previous work [50] on the divergence free part. In [50], the spectrum of the divergence free parts was studied only for D = 6 case in detail where the absence of the massless mode was assumed. Furthermore, the massless modes in higher dimensional models (D > 6) were not understood very well in [50]. 3.2.3 The extra dimensional component Aa (3.53) (3.51) (3.52) (3.53) hese can easily be generalized in generic D dimensions as D[aα(0) b] = 0, (3.54) (3.54) for all a, b = {4, · · · , D −1}. By using the definition in eq. (3.4) and the assumptions β0 ̸= 0, we can rewrite this as for all a, b = {4, · · · , D −1}. By using the definition in eq. (3.4) and the assumptions β0 ̸= 0, we can rewrite this as Bab ≡∂a α(0) b β0 ! −∂b α(0) a β0 ! = 0. (3.55) (3.55) Let us take any three indices from {4, · · · , D −1}, say 4, 5, 6. For this choice, B45 = B56 = B46 = 0 is just a vorticity zero condition to the three vector  α(0) 4 β0 , α(0) 5 β0 , α(0) 6 β0  . The same is true for any choice of three indices. Therefore, from the conventional Stokes’ theorem in three spatial dimensions, the massless condition (3.55) means that there exists a potential −λ(y) β0(y) by which any α(0) a can be expressed as α(0) a β0 = ∂a  −λ β0  ⇔ α(0) a = Daλ. (3.56) (3.56) – 18 – Finally, we have to verify if this is divergence-free or not. Indeed, it is a divergence part which can be seen as Z dD−4y ⃗α(0) · ⃗Adf = Z dD−4y ⃗Dλ · ⃗Adf = Z dD−4y λ ⃗D† ⃗Adf = 0. (3.57) (3.57) Namely, the operator H has no divergence-free zero modes in generic D dimensions.3 Namely, the operator H has no divergence-free zero modes in generic D dimensions.3 In order to clarify massive modes of the divergence-free parts, firstly, let us introduce the eigenvectors ¯f(n)(y) and eigenvalues ¯m2 D,n of the N 2  × N 2  Hermitian operator ¯H = DD† dual to H as In order to clarify massive modes of the divergence-free parts, firstly, let us introduce the eigenvectors ¯f(n)(y) and eigenvalues ¯m2 D,n of the N 2  × N 2  Hermitian operator ¯H = DD† dual to H as ¯H ≡DD†, ¯H ¯f(n) = ¯m2 D,n ¯f(n), (3.58) (3.58) JHEP10(2019)098 JHEP10(2019)098 where ¯f(n) is a N 2  vector whose component is ¯f(n) ˜a (¯a = 1, 2, · · · , N 2  ). 3.2.3 The extra dimensional component Aa Then it is straightforward to show where ¯f(n) is a N 2  vector whose component is ¯f(n) ˜a (¯a = 1, 2, · · · , N 2  ). Then it is straightforward to show HD† ¯f(n) = ¯m2 D,nD† ¯f(n), ( ¯mD,n ̸= 0). (3.59) (3.59) A nice thing for this is that the divergence-free condition is automatically satisfied for any ¯f(n) as   D† a  D† ¯f(n) a = 0. (3.60) (3.60) This can be proved by acting D† a on (D†)a¯a given in eqs. (3.51)–(3.53) as D† a(D†)a¯a = 0, (D)¯aaDa = 0. (3.61) (3.61) Expanding the divergence-free parts as Expanding the divergence-free parts as Expanding the divergence-free parts as ⃗A bdf = X n̸=0 L(n)(x)D† ¯f(n) ¯mD,n , (3.62) (3.62) and plugging this into the quadratic Lagrangian and integrating it over the extra dimen- sions, we get Z dD−4y 1 2A bdf a Γdf abA bdf b = −1 2 X n̸=0 L(n) □+ ¯m2 D,n  L(n). (3.63) (3.63) This expression is formally valid for any β. This expression is formally valid for any β. Unfortunately, it is still not clear the relation between the eigenvalue m2 D,n of the ⃗D† ⃗D operator and ¯m2 D,n of the ¯H = DD† operator. For this point, the D = 6 case is especially simple as ¯H D=6 = DD† D=6 = DaD† a. (3.64) (3.64) We briefly summarize the gauge sector with figure 3. Similarly to the 5D case, there are only two massless states in the low energy effective theory in four dimensions: the one is the gauge field A(0) µ and the other is the U(1) NG field θ(0). In addition to the infinite KK towers of A(KK) µ (eating a(KK)), θ(KK), there newly appear another KK towers of A bdf(KK) a . 3We should mention about the result of the previous work [50] on the divergence free part. In [50], the spectrum of the divergence free parts was studied only for D = 6 case in detail where the absence of the massless mode was assumed. 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sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">ACeHichVHLSgMxFD0d3/V7UZwUyz1sSmpCIor0Y3QjVarQlvLzJi2Q+fFTFqoQ3/AH3DhQhREi5/hxh9w4SeISwVBXHg7HRAt6g1JTk7uTlJFvXMHY0jq6e3rHxgcCg+PjI6NRyYm91yr5qg8q1q65Rwost1zeRZoQmdH9gOlw1F5/tKdaO9v1/njqtZ5q5o2LxgyGVTK2mqLIgqRqJ5UeFCPvTmvbxjxNLp5kKzGImzJPMj1g1SAYgjiC0rco08jmBRQ0GOEwIwjpkuNRySIHBJq4AjziHkObvczQRJm2NsjhlyMRWaSzTKhewJq3bNV1frdIpOnWHlDEk2ANrsRd2z27ZE/v4tZbn12h7adCsdLTcLo6fTO28/asyaBaofKn+9CxQworvVSPvts+0b6F29PXj05ed1UzCm2WX7Jn8X7BHdkc3MOuv6tU2z5whTB+Q+vnc3WBvMZkivL0UX1sPvmIQ05jBPL3MtawiS1k6dwGznGDVuhdiklz0kInVQoFmi+hbT4CXZAkWc=</latexit><latexit 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sha1_base64="UbRQlY4gfmVHSnP6JHUn5F/PZQ=">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</latexit><latexit 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sha1_base64="H0GKair8Idz8EsDhAuK8O/T6wTs=">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</latexit> d(KK) <latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit><latexit sha1_base64="PzCJug5/tInFPStPyEVx7utmgPs=">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</latexit> q(KK) <latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit sha1_base64="ID3obeMy85UDzTurEjMPOMa1J9Q=">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</latexit><latexit 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sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">ACanichVG7SgNBFD1ZXzG+YmwUGzFGrMJEBMUqaGMZE2MCSQi762Qdsi92NwEN+QE7K8FUCiLiZ9j4AxZ+gminYGPhzWZBNKh3mJkzZ+65c2ZGsXheow9hqSBwaHhkfBoZGx8YnIqOh3bd62Go/K8aumWU1Rkl+vC5HlPeDov2g6XDUXnBaW+3d0vNLnjCsvc845sXjFkzRQ1ocoeUYWyIjSt3K5G4yzJ/FjoB6kAxBFExopeo4wDWFDRgAEOEx5hHTJcaiWkwGATV0GLOIeQ8Pc52oiQtkFZnDJkYus0arQqBaxJ625N1erdIpO3SHlAhLsgd2wV3bPbtkT+/i1Vsuv0fVyRLPS03K7OnUym3v/V2XQ7OHwS/WnZw81bPheBXm3faZ7C7Wnbx6fveY2s4nWMrtkz+T/gj2yO7qB2XxTr3Z5toMIfUDq53P3g/3VZIrw7lo8vRV8RjzWMQKvfc60thBnf3SnO0Qm9SDFpTprvpUqhQDODbyEtfQKLG4yK</latexit> ~D† ~D <latexit 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sha1_base64="2T+32bKQ/V+imyfnJlepMTiL5k=">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</latexit><latexit sha1_base64="2T+32bKQ/V+imyfnJlepMTiL5k=">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</latexit><latexit sha1_base64="2T+32bKQ/V+imyfnJlepMTiL5k=">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</latexit> ⇠~D† ~D <latexit 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sha1_base64="MO7Gcha3gPI4DsiKDd6ojv1iko=">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</latexit><latexit sha1_base64="MO7Gcha3gPI4DsiKDd6ojv1iko=">ACfnichVHLSsNAFD3Gd31F3ShuiqXFjXUiguJK1IVLX1XB1pKk0zqYF0ka1CLu/QEXrhRERNCPcOMPuOgniMsKblx4mwZEi3pDZs49c8+dMzOaYwjPZ6zaIrW2tXd0dnXHenr7+gfkwaEtzy67Os/otmG7O5rqcUNYPOML3+A7jstVUzP4tnawVF/fDrjrCdva9I8cnjPVkiWKQld9ovLyaPZQxLMB1+PLe9mCWipxN0rzcoKlWRjxZqBEIEoVm35BlkUYENHGSY4LPiEDajw6NuFAgaHuBwqxLmERLjOcYIYactUxalCJfaAxhJluxFrUV7v6YVqnXYx6HdJGUeSPbNbVmNP7I69sI9fe1XCHnUvRzRrDS138gNnIxv/6pMmn3sf6n+9OyjiLnQqyDvTsjUT6E39MHxeW1jfj1ZSbEr9kr+L1mVPdIJrOBNv17j6xeI0QMoP6+7GWxNpxXCazOJhcXoKbowhnFM0H3PYgErWEWG9j3FNe7xIEFKSZPSVKNUaok0w/gW0twnj4CSPw=</latexit><latexit 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sha1_base64="wUDwlxnBG8ZXwOIlAztEXKrus=">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</latexit> hamiltonian L(KK) <latexit 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sha1_base64="fZr/oibWFl4EQNPFKJPfWXheoc=">ACj3ichVG7SgNBFD1ZXzE+kmgj2ASDEhuZiBCxkKCNEos8TBQ0yu46iUv2xe4mEJf8gD+gYKVgIfb+gI0/YJFPEsFGwvbhZERb3DzJw5c8+dM1zJVBXbYawbEvr6BwaHwsORkdGx8WgsPlGxjaYl87JsqIa1K4k2VxWdlx3FUfmuaXFRk1S+IzXWvfudFrdsxdC3nbJq5pY15WaIosOUQdbB27K3be0RC7Xme8cxpJsgfmR+AnSAUgiLwRu8M+jmBARhMaOHQ4hFWIsGnsIQ0Gk7gqXOIsQop/z9FBhLRNyuKUIRLboLVOp72A1ens1bR9tUyvqDQtUiYwyx7ZDXthD+yWPbH3X2u5fg3PS5t2qafl5mH0dKr09q9Ko93B8afqT8Oalj2vSrk3fQZ7xdyT986OXsprRn3Tl2xZ7J/yXrsnv6gd56la8LvHjxhx+JvHjtSX9vxk9QWVxIEy4sJbNrQaPCmMYMUtSNDLYQB5lqm7hHJe4EuJCRlgVsr1UIRoJvElhM0PHb2UwA=</latexit> Figure 3. A brief summary of the effective fields localized on a topological soliton by a neutral stabilizer H in higher dimensional models. JHEP10(2019)098 Figure 3. A brief summary of the effective fields localized on a topological soliton by a neutral stabilizer H in higher dimensional models. Figure 3. A brief summary of the effective fields localized on a topological soliton by a neutral stabilizer H in higher dimensional models. 4 Localization by a charged stabilizer in D = 5 In this section, we will again consider five dimensional models in which the stabilizer h is not neutral but has a charge to the would-be localized U(1) gauge field. Namely, we slightly modify the Lagrangian Ls in eq. (2.4) as Ls = DMHDMH∗+ ∂MT∂MT −V (H, T), (M = 0, 1, 2, 3, 4), (4.1) (4.1) with the conventional covariant derivative DMH = ∂MH + iqAMH. (4.2) (4.2) As before, we adopt the notation that the gauge coupling constant is absorbed in the gauge field AM, and q stands for a charge of H to the U(1) gauge transformation. Except for the change ∂MH →DMH, we will not modify the Lagrangian (2.1). Thus, the Lagrangian L respects the five dimensional Lorentz symmetry and the U(1) gauge symmetry. The charged stabilizer H now interacts with the U(1) gauge field AM through both the covariant derivative and the function β(H) in front of the F2 term. This is a seed for a mixture of the Higgs mechanism which takes place inhomogeneously, and the localization of the gauge field on the domain wall. This is what we will clarify in this section. The Euler-Lagrange equations are slightly modified as DMDMH + ∂V ∂H∗= −2β ∂β ∂H∗FMNFMN, (4.3) ∂M∂MT + ∂V ∂T = 0, (4.4) ∂M β2FMN = iq HDNH∗−H∗DNH  . (4.5) (4.3) (4.5) Note that we can set H to be real, and then AM = 0 solves the third equation. The first and second equations with AM = 0 are identical with those in the previous section, so that Note that we can set H to be real, and then AM = 0 solves the third equation. The first and second equations with AM = 0 are identical with those in the previous section, so that – 20 – the background soliton configuration with T = T0(y) and H = H0(y) (H0 is real) remains as the solution. In what follows, we will assume H0 ̸= 0. Let us next perturb the background solution as before. The fluctuations are introduced as T = T0 + τ, H = eiϑ(H0 + h), and AM itself stands for the small fluctuation. We will obtain a quadratic Lagrangian for the fluctuations for figuring out mass spectra. A difference from the previous model with the neutral scalar resides only in the covariant derivative as DMH = eiϑ {∂M(H0 + h) + iH0(∂Mϑ + qAM)} . 4 Localization by a charged stabilizer in D = 5 (4.6) (4.6) Namely, a change from the neutral scalar case is realized by just an exchange JHEP10(2019)098 (4.7) ∂Mϑ →DMϑ ≡∂Mϑ + qAM. (4.7) Therefore, the quadratic Lagrangian of the scalar sector can immediately obtained as L(2) s = −⃗ξ T ∂µ∂µ + M2 ⃗ξ + H2 0ϑ  D† µDµ −H−2 0 D† yH2 0Dy  ϑ, (4.8) (4.8) where D† Mϑ = −∂Mϑ + qAM, and ⃗ξ and M2 are defined in eqs. (2.13) and (2.33), respec- tively. Let us rewrite the quadratic Lagrangian with respect to the canonical field θ defined in eq. (2.22) as L(2) s = −⃗ξ T ∂µ∂µ + M2 ⃗ξ + 1 2(∂µθ + q √ 2H0Aµ)(∂µθ + q √ 2H0Aµ) −1 2(Qyθ −q √ 2H0Ay)(Qyθ −q √ 2H0Ay). (4.9) (4.9) Comparing this to eq. (2.23) for the neutral case, the terms with q are added. On the contrary, the gauge sector L(2) g is unchanged since it is independent of q. However, the scalar sector L(2) s newly include the mixing terms between Aµ and θ which we would like to eliminate to diagonalize mass matrices. To this end, we need to modify the gauge fixing term (2.30) in the five dimensions as Comparing this to eq. (2.23) for the neutral case, the terms with q are added. On the contrary, the gauge sector L(2) g is unchanged since it is independent of q. However, the scalar sector L(2) s newly include the mixing terms between Aµ and θ which we would like to eliminate to diagonalize mass matrices. To this end, we need to modify the gauge fixing term (2.30) in the five dimensions as Lξ = −2β2 ξ  ∂µAµ −ξ 1 β2  ∂y β2Ay  + q H0 2 √ 2θ 2 . 4 Localization by a charged stabilizer in D = 5 (4.10) (4.10) We are now ready to write down the quadratic Lagrangian in terms of the canonically normalized field AM = 2β0AM as We are now ready to write down the quadratic Lagrangian in terms of the canonically normalized field AM = 2β0AM as (Ls + Lg + Lξ) quad = −⃗ξ T ∂µ∂µ + M2 ⃗ξ + 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν  D† yDy + q2E2 0  Aν −1 2Ay□Ay −1 2θ□θ −ξ 2  D† yAy + qE0θ 2 −1 2 (Qyθ −qE0Ay)2 , (4.11 2 2 −ξ 2  D† yAy + qE0θ 2 −1 2 (Qyθ −qE0Ay)2 , (4.11) (4.11) – 21 – – 21 – where we defined E0 = H0 √ 2β0 . (4.12) E0 = H0 √ 2β0 . (4.12) Obviously, the scalar fields τ, h ∈⃗ξ stand alone. Therefore, the mass spectrum of ⃗ξ is not affected by whether the stabilizer H is neutral or not. After all, all modifications from the neutral case appear only in the sectors for AM and θ in the specific form qE0. The above Lagrangian includes two important phenomena. The one is the localization of the gauge field Aµ. As we saw in eq. (2.47) in the neutral case, the KK modes A(KK) µ get massive by absorbing a(KK) which essentially resides in Ay. The other is the conventional Higgs mechanism that a gauge field becomes massive by eating a NG scalar field associated with a spontaneously broken symmetry. For our case, roughly speaking, the NG is θ. However, it is not precise since our soliton background is inhomogeneous. Indeed, Ay and θ are mixed in eq. (4.11). Our next task is to diagonalize them, and make clear what field is physical or unphysical. JHEP10(2019)098 The simplest case Let us first consider the simplest example where E0 is a constant. Then, we immediately see from eq. (4.11) that all the mass eigenvalues of Aµ are sifted by a constant as mD,n → q m2 D,n + q2E2 0, (4.13) (4.13) where mD,n is the eigenvalue of D† yDy defined in eq. (2.37). It is important to realize that now the zero eigenvalue is gone. The massless state is now lifted by the non zero mass qE0. 4 Localization by a charged stabilizer in D = 5 This is a peculiar phenomenon which occurs as a consequence of interplay between the localization of gauge fields and the Higgs mechanism. We will explain this in more detail below. For that purpose, let us first note that β0 is proportional to H0 when E0 is constant. This implies Qy = Dy and Q† y = D† y from their definitions in eqs. (2.24) and (2.36). In addition, since the divergence-free part in Ay is not normalizable as is described below eq. (2.52), we eliminate Adf y . Hence, we can always expand Ay = Ad y by the eigenstates {Dyd(n)} of DyD† y as is given in eq. (2.44). At the same time, we expand θ by the eigenstates {d(n)} of D† yDy = Q† yQy as Ay = ∞ X n̸=0 a(n)(x)Dyd(n)(y) mD,n , θ = ∞ X n=0 θ(n)(x)d(n)(y). (4.14) (4.14) Plugging these into the quadratic Lagrangian (4.11) and integrating it over y, we find Leff= L(0) eff+ ∞ X n̸=0  L(n;1) eff + L(n;2) eff  , (4.15) (4.15) with L(0) eff= 1 2A(0) µ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνq2E2 0  A(0) ν −1 2θ(0) □+ ξq2E2 0  θ(0), (4.16) L(0) eff= 1 2A(0) µ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνq2E2 0  A(0) ν 1 L(0) eff= 1 2A(0) µ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµνq2E2 0  A(0) ν −1 2θ(0) □+ ξq2E2 0  θ(0),   ξ   −1 2θ(0) □+ ξq2E2 0  θ(0), (4.16) (4.16) (4.16) – 22 – and L(n̸=0;1) eff = 1 2A(n) µ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν m2 D,n + q2E2 0  A(n) ν −1 2a(n) q  □+ ξ m2 D,n + q2E2 0  a(n) q , (4.17) L(n̸=0;2) eff = −1 2θ(n) q  □+ m2 D,n + q2E2 0  θ(n) q , (4.18) (4.17) (4.18) where we have defined new variables, in order to diagonalize the mixed terms, as JHEP10(2019)098 a(n) q = mD,na(n) + qE0θ(n) q m2 D,n + q2E2 0 , θ(n) q = mD,nθ(n) −qE0a(n) q m2 D,n + q2E2 0 , (n ̸= 0). (4.19) (4.19) The n = 0 part (4.16) is the same form as a common quadratic Lagrangian of the gauge field under the Higgs mechanism in the Rξ gauge. 4 Localization by a charged stabilizer in D = 5 (4.11), let us introduce new variables aq and θq by D† yAy = D† yDy 1 q D† yDy + (qE0)2 aq − 1 r D† yDy −1 + (qE0)−2 θq, (4.21) θ = 1 qE0 1 r D† yDy −1 + (qE0)−2 θq + qE0 1 q D† yDy + (qE0)2 aq. (4.22) (4.21) Note that D† yAy is orthonormal to the zero mode d(0) of D† yDy whereas θ in general has non zero component for d(0). For consistency, we assume that θq is orthonormal to d(0) but aq is not. Then, after little algebras with making use of the identity (4.20), we find Note that D† yAy is orthonormal to the zero mode d(0) of D† yDy whereas θ in general has non zero component for d(0). For consistency, we assume that θq is orthonormal to d(0) but aq is not. Then, after little algebras with making use of the identity (4.20), we find JHEP10(2019)098 D† yAy + qE0θ = q D† yDy + (qE0)2 aq, (4.23) Qyθ −qE0Ay = Kθq, (4.24) (4.23) (4.23) (4.24) where we have defined K = QyqE0 r D† yDy −1 + (qE0)−2. (4.25) (4.25) ith these at hand, the Lagrangian (4.11) reads With these at hand, the Lagrangian (4.11) reads With these at hand, the Lagrangian (4.11) reads L quad = 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν  D† yDy + (qE0)2 Aν −1 2aq h □+ ξ  D† yDy + (qE0)2i aq −1 2θq h □+ K†K i θq. −1 2aq h □+ ξ  D† yDy + (qE0)2i aq −1 2θq h □+ K†K i θq. (4.26) −1 2θq h □+ K†K i θq. (4.26) (4.26) We should emphasis that the mass operator for aq precisely coincides with that of Aµ multiplied by the gauge fixing parameter ξ. Thus, what we need to do is expanding Aν and aq by the eigenfunction d(n) q of the operator D† yDy + (qE0)2 h D† yDy + (qE0)2i d(n) q = m2 Dq,nd(n) q , (4.27) (4.27) as Aµ = ∞ X n=0 A(n) µ (x)d(n) q (y), aq = ∞ X n=0 a(n) q (x)d(n) q (y). (4.28) (4.28) Plugging these into eq. (4.26), we get the formally same equations as eqs. (4.16) and (4.17) with the identification θ(0) = a(0) q . 4 Localization by a charged stabilizer in D = 5 Namely, it expresses that the longitudinal mode of A(0) µ becomes physical by eating the Nambu-Goldstone mode θ(0). As the conventional Higgs mechanism, this occurs via the coupling qAµH in the covariant derivative DMH. On the other hand, regardless of the value of q, the normalized physical vector fields A(0) µ appears on the domain wall thanks to the generalized gauge kinetic term β2FMNFMN. This is the peculiar phenomenon as the consequence of interplay of the localization of the massless gauge field and the Higgs mechanism. The same can be said to the massive modes A(n̸=0) µ . Indeed, eq. (4.17) has the same structure as eq. (4.16). Instead of eating the genuine Nambu-Goldstone mode θ(n), the KK mode A(n̸=0) µ gets massive by absorbing a(n̸=0) q which is the linear combination of a(n) and θ(n). The other scalar field θ(n) q orthonormal to a(n) q appears as a physical massive scalar field on the domain wall. In summary, there is the unique physical light vector field A(0) µ whose mass square is q2E2 0. In addition, there are the physical heavy KK vector A(n̸=0) µ and heavy KK scalar θ(n̸=0) q whose masses are separated from the lightest mass qE0 by Ωof order of the inverse of the domain wall width. Since the two mass scales independently originate, one can freely set their scales. For example, for a phenomenological use, we may set E0 of order the electroweak scale, whereas the domain wall scale Ωis taken to be much higher scale like GUT or the Planck scale. In such situation, only the light massive gauge field A(0) µ is relevant in the low energy effective theory on the domain wall [51]. The generic case After getting an intuitive and transparent understanding through the simplest example, let us next consider the generic case where E0 is not a constant. We need to go back to eq. (4.11). The crucial difference from the simplest case is that Qy and Dy are different operators. However, they relate through E0Q† y = D† yE0 . (4.20) (4.20) – 23 – In order to eliminate mixed terms of Ay and θ in eq. 4 Localization by a charged stabilizer in D = 5 In general, its mass is independent of the domain wall width, so that it is under control in the sense that it can be light or heavy according to β. So A(0) µ is qualitatively different from all other superheavy KK modes. 4 Localization by a charged stabilizer in D = 5 Interplay of the localization of gauge field and the Higgs mechanism works as follows: the massless gauge field A(0) µ absorbs a(0) q and gets non zero mass mDq,0. The higher KK gauge fields A(n̸=0) µ also absorbs a(n̸=0) q and becomes heavier than the neutral case by mD,n →mDq,n. We should note that the eating and eaten fields have the exactly same wave functions d(n) q . Figure 4 briefly summarizes the gauge sector. There are no massless states in the low energy effective theory in four dimensions as a consequence of the local Higgs mechanism – 24 – Aµ <latexit sha1_base64="XSV3qU0cknvS+cOgQL/l9pzqeAE=">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</latexit><latexit 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sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">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</latexit><latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">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</latexit> light massive vector heavy massive vector unphysical massive scalar β−1 0 <latexit 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Figure 4. A brief summary of the effective fields localized on a topological soliton by a charged stabilizer H in five-dimensional models. 5D JHEP10(2019)098 Figure 4. A brief summary of the effective fields localized on a topological soliton by a charged stabilizer H in five-dimensional models. that the massless gauge field A(0) µ eats the U(1) NG field θ(0). In general, its mass is independent of the domain wall width, so that it is under control in the sense that it can be light or heavy according to β. So A(0) µ is qualitatively different from all other superheavy KK modes. that the massless gauge field A(0) µ eats the U(1) NG field θ(0). 5 Localization by a charged stabilizer in D ≥5 We now come to analyze the most generic models with the charged stabilizer H. Namely, we will take the generic dimensions D ≥5, and the generic function for β(H). The main difference from section 3 is that the stabilizer is not neutral but has a charge q to the would-be localized gauge field AM. Furthermore, as we saw in section 4, the extension from D = 5 to D ≥6 is not straightforward but we need new analysis for the divergence free parts Adf a which would supply physical scalar fields unlike the divergence part. Let us begin with describing the Lagrangian again. The Lagrangian we will analyze in this section is same as the one in eq. (2.1). We take the same gauge kinetic part as L0 given in eq. (2.2). However, for the scalar part, instead of Ls in eq. (2.4), we consider Ls given in eq. (4.1) with M = 0, 1, 2, · · · , D −1. As before, we perturb the background configuration T0 and H0, and introduce small fluctuations τ, ϑ, h, and AM by T = T0 + τ, H = eiϑ(H0 + h). The quadratic Lagrangian for the scalar part reads L(2) s = −⃗ξ T □+ M2 ⃗ξ + H2 0ϑ  D† µDµ −H−2 0 D† aH2 0Da  ϑ, (5.1) (5.1) where DMϑ = ∂Mϑ+qAM, D† Mϑ = −∂Mϑ+qAM, and ⃗ξ and M2 are same as those given in eq. (3.25). Compared to eq. (4.8) in D = 5, the change is just Dy →Da (a = 4, 5, · · · , D−1). Accordingly, eq. (4.9) is naturally generalized as ˜L(2) = −⃗ξ T □+ M2 ⃗ξ + 1 2(∂µθ + q √ 2H0Aµ)(∂µθ + q √ 2H0Aµ) −1 2(Qaθ −q √ 2H0Aa)(Qaθ −q √ 2H0Aa), (5.2) (5.2) – 25 – – 25 – with the canonically normalized field θ = √ 2H0ϑ defined in eq. (2.22). Similarly, we also extend the gauge fixing term as with the canonically normalized field θ = √ 2H0ϑ defined in eq. (2.22). Similarly, we also extend the gauge fixing term as Lξ = −2β2 ξ  ∂µAµ −ξ 1 β2  ∂a β2Aa  + q H0 2 √ 2θ 2 . 5 Localization by a charged stabilizer in D ≥5 (5.3) (5.3) Correcting all the pieces Ls, Lg, and Lξ, and using the normalized field AM = 2β0AM, we reach the following quadratic Lagrangian L quad = −⃗ξ T □+ M2 ⃗ξ + 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν  D† aDa + q2E2 0  Aν −1 2Aa□Aa −1 2θ□θ −ξ 2  D† aAa + qE0θ 2 −1 2 (Qaθ −qE0Aa)2 −1 2AaHabAb. (5.4) JHEP10(2019)098 (5.4) Up to here, the quadratic Lagrangian is formally trivial extension of the five dimensional case given in eq. (4.11) except for the last term with H defined in eq. (3.44). However, separating multiple fields Ad a, Adf a and θ into physical and unphysical degrees of freedom is not an easy task due to the mixings among them. As in the five dimensions, the quadratic Lagrangian include Qa and Da which are related by E0Q† a = D† aE0 . (5.5) (5.5) An idea is unifying the extra dimensional gauge fields Aa and the phase θ within a N + 1 component vector ⃗A as ⃗ ! ⃗A = ⃗A θ ! . (5.6) (5.6) In addition, we extend ⃗D and H to ⃗D and H which act on ⃗A by addition, we extend ⃗D and H to ⃗D and H which act on ⃗A by ⃗D = ⃗D qE0 ! , H = H + q2E2 01D−4 −qE0 ⃗Q −q ⃗Q†E0 ⃗Q† ⃗Q ! . (5.7) (5.7) Similarly to eq. (3.23), we have Similarly to eq. (3.23), we have H ⃗D =  H ⃗D + q2E0  E0 ⃗D −⃗QE0  −q ⃗Q†  E0 ⃗D −⃗QE0   = 0, (5.8) (5.8) where we used eqs. (3.23) and (5.5). It is straightforward to show the following equations to hold ⃗A†H ⃗A = ⃗A† H + q2E2 0  ⃗A −qE0 ⃗A† ⃗Qθ −qθ ⃗Q†E0 ⃗A + θ ⃗Q† ⃗Qθ = ⃗A†H ⃗A +  ⃗Qθ −qE0 ⃗A †  ⃗Qθ −qE0 ⃗A  , (5.9) ⃗D†⃗A = ⃗D† ⃗A + qE0θ, (5.10) ⃗D†⃗D = ⃗D† ⃗D + q2E2 0. 5 Localization by a charged stabilizer in D ≥5 (5.11) ⃗A†H ⃗A = ⃗A† H + q2E2 0  ⃗A −qE0 ⃗A† ⃗Qθ −qθ ⃗Q†E0 ⃗A + θ ⃗Q† ⃗Qθ = ⃗A†H ⃗A +  ⃗Qθ −qE0 ⃗A †  ⃗Qθ −qE0 ⃗A  , (5.9) (5.9) ⃗D†⃗A = ⃗D† ⃗A + qE0θ, ⃗D†⃗A = ⃗D† ⃗A + qE0θ, ⃗D†⃗D = ⃗D† ⃗D + q2E2 0. ⃗D†⃗D = ⃗D† ⃗D + q2E2 0. (5.11) (5.11) – 26 – – 26 – Then, we can rewrite the quadratic Lagrangian (5.4) into the following compact form as L quad = −⃗ξ T □+ M2 ⃗ξ + 1 2Aµ  ηµν□−  1 −1 ξ  ∂µ∂ν + ηµν⃗D†⃗D  Aν −1 2 ⃗A†  □+ H + ξ⃗D⃗D† ⃗A. (5.12) (5.12) Note that the gauge sector (the second and third lines) formally coincide with the quadratic Lagrangian of the gauge part in the neutral case eq. (3.19) with Γs given in eqs. (3.20) and (3.21). Therefore, we can repeat the almost same procedures to decompose physical and unphysical degrees of freedom from ⃗A. Firstly, let us define a projection operator Note that the gauge sector (the second and third lines) formally coincide with the quadratic Lagrangian of the gauge part in the neutral case eq. (3.19) with Γs given in eqs. (3.20) and (3.21). Therefore, we can repeat the almost same procedures to decompose physical and unphysical degrees of freedom from ⃗A. Firstly, let us define a projection operator JHEP10(2019)098 P = ⃗D  ⃗D†⃗D −1 ⃗D†. (5.13) (5.13) Then we decompose ⃗A as ⃗A = ⃗Ad + ⃗Adf, ⃗Ad ≡P⃗A, ⃗Adf ≡(1 −P) ⃗A. (5.14) (5.14) Since the projection operator includes  ⃗D†⃗D −1 , we should check if it is always regular or not. It would be ill-defined when  ⃗D†⃗D −1 acts on a zero mode of ⃗D†⃗D. However, it is obvious that ⃗D†⃗D = ⃗D† ⃗D + q2E2 0 does not have zero eigenstates unless qE0 = 0. Thus, we proved that the projection operator P is well-defined as long as q ̸= 0. Since the projection operator includes  ⃗D†⃗D  , we should check if it is always regular or not. It would be ill-defined when  ⃗D†⃗D −1 acts on a zero mode of ⃗D†⃗D. However, it is obvious that ⃗D†⃗D = ⃗D† ⃗D + q2E2 0 does not have zero eigenstates unless qE0 = 0. 5 Localization by a charged stabilizer in D ≥5 Thus, we proved that the projection operator P is well-defined as long as q ̸= 0. From eqs. (5.8) and (5.14), we find From eqs. (5.8) and (5.14), we find H⃗Ad = 0, ⃗D†⃗Adf = 0. (5.15) (5.15) The divergence free part can be decomposed as The divergence free part can be decomposed as The divergence free part can be decomposed as ⃗Adf = β−1 0 ⃗η 0 ! + ⃗A bdf. (5.16) (5.16) The first term in the right hand side diverges at the spatial infinity, so we remove it by hand. With these at hand, now, we can rewrite ⃗A†  □+ H + ξ⃗D⃗D† ⃗A = ⃗A bdf† (□+ H) ⃗A bdf + ⃗Ad†  □+ ξ⃗D⃗D† ⃗Ad = ⃗A bdf† (□+ H) ⃗A bdf + a†  □+ ξ⃗D†⃗D  a, (5.17) e defined a ≡ 1 p ⃗D†⃗D ⃗D†⃗A. (5.18) ⃗A†  □+ H + ξ⃗D⃗D† ⃗A = ⃗A bdf† (□+ H) ⃗A bdf + ⃗Ad†  □+ ξ⃗D⃗D† ⃗Ad = ⃗A bdf† (□+ H) ⃗A bdf + a†  □+ ξ⃗D†⃗D  a, (5.17) (5.17) where we defined where we defined a ≡ 1 p ⃗D†⃗D ⃗D†⃗A. (5.18) (5.18) Thus, we again run into the coincidence between the mass determining operator ⃗D†⃗D for Aµ and ξ⃗D†⃗D for a. This implies that a is eaten by Aµ to give non zero masses. For the divergence free part, we mimic the factorization done in eq. (3.45). In this case, H can be factorized as H = D†D, (5.19) (5.19) – 27 – – 27 – with with D = D 0 qE01N −⃗Q ! , (5.20) D = D 0 qE01N −⃗Q ! , (5.20) (5.20) where D’s are given in eqs. (3.46)–(3.48). The size of D is N+1 2  × (N + 1). Let us study a zero mode of H which satisfies H⃗f (0) = 0 ⇔ D⃗f (0) = 0 ⇔ ⃗f (0) = ⃗Dg, (5.21) (5.21) with an arbitrary scalar function g. One can directly verify this as D⃗D = D 0 qE01N −⃗Q ! ⃗D qE0 ! = D ⃗D qE0 ⃗D −⃗Q(qE0) ! = 0, (5.22) JHEP10(2019)098 JHEP10(2019)098 (5.22) where we used eqs. (3.61) and (5.5). This implies that the divergence-free part is orthogonal to ⃗f (0) because Z dD−4y⃗f (0) · ⃗Adf = Z dD−4y ⃗Dg · ⃗Adf = Z dD−4y g⃗D†⃗Adf = 0. 5 Localization by a charged stabilizer in D ≥5 <latexit sha1_base64="CojLpYipNA61DFAVmlDbF02V0k=">ACanichVG7SgNBFD1ZXzG+YmwUGzFGrMJEBMUqaGMZE2MCSQi762Qdsi92NwEN+QE7K8FUCiLiZ9j4AxZ+gminYGPhzWZBNKh3mJkzZ+65c2ZGsXheow9hqSBwaHhkfBoZGx8YnIqOh3bd62Go/K8aumWU1Rkl+vC5HlPeDov2g6XDUXnBaW+3d0vNLnjCsvc845sXjFkzRQ1ocoeUYWyIjSt3K5G4yzJ/FjoB6kAxBFExopeo4wDWFDRgAEOEx5hHTJcaiWkwGATV0GLOIeQ8Pc52oiQtkFZnDJkYus0arQqBaxJ625N1erdIpO3SHlAhLsgd2wV3bPbtkT+/i1Vsuv0fVyRLPS03K7OnUym3v/V2XQ7OHwS/WnZw81bPheBXm3faZ7C7Wnbx6fveY2s4nWMrtkz+T/gj2yO7qB2XxTr3Z5toMIfUDq53P3g/3VZIrw7lo8vRV8RjzWMQKvfc60thBnf3SnO0Qm9SDFpTprvpUqhQDODbyEtfQKLG4yK</latexit><latexit 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A brief summary of the effective fields localized on a topological soliton by a charged stabilizer H in higher dimensional models. JHEP10(2019)098 Figure 5. A brief summary of the effective fields localized on a topological soliton by a charged stabilizer H in higher dimensional models. vector field A(0) µ . All other physical degrees of freedom reside in A(KK) µ and the divergence- free components ⃗A bdf(KK). They are superheavy whose masses are of order inverse of the domain wall width. vector field A(0) µ . All other physical degrees of freedom reside in A(KK) µ and the divergence- free components ⃗A bdf(KK). They are superheavy whose masses are of order inverse of the domain wall width. Before closing this section, let us make a comment on the divergence free part for a model with a constant E0 = H0/( √ 2β0). From the condition ⃗D†⃗Adf = 0, we find θ = −1 qE0 ⃗D† ⃗A = −1 qE0 ⃗D†  ⃗Ad + ⃗Adf = −1 qE0 ⃗D† ⃗Ad. (5.28) (5.28) Therefore, we can express the divergence free part as ⃗Adf = ⃗Adf 0 ! + ⃗Ad −1 qE0 ⃗D† ⃗Ad ! = D† 0 ! ¯f + 1 −1 qE0 ⃗D† ! ⃗Ad, (5.29) (5.29) where we used ⃗Adf = D† ¯f from eq. (3.61). Note that the first and the second terms in the right hand side are orthogonal each other. This can be easily verified as D† 0 !† ⃗D( ⃗D† ⃗D)−1 −1 qE0 ! = D ⃗D( ⃗D† ⃗D)−1 = 0, (5.30) (5.30) where we used D ⃗D = 0 from eq. (3.61). Since E0 is constant, ⃗D = ⃗Q. Then we have H D† 0 ! 5 Localization by a charged stabilizer in D ≥5 (5.23) (5.23) Now, we consider a dual operator Now, we consider a dual operator ¯H = DD†, ¯H¯f(n) = ¯m2 D,n¯f(n), (5.24) (5.24) where ¯f(n) is a N+1 2  vector. Then one can easily verify the following equations H  D†¯f(n) = ¯m2 D,n  D†¯f(n) , ⃗D†  D†¯f(n) = 0. (5.25) (5.25) Thus, the divergence-free component ⃗A bdf can be decomposed by the divergence-free eigen- functions D†¯f(n) of H as D†¯f(n) ⃗A bdf = X n L(n)(x)D†¯f(n) ¯mD,n , (5.26) (5.26) and the divergence-free part reads Z dD−4y ⃗A bdf† (□+ H) ⃗A bdf = X n L(n) □+ ¯m2 D,n  L(n). (5.27) (5.27) n Hence, the formulae for the charged stabilizer are the same as those for the neutral stabilizer if we replace  ⃗Ad, ⃗A bdf, ⃗D, D, H, ¯H  by  ⃗Ad, ⃗A bdf, ⃗D, D, H, ¯H  .     Let us compare the results in 5 dimensions given in section 4 and in higher dimensions obtained in this section. In the five dimensional case, we decomposed the physical (θq) and unphysical (aq) degrees of freedom as given in eq. (4.26). However, the mass square operator K†K is the complicated operator, so that it is difficult to obtain eigenvalues in reality. Compared to this, the generic formula given here is better since obtaining mass eigenvalues of ⃗A bdf is relatively easier. This is because its mass square operator H remains simple as a consequence of unifying ⃗A and θ in ⃗A. Figure 5 briefly summarizes the gauge sector. As in the 5D case, there are no massless states in the low energy effective theory in four dimensions. 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(6.1) (6.1) Here, T4 and T5 are real scalar fields, and H is a complex scalar field. There exist four discrete vacua T4 = ±v and T5 = ±v with H = 0. Thus, we have two kinds of domain walls associated with the discrete symmetry Z2 × Z2: the one made of T4 and the other made of T5. The domain walls, in general, are not parallel each other, and intersect at an angle. Hereafter, we will concentrate on the intersecting domain walls at 90 degree, see refs. [56–59] for the intersecting domain walls in supersymmetric models. JHEP10(2019)098 Similarly to the single domain wall studied in section 2.2, each domain wall can induce local condensation of H according to values of the parameters. To quickly see this, let us make an ansatz T4 = v tanh Ωx4, T5 = v tanh Ωx5, H = 0. (6.2) (6.2) We fix T4 and T5 by hand, and perturb H by H = 0 + h (for simplicity, we will omit the U(1) NG mode and set h to be real). Then, we find the Schr¨odinger potential for h as We fix T4 and T5 by hand, and perturb H by H = 0 + h (for simplicity, we will omit the U(1) NG mode and set h to be real). Then, we find the Schr¨odinger potential for h as Vh = Ω2 −2λ2v2 sech2Ωx4 + sech2Ωx5 . (6.3) (6.3) Depth of the potential is two folds: Vh →Ω2 −2λ2v2 inside the each wall, and Vh → Ω2 −4λ2v2 at the wall intersection. Thus, we expect that a tachyonic mode of h appears, and it is localized either on the domain walls or only at the intersecting point according to λv/Ω. In order verify this observation, we numerically solved equations of motion for the model (6.1). The numerical solutions are shown in figure 6. We found three qualitatively different configurations. The first solution (the left column of figure 6) has no H condensations at all. This appears when Ωis sufficiently larger than λv. The second solution has finite H condensation only around the intersecting point (the middle column of figure 6). 5 Localization by a charged stabilizer in D ≥5 = D† 0 !  ¯H + q2E2 01 N 2   , (5.31) H 1 −1 qE0 ⃗D† ! = 1 −1 qE0 ⃗D† !  ⃗D ⃗D† + q2E2 01N  , (5.32) (5.31) (5.32) where we used eq. (3.61) for ⃗D†D† = 0 and eq. (3.38) for H ⃗Ad = 0. Hence, to see the physical spectra in ⃗Adf, we need to expand ¯f by the eigenstates of ¯H operator, and expand ⃗Ad by the eigenstates of ⃗D ⃗D† operator. – 29 – – 29 – 6.1 Intersection of domain walls The third solution has infinite H condensation along the domain walls (the right column of figure 6). For our purpose of constructing four dimensional low energy theory, we prefer the finite condensation of H whose codimension is two in six dimensions. Therefore, we will consider solutions of the type of middle column of figure 6. Unfortunately, we do not have an analytic solution of the intersecting domain walls with a finite and non-zero condensation of H. However, for an appropriate choice of parameters λ, v and Ω, we can make a simple separated approximation Happrox = a sech Ω′x4 sech Ω′x5, (6.4) (6.4) with a and Ω′ being approximation parameters. We assume Ω′ is the same order of Ω. This product ansatz works very well as can be seen in figure 7 where we compare the numerical solution and the approximation with appropriate a and Ω′. – 30 – no condensations condensation at intersection condensation inside walls T1 <latexit sha1_base64="jXoyxhM8k/vfU0MRSTU8zAMgns=">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</latexit><latexit 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sha1_base64="u41vLzM7c74vqPuleLchk1DqiQ=">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</latexit> Figure 6. Three typically different numerical solutions. T1,2 and H are plotted on the x4-x5 plane. As a benchmark, we take Ω= 2 and λ = 1. We also take v = 1.1, 1.9, and 2.5 for the left-, middle-, and right-column, respectively. JHEP10(2019)098 Figure 6. Three typically different numerical solutions. T1,2 and H are plotted on the x4-x5 plane. As a benchmark, we take Ω= 2 and λ = 1. We also take v = 1.1, 1.9, and 2.5 for the left-, middle-, and right-column, respectively. (a) numerical solution (b) approximation Figure 7. The left panel shows a numerical solution for (Ω, λ, v) = (2, 1, 1.5). The right panel is a plot of the separated approximation with (a, Ω′) = (0.6, √ 2) in eq. (6.4). (b) approximation (a) numerical solution (b) approximation (b) approximation (a) numerical solution Figure 7. The left panel shows a numerical solution for (Ω, λ, v) = (2, 1, 1.5). The right panel is a plot of the separated approximation with (a, Ω′) = (0.6, √ 2) in eq. (6.4). – 31 – With the above separable background condensation in eq. 6.1 Intersection of domain walls (6.4) at hand, we will now investigate localization of the gauge field on the intersecting point through the Lagrangian Lg = −β2FMNFMN, (M, N = 0, 1, 2, 3, 4, 5), (6.5) (6.5) with β = |H| 2µ → β0 ≃a 2µsech Ω′x4 sech Ω′x5 . (6.6) (6.6) The separable property of the approximate function β0 in x4 and x5 will help us to obtain the mass spectra below. The separable property of the approximate function β0 in x4 and x5 will help us to obtain the mass spectra below. JHEP10(2019)098 6.1.1 Neutral stablizer Here, we study the mass spectra of θ, Aµ, and Aa for the model with the neutral stabilizer H. All the formulae are given in section 3. As is given in eq. (3.26), the mass spectrum for θ is determined by Q† aQa. Similarly, the mass spectrum of Aµ is determined by D† aDa from eq. (3.30). In general, Qa and Da are different, but for the special choice of β proportional to |H| in eq. (6.6) they are identical. To obtain their mass spectra, we will make use of the separable approximation for β0 in eq. (6.6). In this approximation, we have Da ≃−∂a + ∂a sech Ω′xa sech Ω′xa → D† aDa ≃ X a=4,5  −∂2 a + Ω′2 1 −2 sech 2Ω′xa . (6.7) (6.7) Hence, the eigenvalue equation D† aDadn = m2 D,ndn can be solved by separation of variables about x4 and x5. The separated equations are identical to eq. (2.25) which we have already analytically solved. There exists the unique zero eigenstate mD,0 = 0, d(0) ∝sech Ω′x4 sech Ω′x5. (6.8) (6.8) All the excited states are continuum scattering modes as eq. (2.27) whose masses are given by All the excited states are continuum scattering modes as eq. (2.27) whose masses are given by mD(k4, k5)2 =  k2 4 + Ω′2, k2 5 + Ω′2, k2 4 + k2 5 + 2Ω′2 . (6.9) b (6.9) The mass spectrum of the divergence-free part A bdf a is determined by H from eq. (3.39), with D =  D5 −D4  , H = D†D = D† 5D5 −D† 5D4 −D† 4D5 D† 4D4 ! . (6.10) (6.10) We have shown in section 3.2.3 that the mass spectrum of H is identical to that of ¯H which can again be solved by separation of variables in x4 and x5. For the specific β0 given in eq. (6.6), the problem becomes even simpler since ¯H has a constant potential: We have shown in section 3.2.3 that the mass spectrum of H is identical to that of ¯H which can again be solved by separation of variables in x4 and x5. For the specific β0 given in eq. (6.6), the problem becomes even simpler since ¯H has a constant potential: ¯H = DD† = DaD† a = −∂2 a + 2Ω′2. 6.1.2 Charged stabilizer We next study the same model as eq. (6.1), but now the stabilizer H is not neutral. So, we replace ∂MH by DMH. The mass spectrum of Aµ in this case is determined by ⃗D†⃗D = D† aDa + q2E2 0, see eq. (5.12). For the choice of β in eq. (6.6), E0 is a constant E0 = H0 √ 2 β0 = √ 2 µ. (6.13) (6.13) Thus, the masses of A(n) µ are all shifted by the constant √ 2 qµ from those of the neutral case. Namely, there is only one bound state A(0) µ which gets mass √ 2 qµ by the Higgs mechanism which locally occurs at the intersection point. Thus, the masses of A(n) µ are all shifted by the constant √ 2 qµ from those of the neutral case. Namely, there is only one bound state A(0) µ which gets mass √ 2 qµ by the Higgs mechanism which locally occurs at the intersection point. JHEP10(2019)098 The remaining fields θ and Aa are unified in ⃗A, and the physical degrees of freedom are confined in ⃗A bdf. The mass spectrum of ⃗A bdf are identical to the eigenvalues of H: D =    D5 −D4 0 qE0 0 −D4 0 qE0 −D5   , (6.14) H = D†D =    D† 5D5 + q2E2 0 −D† 5D4 −qE0D4 −D† 4D5 D† 4D4 + q2E2 0 −qE0D5 −qE0D† 4 −qE0D† 5 D† 4D4 + D† 5D5   . (6.15) D =    D5 −D4 0 qE0 0 −D4 0 qE0 −D5   , (6.14) (6.14) H = D†D =    D† 5D5 + q2E2 0 −D† 5D4 −qE0D4 −D† 4D5 D† 4D4 + q2E2 0 −qE0D5 −qE0D† 4 −qE0D† 5 D† 4D4 + D† 5D5   . (6.15) (6.15) Following the general arguments of section 5, the eigenvalues of H coincides with ¯H whose explicit form is given by ¯H = DD† =    D4D† 4 + D5D† 5 qE0D5 −qE0D4 qE0D† 5 D4D† 4 + q2E2 0 D4D† 5 −qE0D† 4 D5D† 4 D5D† 5 + q2E2 0   . (6.16) (6.16) Hence, in contrast to H and ¯H in the neutral case, there are no practical advantages to deal with ¯H instead of H. 6.1.1 Neutral stablizer (6.11) (6.11) Therefore, there are no bound states and the mass spectrum is given by ¯m2 D,n = k2 4 + k2 5 + 2Ω′2. (6.12) (6.12) Thus, we conclude that the massless bound states localized at the intersection point are the four dimensional gauge field A(0) µ and the Nambu-Goldstone field θ(0). All other KK states from AM and θ are superheavy with the mass of order Ω′ and are not localized. – 32 – 6.1.2 Charged stabilizer In order to obtain the mass spectra of the divergence free part, we make use of the generic argument given at the end of the section 5. According to them, the divergence free part can be decomposed into two orthogonal components as eq. (5.29). The mass spectrum for the component associated with ¯f of (5.29) corresponds to the eigenvalues of ¯H + 2q2µ2, and the one for the other component ⃗Ad corresponds to the eigenvalues of ⃗D ⃗D† + 2q2µ212. In the six dimensions, we have ¯H = DaD† a and ⃗D ⃗D† =  D4D† 4 D4D† 5 D5D† 4 D5D† 5  . Note that the non-zero eigenvalues of DaD† a are identical to those of ⃗D† ⃗D = D† aDa, if β0 is separable. On the other hand, the non-zero eigenvalues of ⃗D ⃗D† and ⃗D† ⃗D are always identical. Therefore, for the separable β0, the two orthogonal components in the divergence free part ⃗Adf (the first and the second term of eq. (5.29)) are degenerate with eigenvalues of DaD† a + 2q2µ2 = −∂2 a + 2Ω′2 + 2q2µ2. Therefore, no light bound states exists and all the massive modes are heavy scattering modes whose masses are of order O(Ω′) ∼O(Ω). – 33 – 6.2 Axially symmetric case Our next example has β0 that is not separable but is axially symmetric in the x4-x5 plane. To be concrete, we assume the following Gaussian H = ae−Ω2r2, r2 = (x4)2 + (x5)2. (6.17) (6.17) Furthermore, we consider a specific β as before β = |H| 2µ → β0 = a 2µe−Ω2r2. (6.18) (6.18) JHEP10(2019)098 6.2.1 Neutral stablizer As before, we concentrate on θ, Aµ, and Aa. All the formulae are given in section 3. For our special choice of β proportional to |H| in eq. (6.18), θ and Aµ have the same mass eigenvalues of Da = −∂a + ∂ae−Ω2r2 e−Ω2r2 → D† aDa = −∂2 r −1 r∂r −1 r2 ∂2 φ + 4Ω2 Ω2r2 −1  , (6.19) (6.19) with x4 + ix5 = reiφ. The Schr¨odinger potential is asymptotically 4Ω4r2, so all the eigenstates are bound states. Eigenfunctions and eigenvalues of D† aDadnl = m2 D,nldnl are given by with x4 + ix5 = reiφ. The Schr¨odinger potential is asymptotically 4Ω4r2, so all the eigenstates are bound states. Eigenfunctions and eigenvalues of D† aDadnl = m2 D,nldnl are given by dnl = s 2|l|+1(n −|l|)! π(n!)3 Ω|l|+1r|l|L|l| n 2Ω2r2 e−Ω2r2+ilφ, (6.20) L|l| n (ξ) ≡d |l| dξ |l| e ξ d n dξ n ξ ne−ξ, (6.21) mD,nl = 2 p 2n −|l| Ω, (6.22) (6.20) (6.21) (6.22) with n is semi-positive integer and l is an integer of |l| ≤n. L|l| n is the associated Laguerre polynomials. The zero mode is unique with (n, l) = (0, 0) with the wave function with n is semi-positive integer and l is an integer of |l| ≤n. L|l| n is the associated Laguerre polynomials. The zero mode is unique with (n, l) = (0, 0) with the wave function d00 ∝e−Ω2r2. (6.23) d00 ∝e−Ω2r2. (6.23) The mass spectrum of the divergence-free part A bdf a is determined by H from eq. (3.39). We have shown in section 3.2.3 that the mass spectrum of H is identical to that of ¯H. In six dimensions, ¯H is especially simple as ¯H = DD† = DaD† a = D† aDa + 8Ω2. (6.24) (6.24) Therefore, the mass spectrum of Adf a is given by ¯m2 D,nl = m2 D,nl + 8Ω2. (6.25) ¯m2 D,nl = m2 D,nl + 8Ω2. (6.25) – 34 – – 34 – 6.2.2 Charged stablizer Next we consider the case that the stabilizer H is charged. The masses of Aµ are identical to eigenvalues of the operator D† aDa = D† aDa + q2E2 0. For β in eq. (6.18), E0 = √ 2 qµ is constant. So, the effect of changing the neutral H by the charged H is just shift of all the eigenvalues m2 D,nl of D† aDa by the constant 2q2µ2. This is the consequence of the local Higgs mechanism. According to the generic arguments in section 5, the other physical degrees of freedom live in the divergence-free part ⃗A bdf. It can be further decomposed to two components orthogonal to each other: the component associated with ¯f and the other component associated with ⃗Ad of (5.29). The former has the eigenvalues of ¯H + 2q2µ2, and the latter has the eigenvalues of ⃗D ⃗D† + 2q2µ212. In the six dimensions, we have ¯H = DaD† a and its eigenvalues are given in eq. (6.25). On the other hand, the non-zero eigenvalues of ⃗D ⃗D† and ⃗D† ⃗D = D† aDa are always identical, which is given in eq. (6.22). Therefore, the mass spectra in ⃗A bdf are m2 D,nl + 8Ω2 + 2q2µ2 and m2 D,nl + 2q2µ2 with (n, l) ̸= (0, 0). JHEP10(2019)098 7 Conclusion In this paper we investigated localization of the gauge fields via the field dependent gauge kinetic term (1.1) in details. We considered two cases that the stabilizers are neutral and charged. For the neutral case, we improved previous analysis done in refs. [37, 44–49], and especially analysis on the divergence-free parts becomes better, see section 2 for D = 5, and section 3 for generic D ≥5. We also studied the models with charged stabilizers. The charged stabilizers are locally condensed inside a topological soliton, so that they localize the gauge fields and at the same time they give a finite mass to the localized gauge fields similarly to the conventional Higgs mechanism. In order to determine physical mass spectra, we need to diagonalize complicated mixings between the four-dimensional gauge fields, Nambu-Goldstone fields, and the extra-dimensional gauge fields which are further decomposed into the divergence and divergence-free parts. We developed complete and self-contained formula with which one can clearly separate physical and unphysical degrees of freedom for generic models in generic D ≥5 dimensions. When we want massless gauge fields on a topological soliton, all we have to do is preparing neutral stabilizers which interact with the would-be localized gauge fields via eq. (1.1). On the other hand, if we want to have massive gauge bosons on a topological soliton, it can be realized by just replacing the neutral stabilizers with the charged ones. An attempt of identifying the charged stabilizer with the SM Higgs boson in the D = 5 model was studied in ref. [51]. Let us make a comment on localized gauge fields on domain walls in the Higgs vacua [59–68]. When a domain wall interpolates two discrete Higgs vacua where the gauge symmetry is broken, the gauge symmetry is approximately recovered inside the domain wall. Nevertheless, the localized gauge field on the domain wall never becomes massless. The lowest mass of localized gauge field is inevitably of order inverse of the domain wall that is the same order of all the KK modes. Therefore, in principle, we cannot distinguish the lightest massive gauge bosons from the other KK modes. In contrast, the solitons in – 35 – this work live in the confining vacua where the gauge symmetry is not broken. 7 Conclusion As we shown in this work, the lightest mass of localized gauge bosons is controlled only by the charge of the stabilizer, and it is nothing to do with the soliton width. Therefore, we can introduce two independent mass scales: the one is the lightest gauge boson mass and the other is superheavy mass of the KK towers. For phenomenological purpose, see for example ref. [51], our model has an advantage compared to other models with topological solitons in the Higgs phase. As a future direction, it might be interesting to study the intersections of domain walls studied in section 6. In this work, we only considered the intersection of two domain walls at right angle. In general, we can consider multiple domain walls, for example, three domain walls intersect at three different intersection points. We can also include fermions, and investigate whether such model provides a realist four dimensional model like intersecting D-branes [69]. JHEP10(2019)098 Acknowledgments M. E. thanks to Masato Arai, Filip Blaschke, and Norisuke Sakai for fruitful discussions throughout long collaboration, and contributions at the early stage of this work. The work is supported in part by JSPS Grant-in-Aid for Scientific Research KAKENHI Grant No. JP16H03984 and No. JP19K03839. The work is also supported in part by MEXT KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas Discrete Geometric Analysis for Materials Design No. JP17H06462 from the MEXT of Japan. This work is supported by the Ministry of Education, Culture, Sports, Science (MEXT)-Supported Pro- gram for the Strategic Research Foundation at Private Universities “Topological Science” (Grant No. S1511006). Open Access. 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Cardiotoxicity of Anthracyclines
Frontiers in cardiovascular medicine
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INTRODUCTION Anthracyclines are cytostatic antibiotics (1), introduced into the clinical field in the 1960s. As of 2012, anthracyclines were among the most diffused chemotherapeutic agents, and they still represent the base of treatment in many solid cancers and hematological malignancies (1, 2). Anthracyclines are cytostatic antibiotics (1), introduced into the clinical field in the 1960s. As of 2012, anthracyclines were among the most diffused chemotherapeutic agents, and they still represent the base of treatment in many solid cancers and hematological malignancies (1, 2). *Correspondence: Daniela Cardinale daniela.cardinale@ieo.it Unfortunately, anthracyclines are considered the principal culprit drugs behind chemotherapy-induced cardiotoxicity (1–5). The pathognomonic manifestation of anthracycline-induced cardiotoxicity is a hypokinetic cardiomyopathy progressively leading to heart failure, first described in 1967 (6). The onset of anthracycline-cardiomyopathy, also at the pre-clinical stage, may negatively affect the cardiovascular outcome of patients as also limit the chemotherapeutic strategies (4, 5). Specialty section: This article was submitted to Cardio-Oncology, a section of the journal Frontiers in Cardiovascular Medicine Received: 14 November 2019 Accepted: 18 February 2020 Published: 18 March 2020 Citation: Cardinale D, Iacopo F and Cipolla CM (2020) Cardiotoxicity of Anthracyclines. Front. Cardiovasc. Med. 7:26. doi: 10.3389/fcvm.2020.00026 Specialty section: This article was submitted to Cardio-Oncology, a section of the journal Frontiers in Cardiovascular Medicine Edited by: Canan G. Nebigil, École supérieure de biotechnologie Strasbourg (ESBS), France Keywords: cardiotoxicity, anthracyclines, early detection, troponin, prevention, reversibility, ACE-inhibitors, beta-blockers Reviewed by: Sherry-Ann Brown, Mayo Clinic, United States Giselle Melendez, Wake Forest University, United States Cardiotoxicity of Anthracyclines Daniela Cardinale 1*, Fabiani Iacopo 1 and Carlo Maria Cipolla 2 1 Cardioncology Unit, European Institute of Oncology, IRCCS, Milan, Italy, 2 Cardiology Division, European Institute of Oncology, IRCCS, Milan, Italy 1 Cardioncology Unit, European Institute of Oncology, IRCCS, Milan, Italy, 2 Cardiology Division, European Institute of Oncology, IRCCS, Milan, Italy Cardiotoxicity is a feared side effect that may limit the clinical use of anthracyclines. It may indeed affect the quality of life and survival of patients with cancer, regardless of oncological prognosis. This paper provides an overview of anthracycline-induced cardiotoxicity in terms of definition, classification, incidence, risk factors, possible mechanisms, diagnosis, and treatment. We also report effective strategies for preventing cardiotoxicity. In addition, we discuss limiting current approaches, the need for a new classification, and early cardiotoxicity detection and treatment. Probably, anthracycline-induced cardiotoxicity is a continuous phenomenon that starts from myocardial cell injury; it is followed by left ventricular ejection fraction (LVEF) and, if not diagnosed and cured early, progressively leads to symptomatic heart failure. Anthracycline-induced cardiotoxicity can be detected at a preclinical phase. The role of biomarkers, in particular troponins, in identifying subclinical cardiotoxicity and its therapy with angiotensin-converting enzyme inhibitors (mainly enalapril) to prevent LVEF reduction is a recognized and effective strategy. If cardiac dysfunction has already occurred, partial or complete LVEF recovery may still be obtained in case of early detection of cardiotoxicity and prompt heart failure treatment. Keywords: cardiotoxicity, anthracyclines, early detection, troponin, prevention, reversibility, ACE-inhibitors, beta-blockers REVIEW published: 18 March 2020 doi: 10.3389/fcvm.2020.00026 published: 18 March 2020 doi: 10.3389/fcvm.2020.00026 CLASSIFICATION A previous and more dated classification identified three distinct types of anthracycline-induced cardiotoxicity (Table 2): acute, occurring after a single dose, or a single course, with the onset of symptoms within 14 days from the end of treatment, which is usually reversible; early-onset chronic, occurring within 1 year, the principal form of cardiotoxicity, from a clinical and epidemiological stand-point, presenting as a dilated-hypokinetic cardiomyopathy, with progressive evolution toward heart failure; and late-onset chronic, developing years, possibly decades, after the end of anthracycline therapy. The two chronic forms are considered irreversible, with a poor prognosis and a limited to heart failure therapy. This classification stems back to early 1980s, and it is mainly based on small retrospective studies reporting the occurrence of heart failure symptoms in childhood cancer survivors (12–14). In particular, in a milestone study, Steinherz et al. reported cases of heart failure occurrence many years after the end of anthracycline-chemotherapy, and the percentage of patients with cardiac dysfunction, as well as the severity of the dysfunction itself, increased in parallel with time elapsed from the end of anthracycline administration (14). However, the clinical relevance of such a classification at present is uncertain, especially when referred to adult populations. Previous cardiotoxic cancer treatment Lifestyle risk factors • Prior anthracycline use • Prior radiotherapy to chest or mediastinum • Smoking • High alcohol intake • Obesity • Sedentary habit AF, atrial fibrillation; CABG, coronary artery bypass graft; CAD, coronary artery disease; CV, cardiovascular; LV, left ventricular; LVEF, left ventricular ejection fraction; LVH, left ventricular hypertrophy; PCI, percutaneous coronary intervention; VHD, valvular heart disease. AF, atrial fibrillation; CABG, coronary artery bypass graft; CAD, coronary artery disease; CV, cardiovascular; LV, left ventricular; LVEF, left ventricular ejection fraction; LVH, left ventricular hypertrophy; PCI, percutaneous coronary intervention; VHD, valvular heart disease. In particular, recent findings challenge this old classification, suggesting that anthracycline-induced cardiotoxicity is potentially a continuous phenomenon, starting at the myocardial cell level, followed by progressive functional decline, progressively leading to overt heart failure. (Figure 2) (5, 8, 15). To be practical, anthracycline-associated cardiotoxicity is now thought to occur at the time of first exposure, a hypothesis supported by the finding of troponin release after anthracycline administration (16). Clinical presentation may occur years later the initial damage (16–18). Looking at symptoms, the diagnosis may take years (“late” cardiotoxicity). Considering LVEF reduction, it may take months (“early” cardiotoxicity). Citation: The risk of anthracycline-induced heart failure increases as the cumulative dose administered increases: 3–5% with 400 mg/m2 and as high as 18–48% at 700 mg/m2 (4). However, there is a different level of risk for each patient scheduled for anthracycline therapy: patients less than 5 years old or more than 65 years old, with prior or concurrent chest irradiation, pre-existing heart disease, or already known cardiovascular risk factors, have an increased risk for cardiotoxicity March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org Cardiotoxicity of Anthracyclines Cardinale et al. TABLE 1 | Baseline risk factors for anthracycline-induced cardiotoxicity (4, 7). Current myocardial disease Demographic and other CV risk factors • Heart failure • Asymptomatic LV dysfunction (LVEF <50%) • Evidence of CAD (previous myocardial infarction, angina, PCI or CABG, myocardial ischemia) • Moderate and severe VHD with LVH or LV impairment • Hypertensive heart disease with LV hypertrophy • Hypertrophic cardiomyopathy • Dilated cardiomyopathy • Restrictive cardiomyopathy • Cardiac sarcoidosis with myocardial involvement • Significant cardia arrhythmias (AF, ventricular tachyarrhythmias) • Age (<5 or >65 years) • Family history of premature CV disease (<50 years) • Arterial hypertension • Diabetes mellitus • Hypercholesterolemia Previous cardiotoxic cancer treatment Lifestyle risk factors • Prior anthracycline use • Prior radiotherapy to chest or mediastinum • Smoking • High alcohol intake • Obesity • Sedentary habit AF, atrial fibrillation; CABG, coronary artery bypass graft; CAD, coronary artery disease; CV, cardiovascular; LV, left ventricular; LVEF, left ventricular ejection fraction; LVH, left ventricular hypertrophy; PCI, percutaneous coronary intervention; VHD, valvular heart disease. (Figure 1) (11). So far, the principal mechanisms, with potential differential impact and grade of involvement in different cell types, are oxidative stress, DNA damage, senescence, and cell death. (Figure 1) (11). So far, the principal mechanisms, with potential differential impact and grade of involvement in different cell types, are oxidative stress, DNA damage, senescence, and cell death. (Figure 1) (11). So far, the principal mechanisms, with potential differential impact and grade of involvement in different cell types, are oxidative stress, DNA damage, senescence, and cell death. MECHANISMS The specific mechanisms of anthracycline cardiotoxicity still remain unclear. A potential mechanism is the generation of reactive oxygen species (ROS), changes in iron metabolism, and Ca2þ signaling. In 2014, topoisomerase (Top) 2β was indicated as the critical mediator of anthracycline’s cardiac toxic effect (9). Top2 can uncoil deoxyribonucleic acid (DNA) filaments during DNA replication, transcription, or recombination. The anthracycline inhibition of Top2β causes mitochondrial dysfunction and leads to activation of cell death pathways and ROS deposit (2, 3, 10). CLASSIFICATION With the use of circulating biomarkers, such as troponin (pre-clinical myocardial cell damage), prompt identification of cardiotoxicity is possible, allowing for an “acute” form. So far, we are probably observing the evolving stages of the same phenomenon and not three distinct diseases (15, 17, 18). (Table 1) (4, 7). Moreover, anthracycline-induced cardiotoxicity risk increases with the use of other agents that may increase its incidence. In particular, trastuzumab, while very effective in treating breast cancer, interferes with myocyte survival pathways, crucial in countering the toxic effects of anthracyclines (5, 7, 8). Frontiers in Cardiovascular Medicine | www.frontiersin.org DIAGNOSIS AND DEFINITION The cardiomyocyte has always been considered the main cellular target of anthracycline toxic effect in the heart, as their destruction results in the progressive development of cardiac dysfunction. More recently, however, other cell types—such as cardiac progenitor cells, cardiac fibroblasts, and endothelial cells—have been identified as potential additional targets, creating a more complex and intriguing scenario in the pathogenesis of anthracycline-induced cardiomyopathy The diagnosis of anthracycline-induced cardiotoxicity has remained the same over the last 60 years. It has always been based on heart failure symptoms, and, later, also on evidence of LVEF drop (echocardiography or multi-gated acquisition scans) (4, 18). A former definition adopted was an LVEF absolute decrease higher than 10% points, associated with a decline <50% (5). More recently, the consensus [Plana et al. (19)] defined it March 2020 | Volume 7 | Article 26 2 Cardiotoxicity of Anthracyclines Cardinale et al. FIGURE 1 | Graphical representation of several doxorubicin-targeted cell types, with potential side effects and cellular and molecular events evoked by the drug. From Cappetta et al. (11). FIGURE 1 | Graphical representation of several doxorubicin-targeted cell types, with potential side effects and cellular and molecular events evoked by the drug. From Cappetta et al (11) FIGURE 1 | Graphical representation of several doxorubicin-targeted cell types, with potential side effects and cellular and molecular events evoked by the drug. From Cappetta et al. (11). TABLE 2 | Old classification of anthracycline-induced cardiotoxicity (7, 12–14). Characteristics Acute cardiotoxicity Early-onset chronic cardiotoxicity Late-onset chronic cardiotoxicity Onset During or within 2 weeks after AC treatment Within 1 year after the completion of AC treatment >1 year after the completion of AC treatment Dose dependent Unknown Yes Yes Clinical features Depression of myocardial contractility Dilated/Hypokinetic cardiomyopathy Dilated/Hypokinetic cardiomyopathy Course Usually reversible Usually irreversible Usually irreversible Refractory to traditional heart failure therapy Refractory to traditional heart failure therapy Poor prognosis Poor prognosis TABLE 2 | Old classification of anthracycline-induced cardiotoxicity (7, 12–14). as an LVEF decrying >10% points, with a final value <53% (19). In patients at low risk—i.e., without risk factors or a negative cardiovascular history, with an indication to receive a low dose of anthracyclines (total cumulative dose ≤240 mg/m²) or standard dose followed by trastuzumab-based regimens— cardiac monitoring is not suggested by the American Society of Clinical Oncology guidelines. Moreover, they suggest a diagnosis of cardiotoxicity based on clinical symptoms (20). DIAGNOSIS AND DEFINITION Reasons comprise “medicalization, the possibility of causing stress and anxiety, and costs” to be incurred (20, 21). Otherwise, the international cardiological guidelines recommend monitoring of cardiac function by serial LVEF measurements, but do not provide an accurate indication on timing, frequency, modalities, and long-term schedule (7). Moreover, a diagnosis based on symptoms or asymptomatic decrease of LVEF is not only delayed, but also potentially prevents any form of effective prevention, as the cardiac damage may be no longer reversible (17, 18). A recent study evaluating a significant (n = 2,625) population scheduled for anthracycline therapy showed that close monitoring of LVEF after chemotherapy allowed nearly all (98%) cases of cardiotoxicity to be identified within the first 12 months of follow-up (15). In addition, early treatment with angiotensin-converting enzyme (ACE)-inhibitors (enalapril) and beta-blockers (carvedilol or bisoprolol) enabled normalization of cardiac function in most cases (82%), but only 11% of patients who had renormalized LVEF had full recovery—i.e., the same LVEF value as before the start of anthracyclines—while the final LVEF value in 71% of patients remained below the baseline value (Figure 3). These findings confirm that this approach is limited in identifying reversible cardiotoxicity, probably because left ventricular compensation mechanisms have been exhausted (8). Of great importance, the evidence of a normal LVEF does not exclude the risk of future deterioration of cardiac function. Frontiers in Cardiovascular Medicine | www.frontiersin.org TREATMENT The historical concept that anthracycline-induced cardiotoxicity is irreversible, with a reported mortality rate up to 60% within 2 Frontiers in Cardiovascular Medicine | www.frontiersin.org March 2020 | Volume 7 | Article 26 3 Cardinale et al. Cardiotoxicity of Anthracyclines FIGURE 2 | Possible strategies for cancer drug-induced cardiotoxicity detection, prevention, and treatment. AC, anthracyclines; ACEI, angiotensin-converting enzyme inhibitors; BB, beta-blockers; CV, cardiovascular; GLS, global longitudinal strain; HF, heart failure; LVD, left ventricular dysfunction; RAS, renin-angiotensin system. From Cardinale et al. (8). FIGURE 2 | Possible strategies for cancer drug-induced cardiotoxicity detection, prevention, and treatment. AC, anthracyclines; ACEI, angiotensin-converting enzyme inhibitors; BB, beta-blockers; CV, cardiovascular; GLS, global longitudinal strain; HF, heart failure; LVD, left ventricular dysfunction; RAS, renin-angiotensin system. From Cardinale et al (8) Up until 2010, the response to heart failure therapy of patients with anthracycline-induced cardiotoxicity hadn’t been thoroughly investigated. Moreover, these kind of patients have been excluded from large randomized trials evaluating the impact of current heart failure therapies (8). FIGURE 3 | LVEF in patients with cardiotoxicity and with partial (triangle) or full (square) recovery with heart failure therapy. Data are mean ± SD. CT, chemotherapy; HF, heart failure. From Cardinale et al. (15). FIGURE 3 | LVEF in patients with cardiotoxicity and with partial (triangle) or full (square) recovery with heart failure therapy. Data are mean ± SD. CT, chemotherapy; HF, heart failure. From Cardinale et al. (15). The effectiveness of ACE-inhibitors and beta-blockers has been prospectively assessed in two extensive papers (15, 31). In 201 patients with anthracycline-induced cardiotoxicity, an inverse relationship in terms of LVEF improvement has been found between the time interval from the end of chemotherapy and the beginning of heart failure therapy (Figure 4A) (31). LVEF recovery rate was 64% in those treated early (i.e., within 2 months after the end of chemotherapy); later on, however, this percentage rapidly decreased, with no complete recovery after 6 months. After 12 months, obtaining even partial LVEF improvement was almost impossible (Figure 4B) (31). It emerges that cardiotoxicity is not irreversible, but that reversibility is a matter of time, depending on early diagnosis, allowing prompt treatment. Furthermore, these findings, based on standard cardiac symptoms surveillance, might miss this change (8). FIGURE 3 | LVEF in patients with cardiotoxicity and with partial (triangle) or full (square) recovery with heart failure therapy. Data are mean ± SD. CT, chemotherapy; HF, heart failure. From Cardinale et al. TREATMENT (B) Relationship between maximal LVEF during the follow-up period and log time elapsed from chemotherapy and the start of treatment [time-to-heart failure (HF) treatment]. From Cardinale et al. (31). In summary, we can assert that troponin evaluation in patients treated with anthracyclines allows for: 1. Prediction of the development of future left ventricular dysfunction; 2. Prediction of left ventricular dysfunction severity, because the peak value of troponin is closely related to the extent of LVEF reduction; 3. Stratification of cardiac risk after anthracyclines and tailoring of the schedule of post-chemotherapy monitoring of cardiac function; 4. Identification of cardiotoxicity prone patients, in whom a cardioprotective therapy can be considered; and vast majority of cases during the first year after chemotherapy, with normalization of LVEF (final value of LVEF >50%) in 82% of cases (15). However, only 11% of patients had a complete restoration (i.e., final LVEF equal to baseline). This highlights the need for detection methods able to identify early cardiotoxicity and for strategies aimed at preventing the development and the progression of left ventricular dysfunction. 5. Exclusion of most patients from prolonged cardiologic surveillance. On the other hand, the identified weakness points are: 1. Repeated assessments of troponins are needed to detect positivity; 1. Repeated assessments of troponins are needed to detect positivity; 2. The ideal timing for troponin detection must still be defined; TREATMENT (15). years of diagnosis, is now reconsidered. In particular, this belief is based on seminal studies in which heart failure therapeutic strategies were limited (i.e., digoxin, diuretics), or on studies with small populations, retrospective design, short follow-up, or on case reports (22–30). On the contrary, close monitoring and timely treatment with HF therapies have reported that they are critical for functional recovery in a non-selected population treated with anthracycline, allowing early detection of cardiotoxicity in the March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 4 Cardiotoxicity of Anthracyclines Cardinale et al. FIGURE 4 | (A) Percentage of patients who recovered (Responders), according to the time elapsed from anthracycline administration and the start of heart failure therapy. (B) Relationship between maximal LVEF during the follow-up period and log time elapsed from chemotherapy and the start of treatment [time-to-heart failure (HF) treatment]. From Cardinale et al. (31). causes/etiologies (32). Troponin has many advantages: elevated cardiac specificity, high sensitivity, availability, and costs respective to imaging methods. Moreover, there are limited variability issues. In this field, several studies have demonstrated that troponins may detect cardiotoxicity in patients treated with anthracyclines (Table 3) (33–56). The most extensive study included 703 cancer patients, in whom Troponin I (TnI) was assessed before and during the first 72 h after chemotherapy (early TnI), and after 1 month (late TnI) (38). Three different troponin release patterns were recognized: Troponin I remained within the normal interval in 72% of patients, rose at only early evaluation in 21%, and increased at early and late assessments in 9%. Patients with no rise in troponin showed little difference in LVEF and had a good prognosis, with a low incidence of significant adverse heart events (MACE) (1%) during follow-up. Alternatively, TnI- positive patients had a higher rate of MACE: In particular, severe cardiac dysfunction and a higher rate of MACE were associated with a persistent TnI elevation compared to patients with only a temporary rise (p < 0.001). Based on the high negative predictive value (99%), TnI has been able to safely identify low-risk patients, limiting the need and subsequent costs of close long-term cardiac monitoring (34, 35, 38). Conversely, TnI-positive patients deserve more stringent monitoring, mainly those showing a persistent TnI increase. FIGURE 4 | (A) Percentage of patients who recovered (Responders), according to the time elapsed from anthracycline administration and the start of heart failure therapy. PRECLINICAL EARLY DETECTION 3. Standardization of routine troponin use in this clinical setting is a current need; and 4. Timing in which a single sampling of troponin could be obtained. 4. Timing in which a single sampling of troponin could be obtained. Today, at an early preclinical stage, we can detect cardiotoxicity long before symptoms of heart failure occur and before an asymptomatic drop in LVEF. Most data relate to cardiac biochemical markers: mainly troponins and echocardiography of tissue Doppler and strain (5, 7, 8). Other Circulating Biomarkers Although patients with pre-treatment levels of natriuretic peptides (BNP and N-terminal prohormone) tend to experience cardiac events (including cardiac dysfunction), the results are sparse (44, 57, 58). Troponin Assessment in Anthracycline-Treated Patients More recently (57), BNP levels were shown to be significantly higher after every anthracycline cycle in Troponin may be considered the gold standard biomarker for myocardial injury and cardiotoxicity from different March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 5 Cardiotoxicity of Anthracyclines Cardinale et al. TABLE 3 | Clinical studies demonstrating Troponins as predictor of anticancer drug-induced left ventricular dysfunction (33–56). Study (year) Patients (n.) Cancer type Drugs Troponin type Cut off Timing of assessment Lipshultz et al. (33) 15* ALL AC T 0.03 ng/mL Before CT; 1–3 days after each dose Cardinale et al. (34) 201 Various HD CT I 0.04 ng/ml 0–12–24–36–72 h after CT Cardinale et al. (35) 232 Breast cancer HD CT I 0.04 ng/ml 0–12–24–36–72 h after CT Auner et al. (36) 30 Hematological HD Cycl T 0.03 ng/ml Before CT; 1–14 days after CT Sandri et al. (37) 179 Various HD CT I 0.04 ng/ml 0–12–24–36–72 h after CT Cardinale et al. (38) 703 Various HD CT I 0.04 ng/ml 0–12–24–36–72 h after CT Specchia et al. (39) 79 Hematological AC I 0.15 ng/ml Before CT; weekly x 4 times Kilickap et al. (40) 41 Various AC T 0.10 ng/ml Before CT; 3–5 days after 1st and last dose Lee et al. (41) 86 Hematological AC I 0.20 ng/ml Before each dose Schmidinger et al. (42) 74 Renal cancer Sunitinib/sorafenib T 0.02 Before CT, bimonthly, symptoms occurrence Cardinale et al. (43) 251 Breast cancer AC, TRZ I 0.04 ng/ml Before and after each cycle Sawaya et al. (44) 43 Breast cancer AC+taxanes+TRZ HS-I 0.015 ng/ml Before CT; after 3 and 6 months during CT Lipshultz et al. (45) 205* ALL AC/AC+dexrazoxane I/T Any detectable amount Before CT; 1–7 days after each dose; end CT Sawaya et al. (46) 81 Breast cancer AC+taxanes+TRZ HS-I 30 pg/mL Before CT; after 3 and 6 months during CT Draft et al. (47) 53 Various AC I 0.06 ng/ml Before CT; after 1, 3, 6 months Mornos et al. (48) 74 Various AC HS-T NA Before CT; after 6, 12, 24, 52 weeks Mavinkurve-Groothuis et al. (49) 60* ALL AC HS-T 0.01 ng/mL Before CT; after 3 and 12 months Ky et al. (50) 78 Breast cancer AC+taxanes+TRZ HS-I NA Before CT; after 3 and 6 months during CT Mornos et al. Troponin Assessment in (51) 92 Various AC HS-T NA Before CT; after 12 and 36 weeks Putt et al. (52) 78 Breast cancer AC+taxanes+TRZ HS-I NA Before CT; every 3 months (max 15 months) Zardavas et al. (54) 412 Breast cancer AC+taxanes+TRZ HS-T/US-I 14 ng/L/40 ng/L Before CT; week 13, 25, 52; month 18, 24, 30, 36 Olivieri et al. (54) 99 Lymphoma AC/lipoAC US-I 0.08 ng/ml Before CT; 1, 24–72 h after each cycle Kitayama et al. (55) 40 Breast cancer AC/AC+TRZ/TRZ HS-T NA Before CT; every 3 months during CT Shafiet al. (56) 82 Breast cancer AC US-I NA 1, 24 h after each cycle AC, anthracycline-containing chemotherapy; ALL, acute lymphoblastic leukemia; CT, chemotherapy; Cycl, cyclophosphamide; HD, high-dose; LAP, lapatinib; lipoAC, liposomial anthracycline; NA, not available; I, troponin I; T, troponin T; TRZ, trastuzumab; HS, high-sensitive; US, ultra-sensitive *, pediatric population. AC, anthracycline-containing chemotherapy; ALL, acute lymphoblastic leukemia; CT, chemotherapy; Cycl, cyclophosphamide; HD, high-dose; LAP, lapatinib; lipoAC, liposomial anthracycline; NA, not available; I, troponin I; T, troponin T; TRZ, trastuzumab; HS, high-sensitive; US, ultra-sensitive *, pediatric population. Frontiers in Cardiovascular Medicine | www.frontiersin.org Tissue Doppler and Strain Echocardiography subjects following cardiac events, while another study demonstrated an association between an increased BNP at 72 h after chemotherapy and a decrease of LVEF at 1 year (59). Novel echocardiographic methods have emerged as sensitive parameters in the early identification of cardiotoxicity. In particular, introduction of tissue Doppler and strain imaging techniques can detect early subclinical changes in cardiac function, before LVEF falls (4, 7, 19, 51). In this respect, myocardial deformation (strain imaging) has emerged as a sensitive marker for earlier detection of myocardial dysfunction. In particular, 2D (and more recently, 3D) speckle tracking imaging, allowing the evaluation of global myocardial deformation in the longitudinal axis (global longitudinal strain, GLS, %), has become a clinical standard. Several papers demonstrated the value of GLS in detecting subclinical myocardial dysfunction, with prognostic relevance in terms of overt LV dysfunction in cancer patients (66–69). Actually, studies of other biomarkers, including microRNAs (miRNAs), C-reactive protein (CRP), growth differentiation factor-15 (GDF-15), myeloperoxidase (MPO), and galectin- 3 (Gal-3) have not demonstrated an association between pretreatment biomarker levels and cardiovascular outcomes (60, 61). Regarding monitoring for cardiovascular toxicity during therapy, CRP has shown conflicting findings (50). More recently, some reports emerged in the field of microRNAs, in particular for miR-1, showing a trend to earlier detection of cardiotoxicity respective to troponin (62, 63). Another study of patients during a period of 10 years after anthracycline therapy did not find an association with Gal-3 and LV dysfunction. The recent ASE/EACVI consensus defined a relative decrease in GLS of >15% from baseline as an indicator of subclinical LV dysfunction and appropriate use criteria for multi-modality imaging include strain for the evaluation of patient candidates for chemotherapy (19, 70). Finally, the SUCCOUR trial (first randomized controlled trial of GLS-guided therapy introduction) A separate study that included Gal-3 and ST2 found no association with these biomarkers and LVEF 1 year after therapy (64, 65). March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 6 Cardiotoxicity of Anthracyclines Cardinale et al. will better define the role of GLS for surveillance for chemotherapy-related cardiac dysfunction (71). animal models, idarubicin and mitoxantrone also showed a less cardiotoxic profile than doxorubicin (5, 7). animal models, idarubicin and mitoxantrone also showed a less cardiotoxic profile than doxorubicin (5, 7). An Integrated Approach to Biomarkers and Cardiac Imaging Breakthroughs in laboratory technology have allowed for the introduction of more specific and sensitive troponin assay methods (55), which are able to measure minimal amounts (high- sensitivity [HS] dosing systems) of a biomarker that were not detectable with previous methods. This is of pivotal importance, since troponin release as a consequence of anthracycline cardiotoxicity may be minimal, and it is essential to use high- precision dosing systems (72). PRIMARY PREVENTION: REDUCTION OF THE DIRECT CARDIOTOXIC EFFECT (FIGURE 2) g p The hypothesis that iron chelators may reduce the cardiotoxicity induced by anthracyclines suggests that dexrazoxane may be a clinically useful cardioprotective agent (9, 79). Doxorubicin is a potent Top2 inhibitor. In the clinical scenario, many studies demonstrated that dexrazoxane significantly reduces cardiotoxicity in adults and pediatric populations: Patients treated with dexrazoxane had a significantly lower incidence of heart failure than untreated patients. Apart from patients with metastatic breast cancer treated with doses of doxorubicin >300 mg/mq and despite previous findings, dexrazoxane is not routinely used in clinical practice, because suspected of interfering with the anti-tumor effects and by the occurrence of secondary malignancies. In September 2011, the outcome of a referral (80) that recommended several restrictions on dexrazoxane use in both children and adults with cancer was published. However, several new trials on the benefit-risk of dexrazoxane have been published from then (81–83). So far, dexrazoxane results an effective cardioprotector when administered with anthracycline chemotherapy being not associated with a reduction in anti-tumor efficacy or survival or a relevant increased risk of second primary malignancies, and can Tissue Doppler and Strain Echocardiography However, these methodologies are not always readily available in all laboratories and seldom used in the routine evaluation of patients receiving anthracyclines (8). Use of Liposomal Anthracyclines In the heart, liposomes cannot get out from the vascular space because capillaries have tight junctions. As the tendency to accumulate in the heart cells is limited, this may reduce the risk of cardiotoxicity. On the contrary, the liposomes reach high concentrations in the tumor site, leaving the circulatory system where tumor growth damages the capillaries itself (73, 74). The Use of Cardioprotection The use of cardioprotective drugs to reduce the direct cardiotoxic effect is a potential alternative to anthracycline treatment modifications, dosage limitations, or interruptions (4, 5, 8). Limitation of the Maximum Dose of Anthracyclines Present oncologic guidelines recommend limiting the total cumulative dose of anthracyclines to 450–550 mg/ml (4, 8). However, this may limit the effectiveness of anti-cancer treatment. Moreover, significant variability exists in terms of proneness to anthracycline cardiotoxicity, suggesting that genetic variation might modulate the risk (5, 7, 8). Lifestyle Measures Before pharmacologic strategies, primary prevention starts indeed with lifestyle corrective measures. The first HS troponin trial enrolled 45 breast cancer patients who were treated with anthracyclines, taxanes, and trastuzumab (44). International and regional myocardial function was assessed at baseline, every 3 months, with tissue Doppler and strain imaging, combined with troponin. A reduction in the longitudinal strain and an increase in HS troponin were predictive of late left ventricular dysfunction after the end of anthracyclines. Notably, the combined assessment of imaging methods and changes in troponin resulted in an increased specificity (93% combined vs. 73% for each single method). Ky et al. tested a multi-marker approach in a similar population of breast cancer patients receiving the same anti-cancer therapy regimen (50). All levels of the markers increased significantly from baseline (except for NT-proBNP and Galectin-3). However, at the end of anthracycline therapy, only HS troponin absolute values and changes in troponin and myeloperoxidase levels resulted as predictors of further development of left ventricular dysfunctions. Since a strong link exists between cancer and cardiovascular risk factor, addressing smoking and sedentary habits (potentially leading to obesity, with a detrimental role especially in the post- menopausal women), as well as high alcohol intake, is pivotal. A healthy diet has been associated with a protective effect in terms of cancer relapses and cardiovascular disease, while smoking has an ominously detrimental effect. While light to moderate alcohol intake has shown a protective impact in terms of cardiovascular disease, the results in terms of risk of developing cardiotoxicity are conflicting (75–77). Of notice, several pieces of evidence emerged on the protective role of exercise training (and eventually, cardiac rehabilitation) against cardiotoxicity (78). Use of Less Cardiotoxic Anthracycline Analogs g Epirubicin, idarubicin, and mitoxantrone are analogs of anthracyclines that are less cardiotoxic than conventional anthracyclines. Epirubicin cardiotoxicity occurs after higher doses of doxorubicin. However, to obtain the same clinical response, higher doses must be given. In preclinical studies and March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 7 Cardiotoxicity of Anthracyclines Cardinale et al. at follow-up in cancer patients receiving neurohormonal therapies (99). be recommended as a cardioprotector particularly for children and adolescents for whom the development of anthracycline- induced cardiotoxicity could have a crucial prognostic impact. These studies contributed to the CHMP’s decision to remove the contraindication on Cardioxane (84). Beta-Blockers The non-cardioselective beta-blocker carvedilol is cardioprotective against anthracyclines toxicity. In vitro studies and a small randomized clinical trial, the drug was able to prevent the development of ventricular dysfunction (86). In breast cancer patients, carvedilol blunted strain abnormalities and the increase in troponin, preserving diastolic function, after anthracycline use (100). However, the drug failed to prevent an LVEF reduction >10% (101). It appears that carvedilol’s efficacy is linked to its antioxidant activity rather than its beta-blocking action. Indeed, a comparative study of carvedilol and atenolol, a selective β1 antagonist with no antioxidant properties, showed that carvedilol—but not atenolol—prevented mitochondrial damage and mitigated the ultrastructural changes associated with doxorubicin (8, 102). Macedo et al. recently published a systematic review and meta- analysis of nine trials (seven randomized and two retrospective non-randomized trials) on the efficacy of dexrazoxane in patients with breast cancer treated with anthracyclines (with or without trastuzumab). Despite the quality of available evidence remaining low, dexrazoxane was shown to reduce the risk of heart failure and cardiac events, independently from previous exposure to anthracyclines. The oncological response and survival rates were not affected by dexrazoxane (85). Other potentially cardioprotective agents have been studied in animal models and small clinical studies. Preliminary data are promising, but they need to be ratified by further extensive studies (2, 5, 7, 8). Nebivolol, a selective β1 antagonist with vasodilatory properties, started 7 days before anthracyclines and continued for 6 months in 27 patients with breast cancer prevented a significant decrease of LVEF and an increase of NT-proBNP (87). In a retrospective study including 106 breast cancer patients, a reduced incidence of heart failure over a 5-year follow-up period was associated with the continuation of beta-blocker therapy during oncology treatment—including anthracyclines (88). Existing data indicate, from preclinical studies, that The Use of Cardiovascular Agents The Use of Cardiovascular Agents Several heart failure drugs have been shown to be effective in terms of cardioprotection against anthracylines (Table 4) (86–98). Several heart failure drugs have been shown to be effective in terms of cardioprotection against anthracylines (Table 4) (86–98). Overall, a recent meta-analysis of randomized clinical trials of adult patients that underwent chemotherapy and cardiovascular therapies vs. placebo with follow-up (17 trials, 1,984 patients) showed higher (although with small changes) LVEF values TABLE 4 | Cardiovascular drugs showing a prophylactic effect against anticancer therapy-induced LVD in adult cancer populations. Study (year) Study design/follow-up N Cancer type Drugs Intervention Results BETA-BLOCKERS Kalay et al. (86) RCT/6 months 50 Various AC Carvedilol No LVEF↓ Kaya et al. (87) RCT/6 months 45 Breast cancer AC Nebivolol No LVEF and NT-proBNP↑ Seicean et al. (88) Retrospective/5 years 318 Breast cancer AC,TRZ Beta-blockers HF ↓ Pituskin et al. (89) RCT/12 months 99 Breast cancer CT+TRZ Bisoprolol No LVEF ↓ ACEI Cardinale et al. (90) RCT/12 months 114 Various HD CT Enalapril No LVEF ↓; MACE incidence ↓ Pituskin et al. (89) RCT/12 months 99 Breast cancer CT+TRZ Perindopril No LVEF ↓ ARB Nakamae et al. (91) RCT/7 days 40 NHL AC Valsartan No LVEDD↑; no BNP and ANP↑; no QT↑ Cadeddu et al. (92) RCT/18 months 49 Various AC Telmisartan No peak strain rate ↓; no interleukin-6↑ Gulati et al. (93) RCT/1.5–16 months 120 Breast cancer AC+Tx+TRZ Candesartan No LVEF ↓ ALDOSTERONE ANTAGONISTS Akpek et al. (94) RCT/6 months 83 Breast cancer AC Spironolactone No LVEF↓; no TNI and BNP↑; ACEI + BETA-BLOCKERS Bosh et al. (95) RCT/6 months 90 Hematological AC Enalapril + carvedilol No LVEF↓; death↓; HF ↓ STATINS Acar et al. (96) RCT/6 months 40 Hematological AC Atorvastatin No LVEF↓ Seicean et al. (97) Retrospective/5 years 67 Breast cancer AC Statins No HF ↓ Chotenimitkhun et al. (98) PO 51 Various AC Atorvastatin/simvastatin No LVEF↓ ACEI, angiotensin-converting enzyme inhibitor; ANP, atrial natriuretic peptide; ARB, angiotensin receptor blocker; BNP, brain natriuretic peptide; HD CT, high-dose chemotherapy; LVD, left ventricular dysfunction; LVEF, left ventricular ejection fraction; LVEDD, left ventricular end-diastolic diameter; HF, heart failure; MACE, major adverse cardiac events; NHL, non Hodgkin lymphoma; NT-proBNP, N-terminal-proBNP; QT, QT interval; PO, prospective observational; RCT, randomized controlled trial; Tx, taxanes; TNI, troponin I; TRZ, trastuzumab. Perspectives d A recent study identified the molecular and cellular signature of dose-dependent, doxorubicin-mediated cardiotoxicity and provided evidence that prokineticin receptor (PKR-1)-1, acting at myocardial and vascular level, is a promising target to combat cardiotoxicity of cancer treatments (104). Since G protein-coupled receptors (GPCRs) are a target of 40% of clinically used drugs and newly identified cardioprotective agents that bind GPCRs of adrenalin, adenosine, melatonin, ghrelin, galanin, gpelin, prokineticin, and cannabidiol may further aid in the cardioprotective task (105). The combination of enalapril and carvedilol have been tested in the OVERCOME study (preventiOn of left-ventricular dysfunction with enalapril and carvedilol). The study involved 90 patients treated with anthracyclines, with malignant hemopathies. LVEF didn’t change in the intervention group after 6 months, but decreased significantly in controls. In addition, the intervention group had a lower rate of combined death or heart failure or death, heart failure, and a final LVEF of <45 % (95). The Use of Cardiovascular Agents ACEI, angiotensin-converting enzyme inhibitor; ANP, atrial natriuretic peptide; ARB, angiotensin receptor blocker; BNP, brain natriuretic peptide; HD CT, high-dose chemotherapy; LVD, left ventricular dysfunction; LVEF, left ventricular ejection fraction; LVEDD, left ventricular end-diastolic diameter; HF, heart failure; MACE, major adverse cardiac events; NHL, non Hodgkin lymphoma; NT-proBNP, N-terminal-proBNP; QT, QT interval; PO, prospective observational; RCT, randomized controlled trial; Tx, taxanes; TNI, troponin I; TRZ, trastuzumab. March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 8 Cardiotoxicity of Anthracyclines Cardinale et al. cardio-specific beta blockers offer superior protection against anthracycline damage than non-cardioselective ones (8). Statins The effect of statins on cardiotoxicity of anthracyclines is most likely due to their pleiotropic effect, and in particular, to their antioxidant properties (8). Forty hematologic cancer patients with no history of heart disease were randomized to receive atorvastatin or placebo before the onset of anthracyclines (95). The dosage was 40 mg/day, regardless of the levels of cholesterol, and lasted for 6 months. During the follow-up, a reduction of the high-sensitivity reactive C protein level and no significant changes in LVEF were observed in the statin group. PREVENTION IN SELECTED HIGH-RISK PATIENTS Prevention may be an option for all patients who are candidates for cardiotoxic therapy (primary prevention) or restricted to patients with preclinical symptoms of cardiotoxicity, with the advantage of limiting prophylactic therapy to a small number of patients (also reducing the side effects of preventive therapy, i.e., hemodynamic effects) (Figure 2). ACE-Inhibitors and Sartans Experimental data demonstrated a crucial role of the renin- angiotensin system (RAS) in the development and progression of cardiomyopathy induced by anthracyclines (90). Valsartan, administered in combination with anthracyclines, blunted natriuretic peptides increase, the increase in chamber size in patients with non-Hodgkin’s lymphoma treated doxorubicin (91). The authors hypothesized a direct inhibition of the drug, independent from hemodynamic effects (8, 90). g g p Conversely, the LVEF value in the control group resulted in a significant reduction from the baseline. The protective effect of statins also emerged when chemotherapy was started in patients already receiving statins for the prevention of cardiovascular disease (96). In a retrospective observational study of 67 breast cancer patients treated with anthracycline, statin therapy continued to be associated with significant reduction in the risk of heart failure and cardiac-related mortality during follow-up. More recently, patients on statin therapy for the prevention of cardiovascular disease reported a smaller drop in LVEF at 6 months in a retrospective observational study, including 51 patients with breast cancer or hematological malignancies treated with anthracyclines (97). Telmisartan, started before epirubicin, was able to prevent strain reduction and inflammatory markers increase because of its RAS blocking action, but also because of its anti-inflammatory and anti-oxidant properties (92). In the PRADA (Prevention of Cardiac Dysfunction during Adjuvant Breast Cancer Therapy) trial candesartan—but not metoprolol—administrated with adjuvant chemotherapy including anthracyclines, with or without trastuzumab, can protect against an early decline in LVEF, assessed with cardiac MRI (93). The MANTICORE-101 study (Multi-disciplinary Approach to Novel Therapies in Cardiology Oncology Research) tested the use of perindopril vs. bisoprolol in the prevention of left ventricular remodeling, defined as an increase in end-diastolic diameters and primary study point, and of left ventricular dysfunction in HER2+ breast cancer patients treated with trastuzumab prior to anthracycline (89). Neither drug prevent left ventricular remodeling; however, the use of both drugs was associated with a preserved left-ventricular function in multi- variate analysis. Aldosterone Antagonists A recent randomized trial, including 43 breast cancer patients, evaluated the use of spironolactone vs. placebo. Spironolactone was started 1 week before anthracyclines. Three weeks after the end of chemotherapy, the treated group did not show relevant variations in LVEF and rise in troponin I and NT-proBNP (94). In ELEVATE (Effect of Eplerenone on Left Ventricular Diastolic Function in Women Receiving Anthracyclines for Breast Cancer), a recent randomized placebo-controlled trial, administration of eplerenone for 6 months was not associated with significant differences in ventricular function compared with placebo in patients with breast cancer treated with anthracyclines (103). A randomized trial has tested the cardioprotective capacity of enalapril, involving 473 patients with different types of cancers treated with high-dose chemotherapy (90). 114 patients showed an increase in troponin and were randomized for treatment with or without enalapril. After the end of chemotherapy, enalapril was begun, titrated as tolerated, and continued for 1 year. No patients in the enalapril-treated group showed a decrease in LVEF by 10 absolute points below the value of 50%—the study’s primary endpoint—and the incidence of major cardiac events was remarkably small (Figure 5). Of note, in the enalapril community, the LVEF value was still the same as the baseline March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 9 Cardiotoxicity of Anthracyclines Cardinale et al. groups. Only three patients experienced cardiotoxicity defined as a 10% reduction in LVEF, below 50% value. value in 80% of cases after a follow-up duration of 12 months, showing that enalapril can be a very effective drug in the complete preservation of systolic function in this population. In brief, the main result of the study was that the two approaches appear to be similarly effective in preventing left ventricular dysfunction and adverse cardiac events, endorsing the use of enalapril in averting anthracycline-induced cardiotoxicity, irrespectively from the strategy used. Two studies are currently evaluating the efficacy of carvedilol as a preventive therapy in a selected patient with a deterioration in the strain parameter. For Research NCT02177175 (Carvedilol for the Prevention of Anthracyclines/Anti-HER2 Therapy- Associated Cardiotoxicity between Women with HER2+ breast cancer Using Myocardial Strain), the primary endpoint is the identification of a reduced LVEF value during the 1-year follow- up. At Northwestern University of Chicago, the research is still hiring. Which strategy is best? Secondary prevention (i.e., troponin driven) has the limitation of repeated blood samplings. Aldosterone Antagonists Nevertheless, considering the high negative predictive value of troponin (34, 35, 37, 38), this strategy appears warranted and cost-effective, as it permits the exclusion of low-risk patients (patients without troponin rise, the vast majority) from long- term monitoring programs based on imaging techniques with a relevant cost–benefit ratio by reducing “medicalization, distress, PRIMARY VS. SECONDARY PREVENTION Enalapril, which began early after the increase in troponin during anthracycline chemotherapy and continued for 12 months, is an effective therapy to avoid left ventricular dysfunction and subsequent heart events (90). Repeated assessment, however, is needed to detect an increase in troponin, as the marker may increase at different times after infusion with therapy (dose of anthracycline and schedules). Primary prevention, applied to all anthracycline-treated patients, does not pose this downside. The ICOSONE (International CardioOncology Society-One) randomized trial prospectively compared the efficacy of two different approaches, to test whether enalapril, initiated in all patients before chemotherapy (Prevention Group), was able to prevent troponin rise and further the development of left ventricular dysfunction, and to test whether this strategy was more successful than enalapril initiated only after troponin elevation during chemotherapy (Troponin-triggered Group) (106). The study included 273 patients from 21 different Centers of Oncology. The most-often administered anthracyclines were epirubicin and doxorubicin. During chemotherapy and the 12-month follow-up, no significant reduction in LVEF and a minimal incidence of cardiovascular events were detected in both TABLE 5 | Pros and Cons of primary prevention vs. secondary prevention with enalapril (83). Primary prevention with enalapril Enalapril in troponin + patients PROS: • Very low incidence LVD & MACE • Troponin assessment not required PROS: • Very low incidence LVD & MACE • Monitoring during up-titration in about 20% pts • Only pts at high-risk exposed to side effects • FU monitoring not required in troponin negative patients • Low cost-benefit ratio CONS: • Monitoring during up-titration in 100% • All pts exposed to side effects • FU monitoring required in all pts • High cost-benefit ratio CONS: • Repeated TNI assessment LVD, left ventricular dysfunction; MACE, major adverse cardiac events; FU, follow-up; TNI, troponin I. TABLE 5 | Pros and Cons of primary prevention vs. secondary prevention with enalapril (83). REFERENCES 10. Vejpongsa P, Yeh ET. Prevention of anthracycline-induced cardiotoxicity: challenges and opportunities. J Am Coll Cardiol. (2014) 64:938–45. doi: 10.1016/j.jacc.2014.06.1167 1. Octavia Y, Tocchetti CG, Gabrielson KL, Janssens S, Crijns HJ, Moens AL. 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Primary prevention with enalapril • Only pts at high-risk exposed to side effects FIGURE 5 | (A) Percentage of patients developing cardiac dysfunction in the enalapril-treated group (ACEI Group) and controls. (B) Incidence of cardiac events in patients treated with ACEI Group and in Controls. Modified from Cardinale et al. (90). March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 10 Cardiotoxicity of Anthracyclines Cardinale et al. anxiety, and costs” (21). Primary prevention, although not needing a repeated evaluation of troponin during chemotherapy, can be hard in terms of clinical surveillance during the drug up- titration to include 100% of patients. Finally, it may expose to potential side effects all those low-risk subjects for cardiotoxicity (Table 5) (106). inhibitors occurrence appears to be an effective method to prevent anthracycline-related left ventricular dysfunction and cardiac events. Finally, adoption of internal procedures, shared in a multi-disciplinary team, may actively aid in optimizing patient management. In this respect, a direct relationship with the laboratory medicine service for the assessment of troponin values during chemotherapy and the availability of a cardiologist and a dedicated nurse staff should always mix with an active collaboration with the referral oncologist/hematologist (possibly, surgeon) for updates and remains of pivotal importance (107, 108). AUTHOR CONTRIBUTIONS DC, FI, and CC contributed conception, design of the review, and wrote the first draft. All authors contributed to manuscript revision, read, and approved the submitted version. CONCLUSION Anthracycline-induced cardiotoxicity is still a significant problem that compromises the quality of life and overall survival of cancer patients. However, recent findings demonstrate that this form of cardiomyopathy is mostly reversible with early detection and prompt therapeutic introduction strategy. Probably, anthracycline-induced cardiotoxicity is a single and continuous phenomenon, from cellular to clinical stage, starting with myocardial cell injury, followed by progressive LVEF decline and, potentially, overt heart failure. The current standard for monitoring cardiac function (periodic assessment of LVEF), detects cardiotoxicity at a late stage when a significant impairment has already occurred, precluding the chance of effectively prevent and treat its development. FUNDING The present paper was funded by the European Institute of Oncology. The present paper was funded by the European Institute of Oncology. The use of troponins to identify patients with subclinical cardiotoxicity combined with early treatment with ACE- REFERENCES N Engl J Med. (2000) 342:1077–84. doi: 10.1056/NEJM200004133421502 41. 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(2011) 58:988–9. doi: 10.1016/j.jacc.2011.05.025 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. 97. Seicean S, Seicean A, Plana JC, Budd GT, Marwick TH. Effect of statin therapy on the risk for incident heart failure in patients with breast cancer receiving anthracycline chemotherapy: an observational clinical cohort study. J Am Coll Cardiol. (2012) 60:2384–90. doi: 10.1016/j.jacc.2012. 07.067 Copyright © 2020 Cardinale, Iacopo and Cipolla. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). 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. 98. Chotenimitkhun R, D’Agostino R Jr, Lawrence JA, Hamilton CA, Jordan JH, Vasu S, et al. Chronic statin administration may attenuate early anthracycline-associated declines in left ventricular ejection function. Can J Cardiol. (2015) 31:302–7. doi: 10.1016/j.cjca.2014.11.020 March 2020 | Volume 7 | Article 26 Frontiers in Cardiovascular Medicine | www.frontiersin.org 14
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Regulatory T cell-deficient scurfy mice develop systemic autoimmune features resembling lupus-like disease
Arthritis research & therapy
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Abstract Introduction: Scurfy mice are deficient in regulatory T cells (Tregs), develop a severe, generalized autoimmune disorder that can affect almost every organ and die at an early age. Some of these manifestations resemble those found in systemic lupus erythematosus (SLE). In addition, active SLE is associated with low Treg numbers and reduced Treg function, but direct evidence for a central role of Treg malfunction in the pathophysiology of lupus-like manifestations is still missing. In the present study, we characterize the multiorgan pathology, autoantibody profile and blood count abnormalities in scurfy mice and show their close resemblances to lupus-like disease. Methods: Scurfy mice have dysfunctional Tregs due to a genetic defect in the transcription factor Forkhead box protein 3 (Foxp3). We analyzed skin, joints, lung and kidneys of scurfy mice and wild-type (WT) controls by conventional histology and immunofluorescence (IF) performed hematological workups and tested for autoantibodies by IF, immunoblotting and enzyme-linked immunosorbent assay. We also analyzed the intestines, liver, spleen and heart, but did not analyze all organs known to be affected in scurfy mice (such as the testicle, the accessory reproductive structures, the pancreas or the eyes). We transferred CD4+ T cells of scurfy or WT mice into T cell-deficient B6/nude mice. Results: We confirm previous reports that scurfy mice spontaneously develop severe pneumonitis and hematological abnormalities similar to those in SLE. We show that scurfy mice (but not controls) exhibited additional features of SLE: severe interface dermatitis, arthritis, mesangioproliferative glomerulonephritis and high titers of anti-nuclear antibodies, anti-double-stranded DNA antibodies, anti-histone antibodies and anti-Smith antibodies. Transfer of scurfy CD4+ T cells (but not of WT cells) induced autoantibodies and inflammation of lung, skin and kidneys in T cell-deficient B6/nude mice. Conclusion: Our observations support the hypothesis that lupus-like autoimmune features develop in the absence of functional Tregs. CD4+ effector T (Teff) cells, which infiltrate tissues, re- cruit other inflammatory cells and ultimately lead to tissue damage [4]. Also, B cells are activated and high levels of immunoglobulins are present in the serum ([2,5]; reviewed in [3]). The contribution of B cells and autoantibodies for inflammation pathogenesis in scurfy mice was recently highlighted. B cell-deficient scurfy mice have less chronic inflammation and prolonged survival, and B cell transfer into these mice restores autoimmunity [6]. © 2015 Hadaschik et al.; licensee BioMed Central. 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. 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 Interestingly, in the bone marrow, scurfy mice have fewer B cells and higher numbers of cells of the myeloid lineage as com- pared with wild-type (WT) littermates [7,8]. In a recent publication it was shown that these effects depend on Regulatory T cell-deficient scurfy mice develop systemic autoimmune features resembling lupus-like disease Eva N Hadaschik1†, Xiaoying Wei1,2†, Harald Leiss3, Britta Heckmann1, Birgit Niederreiter3, Günter Steiner3, Walter Ulrich4, Alexander H Enk1, Josef S Smolen3 and Georg H Stummvoll3* RESEARCH ARTICLE Open Access Open Access * Correspondence: georg.stummvoll@meduniwien.ac.at †Equal contributors 3Department of Rheumatology, Medical University of Vienna, Wahringer Gurtel 18-20, 1090 Vienna, Austria Full list of author information is available at the end of the article Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 DOI 10.1186/s13075-015-0538-0 Introduction Scurfy mice have a missense mutation in the transcrip- tion factor Forkhead box protein 3 (Foxp3) gene and therefore lack functional CD4+Foxp3+ regulatory T cells (Tregs) and develop a lymphoproliferative disease with multiorgan inflammation, especially in the skin, the lung and the liver ([1,2]; reviewed in [3]). A main mediator of inflammation is the unrestrained activity of autoreactive * Correspondence: georg.stummvoll@meduniwien.ac.at †Equal contributors 3Department of Rheumatology, Medical University of Vienna, Wahringer Gurtel 18-20, 1090 Vienna, Austria Full list of author information is available at the end of the article Page 2 of 12 Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 but not typically involved in SLE (such as the testicles or the accessory reproductive structures, the pancreas or the eyes) [16]. granulopoietic effector cytokines (granulocyte macrophage colony-stimulating factor, tumor necrosis factor, interleu- kin 6 (IL-6)) and that Tregs do not directly affect B lym- phopoiesis, but that they reduce the production of granulopoietic cytokines by suppressing the respective Teff cells [7]. We show that Treg-deficient scurfy mice indeed share typical features of SLE, as they are positive for anti- nuclear antibodies (ANAs) and anti-double-stranded DNA (anti-dsDNA), anti-histone and anti-Smith (anti- Sm) antibodies (Abs). In addition, they are anemic and lymphopenic and develop pneumonitis, nephritis, arth- ritis and hyperkeratotic skin lesions that histologically re- semble cutaneous lupus erythematosus. Furthermore, transfer of CD4+ T cells from scurfy mice, but not from WT controls, induced autoantibody production as well as pneumonitis, nephritis and severe skin disease in CD4+ T cell-deficient B6/nude mice. As their main effect, Treg cells are crucial for main- taining peripheral tolerance [9,10]. The most important subset are CD4+ cells that constitutively express the IL-2 α-chain (CD25) and Foxp3 [11]. Not only is Foxp3 a use- ful Treg marker (which allows differentiation from acti- vated CD4+ Teff cells), but its stable expression is required for Treg differentiation and function [12], as Foxp3 defi- ciency leads to a severe autoimmune-mediated multiorgan inflammation in mice [1,2] and to the related IPEX syn- drome (immune dysregulation, polyendocrinopathy, enter- opathy, X-linked) in humans [2,13-16]. Tregs mainly suppress T cells, but there is evidence that they also target a variety of other immune cells, such as B cells and den- dritic cells (DCs) [9,11,17]. Because scurfy mice exhibit more autoimmune fea- tures than are typical for SLE, we do not claim that the scurfy mouse is a lupus model. Introduction However, our experi- ments foster the hypothesis that lack of Treg function and the consequent lack of peripheral tolerance lead to systemic autoimmune features resembling those in SLE. Scurfy mice develop a severe, generalized autoimmune disorder that can affect almost every organ system, in- cluding the conjunctiva, the liver and the reproductive system (testicles and accessory reproductive structures) [2,3,16]. Older reports also describe inflammation of the intestines and (as in human IPEX) of the pancreas, whereas newer ones do not [2,3]. Some of the auto- immune features in scurfy mice closely resemble those found in systemic lupus erythematosus (SLE), such as pneumonitis, whereas other typical characteristics of SLE, such as nephritis, have not been reported [2,3]. In line with this, impaired Treg function was observed in human SLE and decreased frequencies and function of Tregs correlate inversely with clinical disease activity ([9,18,19]; reviewed in [20]). In addition, a homeostatic imbalance of Tregs and conventional T cells has been described in experimental lupus, and the transfer of CD4+CD25+Foxp3+ Tregs was reported to prolong drug- induced remission [21,22]. Scurfy mice Female heterozygous B6.Cg-Foxp3sf/J (scurfy) mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and bred to C57BL/6 WT male mice to gen- erate hemizygous male B6.Cg-Foxp3sf/Y (scurfy) off- spring). C57BL/6 WT male littermates were used as controls. As recipients for transfer experiments, B6.Cg-Foxn1nu/J (nude) (B6/nude) mice were purchased from The Jackson Laboratory. All mice were held under specific pathogen- free conditions at the central animal facility of the Interfa- cultary Biomedical Faculty, University of Heidelberg, Germany. Animal work was performed under the animal protocol (35-9185.81/G2010/10) approved by the local animal care committee (Regierungspräsidium Karlsruhe). Detection of autoantibodies As in scurfy mice, autoreactive T cells also play a cen- tral role in SLE pathogenesis in vivo because they are ex- panded, infiltrate affected organs and provide help for B cell activation. As a consequence, B cells are hyperreac- tive and produce (auto)antibodies [23-28]. Serum samples were taken from scurfy and WT mice on day 21 of life. For evaluation of autoantibodies by im- munofluorescence (IF), sera were diluted (as indicated in the figure legends) and added to slides precoated with either Crithidia luciliae (dsDNA) or HEp-20-10 cells and primate liver cells, respectively (ANAs) (all from EUROIMMUN, Lübeck, Germany). As a secondary Ab, goat-anti mouse immunoglobulin G (IgG) Alexa Fluor 488 (Invitrogen, Carlsbad, CA, USA), diluted 1:500 in phosphate-buffered saline (PBS), was used. For semi- quantitative analyses, the slides were scored according to fluorescence intensity as follows: 0 = no positive staining, 1 = weakly positive staining, 2 = intermediate positive staining and 3 = strongly positive staining. In order to test the hypothesis that scurfy mice, as a consequence of their Treg deficiency, may exhibit a var- iety of autoimmune features resembling systemic lupus-like disease, we investigated these mice for typ- ical manifestations of SLE. We analyzed for signs of nephritis, pneumonitis, arthritis and the occurrence of typical serum autoantibodies and reevaluated skin manifestations for lupus-like abnormalities. We also analyzed the intestines, liver, spleen and heart, but not all the other organs known to be affected in scurfy mice Page 3 of 12 Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 followed by 30 minutes of blocking with 5% goat serum in Tris-buffered saline (TBS). Slides were incubated with goat anti-mouse IgG Alexa Fluor 488 (Invitrogen) at 1:500 dilution in TBS for 1 hour in the dark. Anti-histone Abs were measured by enzyme-linked im- munosorbent assay (ELISA) (Inova Diagnostics, San Diego, CA, USA). The results are presented in units per milliliter. Horseradish peroxidase–conjugated goat anti-rat Abs (1:2,000 dilution; SouthernBiotech, Birmingham, AL, USA) served as secondary Abs. Further analysis was per- formed by immunoblotting as described elsewhere [29,30]. Urinalysis was done by using the dipstick (Combur 5 Test HC; Roche Diagnostics, Mannheim, Germany) method with a semiquantitative system that allows scoring for ery- throcyturia, leukocyturia and proteinuria from 0 (negative) to + (positive) and ++ (highly positive). Analysis of involvement of inner organs Lungs, kidneys, spleens, hearts, intestines and livers were obtained from scurfy and WT mice; processed according to standard laboratory procedures; and stained with H&E. Kidney sections were also stained with periodic acid-Schiff (PAS) and analyzed by a blinded pathologist experienced in renal pathology of mice (WU). Histological analysis of joints Hind paws were prepared and analyzed by using previ- ously described histopathologic techniques [32-35]. Stain- ing with H&E allowed a general assessment, and toluidine blue (TB) destaining was performed to determine cartilage matrix loss. Tartrate-resistant acid phosphatase (TRAP) staining was performed to identify osteoclasts. Histomor- phometric parameters (area of cartilage destruction, in- flammation and erosion, as well as osteoclast numbers) were quantified by using the OsteoMeasure™image ana- lysis system (OsteoMetrics, Decatur, GA, USA). Additional immunohistochemistry was done for T cells (anti-CD3; Novocastra Laboratories, Newcastle upon Tyne, UK), B cells (anti-CD45 receptor; BD Biosciences PharMingen, San Diego, CA, USA), macrophages (clone F4/80; AbD Serotec, Puchheim, Germany) and granulo- cytes (MCA771G; AbD Serotec) as reported previously [33-35], followed by quantitative analysis of the inflam- matory infiltrate by tissue cytometry using HistoQuest™ software (TissueGnostics, Vienna, Austria) [36,37]. Transfer experiments + CD4+ T cells were isolated from lymph nodes of sick scurfy mice and male WT controls using magnetic activated cell sorting with CD4 microbeads (Miltenyi, Bergisch Gladbach, Germany). Purity of greater than 95% was confirmed by fluorescence-activated cell sorting analysis; CD4+ T cells were washed three times in PBS; and 2 × 106 cells resus- pended in 100 μl were injected into male B6/nude mice via tail vein injections. Four weeks after transfer, recipient mice were analyzed for autoantibody production (ANAs, anti-dsDNA Abs) for signs of inflammatory skin disease and for involvement of inner organs (lung and kidney) as described above. Hematological analysis Scurfy and WT mice were bled at day 21 of life into tubes with sodium citrate to prevent clotting. Blood samples were immediately sent to the University of Heidelberg multidisciplinary center for blood analysis. Scoring of pulmonary inflammation was based on a method published [38] and adapted [39] previously. In brief, for each vessel, we obtained a perimeter score accord- ing to the percentage of vessel perimeter surrounded by cells, calculated the mean width of the infiltrate (cellF soft- ware; Olympus Soft Imaging Solutions, Münster, Germany) and multiplied these values for the final score [38]. Detection of autoantibodies For proteinuria, a score of at least ++ was considered pathologic because healthy mice also showed mild signs of proteinuria under these testing conditions (with a maximum of + positivity). Statistical analysis The data are expressed as mean ± SD. Student’s t-test or Fisher’s exact test (two tailed) was used for comparison of group values and discriminatory measures. One-way ana- lysis of variance was used for repeated measurements of the same variable where appropriate. Wilcoxon’s matched- pairs test was used for the comparison of individual paired values if the distribution was not Gaussian. Significance was analyzed using Prism and InStat software (GraphPad Software, La Jolla, CA, USA), and P-values <0.05 were considered significant. Histological analysis of skin inflammation When the mice were at day 21 of life, routine necropsies were performed for histopathologic evaluation, and skin tissue was fixed in 4% neutral buffered formalin. Fixed tissues were embedded in paraffin, and 5-μm sections were cut and stained with hematoxylin and eosin (H&E). Skin inflammation was scored in a graded fashion as previously described [31]. Scurfy mice spontaneously develop a lupus-like skin phenotype Scurfy mice appear smaller than their WT littermate con- trols and have scaly skin on their ears, eyes and tails (reviewed in [3]). Around day 21 of life, scurfy mice are sig- nificantly smaller than normal and runted and exhibit se- vere skin inflammation (Figure 1a). In contrast to WT For IF analysis, kidneys and back skin tissue samples were embedded in OCT compound and flash-frozen, and 5-μm cryosections were cut and fixed in acetone Page 4 of 12 Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Figure 1 Scurfy mice spontaneously develop severe autoimmune lupus-like skin inflammation. We observed an inflammatory skin disease in scurfy mice that was a consequence of uncontrolled T cell expansion. A macroscopic view of scurfy (Sc) mouse and wild-type (WT) littermate control on day 21 of life (a) and a closer view of the tails of WT mouse (b) and scurfy mouse (c) are shown. Histological examination revealed interface dermatitis with effacement of the dermoepidermal junction and strong lymphohistiocytic inflammatory infiltrates, both of which are key histological features of cutaneous lupus erythematosus. Representative hematoxylin and eosin–stained sections of back skin of WT mouse (d) and sick scurfy mouse (e), as well as a higher magnification image of inflammatory infiltrate in scurfy skin (f), are also shown. (g) Summary of skin pathology scores of scurfy (n = 13) and WT (n = 13) back skin. Representative direct immunofluorescence images show scurfy (h) and WT (i) back skin tissue sections showing linear deposits of murine immunoglobulin only in scurfy skin. Figure 1 Scurfy mice spontaneously develop severe autoimmune lupus-like skin inflammation. We observed an inflammatory skin disease in scurfy mice that was a consequence of uncontrolled T cell expansion. A macroscopic view of scurfy (Sc) mouse and wild-type (WT) littermate control on day 21 of life (a) and a closer view of the tails of WT mouse (b) and scurfy mouse (c) are shown. Histological examination revealed interface dermatitis with effacement of the dermoepidermal junction and strong lymphohistiocytic inflammatory infiltrates, both of which are key histological features of cutaneous lupus erythematosus. Representative hematoxylin and eosin–stained sections of back skin of WT mouse (d) and sick scurfy mouse (e), as well as a higher magnification image of inflammatory infiltrate in scurfy skin (f), are also shown. (g) Summary of skin pathology scores of scurfy (n = 13) and WT (n = 13) back skin. Pneumonitis in scurfy mice All b f (f All but one scurfy mice (five (83%) of 6), but no controls (zero of six) (P = 0.0152), developed pneumonitis charac- terized by alveolar wall thickening, interstitial edema and perivascular and peribronchial (lymphocyte enriched) inflammatory infiltrates and focal hemorrhages resem- bling human and murine lupus pneumonitis [39,43-45] (Figure 2g–j). In analyzing perivascular inflammatory infiltrates in scurfy lungs, we found that the mean per- imeter score was 2.7 ± 1.5 and the width varied from 2 to 22 cell layers thick, with a mean of 47.4 ± 36.8 μm, leading to a significantly elevated total score (Figure 2j). Scurfy mice spontaneously develop a lupus-like skin phenotype Representative direct immunofluorescence images show scurfy (h) and WT (i) back skin tissue sections showing linear deposits of murine immunoglobulin only in scurfy skin. (Figure 2e,f). Urinalysis in a series of 14 scurfy mice showed proteinuria in 21% and erythrocyturia in 29% of mice, but no leukocyturia (data not shown). mice, the tail skin of scurfy mice is scaly and erythema- tous and reveals hyperkeratosis (Figure 1b,c). On histo- logical analysis of inflamed scurfy back skin, the predominant features are interface dermatitis with ef- facement of the dermoepidermal junction (Figure 1e) and strong lymphohistiocytic inflammatory infiltrates (Figure 1f), both of which are histological features charac- teristic of cutaneous lupus erythematosus [40,41]. Using a previously described scoring system for skin pathology that comprises epidermal as well as dermal changes [31], we found significant skin inflammation in all scurfy skin samples, but no WT skin samples (Figure 1g). Using direct IF on cryosections of back skin, we found strong deposits of mouse IgG in the dermoepidermal basement mem- brane zone (similar to the lupus band observed in patients with SLE) in the skin of scurfy mice, but not in that of WT littermate controls (Figure 1h,i). Transfer experiments Scurfy mice also had significantly elevated serum levels of anti-histone Abs in ELISA analysis (145 ± 58 U/ml versus 66 ± 36 U/ml; P = 0.0031). A detailed immunoblot analysis of autoantibody suptypes revealed that 80% of scurfy (but not WT controls) had Abs against Sm anti- gen (8 of 10 versus 0 of 10; P = 0.0007) and that 90% were positive for U1 ribonucleoprotein (RNP) Abs (di- rected against RNP-A) (P = 0.0001), but did not develop Scurfy mice develop mesangioproliferative glomerulonephritis Hyperreactive spleens and analysis of other inner organs In line with the literature, we also found germinal cen- ter hyperplasia, depletion of lymphocytes in mantle zones and parafollicular areas of scurfy spleens, but not those of WT controls. In addition, scurfy mice, but not WT mice, showed periportal and perisinusoidal inflam- matory infiltrates in the liver. There were no signs of in- flammation in the intestines or the heart [1,2,16,31] (data not shown). Kidneys sections were stained with H&E and PAS and analyzed by direct IF. All but one scurfy mouse devel- oped mesangial glomerulonephritis (eight (89%) of nine) typical of World Health Organization (WHO) class II lupus nephritis, whereas the kidneys of WT mice were not affected (Figure 2a–d) [42]. On the basis of direct IF analysis, the majority of scurfy mice showed murine IgG deposits in the glomerula, whereas WT mice did not Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Page 5 of 12 Page 5 of 12 Figure 2 Development of glomerulonephritis and pneumonitis in the majority of scurfy mice, but not in wild-type mice. Scurfy (Sc) mice developed mesangial glomerulonephritis comparable to World Health Organization class II lupus nephritis in humans. Representative hematoxylin and eosin (H&E)–stained sections of a wild-type (WT) kidney (a) and a scurfy mouse kidney (b), a periodic acid-Schiff stain of a glomerulum from a scurfy mouse kidney (c). (d) Glomerulonephritis occurred in eight (89%) of nine scurfy mice, but not in controls (P = 0.0004). Lung involvement resembling lupus pneumonitis was found in all but one scurfy mouse (83%), but not in controls (P = 0.0152). Representative examples of direct immunofluorescence of a scurfy mouse kidney (e) and a WT kidney (f) are shown. Also shown are representative H&E-stained sections of a WT lung (g) and a scurfy lung (h), a higher-magnification image of a peribronchial inflammatory infiltrate in a scurfy lung (i) and the total lung inflammation score in scurfy and WT mice (j). Figure 2 Development of glomerulonephritis and pneumonitis in the majority of scurfy mice, but not in wild-type mice. Scurfy (Sc) mice developed mesangial glomerulonephritis comparable to World Health Organization class II lupus nephritis in humans. Representative hematoxylin and eosin (H&E)–stained sections of a wild-type (WT) kidney (a) and a scurfy mouse kidney (b), a periodic acid-Schiff stain of a glomerulum from a scurfy mouse kidney (c). Scurfy mice are anemic and lymphopenic Hemoglobin, hematocrit and erythrocyte counts were strongly reduced in scurfy blood in contrast to WT con- trols (Figure 3a–c). Complete blood cell counts revealed severe lymphopenia and leukocytosis in scurfy mice and slight (albeit not significant) changes in thrombocyte counts in comparison to WT mice (Figure 3d–f). Scurfy mice show cartilage degradation and nonerosive arthritis Clinically, the majority of scurfy mice showed moderate, diffuse swelling of the paws, which was hard to distin- guish from subcutaneous edema. In histological analyses, scurfy mice showed increased cartilage degradation com- pared with WT controls, and they developed inflamma- tory infiltrates within the synovial membrane, whereas controls did not (Figure 5a,b,d). No osteoclasts were de- tected within the joint, and therefore no erosions were found (Figure 5c). Histomorphometric analysis revealed that (besides fibroblasts) the inflammatory infiltrate con- sisted mainly of CD3+ T lymphocytes (12.8 ± 2.1%) and B cells (7.4 ± 1.9), but also some neutrophils (3.7 ± 3.4%) and macrophages (3.1 ± 1.9) (Figure 6a–c). Scurfy mice produce autoantibodies to nuclear antigens All sera of scurfy mice contained not only ANA, but also anti-dsDNA-Abs. ANA staining showed a cytoplas- mic and nuclear pattern and some samples were still positive at a dilution of 1:1000, while WT controls were negative for anti-dsDNA-Abs and had no or only weak staining for ANA (Figure 4a-c). Using a semiquantita- tive scoring system, scurfy showed significantly elevated values for both ANA and anti-dsDNA Abs when com- pared with controls (Figure 4d). Scurfy mice develop mesangioproliferative glomerulonephritis (d) Glomerulonephritis occurred in eight (89%) of nine scurfy mice, but not in controls (P = 0.0004). Lung involvement resembling lupus pneumonitis was found in all but one scurfy mouse (83%), but not in controls (P = 0.0152). Representative examples of direct immunofluorescence of a scurfy mouse kidney (e) and a WT kidney (f) are shown. Also shown are representative H&E-stained sections of a WT lung (g) and a scurfy lung (h), a higher-magnification image of a peribronchial inflammatory infiltrate in a scurfy lung (i) and the total lung inflammation score in scurfy and WT mice (j). Abs against Ro or La or against Scl-70 or Jo-1 antigens (data not shown). Transfer experiments Scurfy CD4+ T cells induce autoantibody production in B6/nude mice To evaluate if autoreactive CD4+ T cells from scurfy mice could induce autoantibody production via T cell- mediated B cell help, we transferred purified CD4+ T cells from scurfy mice and WT controls into B6/nude mice, which completely lack CD4+ T cells but possess a Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Page 6 of 12 Figure 3 Hematological analyses reveal anemia and lymphopenia in scurfy mice. Freshly drawn blood of scurfy (Sc) and wild-type (WT) mice was immediately subjected to hematological analyses after being drawn. Scurfy mice were anemic, showing significantly reduced (a) erythrocytes, (b) hemoglobin and (c) hematocrit in comparison to WT controls. Upon analyzing the white blood cell count, we found elevated total leukocytes (e), but reduced lymphocytes (d), in scurfy blood, whereas thrombocytes did not show significant differences (f). The results are shown as mean ± SD for scurfy mice (n = 13) and WT mice (n = 14) from two separate experiments. P-values are given in the figure. Figure 3 Hematological analyses reveal anemia and lymphopenia in scurfy mice. Freshly drawn blood of scurfy (Sc) and wild-type (WT) mice was immediately subjected to hematological analyses after being drawn. Scurfy mice were anemic, showing significantly reduced (a) erythrocytes, (b) hemoglobin and (c) hematocrit in comparison to WT controls. Upon analyzing the white blood cell count, we found elevated total leukocytes (e), but reduced lymphocytes (d), in scurfy blood, whereas thrombocytes did not show significant differences (f). The results are shown as mean ± SD for scurfy mice (n = 13) and WT mice (n = 14) from two separate experiments. P-values are given in the figure. skin disease (seven of seven, 100%) resembling the disease spontaneously occurring in scurfy mice (Figure 8a–d). In addition, four (57%) of seven mice that received scurfy CD4+ T cells developed proteinuria and erythro- cyturia as observed by urinalysis after 4 weeks of CD4+ T cell transfer. Two of these mice also showed typical histo- logical features of mesangioproliferative lupus nephritis in histological analysis (Figure 8e), whereas none of the con- trol mice developed kidney disease. skin disease (seven of seven, 100%) resembling the disease spontaneously occurring in scurfy mice (Figure 8a–d). normal B cell repertoire. Transfer experiments Scurfy CD4+ T cells induce autoantibody production in B6/nude mice Four weeks after transfer, we evaluated the presence of autoantibodies in the sera of re- cipient mice and found ANAs (ten of ten mice, 100%) and anti-dsDNA Abs (ten of ten, 100%) in B6/nude mice that received scurfy CD4+ T cells (Figure 7a,b). Among the B6/ nude mice that received WT CD4+ T cells, only very few showed weak ANA positivity and only two mice showed very weak anti-dsDNA Abs (Figure 7c,d). These results in- dicate that, in the absence of functional Tregs, autoreac- tive CD4+ T cells expand and are able to induce ANAs as well as anti-dsDNA Abs via T cell-mediated B cell help. In addition, four (57%) of seven mice that received scurfy CD4+ T cells developed proteinuria and erythro- cyturia as observed by urinalysis after 4 weeks of CD4+ T cell transfer. Two of these mice also showed typical histo- logical features of mesangioproliferative lupus nephritis in histological analysis (Figure 8e), whereas none of the con- trol mice developed kidney disease. Discussion Scurfy mice lack CD4+Foxp3+ Tregs and thus one crucial mechanism of peripheral tolerance. As a consequence, they die early as a result of a generalized systemic auto- immune disease [4]. Several autoimmune features of scurfy mice closely resemble those found in SLE, and Treg dysfunction has been reported in SLE [19]. Because the Scurfy CD4+ T cells induce organ inflammation in B6/nude mice After transfer of CD4+ T cells from scurfy mice, but not of WT CD4+ cells or PBS, T cell-deficient B6/nude mice de- veloped severe pneumonitis (seven of seven, 100%) and Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Page 7 of 12 Page 7 of 12 Figure 4 High titers of antinuclear antibodies and anti-double-stranded DNA antibodies develop in the absence of functional regulatory T cells. Antinuclear antibodies (ANAs) could be detected in all scurfy (Sc) sera when diluted 1:100 on slides coated with HEp-20-10 cells (upper panels) or primate liver tissue (lower panels) (a). In addition, all scurfy, but no control (wild type (WT)), sera were positive for anti-double-stranded DNA (anti-dsDNA) antibodies (diluted 1:100) on slides precoated with Crithidia luciliae (b). Examples of scurfy and WT sera at different dilutions (c) and a summary of the quantitative analysis of ANA and anti-dsDNA antibody positivity in scurfy and WT sera at the dilution of 1:100 (d) are given. The results are shown as mean ± SD for scurfy (n = 20) and WT (n = 20) mice. P-values are given in the figure. Figure 4 High titers of antinuclear antibodies and anti-double-stranded DNA antibodies develop in the absence of functional regulatory T cells. Antinuclear antibodies (ANAs) could be detected in all scurfy (Sc) sera when diluted 1:100 on slides coated with HEp-20-10 cells (upper panels) or primate liver tissue (lower panels) (a). In addition, all scurfy, but no control (wild type (WT)), sera were positive for anti-double-stranded DNA (anti-dsDNA) antibodies (diluted 1:100) on slides precoated with Crithidia luciliae (b). Examples of scurfy and WT sera at different dilutions (c) and a summary of the quantitative analysis of ANA and anti-dsDNA antibody positivity in scurfy and WT sera at the dilution of 1:100 (d) are given. The results are shown as mean ± SD for scurfy (n = 20) and WT (n = 20) mice. P-values are given in the figure. Figure 4 High titers of antinuclear antibodies and anti-double-stranded DNA antibodies develop in the absence of functional regulatory T cells. Antinuclear antibodies (ANAs) could be detected in all scurfy (Sc) sera when diluted 1:100 on slides coated with HEp-20-10 cells (upper panels) or primate liver tissue (lower panels) (a). In addition, all scurfy, but no control (wild type (WT)), sera were positive for anti-double-stranded DNA (anti-dsDNA) antibodies (diluted 1:100) on slides precoated with Crithidia luciliae (b). Scurfy CD4+ T cells induce organ inflammation in B6/nude mice As a consequence of the unleashed T cell proliferation in this regulatory T cell (Treg)-deficient mouse model, the inflammatory infiltrate was dominated by T cells with lower frequencies of granulocytes. (a) A representative immunohistochemical analysis of the hind paw of a scurfy mouse stained with anti-CD3 (upper panel) and neutrophil marker anti-Ly6-B.2 (lower panel) is shown. The quantitative analysis of the inflammatory cellular infiltrate was done by tissue cytometry. A representative scurfy joint is shown in (b) and summarized in (c). T, T cells; B, B cells; mfi, Mean fluorescence intensity; N, Neutrophils; M, Macrophages. The results are shown as mean ± SD for scurfy mice. Figure 6 T cells dominate the inflammatory infiltrate in arthritis in scurfy mice. As a consequence of the unleashed T cell proliferation in this regulatory T cell (Treg)-deficient mouse model, the inflammatory infiltrate was dominated by T cells with lower frequencies of granulocytes. (a) A representative immunohistochemical analysis of the hind paw of a scurfy mouse stained with anti-CD3 (upper panel) and neutrophil marker anti-Ly6-B.2 (lower panel) is shown. The quantitative analysis of the inflammatory cellular infiltrate was done by tissue cytometry. A representative scurfy joint is shown in (b) and summarized in (c). T, T cells; B, B cells; mfi, Mean fluorescence intensity; N, Neutrophils; M, Macrophages. The results are shown as mean ± SD for scurfy mice. the presence of ANA and anti-dsDNA autoantibodies (as well as for anti-histone- and anti-Sm Abs). severe autoimmune disorder seen in scurfy mice (and in human IPEX) includes many more autoimmune features than are typical for SLE (including hypogonadism, pan- creatitis, cholangitis and conjunctivitis), indicating overlap with other autoimmune diseases, the aim of the present study was not clearly at defining the scurfy mouse as a prototypical lupus model. Our aim was to evaluate the hy- pothesis that dysfunction of peripheral tolerance as a con- sequence of Treg malfunction (as seen in scurfy mice) leads to some of the typical features of SLE and therefore represents a lupus-like disease [9]. Pneumonitis is commonly observed in scurfy mice. Perivascular inflammation in scurfy lungs histologically resembles lung involvement in humans as well as that in murine lupus models [39,43-45]. Scurfy CD4+ T cells induce organ inflammation in B6/nude mice Examples of scurfy and WT sera at different dilutions (c) and a summary of the quantitative analysis of ANA and anti-dsDNA antibody positivity in scurfy and WT sera at the dilution of 1:100 (d) are given. The results are shown as mean ± SD for scurfy (n = 20) and WT (n = 20) mice. P-values are given in the figure. Figure 5 Arthritis in scurfy, but not wild-type, joints. All scurfy (Sc; nine of nine), but no control (wild type (WT); zero of nine) mice developed arthritis, as indicated by an inflammatory infiltrate (P < 0.0001). (a) Typical hematoxylin and eosin–stained cross-sections of the hind paws of a scurfy mouse (right panel) and a WT mouse (left panel) are shown. In addition, scurfy mice showed increased cartilage degradation (toluidine blue (TB) staining in (b)), but no osteoclasts were detected within the joint, and therefore no erosions were found (tartrate-resistant acid phosphatase (TRAP) staining in (c)). (d) Graphed data of the quantitative analysis of inflamed area, cartilage damage and eroded area in scurfy and WT mice are shown. The results are shown as mean ± SD for scurfy (n = 9) and WT mice (n = 9). P-values are given in the figure. Figure 5 Arthritis in scurfy, but not wild-type, joints. All scurfy (Sc; nine of nine), but no control (wild type (WT); zero of nine) mice developed arthritis, as indicated by an inflammatory infiltrate (P < 0.0001). (a) Typical hematoxylin and eosin–stained cross-sections of the hind paws of a scurfy mouse (right panel) and a WT mouse (left panel) are shown. In addition, scurfy mice showed increased cartilage degradation (toluidine blue (TB) staining in (b)), but no osteoclasts were detected within the joint, and therefore no erosions were found (tartrate-resistant acid phosphatase (TRAP) staining in (c)). (d) Graphed data of the quantitative analysis of inflamed area, cartilage damage and eroded area in scurfy and WT mice are shown. The results are shown as mean ± SD for scurfy (n = 9) and WT mice (n = 9). P-values are given in the figure. Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Page 8 of 12 Figure 6 T cells dominate the inflammatory infiltrate in arthritis in scurfy mice. Scurfy CD4+ T cells induce organ inflammation in B6/nude mice As typically seen in SLE, scurfy mice developed mesangioproliferative glom- erulonephritis meeting the criteria of WHO class II lupus nephritis, which may have been overlooked in previ- ous analysis if sections were not specifically stained with PAS or by IF [42]. Scurfy mice also developed nonerosive arthritis characterized by a T cell-enriched synovitis and by cartilage damage, thus resembling the arthritic manifes- tations of human SLE [46]. Because of ethical issues re- lated to severe lung involvement, scurfy mice must be analyzed within the first 3 to 4 weeks of life. Therefore, one can only speculate whether their arthritis would re- main nonerosive or if osteoclasts would be attracted into the inflamed joint at a later time point [47]. We confirm previous studies in showing that scurfy mice develop autoimmune characteristics compatible with SLE as pneumonitis, anemia, thrombocytopenia and in- flammatory skin involvement [2,31]. –In addition, we re- port, as new findings underscoring our hypothesis, typical SLE-like phenomena such as glomerulonephritis, lympho- penia and nonerosive arthritis. Moreover, the intensive workup of scurfy skin showed that the cutaneous manifes- tations closely resemble those found in SLE, including the presence of linear IgG deposits resembling a lupus band. Most importantly, however, scurfy mice tested positive for In addition, we characterized the inflammatory skin disease as interface dermatitis with effacement of the dermoepidermal junction and strong lymphohistiocytic Page 9 of 12 Page 9 of 12 Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Figure 7 Transfer of scurfy CD4+ T cells induces autoantibody production in B6/nude mice. Purified CD4+ T cells from lymph node single-cell suspensions of scurfy (Sc) and wild-type (WT) mice were transferred intravenously into immunocompromised B6/nude mice. Four weeks after transfer, the sera (diluted 1:100) of the recipient B6/nude mice were analyzed for the presence of autoantibodies. Antinuclear antibody (ANA) (a and b) and anti-double-stranded DNA (anti-dsDNA) antibodies (c and d) were positive in sera of B6/nude mice after transfer of scurfy CD4+ T cells, but could not be induced by transfer of WT CD4+ T cells or phosphate-buffered saline (PBS) injection. After transfer of scurfy CD4+ T cells from lymph node single-cell suspensions, kidneys of recipient mice showed murine immunoglobulin G deposits in glomerula, whereas recipient mice that received transferred WT CD4+ T cells or PBS did not (e). Scurfy CD4+ T cells induce organ inflammation in B6/nude mice (a), (c) and (e) show one representative stain, and (b) and (d) summarize data of all mice from two independent experiments (n = 10 for scurfy or WT T cell-injected mice, n = 2 for PBS-injected mice). P-values are given in the figure. inflammatory infiltrates, both of which are key histo- logical features of cutaneous lupus [40,41]. interestingly, a deficiency in Treg number and function has also repeatedly been postulated in human and mur- ine SLE [21,51,52]. Therefore, the finding that scurfy mice present with many important characteristics of SLE supports the idea of a pathogenic role of Treg deficiency in this autoimmune disease. In line with this, the adop- tive transfer of Tregs prevented the development of autoimmune disease in scurfy and had protective effects in lupus-prone mice [22,31,53,54]. In line with our hypothesis, we found an SLE-typical autoantibody pattern with ANA and anti-dsDNA, anti- histone and anti-Sm Abs. These autoantibodies have es- caped previous attention and could be detected in our study using sensitive techniques [2,48]. In transfer experiments, we could show that CD4+ T cells of scurfy mice, but not those of WT mice, trans- ferred disease into T cell-deficient B6/nude recipients. This finding underscores the hypothesis that autoreac- tive CD4+ T cells expand in the absence of functional Tregs and that these cells are able to induce lupus-like pathology in lungs, skin and kidneys as well as production of typical autoantibodies via T cell-mediated B cell help. Interestingly, CD4+ T cells from scurfy lymph nodes can also induce myositis and inflammation of the salivary glands (resembling Sjögren’s syndrome) upon transfer into susceptible (RAG-1-knockout) recipients [49,50]. As in SLE, there are signs of strong B cell activation in scurfy mice, as they have splenomegaly with germinal cen- ter hyperplasia and high levels of class-switched IgG auto- antibodies [2]. In a recent publication, authors described using B cell-deficient scurfy mice to show that B cells are important for autoimmune pathology and that therapeutic B cell depletion decreased tissue pathology and increased survival [6]. The B cell activation observed in scurfy mice could be explained either by lack of direct suppression by Tregs or by increased helper stimuli provided by activated autoreactive CD4+ T cells. Scurfy CD4+ T cells induce organ inflammation in B6/nude mice (a), (c) and (e) show one representative stain, and (b) and (d) summarize data of all mice from two independent experiments (n = 10 for scurfy or WT T cell-injected mice, n = 2 for PBS-injected mice). P-values are given in the figure. Figure 7 Transfer of scurfy CD4+ T cells induces autoantibody production in B6/nude mice. Purified CD4+ T cells from lymph node single-cell suspensions of scurfy (Sc) and wild-type (WT) mice were transferred intravenously into immunocompromised B6/nude mice. Four weeks after transfer, the sera (diluted 1:100) of the recipient B6/nude mice were analyzed for the presence of autoantibodies. Antinuclear antibody (ANA) (a and b) and anti-double-stranded DNA (anti-dsDNA) antibodies (c and d) were positive in sera of B6/nude mice after transfer of scurfy CD4+ T cells, but could not be induced by transfer of WT CD4+ T cells or phosphate-buffered saline (PBS) injection. After transfer of scurfy CD4+ T cells from lymph node single-cell suspensions, kidneys of recipient mice showed murine immunoglobulin G deposits in glomerula, whereas recipient mice that received transferred WT CD4+ T cells or PBS did not (e). (a), (c) and (e) show one representative stain, and (b) and (d) summarize data of all mice from two independent experiments (n = 10 for scurfy or WT T cell-injected mice, n = 2 for PBS-injected mice). P-values are given in the figure. Figure 7 Transfer of scurfy CD4+ T cells induces autoantibody production in B6/nude mice. Purified CD4+ T cells from lymph node single-cell suspensions of scurfy (Sc) and wild-type (WT) mice were transferred intravenously into immunocompromised B6/nude mice. Four weeks after transfer, the sera (diluted 1:100) of the recipient B6/nude mice were analyzed for the presence of autoantibodies. Antinuclear antibody (ANA) (a and b) and anti-double-stranded DNA (anti-dsDNA) antibodies (c and d) were positive in sera of B6/nude mice after transfer of scurfy CD4+ T cells, but could not be induced by transfer of WT CD4+ T cells or phosphate-buffered saline (PBS) injection. After transfer of scurfy CD4+ T cells from lymph node single-cell suspensions, kidneys of recipient mice showed murine immunoglobulin G deposits in glomerula, whereas recipient mice that received transferred WT CD4+ T cells or PBS did not (e). Abbreviations Ab: Antibody; DC: Dendritic cell; ELISA: Enzyme-linked immunosorbent assay; Foxp3: Forkhead box protein 3; H&E: Hematoxylin and eosin; IF: Immunofluorescence; IgG: Immunoglobulin G; IL: Interleukin; IPEX syndrome: Immune dysregulation, polyendocrinopathy, enteropathy, X-linked; PAS: Periodic acid-Schiff; PBS: Phosphate-buffered saline; RNP: Ribonucleoprotein; SD: Standard deviation; SLE: Systemic lupus erythematosus; TB: Toluidine blue; TBS: Tris-buffered saline; Teff: Effector T cell; TRAP: Tartrate-resistant acid phosphatase; Treg: Regulatory T cell; WHO: World Health Organization; WT: Wild type. Conclusions h b The absence of functional Tregs is associated with the development of a multiorgan autoimmune disease due to activation of autoreactive CD4+ T cells and additional B cell-mediated disease. The developing autoimmune disease resembles human (and murine) SLE in many re- spects, although scurfy mice develop an even broader spectrum of autoimmune manifestations [3]. Scurfy CD4+ T cells induce organ inflammation in B6/nude mice The latter view is supported by an observation that Treg-depleted Foxp3DTR mice exhibit an expansion of follicular helper T cells that strongly Thus, the systemic lupus-like features observed in scurfy mice appear to be a consequence of Treg dysfunc- tion and uncontrolled CD4+ Teff cell expansion, and, Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 Page 10 of 12 Figure 8 Transfer of scurfy CD4+ T cells induces skin, lung and kidney pathology in B6/nude mice. Four weeks after transfer of purified CD4+ T cells from scurfy (Sc) and wild-type (WT) mice into immunocompromised B6/nude mice, tissues were analyzed by histology. All recipients of scurfy CD4+ T cells showed severe skin inflammation (a and b) and lung inflammation (c and d), whereas recipients of WT CD4+ T cells and PBS-treated recipients did not. Kidney pathology was observed in two of seven recipients of scurfy CD4+ T cells, but in none of the controls (e). Figure 8 Transfer of scurfy CD4+ T cells induces skin, lung and kidney pathology in B6/nude mice. Four weeks after transfer of purified CD4+ T cells from scurfy (Sc) and wild-type (WT) mice into immunocompromised B6/nude mice, tissues were analyzed by histology. All recipients of scurfy CD4+ T cells showed severe skin inflammation (a and b) and lung inflammation (c and d), whereas recipients of WT CD4+ T cells and PBS-treated recipients did not. Kidney pathology was observed in two of seven recipients of scurfy CD4+ T cells, but in none of the controls (e). pathological features described in scurfy mice can be at- tributed to the lack of Treg control. Interestingly (as in SLE), we found not only direct T cell-mediated tissue in- flammation but also B cell hyperreactivity and autoanti- body production, which also fosters the idea that Tregs are important for maintaining peripheral tolerance against B cell-mediated autoimmunity. augmented B cell proliferation, hyperimmunoglobuline- mia and anti-dsDNA autoantibody production [55]. In line with these observations, our data show the induc- tion of autoantibodies in recipient B6/nude mice after transfer of autoreactive scurfy CD4+ T cells, which proves that autoreactive CD4+ T cells expanding in the absence of functional Tregs are responsible for auto- antibody production via T cell-mediated B cell help. These findings provide an important link from missing Treg control as present in scurfy mice to B cell- mediated autoimmune processes in SLE. References Foxp3 regulatory T cells ensure B lymphopoiesis by inhibiting the granulopoietic activity of effector T cells in mouse bone marrow. Eur J Immunol. 2015;45:167–79. 7. Kim S, Park K, Choi J, Jang E, Paik DJ, Seong RH, et al. Foxp3 regulatory T cells ensure B lymphopoiesis by inhibiting the granulopoietic activity of effector T cells in mouse bone marrow. Eur J Immunol. 2015;45:167–79. 32. Hayer S, Redlich K, Korb A, Hermann S, Smolen J, Schett G. Tenosynovitis and osteoclast formation as the initial preclinical changes in a murine model of inflammatory arthritis. Arthritis Rheum. 2007;56:79–88. 8. Riewaldt J, Düber S, Boernert M, Krey M, Dembinski M, Weiss S, et al. Severe developmental B lymphopoietic defects in Foxp3-deficient mice are refractory to adoptive regulatory T cell therapy. Front Immunol. 2012;3:141. 33. Schett G, Tuerk B. 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Acknowledgements W h k Cl S We thank Clemens Scheinecker for critical reading of the manuscript and discussion of the data. ENH received grant support from the Else 21. Humrich JY, Morbach H, Undeutsch R, Enghard P, Rosenberger S, Weigert O, et al. Homeostatic imbalance of regulatory and effector T cells due to IL-2 deprivation amplifies murine lupus. Proc Natl Acad Sci U S A. 2010;107:204–9. Kröner-Fresenius-Stiftung and an international reintegration grant from the European Union. 22. Weigert O, von Spee C, Undeutsch R, Kloke L, Humrich JY, Riemekasten G. CD4 + Foxp3+ regulatory T cells prolong drug-induced disease remission in (NZB × NZW) F1 lupus mice. Arthritis Res Ther. 2013;15:R35. Authors’ contributions JS helped to interpret the data and critically revised the manuscript. GHS conceived and designed the study, performed data analysis and wrote the final manuscript. All authors read and approved the final manuscript. 18. Bonelli M, von Dalwigk K, Savitskaya A, Smolen JS, Scheinecker C. Foxp3 expression in CD4+ T cells of patients with systemic lupus erythematosus: a comparative phenotypic analysis. Ann Rheum Dis. 2008;67:664–71. 19. Bonelli M, Savitskaya A, von Dalwigk K, Steiner CW, Aletaha D, Smolen JS, et al. Quantitative and qualitative deficiencies of regulatory T cells in patients with systemic lupus erythematosus (SLE). Int Immunol. 2008;20:861–8. 20. Brusko TM, Putnam AL, Bluestone JA. Human regulatory T cells: role in autoimmune disease and therapeutic opportunities. Immunol Rev. 2008;223:371–90. Received: 23 September 2014 Accepted: 23 January 2015 Received: 23 September 2014 Accepted: 23 January 2015 Received: 23 September 2014 Accepted: 23 January 2015 25. Hoffman RW. T cells in the pathogenesis of systemic lupus erythematosus. Clin Immunol. 2004;113:4–13. 26. Murata H, Matsumura R, Koyama A, Sugiyama T, Sueishi M, Shibuya K, et al. T cell receptor repertoire of T cells in the kidneys of patients with lupus nephritis. Arthritis Rheum. 2002;46:2141–7. Author details 1 1Department of Dermatology, University of Heidelberg, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany. 2Department of Pathology, Affiliated Zhong-Da Hospital, Southeast University, 87 Dingjia Bridge, Gulou, 210009 Nanjing, China. 3Department of Rheumatology, Medical University of Vienna, Wahringer G rtel 18 20 1090 Vienna A stria 4Department of Patholog 1Department of Dermatology, University of Heidelberg, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany. 2Department of Pathology, Affiliated Zhong-Da Hospital, Southeast University, 87 Dingjia Bridge, Gulou, 210009 Nanjing, China. 3Department of Rheumatology, Medical University of Vienna, Wahringer Gurtel 18-20, 1090 Vienna, Austria. 4Department of Pathology, Hietzing Hospital, Wolkersbergenstrasse 1, 1130 Vienna, Austria. 23. Gottlieb AB, Lahita RG, Chiorazzi N, Kunkel HG. Immune function in systemic lupus erythematosus: impairment of in vitro T-cell proliferation and in vivo antibody response to exogenous antigen. J Clin Invest. 1979;63:885–92. Wahringer Gurtel 18-20, 1090 Vienna, Austria. 4Department of Pathology, Hietzing Hospital, Wolkersbergenstrasse 1, 1130 Vienna, Austria. 24. Koning F, Yokoyama WM, Maloy WL, Stingl G, McConnell TJ, Cohen DI, et al. Expression of Cγ4 T cell receptors and lack of isotype exclusion by dendritic epidermal T cell lines. J Immunol. 1988;141:2057–62. References 1. Godfrey VL, Wilkinson JE, Rinchik EM, Russell LB. Fatal lymphoreticular disease in the scurfy (sf) mouse requires T cells that mature in a sf thymic environment: potential model for thymic education. Proc Natl Acad Sci U S A. 1991;88:5528–32. 27. Scheinecker C, Zwölfer B, Köller M, Männer G, Smolen JS. Alterations of dendritic cells in systemic lupus erythematosus: phenotypic and functional deficiencies. Arthritis Rheum. 2001;44:856–65. 2. 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Eur J Immunol. 2012;42:2305–10. 5. Huter EN, Natarajan K, Torgerson TR, Glass DD, Shevach EM. Autoantibodies in scurfy mice and IPEX patients recognize keratin 14. J Invest Dermatol. 2010;130:1391–9. 30. Stummvoll GH, Fritsch RD, Meyer B, Hoefler E, Aringer M, Smolen JS, et al. Characterisation of cellular and humoral autoimmune responses to histone H1 and core histones in human systemic lupus erythematosus. Ann Rheum Dis. 2009;68:110–6. 6. Aschermann S, Lehmann CH, Mihai S, Schett G, Dudziak D, Nimmerjahn F. B cells are critical for autoimmune pathology in Scurfy mice. Proc Natl Acad Sci U S A. 2013;110:19042–7. 6. Aschermann S, Lehmann CH, Mihai S, Schett G, Dudziak D, Nimmerjahn F. B cells are critical for autoimmune pathology in Scurfy mice. Proc Natl Acad Sci U S A. 2013;110:19042–7. 31. Huter EN, Punkosdy GA, Glass DD, Cheng LI, Ward JM, Shevach EM. TGF-β- induced Foxp3+ regulatory T cells rescue scurfy mice. Eur J Immunol. 2008;38:1814–21. 7. Kim S, Park K, Choi J, Jang E, Paik DJ, Seong RH, et al. Authors’ contributions ENH participated in the design of the study, carried out part of the histological and IF analyses, performed data analysis and drafted the manuscript. XW carried out part of the histological and IF analyses, performed data analysis and drafted the manuscript. HL performed quantitative analysis of the arthritic inflammatory infiltrate by tissue cytometry and helped in drafting the manuscript. BH did genotyping, urinalysis and hematological analysis of mice; carried out histological workups (all organs except for the paws); and helped in drafting the manuscript. BN did histological workup of the paws (H&E, TB and TRAP staining) and additional immunohistochemistry (T cells, B cells, macrophages The data presented herein support the hypothesis that the lack of peripheral tolerance can lead to SLE-like fea- tures and thus underline an important role of Tregs in the pathogenesis of SLE, as suspected on the basis of pre- vious reports on defective Treg function in active lupus [9]. The genetic defect in scurfy mice is precisely charac- terized and affects only Foxp3+ Tregs; consequently, all Page 11 of 12 Page 11 of 12 Hadaschik et al. Arthritis Research & Therapy (2015) 17:35 17. DiPaolo RJ, Brinster C, Davidson TS, Andersson J, Glass D, Shevach EM. Autoantigen-specific TGFβ-induced Foxp3+ regulatory T cells prevent autoimmunity by inhibiting dendritic cells from activating autoreactive T cells. J Immunol. 2007;179:4685–93. and granulocytes) and helped in drafting the manuscript. GS performed detailed analysis of autoantibodies by ELISA and immunoblotting and helped in drafting the autoantibodies part of the manuscript. WU is a pathologist experienced in renal pathology of mice; he analyzed kidney specimens and helped in designing the respective figures and their description and in drafting the manuscript. AHE participated in the design of the study and critically revised the manuscript. JS helped to interpret the data and critically revised the manuscript. GHS conceived and designed the study, performed data analysis and wrote the final manuscript. All authors read and approved the final manuscript. and granulocytes) and helped in drafting the manuscript. GS performed detailed analysis of autoantibodies by ELISA and immunoblotting and helped in drafting the autoantibodies part of the manuscript. WU is a pathologist experienced in renal pathology of mice; he analyzed kidney specimens and helped in designing the respective figures and their description and in drafting the manuscript. AHE participated in the design of the study and critically revised the manuscript. References Selective CDK4/6 inhibition with tumor responses by PD0332991 in patients with mantle cell lymphoma. Blood. 2012;119:4597–607. 15. Wildin RS, Smyk-Pearson S, Filipovich AH. Clinical and molecular features of the immunodysregulation, polyendocrinopathy, enteropathy, X linked (IPEX) syndrome. J Med Genet. 2002;39:537–45. 38. McKenzie Jr WN, Sunderrajan EV, Kavanaugh JL, Braun S, Ansbacher L, Walker SE. Sex hormones modulate the response of pulmonary perivascular inflammation to cyclophosphamide therapy in MRL/MpJ-lpr/lpr mice. Am J Pathol. 1988;131:530–8. 16. Lyon MF, Peters J, Glenister PH, Ball S, Wright E. 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Arthritis Research & Therapy (2015) 17:35 References Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and take full advantage of: Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review
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The Managerial Competence Of The Madrasa Head In Improving Teacher Professionalism And Performance At Mi Al-Maarif Bojongsari, Cilacap District
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The Managerial Competence Of The Madrasa Head In Improving Teacher Professionalism And Performance At Mi Al-Maarif Bojongsari, Cilacap District p Slamet Pamuji 1 , Sun Limei2 1UIN Prof. K.H. Saifuddin Zuhri Purwokerto, Indonesia 1UIN Prof. K.H. Saifuddin Zuhri Purwokerto, Indonesia 2 Goethe University Frankfurt, Germany 2 Goethe University Frankfurt, Germany 2 Goethe University Frankfurt, Germany Citation: Pamuji, S., & Limei, S. (2023). The Managerial Competence Of The Madrasa Head In Improving Teacher Professionalism And Performance At Mi Al-Maarif Bojongsari, Cilacap District (a case study in Lateri Village, Baguala District, Ambon City). Pengabdian: Jurnal Abdimas, 1(2), 72–82. https://doi org/10 55849/abdimas v1i2 117 ABSTRACT Background. Professional Madrasah Principals in the new paradigm of education management will have a positive impact and fundamental changes in the reform of the education system in Madrasas. Purpose. This quantitative study In addition to this, becoming a professional headmaster needs to start with a professional appointment as well. Method. This study uses a qualitative descriptive approach, namely research procedures that produce data descriptions in the form of words, spoken, or a person's behavior. Results. The result is that professionalism has good performance, so the competence of the principal here is very good in improving teacher performance and professionalism. a) Creating a program involving all school members is a form of leadership in human resources as human beings who need to be respected.. b) In achieving the school's vision and mission, the principal of the MI Al-Ma'arif Bojongsari school has delegated authority to teachers and administrative staff as a mirror of modified leadership. c) In improving the competence of pedagogic teachers, the principal of the MI Al-Ma'arif Bojongsari Conclusion. The efforts made by teachers in improving pedagogic competence are teachers have realized that the work of the teacher is a profession that needs to be improved. Efforts made by teachers in improving pedagogic competence, in addition to following the program that has been implemented by the school. Pengabdian: Jurnal Abdimas https://journal.ypidathu.or.id/index.php/abdimas P - ISSN: 2987-8470 E - ISSN: 2987-7105 Pengabdian: Jurnal Abdimas https://journal.ypidathu.or.id/index.php/abdimas P - ISSN: 2987-8470 E - ISSN: 2987-7105 | Research Papers Erformance, Managerial Competence, Professionalism Erformance, Managerial Competence, Professionalism Citation: Pamuji, S., & Limei, S. (2023). The Managerial Competence Of The Madrasa Head In Improving Teacher Professionalism And Performance At Mi Al-Maarif Bojongsari, Cilacap District (a case study in Lateri Village, Baguala District, Ambon City). Pengabdian: Jurnal Abdimas, 1(2), 72–82. https://doi.org/10.55849/abdimas.v1i2.117 INTRODUCTION Professional madrasah principals in the new paradigm of education management will have a positive impact and quite fundamental changes in the renewal of the education system in madrasas. Reliable managerial skills are able to bring a healthy and dynamic madrasah atmosphere (Winder & Tempier, 2018). Creating the attitude and spirit and professionalism of teachers also depends a lot on the leadership of the madrasah head. Teachers or other staff will be able to work well and enthusiastically if the madrasah principal is able to apply his leadership effectively (Foster, 2011). Therefore, to improve the professionalism of teachers, it is necessary to pay attention to the leadership of the madrasah principal. Correspondence: Slamet Pamuji, pamujislamet25@gmail.com Received: June 12, 2023 Accepted: June 15, 2023 Published: June 29, 2023 Slamet Pamuji, pamujislamet25@gmail.com Received: June 12, 2023 Accepted: June 15, 2023 Published: June 29, 2023 Slamet Pamuji, pamujislamet25@gmail.com Slamet Pamuji, Sun Limei The Managerial Competence of The Madrasa... | Research Papers In the study of education management, the activity of mobilizing others is leadership (PINHEIRO dkk., 2021). Leadership that determines direction and goals, provides guidance and creates a work climate that supports the implementation of the overall administrative process and teaching and learning activities. In the study of education management, the activity of mobilizing others is leadership (PINHEIRO dkk., 2021). Leadership that determines direction and goals, provides guidance and creates a work climate that supports the implementation of the overall administrative process and teaching and learning activities. As a manager, the madrasah head has more skills or generalist knowledge (de Jong dkk., 2022). Because he will be a role model for his subordinates who will enforce obligations completely and perfectly in his leadership. Therefore, the madrasah head as a manager is required to have a conceptual framework related to strategic matters, namely the ability to educate teachers and employees (Buchholtz & Sinstad, 2021). In this case, the madrasah head is the component that most determines the success or failure of the madrasah in delivering competitive (Villegas-Torres & Lengeling, 2021a) teachers who are ready to compete in producing quality output in educational challenges, because in the hands of the madrasah head, curriculum, learning resources, infrastructure and learning climate become something meaningful in improving good teacher performance (Gabriela dkk., 2022; Kartel dkk., 2022; Qureshi dkk., 2022). In addition, teachers are also the spearhead of the implementation of the decisions and policies set by the madrasah head. Teacher performance or work performance (performance) is the result achieved by the teacher in carrying out the tasks assigned to him based on skills, experience, and seriousness and the use of time (Enikolopov dkk., 2020). Teacher performance will be good if the teacher has implemented elements consisting of loyalty and high commitment to teaching duties (Villegas-Torres & Lengeling, 2021b), mastering and developing learning materials, discipline in teaching and other tasks, creativity in the implementation of teaching, cooperation with school residents, leadership that is a role model for students, good personality, honest and objective in guiding students, and responsibility for their duties. The Managerial Competence of The Madrasa... The Managerial Competence of The Madrasa... | Research Papers implementation of madrasah programs. The lack of madrasah's relationship with the community causes public perception to position teachers as the main key to educational success or failure. Lack of monitoring and evaluation carried out by the madrasah head of the madrasah program. implementation of madrasah programs. The lack of madrasah's relationship with the community causes public perception to position teachers as the main key to educational success or failure. Lack of monitoring and evaluation carried out by the madrasah head of the madrasah program. Based on the situation in the field, the competence carried out by the principal shows an increase in good things so that it can also be seen that the skills or performance of teachers show an improved state (Hartini dkk., 2022; Ilham dkk., 2022; Safitri dkk., 2022). This statement is in accordance with the initial observations as described above, there are several reasons that encourage the author to conduct this research including progress in the field of education requires education managers who are able to manage education units and are able to improve teacher performance in achieving educational goals, and some madrasah principals in Indonesia are weak in supervision and managerial competencies (Najeed dkk., 2022; Nopiana dkk., 2022). Third, the public perception has been positioning teachers as the main key to the success or failure of education, even though a teacher is only one component in the education unit at school. In addition to the teacher, the principal is a party that plays an equally important role. Fourth, empirical studies with this theme are interesting to do considering the rapid development of management science and theory, especially education management. Based on the problems that have been described in the background of the problem above, and due to the limitations of time, funds, energy and theories and so that this research can be carried out in depth, not all problems that have been identified will be studied (Dianovi dkk., 2022; Rahmah dkk., 2022; Rohmalimna dkk., 2022). Researchers provide limitations, where research will be conducted on "Managerial Competence of Madrasah Principals in an effort to improve professionalism and teacher performance at MI Al-Maarif Bojongsari Cilacap Regency". Correspondence: In addition to this, becoming a professional headmaster needs to start with a professional appointment as well. In fact (Kadwa & Alshenqeeti, 2020), there needs to be a rigorous selection within a certain time and selection based on those who have been in the school for a long time (Poskitt, 2020). This will create a democratic climate conducive to the creation of optimal learning to develop children's potential. This is the only way to develop professional principals who are ready to push the vision into action of the new paradigm (Dewi S dkk., 2022; Hikmah dkk., 2022; Keshav dkk., 2022). In relation to teacher professionalism, a teacher must have academic qualifications, competencies, an educator certificate, be physically and mentally healthy, and have the ability to realize national education goals . Teacher competencies include: pedagogical competence, personality competence, social competence and professional competence obtained through professional education. The problem of teacher professional competence is one of the competencies that must be possessed by every teacher in any level of education. Based on preliminary observations made by researchers at MI Al-Maarif Bojongsari, Cilacap Regency, several problems were found in the implementation of the principal's duties as a manager which caused the madrasah principal's managerial duties to not be carried out optimally, including planning, the difficulty faced by the madrasah principal in planning is that the madrasah principal has difficulty in gathering opinions from teachers and employees to make decisions in a plan due to the lack of a culture of initiative from teachers and employees to give their opinion (Anoum dkk., 2022; Demina dkk., 2022; Firman dkk., 2022). Directing, the difficulties faced are the different perspectives, habits, willingness and skills of teachers make it difficult for the madrasah head in an effort to unite the vision and mission towards achieving madrasah goals (Oladrostam dkk., 2022). Supervision, the difficulties faced are the many administrative tasks that are the responsibility of the madrasah principal, causing less focus on the madrasah principal's supervision of the Abdimas | Vol. 1 | No. 2 | 2023 67 RESULT AND DISCUSSION Managerial Competence Managerial Competence RESEARCH METHODOLOGY This research conducted is included in field research. Field research, namely research in which data collection is carried out in the field, such as in the community environment, institutions and community organizations and educational institutions both formal and non-formal. The type of field research is qualitative research. Qualitative research is research that intends to understand the phenomenon of what is experienced by the research subject, for example behavior, perception, motivation, action, holistically, and by means of descriptions in the form of words and language, in a special natural context and by utilizing various scientific methods. This research takes data from the research site, namely by using data collection techniques of observation, interviews, and documentation. Researchers carried out the data analysis stage from the acquisition of field data obtained from observations, interviews and documentation. Data analysis is made by reviewing, organizing, analyzing, dissecting, finding patterns, and reporting systematically. The Managerial Competence of The Madrasa... The Managerial Competence of The Madrasa... | Research Papers cannot be seen. Skill and knowledge are outer competencies (surface) while motive, trait, self image and social role are hidden competencies that are not visible to the naked eye, but determine a person's success. In general, the term HR competency is referred to as capability to perform which indicates that HR competency consists of various variables. cannot be seen. Skill and knowledge are outer competencies (surface) while motive, trait, self image and social role are hidden competencies that are not visible to the naked eye, but determine a person's success. In general, the term HR competency is referred to as capability to perform which indicates that HR competency consists of various variables. Competence is a collection of knowledge, skills and attitudes that exist in a person to perform activities effectively in a job or job function which is the standard expected of employees. Competencies are also used for individuals to guide self-improvement. HR competencies can be divided into two, namely those that are visible, such as knowledge competencies and skill competencies and invisible competencies (hidden competencies) such as self-concept, traits and motives, all of which can be categorized in attitude variables (Noer dkk., 2023). Boyatzis defines competency as "the fundamental characteristics of a person that cause or give rise to effective and outstanding performance." This competence is determined by the factors of motives, traits, self-concept, knowledge, skills that will determine and distinguish between people who have superior or average performance, or effective and ineffective performance. Because this variable is difficult to measure, Spencer and Spencer further developed these competencies into six competency groups that can predict superior performance, each consisting of 2-5 competencies. The competencies required from one job to another are different. Spencer and Spencer formulated competencies for each field of work, for example technicians and professionals, sales people, helping and humanservice workers, managers and entrepreneurs. In this study, managerial competency is used. The indicators that competent managers must have are as follows: Impact and Influence, Achievement orientation, Teamwork and cooperation, Analytical thinking, Initiative, Developing Others, Self Confidence. Directiveness / Assertiveness, information Seeking, Team Leadership, Conceptual Thinking. The Managerial Competence of The Madrasa... Profesionalisme Professionalism is the condition, direction, value, purpose, and quality of an expertise and authority related to a person's livelihood According to the American Webster dictionary, Professionalism is "a behavior, an objective or a series of qualities that are adequate or describe the style of a profession (the conduct, aims, qualities, that characterize a profession). aimsr qualities, that characterize a profession). Professionalism contains two elements, namely the element of expertise, and the element of vocation, the element of technical skill and ethical maturity, the element of reason and morals. And both of them are the rounded elements of leadership. Thus, talking about professionalism cannot be separated from the issue of leadership in a broad sense. A profession provides services based on science that is only understood by certain people who are systematically formulated and applied to meet client needs. So the profession is a scientific job to meet the needs of members of society. Furthermore, "professionalism is an idea, flow or opinion that a profession must be carried out by professionals with reference to the norms of professionalism. So professionalism is primarily a matter of attitude. Not a set of competencies. A true professional is a technician who truly cares. Furthermore, it is said that true professionalism implies a pride in work commitment to quality, dedication to the interests of clients, and a genuine desire to help. Managerial Competence The study of competence was initiated by Mc Clelland in his article entitled Testing for Competence Rather than Intelligence. Through several studies Clelland concluded that aptitude tests traditionally used by psychologists to predict performance, in fact cannot predict job performance, because the results are often biased (Hermansyah dkk., 2023; Nadya dkk., 2022). Likewise, test results and references cannot also predict a person's success in work. Mc Clelland found a deeper measurement model called competence. Competencies are characteristics that exist in individuals that are related to the reference criteria for effective and or superior performance in work situations. Competence is illustrated like an iceberg, the surface can be identified, while the bottom / inside Abdimas | Vol. 1 | No. 2 | 2023 68 The Managerial Competence of The Madrasa... The Managerial Competence of The Madrasa... | Research Papers concept that is the operational effectiveness of an organization, part of the organization, and its employees based on predetermined standards and criteria. Because organizations are basically run by humans, performance is actually human behavior in carrying out its role in an organization to meet predetermined standards of behavior in order to produce the desired actions and results. concept that is the operational effectiveness of an organization, part of the organization, and its employees based on predetermined standards and criteria. Because organizations are basically run by humans, performance is actually human behavior in carrying out its role in an organization to meet predetermined standards of behavior in order to produce the desired actions and results. Teacher performance has certain specifications. Teacher performance can be seen and measured based on the specifications or competency criteria that each teacher must have. In relation to teacher performance, the form of behavior in question is the teacher's activities in the learning process. With regard to teacher performance standards, Sahertian as quoted by Kusmianto in the teacher performance assessment guidebook by supervisors explained that: Teacher performance standards relate to the quality of teachers in carrying out their duties such as: (1) working with individual students, (2) lesson preparation and planning, (3) utilizing learning media, (4) involving students in various learning experiences, and (5) active leadership from the teacher. From the various definitions above, it can be concluded that the definition of the concept of teacher performance is the result of work or work performance carried out by a teacher based on the ability to manage teaching and learning activities, which include lesson planning, lesson implementation, lesson evaluation and fostering interpersonal relationships with students. Based on the results of interviews with principals, the way the principal improves teachers' pedagogical competence is by preparing the School Work Plan and Budget (RKAS). In the plan, a program to improve teachers' pedagogical competence is made. To realize the work plan, the principal makes a TEAM consisting of two teams, namely, the school development team (TPS) and the Curriculum Development Team (TPK). This team translates the school work plan into a program of activities. TPS makes programs related to the future development of the school, including planning the needs of school facilities and infrastructure. While TPK makes programs related to improving teacher competence, including pedagogic competence. Teacher Performance Performance is an activity carried out by each individual in relation to achieving planned goals. In this regard, there are several definitions of performance. Smith in stating that performance is .output drive from processes, human or otherwise. Performance is the result or output of a process. It is further stated by Mulyasa that performance can be interpreted as work achievement, work implementation, work achievement, work results or performance. Performance is a universal Abdimas | Vol. 1 | No. 2 | 2023 69 The Managerial Competence of The Madrasa... The Managerial Competence of The Madrasa... | Research Papers pedagogic competence is based on the National Education (Los, t.t.) Permit to empower school resources. This empowerment of school resources is to support the process standards implemented by the school, because in the process standards, teachers are required to make syllabus, lesson planning, lesson implementation, learning outcomes assessment, and others. pedagogic competence is based on the National Education (Los, t.t.) Permit to empower school resources. This empowerment of school resources is to support the process standards implemented by the school, because in the process standards, teachers are required to make syllabus, lesson planning, lesson implementation, learning outcomes assessment, and others. For this reason, teachers are required to have pedagogic competencies related to learning process activities. The principal's consideration to improve the pedagogic competence of this teacher, so that teachers are really able to implement the contents of Permendiknas RI No. 14 of 2007 concerning process standards, because with process standards teachers are required to be able to manage learning, understanding of students, utilizing learning evaluation technology, and developing students. The demand for teachers to have the ability to carry out the learning process in accordance with Permendiknas No. 14 of 2007 concerning process standards, so that the Graduate Competency Standards can be achieved. Graduate Competency Standards are qualifications of graduate abilities that include knowledge attitudes and skills. The basis for improving teachers' pedagogical competence is the issuance of Law No. 20 of 2003 concerning the National Education System. This law provides updates to the learning process. The term student is not used in this law, the word student is replaced by learner. This shows that in education, students are required to be active in participating in the learning process. With the demand for learner activeness, the teaching and learning process needs serious attention and shifts to a learning process. In improving pedagogic competence is a professional demand and demands of the law. The legal basis for teachers in improving pedagogic competence is law No. 14 of 2005 concerning teachers and lecturers. Teachers as a profession need to improve pedagogic, as a basis for considering teachers to improve pedagogilk competence, is the demands of the profession with the issuance of Permendiknas No. 23 of 2006 concerning graduate competency standards and Permendiknas No. 41 of 2007 concerning process standards, because the two Permendiknas are interrelated candy. The Managerial Competence of The Madrasa... Teachers need to have adequate pedagogic competence, so that teachers can implement Permendiknas No 41 of 2007 concerning education process standards. In the education process standards, teachers are required to make learning plans, implement learning plans and evaluate the results of the learning process, this is Mulyasa's ability to manage learning. The success of the school is strongly influenced by the leadership of the principal. Leadership is the ability to move, influence, motivate, invite, direct, advise, guide, order, command, prohibit and even punish and foster with the intention that humans as management media want to work in order to achieve goals efficiently and effectively ". Principals must be able to mobilize all school residents, be it teachers, administration or other school residents, mobilizing is an activity of the principal in influencing school residents so that school activities can run as expected. In addition to the principal influencing by moving, the principal also needs to provide motivation, so that activities carried out by school residents increasingly show effective and efficient results. Therefore, the role of the principal is very important. The Managerial Competence of The Madrasa... The team formed by the principal has the task of elaborating the activity plan in the form of programs. The formation of this team is done through deliberation in a teachers' council meeting involving all teachers and supervisors. In particular, the curriculum development team (TPK) develops programs related to improving teachers' pedagogical competence through In House Training (IHT). In this IHT activity, teachers are guided to make learning tools, learning media, making questions and post-learning evaluations. In addition to IHT activities, to improve teachers' pedagogical competence, principals also conduct classroom supervision, send teachers to participate in upgrading and subject teacher meetings (MGMP). There are several legal bases that guide principals to improve teachers' pedagogical competence, namely Law No. 20 of 2003 concerning the national education system, Law No. 14 of 2005 concerning teachers and lecturers, Government Regulation No. 13 of 2007 concerning principal standards, Permendiknas RI No. 16 of 2007 concerning Academic Qualification Standards and Teacher Competencies, Permendiknas RI No. 19 of 2007 concerning education management standards. As a consideration for school principals in improving teachers' pedagogic competence, the findings in this study are Permendiknas RI No 23 of 2006 concerning Graduate Competency standards and Permendiknas RI No 41 of 2007 concerning process standards. To improve teachers' pedagogic competence, principals must have adequate knowledge and competence. With adequate knowledge and competence, principals can consider very important factors as a basis for improving pedagogic competence. In Permendiknas RI No 13 of 2007 concerning principal standards, it is explained that school principals have various competencies including managerial competencies that function to lead schools in order to optimally utilize school resources, manage teachers and staff in order to optimally empower human resources. The principal's consideration in improving teachers' Abdimas | Vol. 1 | No. 2 | 2023 70 ACKNOWLEDGEMENT This is a short text to acknowledge the contributions of specific colleagues, institutions, or agencies that aided the efforts of the authors. CONCLUSION From the exposure of the research results above, several conclusions can be drawn as follows: 1. How principals in improving teacher competence: a) Making programs by involving all school members is a form of leadership of human resources as people who need to be respected. Principals always involve teachers in the preparation of the program, this shows that the principal applies democratic leadership by fostering and developing a common life in togetherness through cooperation that mutually recognizes, mutually appreciates and respects the strengths and weaknesses of each individual. b) In achieving the vision and mission of the school, the principal of Abdimas | Vol. 1 | No. 2 | 2023 71 AUTHORS’ CONTRIBUTION or 1: Conceptualization; Project administration; Validation; Writing - review and editing Author 1: Conceptualization; Project administration; Validation; Writing - review and editing. Author 2: Conceptualization; Data curation; In vestigation Author 1: Conceptualization; Project administration; Validation; Writing - review and editing. Author 2: Conceptualization; Data curation; In-vestigation. Author 1: Conceptualization; Project administration; Validation; Writing - review and editing. Author 2: Conceptualization; Data curation; In-vestigation. Author 2: Conceptualization; Data curation; In-vestigation. The Managerial Competence of The Madrasa... | Research Papers MI Al-Ma'arif Bojongsari has delegated authority to teachers and administrative staff as a mirror of democratic leadership, where the responsibility for the tasks that have been delegated lies in the hands of teachers and administrative staff, because the principal is the leader of the school. The creation and implementation of these programs is a way done by the principal in improving the pedagogic competence of teachers, the principal of MI Al-Ma'arif Bojongsari. c) In improving the pedagogic competence of teachers, the principal of MI Al-Ma'arif Bojongsari has formed a curriculum development team (TPK) which is tasked with outlining the program contained in the school's activity and budget plan (RKAS). The efforts made by teachers in improving pedagogic competence are teachers have realized that the work of the teacher is a profession that needs to be improved. Efforts made by teachers in improving pedagogic competence, in addition to following the program that has been implemented by the school. Teachers also try to improve competence by learning on their own through books and the internet, informal discussions between teachers, attending training, training, seminars, subject teacher meetings. Seeing the efforts made by MI Al-Ma'arif Bojongsari teachers, it can indeed improve pedagogic competence so that it can improve understanding of students. By understanding the character of students, teachers can more easily provide guidance and guidance. The Managerial Competence of The Madrasa... | Research Papers Firman, F., Alef, R., & Eric, M. (2022). Use Of Zoom Meeting Applications to Memorize the Qur’an Online. Journal International Inspire Education Technology, 1(2), 99–110. https://doi.org/10.55849/jiiet.v1i2.92 Foster, R. (2011). Teachers’ Professional Identity. 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A theoretical framework for analyzing training situations in mathematics teacher education. Winder, C. G., & Tempier, F. (2018). A theoretical framework for analyzing training situations in mathematics teacher education. Copyright Holder : © Slamet Pamuji et al. (2023). First Publication Right : © Pengabdian: Jurnal Abdimas This article is under: Abdimas | Vol. 1 | No. 2 | 2023 74
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General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal 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. Citation (APA): Libianchi, P., Brunskog, J., Agerkvist, F., & Shabalina, E. (2023). Active noise control at low frequencies for outdoor live music events using the conjugate gradient least square method. Applied Acoustics, 205, Article 109235. https://doi.org/10.1016/j.apacoust.2023.109235 Downloaded from orbit.dtu.dk on: Oct 24, 2024 Downloaded from orbit.dtu.dk on: Oct 24, 2024 Downloaded from orbit.dtu.dk on: Oct 24, 2024 Active noise control at low frequencies for outdoor live music events using the conjugate gradient least square method Libianchi, Pierangelo; Brunskog, Jonas; Agerkvist, Finn; Shabalina, Elena Published in: Applied Acoustics Link to article, DOI: 10.1016/j.apacoust.2023.109235 Document Version Publisher's PDF, also known as Version of record General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. a r t i c l e i n f o Keywords: Active noise control Sound field control Outdoor live music events Conjugate gradient least square Active set-type method Keywords: Active noise control Sound field control Outdoor live music events Conjugate gradient least square Active set-type method  2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Pierangelo Libianchi a,b,⇑, Jonas Brunskog a, Finn Agerkvist a, Elena Shabalina b Pierangelo Libianchi a,b,⇑, Jonas Brunskog a, Finn Agerkvist a, Elena Shabalina b a Acoustic Technology Group, Department of Electrical and Photonics Engineering, Technical University of Denmark, Building 352, Ørsteds Plads, Kongens Lyngby DK-2800, Denmark b d&b audiotechnik GmbH & Co. KG, Eugen-Adolff-Str. 134, Backnang 71522, Baden Wüttember, Germany ⇑Corresponding author. E-mail address: pielbia@dtu.dk (P. Libianchi). a r t i c l e i n f o Article history: Received 27 October 2022 Received in revised form 1 January 2023 Accepted 20 January 2023 Article history: Received 27 October 2022 Received in revised form 1 January 2023 Accepted 20 January 2023 Sound field control can be applied to the problem of reducing noise emissions from outdoor live music events. One method employed in this type of applications is pressure matching. Different approaches can be used to find a solution to this problem. Many of these methods can provide reduction of more than 10 dB in the frequency range of a subwoofer, between 30 and 120 Hz, thus reducing the loudness to half the original. Such a performance is adequate, but it comes with drawbacks and/or practical limitations such as side lobes that can create new problems in new areas, computational cost, difficult parameter selection, etc. The method proposed here uses the conjugate gradient least square to compute a solution while providing an easier way to find a suitable regularization and at the same time controlling the radiation pattern of the solution to reduce the possibility of side lobes. In addition, the use of an active set-type methods allows to include explicit constraints on the amplitude of the solution to avoid amplification and non-linear behavior of the transducers. After introducing the theory, the performances are compared to other more established methods through simulations and outdoor measurements per- formed at a 2:1 scale to show properties and practical aspects of the method proposed. These experi- ments show that 10 dB insertion loss are achieved over a broad frequency range with peaks larger than 20 dB. We investigate the difference in performance between the different methods and use simu- lated versus measured transfer functions to derive the filters. We also analyze the numerical properties of the solutions provided by the different methods and relate them to the spatial properties of the corre- sponding sound fields. Furthermore, we present a convergence study to evaluate the effect that grids of different resolutions used in the simulations have on the insertion loss for different degrees of regu- larization. Finally, we present also a sensitivity analysis of the proposed method to uncertainties in the speed of sound and show how the regularization directly affects the robustness of the method against such inaccuracies. https://doi.org/10.1016/j.apacoust.2023.109235 0003-682X/ 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Link back to DTU Orbit Link back to DTU Orbit Citation (APA): Libianchi, P., Brunskog, J., Agerkvist, F., & Shabalina, E. (2023). Active noise control at low frequencies for outdoor live music events using the conjugate gradient least square method. Applied Acoustics, 205, Article 109235. https://doi.org/10.1016/j.apacoust.2023.109235 Applied Acoustics 205 (2023) 109235 https://doi.org/10.1016/j.apacoust.2023.109235 0003-682X/ 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://c 1. Introduction In this paper we propose a method based on the conjugate gradi- ent least square (CGLS) as an alternative that can provide similar performance to the aforementioned approaches but avoiding some of the drawbacks, making it better suited to a practical application. The method should be computationally efficient and produce a solution for all frequencies in a short time: the weather conditions change with time and affect sound propagation, thus modifying the transfer functions [10]. A solution is most effective when the actual weather conditions match the ones encountered when the transfer functions were measured or simulated [7]. An additional challenge is to avoid high gain filters that produce non-linearities in the loud- speakers, thus leading to distortion. The system here is assumed to be linear and any deviation from this assumption will negatively impact the performance. In general, this is less of a problem if the secondary sources are the same as the primary sources and/ or if the distance between them is large. A thorough discussion about this aspect is beyond the scope of this paper. The paper is organised as follows: In Section 2 we show how the drawbacks of the subspace/projection methods can be avoided using the Krylov subspace that can be efficiently accessed using the conjugate gradient least square. A similar approach was used in [19] where the conjugate gradient (CG) was used to find a basis for an acoustic contrast application as a less expensive alternative to other methods. It offered a large reduction in complexity at the cost of a reduction in performance. In this case, we use the conju- gate gradient least square algorithm to directly compute the solu- tion at each frequency without necessarily worsening the performance. We also show that a way to include explicit ampli- tude constraints without incurring in the computational cost asso- ciated with a convex optimization problem using an active set-type method. We also provide an alternative to the selection of a regu- larization parameter using problem specific stopping criteria that can be easily implemented given the iterative nature of the algo- rithm. The use of stopping criteria additionally helps to control the radiation pattern as it is explained in details in Section 4.1. The theory presented here is then be validated through measure- ments in Section 3 where we employed filters obtained using both measured and simulated transfer functions H and primary field p. 1. Introduction control systems has been studied to weaken the noise emissions from live events using additional control sources placed behind the audience [7,8]. These methods apply ad hoc filters to the con- trol sources to create an anti-field that, through destructive inter- ference, reduces the noise emissions generated by the sources at the stage in a given area, usually referred to as dark zone. A com- mon way to derive these filters is by solving a pressure matching problem which consists of minimizing jjHq þ pjj2 2, where H 2 CMN is the transfer function matrix between M receivers in the dark zone and N control sources, q 2 CN is the vector with the complex amplitude coefficients of the transfer functions for N control sources and finally p 2 CM is the vector of the primary pres- sure field at the M receivers in the dark zone. This approach was first introduced in [9] which also provides a study of the influence of the secondary (control) array on the sound field in the audience The effects that noise has on the health and well-being of indi- viduals is more clear now than ever [1]. The legislation is also fol- lowing suit and becoming more and more restrictive [2]. Outdoor live events present a special case of noise source that comes with particular challenges and characteristics. Sound at these events usually contains a strong low frequency component (30 to 120 Hz [3,4]) that can travel over large distances with minimal attenuation from the atmosphere [5]. At the same time, these com- ponents are integral to the experience of the audience and cannot simply be tuned down [6]. In the last years, the use of active noise https://doi.org/10.1016/j.apacoust.2023.109235 0003-682X/ 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 area using a double layer of control sources or a single layer of car- dioid subwoofers. The performance of such a system was further investigated in [8] which present results from different practical applications with different degrees of complexity: presence of buildings and large time frames with changing weather conditions which affects the transfer functions and thus the final result [10]. 1. Introduction The lower dimensional representa- tion is obtained through a decomposition of H using either the singular value decomposition, eigenvalues decomposition or principal components analysis. A subset of the basis vectors is then used to compute the solution. The main advantage of this method is the potential of controlling the radiation patter by selecting basis vectors with the desired spatial properties. The drawbacks come from the need of performing the decom- position at each frequency, which can be computationally expensive for large-scale problems and is likely to introduce audible spectral artifacts. The lack of amplitude constraints on the solution and the basis vector selection that can be hard to automate and time consuming to perform manually.  Subspace/projection methods: This family of methods uses a lower dimensional representation of H and then project p on it to find the solution [18]. The lower dimensional representa- tion is obtained through a decomposition of H using either the singular value decomposition, eigenvalues decomposition or principal components analysis. A subset of the basis vectors is then used to compute the solution. The main advantage of this method is the potential of controlling the radiation patter by selecting basis vectors with the desired spatial properties. The drawbacks come from the need of performing the decom- position at each frequency, which can be computationally expensive for large-scale problems and is likely to introduce audible spectral artifacts. The lack of amplitude constraints on the solution and the basis vector selection that can be hard to automate and time consuming to perform manually. One of the challenges in this type of applications is to avoid that the sound field generated by the control sources spills into the audience area; the control system should go undetected by the audience to not affect their experience. To do so, it is possible to use a double array: one array to reduce the level in the dark zone and one array to limit the effects in the audience area [11]. This approach was first applied to this problem in [12]. The problem has been reformulated as a double objective minimization problem allowing to control the balance between the reduction of the pres- sure levels in the dark zone and the spill of the control source in the audience area. However, [9] showed that it is sufficient to use a single layer if the subwoofers have a cardiod directivity pattern. 1. Introduction Here, the results obtained from the method proposed are also be compared to the ones obtained with least square with Tikhonov regularization and automatic search methods and constrained con- vex optimization. The methods are compared in term of the inser- tion loss they provide, the spatial properties of the corresponding secondary sound fields, including the connection between spatial and numerical properties of the method, and their computation time. In addition, we provide an analysis of the robustness of the method to uncertainties in the speed of sound in Section 4.2 and a convergence analysis using grid of receivers with different resolutions in Section 4.3. The pressure matching problem can be formulated and solved in different ways, each one with its pros and cons:  Least square problem with Tikhonov regularization: This method is computationally efficient [13] and has been used effectively in this type of applications [7]. The main drawback is that the only way to avoid filters with high gain or to control the radiation pattern of the secondary array is through the reg- ularization parameter. Automatic search methods like l-curve [14], generalized cross validation (GCV) [15] or normalized cumulative periodogram (NCP) [16] can find the best compro- mise between accuracy and amplitude of the solution. The fil- ters generated by this compromise might still have a gain too large for this type of application and/or an undesirable radiation patter. This makes it necessary, at least for this type of applica- tion, to manually adjust the gain of the solutions obtained from these methods or to manually search for the best regularization parameter. Furthermore, the regularization parameter is also the only way to control the radiation pattern of the secondary array which, if not taken into account, can lead to side-lobes that can potentially increase noise emissions outside of the dark zone.  Least square problem with Tikhonov regularization: This method is computationally efficient [13] and has been used effectively in this type of applications [7]. The main drawback is that the only way to avoid filters with high gain or to control the radiation pattern of the secondary array is through the reg- ularization parameter. Automatic search methods like l-curve [14], generalized cross validation (GCV) [15] or normalized cumulative periodogram (NCP) [16] can find the best compro- mise between accuracy and amplitude of the solution. 1. Introduction In both these works, the primary sound field p and the secondary transfer functions H necessary to compute the filters are measured. An alternative is provided in [7], where the transfer functions are modelled using a spherical harmonic expansion. The coefficient of each mode and the effective speed of sound, related to wind speed and temperature on the ground, have been cast as stochastic variables. The propagation model is then combined with measured data to find the best estimates for such variables. With this approach the results generalize better than if using only measure- ments. Furthermore, it drastically reduces the number of measure- ments needed to compute the filters.  Convex optimization: This method allows to include explicit constraints on the amplitude of the solutions [17]. This restrict the search for a solution in a feasible set that do not violates the constraints. The constraints are therefore applied from the beginning and not after finding a solution which makes it potentially the most accurate option. The main drawbacks are its computational cost, the difficulty in controlling the radiation pattern and, when there are many control sources, it might not find a feasible solution. In this case, the constraints on the amplitude of the solution have to be relaxed. A new constraint is defined over the array effort but it does not strictly avoid high gains in some of the sources in the asrray.  Convex optimization: This method allows to include explicit constraints on the amplitude of the solutions [17]. This restrict the search for a solution in a feasible set that do not violates the constraints. The constraints are therefore applied from the beginning and not after finding a solution which makes it potentially the most accurate option. The main drawbacks are its computational cost, the difficulty in controlling the radiation pattern and, when there are many control sources, it might not find a feasible solution. In this case, the constraints on the amplitude of the solution have to be relaxed. A new constraint is defined over the array effort but it does not strictly avoid high gains in some of the sources in the asrray.  Subspace/projection methods: This family of methods uses a lower dimensional representation of H and then project p on it to find the solution [18]. 2.1. Krylov subspace and CGLS The more iteration the smaller the residual but also at the same time the larger the energy in the solution, jjqðkÞjj2 6 jjqðkþ1Þjj2; jjHqðkÞ  pjj P jjHqðkþ1Þ  pjj: ð5Þ ð5Þ Kk  spanfHHp; ðHHHÞHHp; . . . ; HHH  k1 HHpg: ð1Þ ð1Þ The main consequence is that it is not necessary to find a truncation order or the value of a regularization parameter but it is possible to include stopping criteria suited to the problem; the algorithm will stop when these criteria are met. This allows to avoid the practical limitation encountered with a least mean square solution with Tikhonov regularization since its execution can be automated while fulfilling the amplitude or other requirement that a problem might present. Furthermore, this criteria can be more refined and not lim- ited to looking for the best balance between amplitude of the solu- tion and amplitude of the residual as done by GCV, NCP and l-curve. For instance, they can be used to easily control the radiation pattern of the secondary array as other subspace/projection methods and opposite to the least square solutions as it will be explained in Section 2.2. The main consequence is that it is not necessary to find a truncation order or the value of a regularization parameter but it is possible to include stopping criteria suited to the problem; the algorithm will stop when these criteria are met. This allows to avoid the practical limitation encountered with a least mean square solution with Tikhonov regularization since its execution can be automated while fulfilling the amplitude or other requirement that a problem might present. Furthermore, this criteria can be more refined and not lim- ited to looking for the best balance between amplitude of the solu- tion and amplitude of the residual as done by GCV, NCP and l-curve. For instance, they can be used to easily control the radiation pattern of the secondary array as other subspace/projection methods and opposite to the least square solutions as it will be explained in Section 2.2. This subspace is built iteratively, with k being the number of iterations, and its components are based on increasing powers of the covariance matrix HHH and projections of the primary pressure field HHp. 1. Introduction The fil- ters generated by this compromise might still have a gain too large for this type of application and/or an undesirable radiation patter. This makes it necessary, at least for this type of applica- tion, to manually adjust the gain of the solutions obtained from these methods or to manually search for the best regularization parameter. Furthermore, the regularization parameter is also the only way to control the radiation pattern of the secondary array which, if not taken into account, can lead to side-lobes that can potentially increase noise emissions outside of the dark zone. 2 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 where ci are weights scaling the corresponding i-th Krylov basis vector. The SVD decomposition of the transfer function matrix is H ¼ URVH, which means that HHH ¼ VR2VH. A relation between the CGLS algorithm and the SVD decomposition can be found by rewriting H in Eq. (3) in terms of its singular values and singular vectors, 2.1. Krylov subspace and CGLS The use of subspace/projection methods is interesting for this application since they allow the selection of basis vectors with desirable spatial properties to control the radiation pattern of the secondary array. Thus, with these methods it is possible to limit radiation outside the dark zone. The drawback of having to per- form a decomposition at each frequency can be mitigated by pro- viding a set of basis vectors such as the ones in a discrete cosine transform (DCT), discrete Fourier transform (DFT), a plane wave decomposition (PWD) or a random matrix instead of computing the Singular Value Decomposition (SVD) [13]. The main disadvan- tage of this approach is that such basis vectors are not adapted to the problem, in other words, it might be necessary to use many components of the basis to be able to properly model the problem. For example, if we consider a sound field created by an array with large spatial variation, either because in its near field or due to spa- tial aliasing, it can require the superposition of many basis vectors from a DFT, with different frequencies, to model it accurately. We would like, instead, to find a basis where the first few vectors allow us to model the main features of such sound field. A basis like this is provided by the Krylov subspace, which is defined as: qðkÞ ¼ ðc1 þ c2VR2VH þ c3VR4VH þ . . . þ ckVR2ðk1ÞVHÞVRUHp ¼ Vðc1R2 þ c2R4 þ c3R6 þ . . . þ ckR2kÞR1UHp ¼ VUðkÞR1UHp ð4 ð4Þ which means that the CGLS solution is a solution to an inverse prob- lem where the singular values are filtered by the coefficients in UðkÞ. In this way it is possible to see how the CGLS algorithm applies a regularization to the problem that depends on the number of itera- tions. This is similar to a truncated singular value decomposition (TSVD, where the coefficients are 1 before truncation and 0 after) or a Tikhonov regularized least square (where the i-th coefficient is given by r2 i =ðk2 þ r2 i Þ). The main difference is that the role of the regularization parameter here is played by the number of iter- ations. 2.1. Krylov subspace and CGLS The value of k also defines the dimension of the subspace and it cannot exceed rankðHÞ since any additional iteration would add vectors that are not linearly independent. The problem of the Krylov subspace is that increasing powers of the covariance matrix HHH result in vectors that are richer in the direction of the first right singular vector of H [13]; this is the vec- tor corresponding to the largest singular value. The basis obtained in this way would have components that are not orthogonal. A modified Gram-Schmidt algorithm can be used to obtain a new basis whose vectors follow the directions of the right singular vec- tors of H thus providing a better representation. This might seem more cumbersome than computing the SVD and selecting the basis vectors. However, the conjugate gradient (CG) algorithm [20] applied to the normal equations HHHq ¼ HHp, associated to the unregularized least square problem jjHq  pjj2 2, actually computes a solution that lies in the Krylov subspace without the need to orthonormalize and store all the basis vectors [13]. It turns out that this is exactly what the conjugate gradient least square (CGLS) algorithm does. This algorithm is more expensive than CG but is still very efficient since it requires two matrix–vector products per iteration and its memory allocations is essentially independent of the number of iterations [21]. Furthermore, it allows to solve problems where H is not necessarily square or positive definite without the need to explicitly compute HHH. Even though it is beyond the scope of this paper, it is worth knowing that CGLS also allows the use of a Bayesian preconditioner to provide a priori knowledge of the solution [22]. This can be use- ful, for example, to control how the energy in the solution is dis- tributed between the different sources to avoid over-driving a subset of them. On the other hand, one has to consider the side- effects of doing so as it will also change the radiation pattern of the secondary array and possibly increase radiation towards the sides. 2.3. Active set-type method The solution provided by Eq.(2) contains the complex filters coefficients to be applied to each secondary source at a given fre- quency. These filters should not amplify the driving signal to the point where non-linear effects from the transducers become sig- nificant. This means that the gain applied to each source should be smaller or equal to a user defined threshold (in this case set to 1, so jqij 6 1 or 20log10ðjqijÞ < 0 dB). The stopping criteria allow, to some extent, to control the amplitude of the solution. In this way one can stop the algorithm when any component of the solution becomes larger than the user defined threshold. Even if this is an improvement over other methods, it does not provide explicit amplitude constraints and could prevent the use of a meaningful solution because it violates the amplitude require- ments even by a small amount. The active set-type method intro- duced in [26] allows to include explicit amplitude constraints on the solution of the CGLS algorithm. So, once one obtains a CGLS solution complying with user requirements but that violates the amplitude constraints, the active set-method can be employed to find a correction that allows the solution to fulfill the ampli- tude limits. The main idea is to fix the coefficients that are equal to the constraints and redistribute the energy from the coeffi- cients that are larger than the threshold to the ones that are smaller. This is done by computing a correction ~y to be applied to the solution allowing it to fulfill the constraints. This correction must not affect the coefficients equal to the constraints, i.e. ~yi ¼ 0 for jqij ¼ 1 in this case. The index i of these coefficients are stored in the active set AuðqÞ. The original method applies box con- straints to the solution and hence uses two sets, one for the lower bound and one for the upper bound. Since we are applying the constraints to the magnitude of the solution we are interested only in the upper bound. The primary and secondary sources consisted of two arrays of 6 d&b audiotechnik Y10 loudspeakers that can be considered as omnidirectional in the frequency range of interest. The loudspeak- ers were driven by D80 amplifiers from d&b audiotechnik. 2.2. Number of iterations and spatial properties of the solution The use of the stopping criteria in the CGLS algorithm allows to include problem specific requirements that can go beyond the magnitude of the solution or the amplitude of the residual. It was shown in [23] that the number of iterations of the CGLS algo- rithm can also be used to control the radiation pattern of the con- trol array. In this application, the left and right singular vectors constitute pressure modes and source strength modes [24], respec- tively. The singular values encode the radiation efficiency of each of the modes or amplification factors once inverted [25]. The num- ber of iterations can control the weight that each source strength mode has on the solution and in turns how large is the excitation of each of the pressure modes. The larger the number of iterations the larger are the weights applied to higher order modes. High order pressure modes tends to have a higher spatial frequency The k-iterate solution is the minimizer of the following problem: qðkÞ ¼ min q jjHq  pjj2 2 s:t: q 2 KkðHHH; HHpÞ: ð2Þ qðkÞ ¼ min q jjHq  pjj2 2 s:t: q 2 KkðHHH; HHpÞ: ð2Þ ð2Þ Since the solution qðkÞ provided by the CGLS algorithm consists of a linear combination of the basis vectors in the Krylov subspace [13], it can be written as qðkÞ ¼ c1HHp þ c2ðHHHÞHHp þ . . . þ ckðHHHÞ ðk1ÞHHp; ð3Þ 3 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 and more energy is directed towards the sides. Knowing this, it is possible to control radiation outside of the dark zone by controlling the number of iterations through a specific stopping criterion. For examples, one can monitor the total pressure field at control points outside of the dark zone and stop the algorithm when an increase above a certain threshold is detected. This feature is very impor- tant for this application since it allows to avoid side lobes that could create problems outside of the dark zone. When using least squares with Tikhonov regularization, it would be necessary to compute the solution for multiple regularization parameters to obtain the same result. The range over which one performs this search and the size of the steps would depend on the condition number of the transfer functions matrix, which is both setup and frequency dependent. ^r ¼ H^q  p The method then introduces a matrix D ¼ diagðd1; d2; . . . ; dnÞ with entries: dk ¼ 0; k 2 AuðqÞ 1; otherwise  : ð7Þ 2.2. Number of iterations and spatial properties of the solution On the other hand, the CGLS algorithm searches for the solution in the Krylov subspace that is molded by the transfer function matrix from the get go. The correction sought after is given by ~y ¼ DzðkÞ that can be used to obtain the new alternative solution ^q ¼ q þ ^y. This new solution could also violate the constraints in which case the steps described here should be repeated. Since the residual vector ^r does not decrease monotonically, the algorithm is not guaranteed to termi- nate. This could lead to cycling, however in the current application such behavior has not been encountered so far. Furthermore, since this algorithm redistributes the energy between the coefficients of the solutions, it tends to work better when the solution has many coefficients since it offers more degrees of freedom. Solutions with few coefficients might not exploit the advantages offered by this method and it might not offer any improvement over just reducing the amplitude of the solution by an offset. 2.3. Active set-type method The spacing between the sources was 1 m, corresponding to 2 m on a real scale, which is a realistic spacing for a real setup. The dark zone started 5 m from the control sources which in turn were placed at 20 m from the primary sources. To evaluate the perfor- mances in the dark zone (DZA from now), 24 microphones were arranged in 8 rows of 3 with 0.5 m spacing between them. Further- more, an array of 8 microphones (BA), also spaced 0.5 m, was placed 45 m from the primary sources to evaluate the level reduc- tion beyond the dark zone and two arrays of 16 microphones spaced 1 m were placed to the left (LA) and right (RA) of the main axis and at 10 m from it to measure possible side lobes. All the microphones were Beyer Dynamics MM1 provided with wind shields. The microphones were then connected to four Yamaha Tio 1608-D interfaces that performed the analog to digital conver- sion and returned the signal through a Dante network. The refer- ence signal fed to the loudspeakers and the signal measured at the microphones were processed in MATLAB and distributed using a Dante virtual sound-card at a sampling frequency of 48 kHz. MATLAB was also used to compute the ideal filters from the differ- ent algorithms. These filters were then implemented as arbitrary- phase finite impulse response (FIR) filters and uploaded directly to the DSP integrated in the amplifiers. Both the sources and the microphones were placed close to the ground to minimize the interferences from ground reflections in the frequency range of the experiment. The weather data was measured using a Davis Vantage Vue weather station set at a height of 2 meters plus an additional sensor on the ground. The coefficients violating the constraints are clipped to the threshold providing an approximate solution ^q which is used to compute the new residual: ð6Þ 2.4. Experimental methods The strategy proposed in Section 2.1–2.3 has been tested with the experimental setup shown in Fig. 1. Due to space limitations, the experiment was performed with a 2:1 scale so the frequency range has been shifted to the interval starting from 60 Hz and end- ing at 240 Hz and the distances have been halved to be consistent with the new scaling. The experiment was performed outdoor in semi free-field conditions on a football field with a small hill on the left, a set of trees at the back and a hedge with a river behind it on the right as it can seen in Fig. 1b. Table 1 Table 1 Weather conditions during the measurement of the primary field and the transfer functions of the secondary sources. The secondary/control source are numbered from the rightmost with respect to the main axis (bottom in Fig. 1a) to the leftmost (top in Fig. 1a). The wind direction is relative to the main axis of the setup: 0 corresponds to wind blowing in the direction of propagation; 90 blowing towards the right of the main axis and 90 to the left. Index Source Tz¼2m [C] Tz¼0m [C] Wind speed [m/s] Wind direction [] 1 Primary (all) 4.9 4 0.4 135 2 Control 1 4.9 3.9 0 - 3 Control 2 4.9 3.9 0 - 4 Control 3 4.9 3.9 0 - 5 Control 4 4.9 3.9 0 - 6 Control 5 4.9 3.9 0 - 7 Control 6 4.9 3.9 0.4 22.5 A summary of the weather conditions found during such measure- ments is included in Table 1. Having both measurements and sim- ulations allowed to quantify the improvements that the measurements can bring when there are reflections and effects not taken into account by the model. Details of the simulations can be found in Section 2.6. The algorithm proposed here has been evaluated using different number of iterations, ranging from 1 to 3. The active set-type method from [26] was used to limit the magnitude of the filters to 1 (0 dB) even though it was triggered only after three iterations of the CGLS algorithm. In addition, the method proposed has been compared to least square with Tikhonov regularization where the l-curve and GCV have been used to select the regularization parameter and the gain of the solutions has been adjusted when violating the amplitude constraint. The problem has also been for- mulated within a convex optimization framework and solved in MATLAB using the fmincon function. In this case we used two types of constraints, one on the amplitude of each individual source (jqj  1) and one on the array effort (jjqjj2 2 6 0:5). In each case the solution has been computed at 49 different frequencies in 1/24th octave bands. A summary of the methods can be found in Table 2. The table, also shows the running time of each method. These values comprises all the 49 runs to compute the solution The performance of the system have been evaluated computing the insertion loss (IL) at each microphone. 2.5. Performance evaluation and comparison dk ¼ 0; k 2 AuðqÞ 1; otherwise  : ð7Þ The performance of the algorithm was evaluated using filters derived by a primary field p and secondary transfer functions H that were both measured and simulated. Both measurements and simulations used only the sensors in the DZA. The microphones were moved randomly within a circle of 15 cm diameter before evaluating the performance to avoid committing an inverse crime. This matrix allows to not affect the coefficients in the active sets. The CGLS algorithm is then used again to find an approximate solu- tion to the problem: HDz ¼ ^r: HDz ¼ ^r: ð8Þ 4 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 1. Overview of the measurement setup (a) with the 8x3 microphones array in the dark zone (DZA), the array of 8 microphones at the back (BA) and the arrays of 12 microphones on the left and right of the main axis (LA and RA). At the bottom the satellite view of the venue (b) and a picture of the setup (c). Fig. 1. Overview of the measurement setup (a) with the 8x3 microphones array in the dark zone (DZA), the array of 8 microphones at the back (BA) and the arrays of 12 microphones on the left and right of the main axis (LA and RA). At the bottom the satellite view of the venue (b) and a picture of the setup (c). Table 1 They are then averaged over the different evaluation areas: dark zone (DZA), back array (BA), left array (LA) and right array (RA), hILi ¼ 1 N X N n¼1 20 log jpp nj jpt nj   ; ð9Þ ð9Þ where p is the complex pressure at the microphone n within a given area and by the main array alone pp n or by the main and control arrays together pt n. where p is the complex pressure at the microphone n within a given area and by the main array alone pp n or by the main and control arrays together pt n. 5 Applied Acoustics 205 (2023) 109235 P. Libianchi, J. Brunskog, F. Agerkvist et al. Table 2 Summary of the methods tested, their defining equations, parameters, parameter selection method and running time. Table 2 Summary of the methods tested, their defining equations, parameters, parameter selection method and running time. Tag Equation Param search method Param Running time [ms] Mean Standard deviation cglsk¼1 Eq. (2) + [26] k = 1 User def 5.2 1.1 cglsk¼2 Eq. (2) + [26] k = 2 User def 6.1 1.2 cglsk¼3 Eq. (2) + [26] k = 3 User def 25.7 5.3 fminconjqj1 minqjjp  Hqjj2 2 s.t. jqj  b b = 1 User def 2571.2 235.2 fminconjjqjj2 2<0:5 minqjjp  Hqjj2 2 s.t. jjqjj2 2 < b b = 0.5 User def 2204.5 244.6 gcv minqjjp  Hqjj2 2 þkjjqjj2 2 k [15] 3.2 0.7 l  curve minqjjp  Hqjj2 2 þkjjqjj2 2 k [14] 3.0 0.5 Table 2 Summary of the methods tested, their defining equations, parameters, parameter selection method and running time. at each frequency. The statistics are estimated running the algo- rithm in MATLAB 128 times on a Windows 10 laptop PC with Intel Core i7-8750H CPU at 2.20 GHz and using 16 GB of RAM. 3. Results The results presented in this section are all obtained from phys- ical measurements. Simulations are used to generate the filters in Section 3.1 and only in the case of Fig. 3 to calculate also the inser- tion loss. 2.6. Simulations The simulations were performed using the complex directivity point source method (CDPS) [27]. This model relies on free-field conditions, so it does not really match the conditions of the exper- iment due to the obstacles highlighted in Fig. 1b. The simulations were performed reproducing the setup shown in Fig. 1a, using the same loudspeakers, same sensitivity and directivity pattern, a temperature of 5C and no wind to match the weather conditions encountered when the same transfer functions were measured (see Table 1). In a first step, the simulations were used to obtain the primary field p and secondary transfer functions H only within the dark zone (DZA). The point grid in the DZA in the simulation matched the position of the microphones during the measure- ments. These data was used to generated the filters for the control sources using the methods in Table 2. In a second step, the points in the simulated DZA had been moved modifying their coordinates by drawing a correction from a normal distribution, mimicking the shift applied in the real experimental setup. Then, the primary field p and secondary transfer function H have been computed again in the DZA and also at LA, RA, and BA. Then, the different methods have been evaluated applying the filters obtained in the first step to the newly simulated transfer functions and computing the inser- tion loss as defined in Eq. (9). 3.1. Simulated transfer functions 3.1.1. Insertion loss It can still be a problem because the level increase is quite large and if there is a building in such a direction the difference will be very much noticeable. The control point stopping criterium dis- cusses in Section 2.2 and implemented in the CGLS algorithm takes into account such situation. The larger the regularization (see cglsk¼1; cglsk¼2 and l  curve) the closer to 0 the insertion loss. This is because with a stronger regularization, the secondary sound field is more focused on the dark zone with limited radiation outside of it; resulting in a minimal level increase with respect to the primary field alone. The insertion loss at the left and right arrays (LA and RA) are similar but the amplitude and positions of the dips do not totally agree due to the asymmetry of the sound field produced by the different obstacles at the left and right sides of the domain, as it can be seen in Fig. 1b. The algorithms with smaller regularization show an improve- ment beyond the dark zone, at the back array. A possible explana- tion is that, with lower regularization, the secondary field better matches the first one in the dark zone while higher regularization matches only some of the largest spatial features of the primary field but not accurately enough to translate to larger distances and progressively degrade as the mismatch grows. p g y g g It is very important to also see what is happening off-axis. The algorithms that on the paper were supposed to provide the larger insertion loss are also the ones that increase the most the sound pressure level outside of the dark zone in Fig. 1. It can be seen how, as the regularization decreases, the insertion loss become more and more negative thus indicating an increased SPL in these positions. Solutions with weaker regularization excite more higher order pressure modes that present strong radiation off- axis (more in Section 4). The resulting secondary field is more prone to present side lobes. In this instance though, the total sound field, produced by the superposition of the primary and secondary fields, does not present side lobes itself but a level increase where the primary field alone had low sound pressure levels. 3.1.1. Insertion loss In this case only, simulations are used to compute both the filters and the insertion loss are calculated from the simulated filters and simulated transfer functions in the two-step process described in Section 2.4. 3.1.2. Primary and secondary sound fields Section 2.6 and whose results are shown in Fig. 3. To achieve such large reductions, the magnitude and phase of the primary field need to be matched to such an accuracy that is not achievable with all the uncertainties that can be encountered in a real setting. The insertion loss provided by the 3 iterations CGLS method, cglsk¼3, between 100 and 150 Hz are much larger than for any other method. The real sound field in this frequency range present a dip, probably due to interactions with the surrounding obstacles, and the model used for the simulations tends to overestimate the sound pressure level in the DZA. The amplitude match between the primary and the secondary field is poor for most methods lead- ing to a decrease in insertion loss. cglsk¼3 is the only solution where the active set-type method is active. This method redistributes the energy between the coefficients to comply with the constraints without any knowledge of the primary field. In doing so, it intro- duces a phase relationship between the sources in the middle of the array and the one at the extremes that also produce a dip in amplitude in the dark zone. This proves to be a much closer match to the amplitude of the primary field thus producing larger inser- tion loss. The negative insertion loss could be interpreted as side lobes. In this particular case though, the negative insertion loss are caused by dips in the primary field. In Fig. 4 we can see the measurements corresponding to cglsk¼3 as function of microphone position and frequency for the microphone array on the left of the dark zone (LA in Fig. 1a). The sound field that results from the interaction of primary and control sources does not present side lobes. It is increasing the overall level if compared with the primary field alone and is doing so at frequencies and points where the level of the primary field alone was quite low. This suggest that the problem it creates is not as bad as the insertion loss alone might suggest. 3.1.1. Insertion loss This is the main reason for the negative side lobes and it is a result of the choice of the regularization combined with a mismatch between the simulated and the real sound fields as explained in the next section. 3.1.1. Insertion loss The insertion loss produced by the different algorithms using simulated transfer functions are shown in Fig. 2. The insertion loss are calculated from measured pressure fields obtained applying the filters computed from simulated transfer functions. The inser- tion loss in the dark zone provided by the different algorithms are quite close to each other. According to simulations, the differences were supposed to be much larger, as shown in Fig. 3. The insertion loss presented in this figure are the only one in this paper where simulations are used to derive the filters and to calculate the inser- tion loss. Inaccuracies in the model, that fails to take into account reflections, inhomogeneities in the medium and wind, reduced the gap and the overall performance. Solutions obtained using larger regularization such as the CGLS with one iteration, cglsk¼1, and l- curve, that were supposed to give the worst performances, have degraded much less than the others and are more robust to such inaccuracies (more in Section 4.2). On the other hand, fmincon was supposed to provide insertion loss of more than 30 dB over a large frequency range according to the simulations described in Fig. 2. Insertion loss IL from the measurements set with filters derived from simulated transfer functions, see Table 3. Top left: loss averaged over the dark zone. Top right: loss averaged over the array at the back. Bottom left: loss averaged over the left array LA from Fig. 1a. Bottom right: loss averaged over the right array RA in Fig. 1a. 6 Fig. 2. Insertion loss IL from the measurements set with filters derived from simulated transfer functions, see Table 3. Top left: loss averaged over the dark zone. Top right: loss averaged over the array at the back. Bottom left: loss averaged over the left array LA from Fig. 1a. Bottom right: loss averaged over the right array RA in Fig. 1a. 6 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 3. Spatially averaged insertion loss IL in the dark zone. In this case only, simulations are used to compute both the filters and the insertion loss are calculated from the simulated filters and simulated transfer functions in the two-step process described in Section 2.4. Fig. 3. Spatially averaged insertion loss IL in the dark zone. 3.2. Measured transfer functions This is confirmed by the measurements at the array at the back (BA, in Fig. 1a). Here the performances from the measured transfer functions degrade more than with simulations. errors which cause the drop in performance due to the model mis- match described in Section 3.1. Finally, the losses in the dark zone using 3 iterations are shown in Fig. 5c and they have an overall trend similar to the previous ones. This solution further reduce the residual providing larger insertion loss than cglsk¼1 and cglsk¼2. The performance from simu- lated transfer functions is now closer to the measured ones between 100 and 150 Hz. As explained in Section 3.1, the active set-type method introduce a phase relationship between the sec- ondary sources that produce a dip in level in such frequency range. This counterbalance the model overestimating the amplitude of the sound field in this region and range, providing a better match between the primary and secondary fields. The performance in this case is limited by the fact that the solution hits the amplitude con- straints and it is even more sensitive to uncertainties. We can see here that the insertion loss reach peaks of more than 25 dB and is above 10 dB over the entire frequency range. At the back, the per- formance of the measured transfer functions is similar to the ones obtained with two iterations. When simulated transfer function are used instead, the insertion loss are worse than with 2 itera- tions. cglsk¼3 is even more sensitive to uncertainties due to the weaker regularization. The changes in the interference pattern out- side of the dark zone introduce a larger drop in performance than in the previous case. g Increasing the number of iterations to 2 improves the perfor- mance of both sets of filters in the dark zone as it can be seen in Fig. 5b. The set derived from the measured transfer functions pro- vide very irregular performance over frequency but it still presents an improvement over simulations. This solution can provide better results than the one iteration version but it is more sensitive to inaccuracies. The weather conditions changed from the time when the transfer functions were measured to the time when the inser- tion loss were obtained. 3.2. Measured transfer functions While the temperature did not change, the direction of the wind changed approximately 110 degrees while keeping its speed (see Table 3, entry number 23 compared to Table 1). Considering this shift, the accuracy of the match between primary and secondary field can change rather quickly with fre- quency and/or space since it does not only affect the direct field but also the reflections and thus the interference pattern. This can cause abrupt changes in the performance considering the high level of reduction reached here (up to 24 dB). However, even if there are large drops, the insertion loss are over 10 dB for most fre- quencies. The simulated transfer functions provide a smaller reduction but are not as irregular. This smoothness is due to the lack of reflections in the simulations. When there is a difference between the weather conditions used to compute the filters and the real one, their impact on the results are not as big. This is because these filters are matching only the direct field that does not changes as much as the interference pattern. In addition, also here the largest difference is between 100 and 150 Hz. The reason is the same as with cglsk¼1. This time the difference is even larger and this is due to the increased number of iterations. We can see here that when the propagation paths are accurately characterized, the increased accuracy of the algorithm lead to larger insertion loss. On the other hand, the algorithm is also more sensitive to For all the algorithm tested, not only for cglsk¼1 and cglsk¼2 but also the other, the insertion loss at LA and RA from measured trans- fer functions closely match the results from simulated transfer functions in Fig. 2. The only exception is cglsk¼3. This is the reason why we show these results only for this case. The performance of the filters derived from measured transfer functions do not pro- duce a large increases of the sound pressure level off axis. On the other hand, there is a large increase when the simulated transfer functions are used instead. The background noise in the measured transfer functions actually improve the conditioning of the corre- sponding transfer function matrix. The higher spatial frequency associated with the noise field increases the amplitude of the high order singular values. 3.2. Measured transfer functions To study the effect that simulated or measured transfer func- tions have on the performance of the system, a new set of filters has been computed using the measured transfer functions from Table 1. The resulting insertion loss have been compared to the ones obtained by using simulated transfer functions. We omitted the graphics corresponding to the LA and RA for cglsk¼1 and cglsk¼2 for clarity since the results using measured and simulated transfer functions match very closely. The results for cglsk¼1 are shown in Fig. 5a. The difference is quite noticeable in the dark zone. The measured transfer functions provide a better perfor- mance on average even though not much larger than with the sim- ulated ones. Measuring the transfer functions provides an accurate description of the sound field in the dark zone. The main difference is located between 100 and 150 Hz due to a model mismatch. The 7 7 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 60 80 100 Fig. 4. Overview of the sound fields and insertion loss IL at the left array (LA in Fig. 1a) for the set of filters obtained with cglsk¼3 and simulated transfer functions. First: primary field; Second: secondary field; Third: total field; Fourth: insertion loss. 60 80 100 Fig. 4. Overview of the sound fields and insertion loss IL at the left array (LA in Fig. 1a) for the set of filters obtained with cglsk¼3 and simulated transfer functions. First: primary field; Second: secondary field; Third: total field; Fourth: insertion loss. Fig. 4. Overview of the sound fields and insertion loss IL at the left array (LA in Fig. 1a) for the set of filters obtained wit primary field; Second: secondary field; Third: total field; Fourth: insertion loss. d insertion loss IL at the left array (LA in Fig. 1a) for the set of filters obtained with cglsk¼3 and simulated transfer functions. First Third: total field; Fourth: insertion loss. model tends to overestimates the amplitude of the sound field between 100 and 150 Hz where the primary field present a dip. The amplitude mismatch results in the drop in performance when using simulated transfer functions. In cases such as this one, where reflections are involved, the interference pattern outside of the measured area will be quite different. Because of this difference, the performance in the dark zone do not generalize well to other areas. 3.2. Measured transfer functions This result in a more stable solution, with a smaller amplitude and that does not hit the amplitude constraints. It behaves as a solution with a stronger regularization with weak radiation off-axis. The worse conditioning of the simulated sec- ondary transfer function matrix lead to a solution with a larger 8 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 5. Insertion loss from the measurements using filters from cglsk¼1 cglsk¼2 and cglsk¼3 for simulated and measured transfer functions. The insertion loss are ave the DZA (left) and at the BA (right) as defined in Fig. 1a. The last row contains the insertion loss at the LA (left) and RA (right) for cglsk¼3. They are not shown in fo case since the results form simulations and measurements closely match. Fig. 5. Insertion loss from the measurements using filters from cglsk¼1 cglsk¼2 and cglsk¼3 for simulated and measured transfer functions. The insertion loss are averaged over the DZA (left) and at the BA (right) as defined in Fig. 1a. The last row contains the insertion loss at the LA (left) and RA (right) for cglsk¼3. They are not shown in for the other case since the results form simulations and measurements closely match. between the predicted and real primary pressure fields. Because of this, the secondary pressure field fails to match the primary field on the sides and it increases the level where the primary field had a small amplitude. This does not occur in the dark zone because it is closer to the main axis and well within the main lobe of both arrays. amplitude that hits the constraints and produce a stronger radia- tion outside the dark zone. This discrepancy between measured and simulated transfer functions only occurs in this case because it is the one with the weakest regularization. All the other solutions based on inverse problems have a stronger regularization and the better conditioning of the measured transfer function matrix does not produce such a striking difference. It does however produce a smaller level increase at LA and RA than the solutions from simu- lations do. The method based on convex optimization are affected differently by the noise and the amplitude of the solution keeps being large thus produce an increase in sound pressure level off- axis. Table 3 Index Transfer functions Array Method Tz¼2m [C] Tz¼0m [C] Wind speed [m/s] Wind direction [] 1 Simulated Both cglsk¼1 4.4 12.6 0 - 2 Simulated Both cglsk¼2 4.4 11.6 0.9 22.5 3 Simulated Both cglsk¼3 4.4 11.2 0.4 135 4 Simulated Both fminconjqj1 4.6 11.1 0.9 180 5 Simulated Both fminconjjqjj2 2<0:5 4.6 11.1 1.3 157.5 6 Simulated Both gcv 4.6 11.1 1.3 157.5 7 Simulated Both l  curve 4.6 11 1.8 157.5 10 Simulated Primary cglsk¼3 4.4 11.2 0.4 135 17 Simulated Control cglsk¼3 4.4 11.2 0.4 135 22 Measured Both cglsk¼1 5 3.7 0 - 23 Measured Both cglsk¼2 5 3.7 0.4 112.5 24 Measured Both cglsk¼3 5 3.7 0.4 112.5 31 Measured Primary cglsk¼3 5 3.7 0.4 112.5 38 Measured Control cglsk¼3 5 3.7 0.4 112.5 Fig. 6. Overview of the primary field at the left array: simulated (left) and measured at two different times (center corresponding to entry 10 and right to entry 31 in Table 3). Fig. 6. Overview of the primary field at the left array: simulated (left) and measured at two different times (center corresponding to entry 10 and right to entry 31 in Table 3). Fig. 6. Overview of the primary field at the left array: simulated (left) and measured at two different times (center correspon Fig. 6. Overview of the primary field at the left array: simulated (left) and measured at two different times (center corresponding to entry 10 and right to entry 31 in Table 3). field at the left array: simulated (left) and measured at two different times (center corresponding to entry 10 and right to entry 31 in It is possible to analyze the solutions obtained using the CGLS or any other method in terms of which pressure modes they excite and in which measure. Using the SVD, one can express the sec- ondary field ps as ond and third plots in the figure both represent the measured pri- mary field but at two different times that had a temperature differ- ence of approximately 8C (entries 10 and 31 in Table 3). They show how a difference in temperature can change the shape of the radiation pattern. ps ¼ Hq ¼ URVHq ¼ Uw; ð10Þ ð10Þ ps ¼ Hq ¼ URVHq ¼ Uw; Now looking at the secondary fields in Fig. Table 3 7 we see how using filters generated by cglsk¼3 from simulations we obtain a good match with the simulated primary field but not with the measured one. The main difference is the large sound pressure level intro- duced by the secondary field in positions and frequencies where the level of the primary field was much lower. This results in the large dips observed in Fig. 5c. When we look at the secondary field generated with cglsk¼3 using measured transfer functions we see how it provides a closer match to the measured primary field with overall lower sound pressure levels. where w ¼ RVHq is a vector of weights or amplification coefficients applied to the pressure modes. We can study why some solution might be problematic outside of the dark zone by looking at the amplitude of the weights and the shape of the corresponding pres- sure modes. Fig. 8 shows the magnitude and phase of the left singular vec- tors, equivalent to pressure modes, of the simulated transfer func- tions H at 125 Hz. The domain used for the simulations was symmetric and as a consequence it can be seen how the odd order modes are also symmetric while the even ones are anti-symmetric. Another important observation regards the energy distribution within each mode. First of all, low order modes have a lower spatial frequency and second, the energy is more focused at the center while it moves towards the sides as the order increases. The differ- ent algorithms and regularization combine these modes in differ- ent ways and with different weights which determine the spatial characteristics of the solutions. Table 3 Table 3 Summary of the weather conditions encountered during the measurements displayed in this paper. The wind direction is relative to the main axis of the setup: 0 corresponds to wind blowing in the direction of propagation; 90 blowing towards the right of the main axis and 90 to the left. The complete table can be found in the supplementary material. Index Transfer functions Array Method Tz¼2m [C] Tz¼0m [C] Wind speed [m/s] Wind direction [] 1 Simulated Both cglsk¼1 4.4 12.6 0 - 2 Simulated Both cglsk¼2 4.4 11.6 0.9 22.5 3 Simulated Both cglsk¼3 4.4 11.2 0.4 135 4 Simulated Both fminconjqj1 4.6 11.1 0.9 180 5 Simulated Both fminconjjqjj2 2<0:5 4.6 11.1 1.3 157.5 6 Simulated Both gcv 4.6 11.1 1.3 157.5 7 Simulated Both l  curve 4.6 11 1.8 157.5 10 Simulated Primary cglsk¼3 4.4 11.2 0.4 135 17 Simulated Control cglsk¼3 4.4 11.2 0.4 135 22 Measured Both cglsk¼1 5 3.7 0 - 23 Measured Both cglsk¼2 5 3.7 0.4 112.5 24 Measured Both cglsk¼3 5 3.7 0.4 112.5 31 Measured Primary cglsk¼3 5 3.7 0.4 112.5 38 Measured Control cglsk¼3 5 3.7 0.4 112.5 Fig. 6. Overview of the primary field at the left array: simulated (left) and measured at two different times (center corresponding to entry 10 and right to entry 31 in Table 3). Summary of the weather conditions encountered during the measurements displayed in this paper. The wind direction is relative to the main axis of the setup: 0 corresponds to wind blowing in the direction of propagation; 90 blowing towards the right of the main axis and 90 to the left. The complete table can be found in the supplementary material. Summary of the weather conditions encountered during the measurements displayed in this paper. The wind direction is relative to the main axis of the setup: 0 corresponds to wind blowing in the direction of propagation; 90 blowing towards the right of the main axis and 90 to the left. The complete table can be found in the supplementary material. 3.2. Measured transfer functions To facilitate the comparison, the primary field from simulation and from measurements at the left microphones array are plotted in Fig. 6. Away from the main axes, the simulated primary field present a dip that moves closer to the main axis as the frequency increases. In the measurements, this dip has a different extension in space and it behaves differently in both space and frequency. The possible reasons for this difference are reflections and a mis- match in the speed of sound due to temperature and wind. The sec- The effect of the regularization and the level increase seen when using the simulated transfer function is also related to a mismatch 9 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Table 3 Summary of the weather conditions encountered during the measurements displayed in this paper. The wind direction is relative to the main axis of the setup: 0 corresponds to wind blowing in the direction of propagation; 90 blowing towards the right of the main axis and 90 to the left. The complete table can be found in the supplementary material. 4.1. Numerical properties of the solutions In this section the focus is brought to the numerical properties of the secondary transfer functions and to the solutions provided by the different algorithms. Fig. 7. Overview of the secondary field at the left array: simulated (left), measured applying the filters from simulations (center, entry 17 in Table 3) and measured applying the filters obtained from measurements (right, entry 38 in Table 3). Fig. 7. Overview of the secondary field at the left array: simulated (left), measured applying the filters from simulations (center, entry 17 in Table 3) and measured applying the filters obtained from measurements (right, entry 38 in Table 3). 10 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 8. Magnitude (top) and corresponding phase (bottom) of the all the pressure modes, both symmetric and anti-symmetric, of the simulated transfer functions at 125 Hz. Fig. 8. Magnitude (top) and corresponding phase (bottom) of the all the pressure modes, both symmetric and anti-symmetric, of the simulated transfer functions at 125 Hz. ng phase (bottom) of the all the pressure modes, both symmetric and anti-symmetric, of the simulated transfer functions at 125 Hz Fig. 8. Magnitude (top) and corresponding phase (bottom) of the all the pressure modes, both symmetric and anti-symmetric, of the Fig. 9. Magnitude of the coefficients from the solutions obtained with simulated transfer functions that are applied to the pressure modes: 1 (left), 3 (center) and 5 (right). Fig. 9. Magnitude of the coefficients from the solutions obtained with simulated transfer functions that are applied to the pressure modes: 1 (left), 3 (center) and 5 (right). m the solutions obtained with simulated transfer functions that are applied to the pressure modes: 1 (left), 3 (center) and 5 (right) Fig. 9. Magnitude of the coefficients from the solutions obtained with simulated transfer functions that are applied to the pressure The solutions from the different algorithms excite these modes with different weights that can be obtained applying Eq. (10). These weights are shown in Fig. 9 as a function of frequency. Con- sidering that in the simulations, both the primary field and the sec- ondary transfer functions are symmetric, the even order modes are not excited at all and have been omitted for clarity. Odd order modes have weights that in general decrease with the order. The first mode has approximately the same amplitude in each solu- tions. 4.1. Numerical properties of the solutions The amplitude of the third mode increases with frequency starting at one order of magnitude lower than the first mode and reaching approximately half its amplitude at the top of the fre- quency range. This is approximately the same for every solutions except for l-curve and cglsk¼1. The l-curve present a slightly smaller amplitude than the other methods. However, cglsk¼1 has an ampli- tude of various orders of magnitude smaller than the first mode except at high frequencies. This mean that for this solution, only the first mode is relevant up to a frequency of approximately 200 Hz, so the third mode can be ignored for all practical purposes. The fifth mode is much smaller than the previous ones. It can be seen here that the solutions where the amplitude of this mode is larger are also the ones that in Fig. 2 had more energy radiated towards the sides. cglsk¼1 is the one radiating the least amount of 11 Applied Acoustics 205 (2023) 109235 P. Libianchi, J. Brunskog, F. Agerkvist et al. loss decreases. Furthermore, the histograms for cglsk¼1 and cglsk¼2 present a sharp rise at high insertion loss. This is a consequence of using the mean speed of sound to also calculate the filters. It fol- lows that error in estimating the speed of sound follows a Gaussian distribution with mean 0 and the same standard deviation as the distribution of the speed of sound. This means that small errors occur more often leading to larger relative frequencies for high insertion loss. Moreover, a sharper increase means that large inser- tion loss are achieved in more realizations hinting to a larger robustness of the method due to a larger tolerance to errors. cglsk¼3 is an exception since it does not show the same sharp rise at high insertion loss. Even when the error is small, in this case the performance is limited by the amplitude constraints and the active-set type method that is triggered only in this case. The per- formance from cglsk¼1 are worse both in absolute and average terms than the others. cglsk¼2 can provide the largest insertion loss when the speed of sound used to compute the filters is accurate. cglsk¼3 provides slightly worse performance in the best case sce- nario. This is again a result of the constraints. 4.2. Sensitivity analysis The weather conditions, specifically temperature and wind and as a consequence the speed of sound, affect the transfer functions between a source and a set of receivers as describe in [10]. The per- formance of an outdoor active noise control system depends on how close the weather conditions are to when the transfer function were measured/simulated as explained in [7]. In this section, we present an analysis of the robustness of the cgls algorithm to inac- curacies in the speed of sound. The filters were computed using simulated transfer functions obtained using a speed of sound of 334.4 m/s corresponding to a temperature of 5C as recorded when the transfer functions were measured during the experimental val- idation. Three different sets of filters were obtained by running the algorithm for 1, 2 and 3 iterations. An additional 512 realizations of the primary field and secondary transfer functions were computed using speed of sounds following a Gaussian distribution with mean 334.4 m/s and a standard deviation of approximately 2.5 m/s. The speed of sound was calculated using the dry air approximation c ¼ 20:05 ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi 273:15 þ T p [28] with T the temperature in C. The distri- bution of speed of sound are shown in Fig. 10. Each set of filters was then applied to each of the 512 realizations of the secondary transfer functions and the resulting insertion loss in the dark zone have been averaged over space and frequency. The relative fre- quency of the insertion loss for k ¼ 1; k ¼ 2 and k ¼ 3 are shown in Fig. 11. g In general, the symmetric distribution of the speed of sound is now asymmetric. The reason is that as the estimation error of the speed of sound increases, regardless if due to underestimation or overestimation, the performance gets worse and the insertion The main take-away from this analysis is that cglsk¼1 is more robust and deliver consistent performance across a larger range of speed of sound even though the mean and absolute insertion loss are smaller than in the other cases. cglsk¼3 fails to deliver the improvement that one might expect by increasing the number of iterations due to the amplitude constraints. cglsk¼2 should be cho- sen if one desires larger insertion loss than the ones cglsk¼1 can provide. Fig. 10. 4.1. Numerical properties of the solutions Since this limitation is intrinsic to the solution and independent from the accuracy of the sound speed, on average the losses tends to be worse than the for cglsk¼2. The shape of the frequency distributions for cglsk¼2 and cglsk¼3 are rather similar and the center of gravity occurs at insertion loss comprised between the mean and the mean minus one standard deviation. The main difference is that cglsk¼3 has a smaller tail at higher insertion loss and larger relative frequencies at the center of gravity. This is reflected in the lower average value and a smaller standard deviation. cglsk¼1 is very different since the center of gravity is well distributed between plus/minus one stan- dard deviation from the mean. Furthermore, the largest insertion loss have the largest relative frequencies. In this case, the mean is smaller than in the other two cases but also the standard devia- tion is considerably smaller meaning that cglsk¼1 is the most con- sistent in terms of performance. energy towards the sides because only the first mode has a large amplitude and it focuses the energy towards the main axis. The dip in the coefficients of the fifth mode is a numerical artifact due to how the modes are sorted in MATLAB. 4.2. Sensitivity analysis Probability distributions of the temperatures (left) and corresponding speed of sound (right) used in the simulations. The dashed line represent the mean and the mean plus/minus one standard deviation. 4.3. Convergence analysis In this section the focus is on the effect that different grid reso- lutions have on the final performance of the algorithm for different number of iterations. The transfer functions used to compute the filters were computed over grids of receivers with resolutions of: 1 m, 0.75 m, 0.5 m, 0.25 m, 0.1 m, 0.05 m and 0.01 m. The filters were then applied to transfer functions simulated over a grid with a resolution of 0.5 m but with receivers at different locations than Fig. 10. Probability distributions of the temperatures (left) and corresponding speed of sound (right) used in the simulations. The dashed line represent the mean and the mean plus/minus one standard deviation. Fig. 11. Histograms with the insertion loss from each of the 512 realizations averaged over space and frequency. Dashed lines show the overall mean and mean plus/minus one standard deviation. Left: cglsk¼1; center: cglsk¼2; right: cglsk¼3. Fig. 11. Histograms with the insertion loss from each of the 512 realizations averaged over space and frequency. Dashed lines show the overall mean and mean plus/minus one standard deviation. Left: cglsk¼1; center: cglsk¼2; right: cglsk¼3. 12 12 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 12. Insertion loss from filters computed using different number of iterations of the CGLS algorithm and secondary transfer functions with different grid reso filters are then applied to either simulated (left) or measured transfer functions (right). Fig. 12. Insertion loss from filters computed using different number of iterations of the CGLS algorithm and secondary transfer f filters are then applied to either simulated (left) or measured transfer functions (right). Fig. 12. Insertion loss from filters computed using different number of iterations of the CGLS algorithm and secondary transfer functions with different grid resolutions. The filters are then applied to either simulated (left) or measured transfer functions (right). the ones used to compute the filters. In addition, the filters were also applied to the transfer functions that were actually measured on the field. Similar conclusions can be drawn when the algorithm ran for 2 iterations. In this case the simulated insertion loss (Fig. 12b are lar- ger than with cglsk¼1 as one might expect. On the other hand, when the filters are applied to real transfer function (Fig. 4.3. Convergence analysis Filters obtained from the different grid resolutions used to obtain the transfer functions fed to the CGLS algorithm with 3 iterations. Left: outermost sources; Middle: second and fifth sources; Right: innermost sources. Fig. 13. Filters obtained from the different grid resolutions used to obtain the transfer functions fed to the CGLS algorithm with 3 iterations. Left: outermost sources; Middle: second and fifth sources; Right: innermost sources. number of secondary sources increases. When more sources are used, the maximum number of iterations increases too. This would result in more discrete steps and smoother changes in the regular- ization. More sources are also beneficial for the active set-type method. More sources means more degrees of freedom, allowing this algorithm to find a better alternative solution. Few degrees of freedom and large violations of the constraints, as it was the case with cglsk¼3, can lead to solutions with discontinuities because the algorithm has to intervene more aggressively with fewer options for redistributing the energy between coefficients. Such disconti- nuities can make the implementation of the filters problematic, they can add signal artifacts and a drop in performance in a limited frequency range that could spoil the overall performance of the system. It was also noticed that the number of iterations should be kept constant across frequency. The reason for this is that differ- ent number of iterations means different energy in the solution. When different number of iterations are used for adjacent frequen- cies, the solution can present jumps that would make it harder to implement the resulting filters. Furthermore, even if the number of iterations is kept constant, this method still provide the advantage of a frequency dependent regularization. As it was seen in Section 2, the regularization provided depends on the filter coefficients that in turn depends on H and p that are both frequency dependent. case there is such a big difference using different grid resolutions, and why this difference is also present in the measured transfer functions, can be found inspecting the actual filters in Fig. 13. In this particular case the solutions hit the amplitude con- straints forcing the active set-type method to kick in and find an alternative solution with a magnitude smaller than one. The solu- tions with grids finer than 0.1 m do not hit the constraints below 100 Hz. 4.3. Convergence analysis 12b), both the gain from a finer grid and the additional iteration fade and the per- formance are quite similar to the ones shown in Fig. 12b. This is due to the fact that this solution is less robust and the real world uncertainties affect all the solutions regardless of the grid size used. In Fig. 12 the insertion loss averaged over the dark zone are shown for the different grid resolutions and number of iterations of the CGLS algorithm. When the filters obtained after 1 iteration are applied to the simulated transfer functions (Fig. 12a), the inser- tion loss increase as the resolution gets finer. The sound field is better captured with finer grids and the resulting anti-field matches the primary field more closely up to approximately 200 Hz where the relation between resolution and performance is not as clear. The results seems to converge for grid resolutions smaller than 0.1 m. When the filters are applied to the measured transfer functions (Fig. 12b), the finer resolutions do not affect the insertion loss. This is due to the fact that for better perfor- mance, the tolerance to errors gets smaller and the real world uncertainties spoil the gain in performance provided by increasing the sampling resolution. As a matter of fact, at some frequencies the coarser grids perform better than the finer ones because they are not modelling finer details and then do not suffer when such details do not exactly match the reality. The situation is different when the algorithm ran for 3 itera- tions. When the filters are applied to simulated transfer functions (Fig. 12b) we see a big difference at low frequencies when grids with a resolution finer than 0.1 m are employed. At mid frequen- cies there is a trend similar to the previous cases where the perfor- mance improves by making the grid finer, reaching convergence for a resolution of 0.1 m. At higher frequencies the effect of the grid resolution on the performance is not clear. When the filters are applied to measured transfer functions (Fig. 12b) we see a trend similar to the one saw when using simulations and, as it happened in the previous two cases, the improvements are not as big as one might expect, except at low frequencies. The reason why in this 13 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 Fig. 13. 4.3. Convergence analysis This is the reason why, up to this frequency, these solu- tions provide much larger insertion loss. Above 100 Hz, all solu- tions hit the constraints and the different grid resolutions do not matter as much anymore and the performance in terms of inser- tion loss drop dramatically. The high frequency inconsistencies might be due to how the active set-type method works. Instead of just clipping the solution, this method fix the coefficients of the solution hitting the constraints, and redistribute the energy between the coefficient above and below the constraints. In this way, it finds an alternative solution with no coefficient larger than the user-defined threshold. For this reason, it is not straightfor- ward to find a relation between grid resolutions and insertion loss. Finer resolutions do not hit the constraints at low frequencies because the corresponding transfer function matrices have larger singular values. Even the high order singular values are close to unity. This means that when they are inverted to compute the solution, they do not boost the amplitude of the filters as much as the singular values corresponding to the coarser grids do, so the corresponding solutions are more stable. This can only be seen with cglsk¼3 because in this case the smaller regularization lead to higher order modes having a larger weight on the solution making the amplitude of the high order singular values more significant. It can be beneficial to use measured transfer function instead of simulations when increasing the number of iterations. Inaccuracies in the model can be amplified and the noise reduction in the dark zone is accompanied by an increase in the sound pressure level outside of it. The disadvantage is that during the day, weather con- ditions can drastically change reducing the improvements. In addi- tion, when there are reflections, solutions obtained using measured transfer functions do not generalize well beyond the dark zone while with simulations, since they only compensate for the direct field, the performance do not degrade as much. This agrees with [7] since the interference pattern generated by reflections in the dark zone does not just propagate beyond it without substantial changes. On the other hand, the direct sound field can be extrapo- lated out of the dark zone and it still constitutes the most promi- nent component of the sound field. 6. Conclusions In Section 3 it was shown that the CGLS based method proposed here provides performance comparable to regularized least square and constrained optimization in terms of insertion loss and to other studies with similar topological complexity. It was also shown how it is possible to include amplitude constraints on the solution using an active set-type method [26] without drastically increasing the computational effort in contrast with constrained convex optimization (Table 2). The advantages of these two meth- ods and their combination increases with the scale of the problem. In Section 2.2 was shown how it is possible to control the directiv- ity pattern of the secondary array by controlling the number of iterations using application-specific stopping criteria. This is an efficient way to incorporate a feature that would normally require careful and manual selection of a regularization parameter in a reg- ularized least square approach, mode selection in a subspace/pro- jection method or additional constraints in a convex optimization setting. The experimental setup described in Section 2.4 was not designed to maximize the loss outside of the dark zone. The main purpose was to compare the different algorithms in terms of inser- tion loss and radiation patterns. Placing the dark zone further away from the secondary sources would have produced better results at the BA and at larger distances in general. A dark zone close to the secondary array present a lower condition number than one fur- ther away [29]. This is due to the fact that there is larger spatial variation in the pressure field due to near field effects and this results in larger singular values for the higher order modes. At the same time, because near field effects are included in the solu- tion, this tends to not generalize well when moving away from the dark zone. Furthermore, the rate of decay of the level of the two sound fields can be quite different leading to an increasing mis- match between primary and secondary field thus performance that degrade with distance. In Section 4.1 was found that the magnitude of the regulariza- tion is not only important to control the amplitude of the solution but also the directivity pattern of the control array. 6. Conclusions A sensitivity study in Section 4.2 also shown how regularization directly affects the robustness of the solution against model inaccuracies, noise in the measurement or uncertainty in the simulation parameter such as the speed of sound. In general, it was noticed that stronger reg- ularization focus the energy of the solution into the dark zone lim- iting the risk of a level increase outside of it thus avoiding creating new problem and complaints in new areas. Even though, on paper, stronger regularization is associated with larger residuals, which translates to lower insertion loss, it was found that this is not nec- essarily the case in practice. Large insertion loss tolerate very small magnitude and phase errors between the primary and secondary fields that are hard to achieve in a dynamic environment with changing weather conditions and possibly reflections from obsta- cles and from the ground. In general, solutions obtained with stronger regularization are recommended. Moreover, it was found that measured transfer functions can provide better insertion loss than simulations. However, the simulated transfer function do bet- ter in complex topologies since they only model the direct field. The measurements include both direct field and reflections which is harder to model correctly thus the tendency of presenting larger errors outside of the dark zone or with changing weather conditions. When the dark zone is placed far from the secondary sources, the far-field is being modelled instead, allowing for a better gener- alization. The improved performance in this case is also related to the wavefronts of the two fields becoming more plane and similar. The drawback is an increase of the condition number. The main consequence is that instability in the solution can occur with a smaller number of iterations. The proposed method is slightly more heavy than regularized least square but still in the same order of magnitude. The increase in the number of iterations has a small effect on the total running time. The active set-type method produce a more noticeable increase but allows to include explicit amplitude constraints. The alternative is constrained convex optimization, although, in this case the running time increases by two orders of magnitude com- pared to cglsk¼3. 5. Discussion tions obtained with a small number of iterations are in general preferable since they tend to be more robust to limitations of the model or inaccurate medium parameters as described in Section 4.2 and therefore present a lower risk of increasing the sound pressure level outside the dark zone. 6. Conclusions However, the running times presented in Table 2 are all considered as acceptable for this type of application since changes in the mean properties of the medium occur on a much larger time scale: from 10 min to approximately 1 h [30]. In this work, we did not include compensations for changing propagation conditions and thus the corresponding variations in the transfer functions. Instead, we run the measurements in small time windows of approximately 10 min, in which we can consider the mean properties of the medium to be quasi-static, to minimize the influence of such changes. The influence of the medium and the robustness of the proposed method has been analyzed in Sec- tion 4.2. However, at short distances, it is possible to correct vari- ations in the transfer functions caused by changes in the propagation conditions as described in [31]. At larger distances the effects of the moving inhomogeneous medium are more com- plex and harder to compensate for. Finally, a convergence study in Section 4.3 showed that grids with higher resolution can provide larger insertion loss due to the increased accuracy in the sampling of the sound field during simulations. In practical applications tough, these gains might be cancelled by a mismatch between the model and the dynamic properties of the propagation paths. Furthermore, it showed that increased grid resolutions results in a better conditioning of the problem allowing to achieve more stable solutions even with a rel- atively large number of iterations. Finally, all filters have been implemented as arbitrary-phase Finite Impulse Response (FIR) filters. The implemented filters do not show pre-ringing or other time-domain artifacts. The filters obtained from simulations look very similar with small differences in time and amplitude, which increases as the regularization decreases, as expected. It is different when using measurements. First, the filters are longer since also the reflections are taken into account. fmincon produces solutions that are different from the other algorithms and present larger oscillations and longer response. The difference between the two fmincon solutions using different constraints is minimal. The rest of the algorithms resem- ble each other closely except for small differences in amplitude and time. Future work should focus on the application of this method in the time domain and/or in combination with an adaptive method to compensate for changes in the propagation conditions in real time. 5. Discussion In Section 2 it was explained how the number of sources deter- mines rankðHÞ which in turns limits the number of iterations of the cgls algorithm. In the experiment presented in Section 2.4, we ran the algorithm a maximum of 3 iterations because of the symmetric nature of the primary field and secondary transfer functions used in the simulations. This symmetry halved the degrees of freedom and subsequent iterations would not have added any new informa- tion or improvement to the solutions. We can also see this in Sec- tion 4.1 where only three of the six pressure modes were active in all the solutions from the different algorithms. In case it is not possible to measure the transfer functions and the primary field, it can be a better option to use simulations and cgls with a low number of iterations. The results obtained in this case are comparable to results obtained in [7] and in [8], for cases with a similar topological complexity. This means that it is possible to avoid measuring the transfer functions, thus reducing the prac- tical limitations for the use of such a system in day-to-day applica- tions. One can also use more advanced modelling tools reducing the gap between simulations and measurements. Furthermore, large insertion loss obtained in simulations are often not achieved in practice due to uncertainties in the modelling parameters. Solu- The iterative nature of this algorithm can be both a strength and a limitation. It is a strength since it makes it easier to select the appropriate regularization by controlling the number of iterations and monitoring relevant performance criteria in between itera- tions. On the other hand, the amount of regularization changes in discrete steps going from very large at the first iteration to almost no regularization. However, this limitation is lessened when the 14 Applied Acoustics 205 (2023) 109235 P. Libianchi, J. Brunskog, F. Agerkvist et al. tions obtained with a small number of iterations are in general preferable since they tend to be more robust to limitations of the model or inaccurate medium parameters as described in Section 4.2 and therefore present a lower risk of increasing the sound pressure level outside the dark zone. References [23] P. Libianchi, F. Agerkvist, E. Shabalina, A conjugate gradient least square based method for sound field control, in: Proceedings of InterNoise21, Proceedings of Inter-noise 2021–2021 International Congress and Exposition of Noise Control Engineering, Institute of Noise Control Engineering, 2021, pp. 1029–1040. doi:10.3397/IN-2021-1736. [1] World Health Organization. Regional Office for Europe, Environmental noise guidelines for the European Region, World Health Organization, 2018. [2] Hill AJ, Shabalina E. Sound exposure and noise pollution at outdoor events. J Audio Eng Soc 2020;68(6):145. [24] Hamdan EC, Fazi FM. Three-channel crosstalk cancellation mode efficiency for sources in the far-field. In: Tew T, Williams D, editors. 2019 AES International Conference on Immersive and Interactive Audio, York, ENGLAND. p. 27–9. [3] Elowsson A, Friberg A. Long-term average spectrum in popular music and its relation to the level of the percussion, in. Audio Eng Soc Convention 2017;142:49–53. http://www.aes.org/e-lib/browse.cfm?elib=18638. [25] Borgiotti GV. The power radiated by a vibrating body in an acoustic fluid and its determination from boundary measurements. J Acoust Soc Am. 1990;88 (4):1884–93. https://doi.org/10.1121/1.400211. [4] Støfringsdal B. Expected sound levels at concert venues for amplified music. Proc Inst Acoust 2018;40(October):654–60. [5] Bass H, Sutherland L, Zuckerwar A, Blackstock D, Hester D. Atmospheric absorption of sound: Further developments (vol 97, pg 680, 1995). J Acoust Soc Am 1996;99(2):1259. https://doi.org/10.1121/1.415223. [26] Morigi S, Reichel L, Sgallari F, Zama F. An iterative method for linear discrete ill-posed problems with box constraints. J Comput Appl Math 2007;198 (2):505–20. https://doi.org/10.1016/j.cam.2005.06.053. [6] Toole F, Sound Reproduction, in: Sound Reproduction: The Acoustics and Psychoacoustics of Loudspeakers and Rooms, 1st Edition, Focal Press, Burlington, 2008, pp. 1–490. doi:10.4324/9780080888019-8. [27] Feistel S. Modeling the radiation of modern sound reinforcement systems in high resolution. RWTH Aachen; 2014. Ph.D. thesis. [28] V.E. Ostashev, D.K. Wilson, Acoustics in moving inhomogeneous media, second edition, Acoustics in Moving Inhomogeneous Media, Second Edition, CRC Press, 2015, cited By:16. URL: www.scopus.com. [7] Heuchel FM, Caviedes-Nozal D, Brunskog J, Agerkvist FT, Fernandez-Grande E. Large-scale outdoor sound field control. J Acoust Soc Am 2020;148 (4):2392–402. https://doi.org/10.1121/10.0002252. y p [29] Nelson P, Yoon S. Estimation of Acoustic Source Strength By Inverse Methods: Part I, Conditioning of the Inverse Problem. J Sound Vib 2000;233(4):643–68. https://doi.org/10.1006/jsvi.1999.2837. [8] Brunskog J, Heuchel F, Caviedes Nozal D, Song MH, Agerkvist FT, Fernandez Grande E, Gallo E, Full-scale outdoor concert adaptive sound field control, Proceedings of the International Congress on Acoustics 2019-Septe (September) (2019) 1170–1177. doi:10.18154/RWTH-CONV-239890. The authors do not have permission to share data. [16] Gomes J, Hansen P. A study on regularization parameter choice in near-field acoustical holography. Acoust Soc Am J 2008;123(5). https://doi.org/10.1121/ 1.2934037. acoustics’08; Conference date: 29–06-2008 Through 04–07-2008 3385–3385. Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Pierangelo Libianchi reports financial support, equipment, drugs, or supplies, and travel were provided by d&b audiotechnik GmbH & Co. KG. Pierangelo Libianchi reports a relationship with d&b audiotechnik GmbH & Co. KG that includes: employment. [17] Boyd S, Vandenberghe L. Convex Optimization. Cambridge: Cambridge University Press; 2004. y [18] T.D. Abhayapala, J. Zhang, P. Samarasinghe, W. Zhang, Limits of noise control over space, in: Proceedings of the 23rd International Congress on Acoustics, no. 1, Aachen, 2019, pp. 47–54. [19] L. Shi, T. Lee, L. Zhang, J.K. Nielsen, M.G. Christensen, A fast reduced-rank sound zone control algorithm using the conjugate gradient method, in: ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, Vol. 2020-May, 2020, pp. 436–440. doi:10.1109/ ICASSP40776.2020.9054461. CRediT authorship contribution statement Pierangelo Libianchi: Conceptualization, Methodology, Soft- ware, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - original draft, Writing - review & editing, Visu- 15 P. Libianchi, J. Brunskog, F. Agerkvist et al. Applied Acoustics 205 (2023) 109235 alization. Jonas Brunskog: Formal analysis, Writing - review & editing, Supervision. Finn Agerkvist: Formal analysis, Writing - review & editing, Supervision, Project administration, Funding acquisition. Elena Shabalina: Formal analysis, Writing - review & editing, Supervision, Project administration, Funding acquisition. [12] F. Heuchel, D. Caviedes Nozal, J. Brunskog, E. Fernandez Grande, F. Agerkvist, An adaptive, data driven sound field control strategy for outdoor concerts, in: Proceedings of 2017 AES International Conference on Sound Reinforcement, Audio Engineering Society, 2017, p. 10. [13] Hansen PC. Discrete Inverse Problems: Insight and Algorithms. USA: Society for Industrial and Applied Mathematics; 2010. [14] Calvetti D, Morigi S, Reichel L, Sgallari F. Tikhonov regularization and the l- curve for large discrete ill-posed problems. J Comput Appl Math 2000;123(1– 2):423–46. https://doi.org/10.1016/S0377-0427(00)00414-3. Acknowledgements [20] Hestenes M, Stiefel E. Methods of conjugate gradients for solving linear systems. J Res National Bureau f Standards 1952;49(6):409. https://doi.org/ 10.6028/jres.049.044. Funding: d&b audiotechnik GmbH & Co. KG. A particular thanks goes to Kilian Köhler for his help with the measurements and to Jonas Wagner and his team for providing the equipment. [21] Calvetti D, Somersalo E. Introduction to Bayesian Scientific Computing, Vol. 2. Tokyo: Springer Japan; 2007. [22] Calvetti D, Pitolli F, Somersalo E, Vantaggi B. Bayes meets krylov: Statistically inspired preconditioners for CGLS. SIAM Review 2018;60(2):429–61. https:// doi.org/10.1137/15M1055061. Data availability [15] Golub GH, Heath M, Wahba G. Generalized cross-validation as a method for choosing a good ridge parameter. Technometrics 1979;21(2):215–23. https:// doi.org/10.1080/00401706.1979.10489751. The authors do not have permission to share data. References [30] Kelly M, Barlas E, Sogachev A. Statistical prediction of far-field wind-turbine noise, with probabilistic characterization of atmospheric stability. J Renewable Sustainable Energy 2018;10(1). https://doi.org/10.1063/1.5012899. [9] Heuchel F, Caviedes Nozal D, Agerkvist FT, Sound Field Control for Reduction of Noise from Outdoor Concerts, Proceedings of the Audio Engineering Society (2018) 8. URL: http://www.aes.org/e-lib/inst/browse.cfm?elib=19833. [31] F.M. Heuchel, D. Caviedes-Nozal, E. Fernandez-Grande, J. Brunskog, F.T. Agerkvist, Adapting transfer functions to changes in atmospheric conditions for outdoor sound field control, Proceedings of the International Congress on Acoustics 2019-Septe (1) (2019) 1178–1183. doi:10.18154/RWTH-CONV- 239982. [10] Caviedes-Nozal D, Heuchel FM, Agerkvist F, Brunskog J, The effect of atmospheric conditions on sound propagation and its impact on the outdoor sound field control, Inter-noise 2019 Madrid - 48th International Congress and Exhibition on Noise Control Engineering (2019). g g ( ) [11] Nelson P, Elliott S. Active Control of Sound. 1st Edition. London: Academic Press Ltd.; 1992. 16
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English
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OsSRK1, a lectin receptor-like kinase, controls plant height by mediating internode elongation in Oryza sativa L
Molecular breeding
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Bin Li  (  binli369@hnu.edu.cn ) Yixing Li  Mudan Qiu  Hao Dong  Xiushan Li  Xuanming Liu  Chongsheng He  Li Li Bin Li  (  binli369@hnu.edu.cn ) Yixing Li  Mudan Qiu  Hao Dong  Xiushan Li  Xuanming Liu  Chongsheng He  Li Li OsSRK1, a Lectin receptor-like kinase, controls plant height by mediating internode elongation in Oryza sativa L. Bin Li  (  binli369@hnu.edu.cn ) Yixing Li  Mudan Qiu  Hao Dong  Xiushan Li  Xuanming Liu Research Article Page 1/15 Page 1/15 Abstract LecRLKs (Lectin receptor-like kinases) is a subfamily of RLKs (receptor like kinase) and takes part in mounds of biological processes in plant-environment interaction. However, the roles of LecRLKs in plant development are still elusive. Here, we showed that OsSRK1, belonging to LecRLK family in rice, had a relative higher expression in internode and stem in comparison with that in root and leaf. LecRLKs (Lectin receptor-like kinases) is a subfamily of RLKs (receptor like kinase) and takes part in mounds of biological processes in plant-environment interaction. However, the roles of LecRLKs in plant development are still elusive. Here, we showed that OsSRK1, belonging to LecRLK family in rice, had a relative higher expression in internode and stem in comparison with that in root and leaf. Importantly, srk1-1 and srk1-2, two genome-edited mutants of OsSRK1using CRISPR/Cas9 system, exhibited obviously a decreased plant height and shorter length of the first internode and second internode compared with those in WT. Subsequently, histochemical sectioning showed that the stem diameter and the cell length in stem are significantly reduced in srk1-1 and srk1-2 compared with WT. Moreover, analyzing the expression of four gibberellin biosynthesis related genes showed that CPS, KAO, KS1 and GA3ox2 expression had similar levels between WT and mutants. Importantly, we further verified that OsSRK1 can directly interact with gibberellin receptor GID1. Together, our results revealed that LecRLKs family member OsSRK1 positively regulated plant height by controlling internode elongation which maybe depended on OsSRK1- GID1 interaction mediated gibberellin signaling transduction. Introduction For example, Pseudomonas syringae DC3000 induced overexpress of LecRK-IX.2, which is depend on FLS2, is required for pathogen defense (Desclos-Theveniau et al. 2012). Aside from the functions of LecRLKs in plant stresses, several LecRLKs have been identified as regulators in seed germination, pollen development and grain yield. However, it is still not be revealed about the specific molecular mechanism of LecRLKs in plant development and growth. LecRLKs (Lectin receptor-like kinases) belonged to RLK family and named after its lectin/lectin-like ectodomain (Wang J. et al., 2019). There are 173 LecRLKs in rice and 75 LecRLKs in Arabidopsis implying they had multiple functions in plant. Consistent with speculation, a large number of works had showed that LecRLKs play crucial roles in plant abiotic and biotic stresses, such as salt stress and pathogen stress (Sun et al. 2020). For example, Pseudomonas syringae DC3000 induced overexpress of LecRK-IX.2, which is depend on FLS2, is required for pathogen defense (Desclos-Theveniau et al. 2012). Aside from the functions of LecRLKs in plant stresses, several LecRLKs have been identified as regulators in seed germination, pollen development and grain yield. However, it is still not be revealed about the specific molecular mechanism of LecRLKs in plant development and growth. In this work, gene expression assay showed that OsSRK1 had a relative higher expression in internode and stem. Furthermore, the mutants of OsSRK1 exhibited obviously decreased plant height and shorter length of the first internode and second internode compared with those in WT. Moreover, using multiple method evidenced that OsSRK1 can directly interact with gibberellin receptor GID1, which regulated GA signaling pathway. Our results revealed that LecRLKs family member OsSRK1 positively regulated plant height by controlling internode elongation which maybe depended on OsSRK1- GID1 interaction. This work lay a solid foundation for new research direction of rice morphological formation and also provided materials for molecular breeding in rice. Plant materials and growth conditions Rice (Oryza sativa ssp. japonica) variety 9522 was used as the wild-type (WT) and the background for all subsequent mutations. The two lines of srk1 mutant were obtained using CRISPR/Cas9 technology as previously described (Zhang et al., 2014). All plants were grown in a paddy field in Hainan and in a greenhouse with a 30/24 ± 1°C day/night temperature, 50 to 70% relative humidity, and a light/dark period of 13 h/11 h. Phylogenetic tree construction Using an amino acid sequence of SRK1 (LOC_Os01g10710), homologous sequences were searched with the BLAST in NCBI (http://www.ncbi.nlm.nih.gov). Sequences of the most similar were downloaded from NCBI and aligned using ClustalX2.1 and Bioedit with default settings. A phylogenetic tree was built with MEGA5 software using the Neighbor-Joining method. Introduction Rice, as the staple food for more than half the population in the world, is the leading food crop and its cultivated areas account for about one third of the total food crop planting areas. Plant height, which caused by stem elongation, is a key factor for lodging resistance and also regulates the grain yield in rice. There are many factors regulating stem elongation, among which the phytohormone gibberellin is one of the most important (wang et al. 2008). Gibberellin precisely controls plant development and growth, including seed germination, hypocotyl elongation, stem elongation and so on (Li et al. 2018). Several reports have indicated that both the synthesis pathway and GA induced signaling pathway can regulate plant height in rice. For instance, the deficiency of GA20ox2 and GA20ox3, two key enzymes for GA synthesis, exhibit dwarf phenotype caused by GA53 accumulation and GA20 and GA1 reduction in rice (Sasaki et al. 2002, Ye et al. 2015, Xue et al. 2013). GA3ox2, another key enzyme for GA synthesis, also regulated plant height by controlling the content of activated GA1 (Itoh et al. 2001, Tong et al. 2014, Hu et al. 2018). Moreover, DOG can regulate cell elongation through balancing the level of activated GA by regulating the transcriptional level of GA3ox2, GA2ox1 and GA2ox3 (Liu et al. 2011). Beside the GA content, GA induced signal transduction also takes part in plant height regulation. For example, the deficiency of GA receptor GID1 caused dwarf phenotype in rice (Ueguchi-Tananja et al. 2005). RLKs also play crucial roles in plant height. The BR receptor BRI1 and its coreceptor BAK1, two important RLKs, synergistically regulated BR signaling dependent internode elongation (Yamamuro et al. 2011, Zhang et al. 2015, Gui et al. 2016). Moreover, another LRR-RLK XIAO also regulated plant height by mediating BR signaling (Jiang et al. 2012). Besides that, a RLK PSRK2 mediated GA signaling to affect internode elongation (Li et al. 2018). Page 2/15 Page 2/15 LecRLKs (Lectin receptor-like kinases) belonged to RLK family and named after its lectin/lectin-like ectodomain (Wang J. et al., 2019). There are 173 LecRLKs in rice and 75 LecRLKs in Arabidopsis implying they had multiple functions in plant. Consistent with speculation, a large number of works had showed that LecRLKs play crucial roles in plant abiotic and biotic stresses, such as salt stress and pathogen stress (Sun et al. 2020). Genetic analysis and histological analysis Plant height and internode length were quantified as previously described (Zhang et al. 2010). Two lines of srk1 transgenic mutant plants (n = 30) and the wild-type control plants (n = 30) were grown in a paddy field, after which the plant main culm was measured at the heading stage. The four elongated internodes (Internode-I, Internode-II, Internode-III, Internode-IV, from top to bottom) were harvested from different individual wild-type and transgenic plants. The statistical tests were performed by t-test, and the variation was expressed as the standard deviation (SD). The second internodes were collected at the tillering stage and the seedling stage, then fixed in FAA (50% ethanol/0.9 M glacial acetic acid/3.7% form- aldehyde, 18:1:1, v/v/v, by vol) overnight at 4 °C, dehydrated with a graded series of ethanol, infiltrated with xylene, and embedded in paraffin. The 9-μm-thick sections were cut and transferred onto poly-L-lysine- coated glass slides, deparaffinized in xylene, stained with 1% safranin and solid green (formulated with 95% ethanol), and then dehydrated through an ethanol series. Light microscopy was performed using a Nikon microscope. Fluorescence imaging analysis For detection of the subcellular localization of SRK1, the pCAMBIA1305-SRK1-GFP was transfected into protoplasts, which were isolated from one-week-old rice leaves through cellulase and macerozyme digestion. The transfected protoplasts were incubated in the dark at 28 °C for 18 h to allow for the expression of the SRK1 proteins. The transfected protoplasts with vector of pCAMBIA1305-GFP was a Page 3/15 Page 3/15 negative control. The VENUS fluorescence in root detection with a confocal microscope (Leica TCS SP8 X, excitation 488 nm; emission 500-550 nm). negative control. The VENUS fluorescence in root detection with a confocal microscope (Leica TCS SP8 X, excitation 488 nm; emission 500-550 nm). GUS staining For construction of the promoter fusion vector pCAMBIA1301- proSRK1::GUS, a 1,536 bp promoter fragment containing the upstream region of ATG and the first exon was amplified using the specific primers proSRK1-F and proSRK1 -R. The proSRK1 fragment was assembled via restriction sites into pCAMBIA1301 (Ohta et al. 1990). Subsequently, the transgenic plants proSRK2::GUS were obtained by transformation of  (Oryza sativa ssp. japonica) variety 9522. Tissues from the homozygous plants were stained with GUS (β-glucuronidase) stain solution as previously described (Jefferson et al. 1986) and images were taken under a Canon camera and Nikon phase-contrast microscope. Total RNA extraction and quantitative PCR assay Total RNA was isolated from rice tissues (root shoot, leaf, lemma/palea, and anthers) at different stages with the Trizol Reagent kit (Invitrogen) according to the manufacturer’s protocol. The stages of rice anthers were classified according to Zhang and Wilson (2009). After treatment with DNase (Promega), the isolated 0.5 mg RNA was reverse transcribed to synthesize first-strand cDNA using the ReverTra Ace- a-First-Strand cDNA synthesis kit (Fermentas). The reverse transcription products were used as templates in the following quantitative PCR. Quantitative PCR analysis of CPS, KS, KAO and GA3ox2 were performed with SYBR Premix EX Taq (TAKARA) on a Bio-Rad detection system. Each experiment was repeated three times. Data acquisition and analyses were per- formed using the method described by Roter-Gene software (Version 6.0; Build 38). Samples were normalized using ACTIN1 expression as described previously (Zhou et al. 2014). Yeast two-hybrid assays (Y2H) Page 4/15 Page 4/15 Y2H assays were performed as described previously (Yu et al., 2010). The cytoplasmic domain of RK1 was amplified and constructed into pGADT7 to make an infusion with GAL4-AD as bait. The full CDS of GID1 was cloned into the prey vector pGBKT7. Different plasmid pairs were co-transformed into yeast cells AH109, respectively. The transformants were dilution plated onto synthetic dropout medium lacking tryptophan/leucine agar (-Trp-Leu) and synthetic dropout medium lacking tryptophan/leucine/histidine (-Trp-Leu-His) supplemented with 10 mM 3-AT (3-Amino-1, 2, 4-triazole) for Y2H assays were performed as described previously (Yu et al., 2010). The cytoplasmic domain of RK1 was amplified and constructed into pGADT7 to make an infusion with GAL4-AD as bait. The full CDS of GID1 was cloned into the prey vector pGBKT7. Different plasmid pairs were co-transformed into yeast cells AH109, respectively. The transformants were dilution plated onto synthetic dropout medium lacking tryptophan/leucine agar (-Trp-Leu) and synthetic dropout medium lacking tryptophan/leucine/histidine (-Trp-Leu-His) supplemented with 10 mM 3-AT (3-Amino-1, 2, 4-triazole) for 3-5 days to test the interaction. tryptophan/leucine/histidine (-Trp-Leu-His) supplemented with 10 mM 3-AT (3-Amino-1, 2, 4-triazole) for 3-5 days to test the interaction. GST pull-down assays The GST-SRK1-CD protein were incubated by GST Sepharose resin for four hours in a tube with the pull- down binding buffer (50 mM Tris-HCl, 150 mM NaCl and 10 mM MgCl2, pH 8.0) at 4°C. GST protein was a negative control. After a brief centrifugation at 100 g for five minutes at 4°C, the buffer was removed, and 1 µg His-GID1 proteins were added to the resin, along with the fresh binding buffer, respectively. Then, the tube was rotated at 4°C for 12 hours for protein binding. Afterwards, the resin was washed for five times with washing buffer (20 mM HEPEs, 40 mM KCl and 1 mM EDTA, pH 8.0) to remove the nonspecifically bound protein, combined with 60 µL washing buffer and 20 µL 4× SDS loading buffer, and boiled for 10 minutes. After centrifugation at 12,000 × g for one minute at 22°C, the supernatant was subjected to immunoblotting analysis. The pull-down was analyzed by western blotting using the GST antibody (CMC, SC-80998) and His antibody (Abmart, M20001). LUC assays to examine interaction To investigate the interaction, SP-nLuc-SRK1 with GID1-cLuc were mixed and infiltrated into N. benthamiana leaves. The plants were grown for 36 h before the infiltrated leaves were sprayed with 1 mM D-luciferin, and then the luciferase signal was detected with a chemiluminescence imaging system (Tanon 5200 Multi, Tanon Biomart). SRK1 gene expression pattern in rice To investigate the SRK1 expression pattern in rice, we performed GUS staining assay in proSRK1-GUS transgenic plant. Histochemical staining showed that GUS was expressed throughout roots, leaves and stems in seedling stage and transition stage from vegetative growth to reproductive growth (Fig. 2a-f). And GUS staining intensity was stronger in internode and stem (Fig. 2d-e). Moreover, the expression level of GUS is higher in panicle at stage I and stage II, then the level decreased with panicle development, but it will not disappear (Fig. 2g). We further verified these results using RT-PCR to directly detecting the transcriptional level of SRK1. As shown in Fig. 2h, SRK1 was expressed in all tissues and stem and internode had a higher expression of SRK1 in comparison with other tissues (Fig. 2h). These results showed that SRK1 had a stronger expression in stem and internode, indicating the function of SRK1 was potentially associated with stem and internode development. The deficiency of SRK1 affected internode elongation To further investigate the function of SRK1, we try to generate genome-edited mutants of OsSRK1 using CRISPR/Cas9 system. Firstly, we designed a 19-nt target sequence (TS237), which between base 254 to base 274 in SRK1 genome. Then we cloned the target sequence into pYLCRISPR/Cas9 vector and generate the vector of pYLCRISPR/Cas9-MT-SRK1. Using callus transformation system, we respectively generated three kinds of mutants for SRK1 named N237-7, N237-13 and N237-23 (Fig. 3a). The sequencing results of the three mutants showed that N237-13 and N237-23 carry large DNA fragment deletions at transmembrane domain and kinase domain that lead to the premature termination of SRK1 mRNA translation (Fig. 3b). We compared the phenotype and agricultural traits between SRK1 mutants and WT. As shown in Fig. 3b and 3k , the average height of srk1-1 and srk1-2 are 58.62±1.82 cm and 60.32±1.79 cm respectively, which are significantly lower than the 72.78±2.30 cm height of WT (Fig. 3b and 3k ). Internode length is closely related with stem length, therefore we detected the internode length in mutants and WT. The first internode length of srk1-1 and srk1-2 are 17.00±0.85 cm and 17.16±0.96 cm respectively and the second internode length of srk1-1 and srk1-2 are13.10±1.13 cm and 14.64±0.69 cm respectively, which are both shorter than those in WT (the first internode length is 23.36±0.88 and the second internode length is 17.22±0.34) (Fig. 3c, 3d and 31). Results The plasma membrane protein SRK1 belongs to LecRLKs family To investigate the function of SRK1, we performed phylogenetic analysis by MEGA v7.0 and Clustal X. SRK1 is founded in Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, Vitis vinifera and Brassica napus, indicating SRK1 is quite conserved in plant. Furthermore, we constructed a phylogenetic tree using SRK1 and its homologs in 13 species (Fig. 1a). The phylogenetic tree contains two subfamilies, one of which was w’a’sestablished in monocotyledons, and the other evolved in dicotyledon. We further aligned the sequences of SRK1 homologs from Oryza sativa L., BGIOSGA002962, ORUFI01G07230, SORBI_3003G025300 and KQL04887. The results revealed that SRK1 shares high sequence similarity with SRK1 proteins of other four plants. Page 5/15 Page 5/15 We analyzed the structure of SRK1 from 13 species mentioned earlier. Except for TraesPAR_01G000100.1 and Zm00001d025065, SRK1 protein containing signal peptide domain, lectin ectodomain, one transmembrane domain and kinase domain belonged to LecRLKs family (Fig. 1b). Whereas, SRK1 in TraesPAR_01G000100.1 and Zm00001d025065 lacking of signal peptide domain belonged to S_TKc family. Then SRK1 localization was analyzed using transient expression system in protoplast. And SRK1-GFP was mainly localized at plasma membrane (Fig. 1c), indicating that SRK1 is a typical plasma membrane localized protein as other LecRLKs. SRK1 directly interacted with the GA receptor GID1 As GA playing an important role in internode elongation, we further detected the four genes related to GA biosynthesis. The results showed that there was no significant changing of CPS, KAO, KS1 and GA3ox2 expressions between the mutants and WT, indicating that the deficiency of SRK1 may not affect the endogenous GA concentration (Fig. S2a-d). Therefore, we further screening the interactors of SRK1 using Y2H screening system. We constructed SRK1-CD-BD by cloning the gene segment which expressing cytosolic domain of SRK1 into pGBKT7 vector. The sequencing results shown that one of the potential interactors is GA receptor GID1. Then, we constructed GID1-AD and verified the screening result by Y2H using ONPG as substrate (Fig. 4a-b). Furthermore, we purified GID1-His and SRK1-CD-GST proteins and GST-pulldown assay showed that SRK1-CD-GST directly interacted with GID1-His in vitro (Fig. 4c). Moreover, we can detect the signals when expression GID1-nLUC and SRK1-cLUC in tobacco together, revealing that SRK1 can interact with GID1 in vivo (Fig. 4d). Together, SRK1 may regulate internode elongation by interacting with GA receptor GID1. SRK1 gene expression pattern in rice Aside from those, the average panicle length of srk1-1 and srk1-2 are 12.70±0.54 cm and 13.10±0.70cm respectively, which are significantly lower than the 15.44±1.35 cm length of WT (Fig. 3b, 3c and 3k). Interesting, there is no significant difference in number of primary Page 6/15 Page 6/15 branches and spikelet per panicle between mutants and WT (Fig. 3m-n). Follow, we analyzed the effective panicle per plant (Fig. S1a), seed length/width (Fig. S1b), and grain weight per plant (Fig. S1c). There is no significant difference in these agronomic traits between WT and mutants. To investigate the reason why the internode lengths of mutants are shorter than those in WT, we analyzed the diameter of the stem and stem cell length using paraffin section. The transverse sectioning of the stem showed that the inner and outer diameter of the stem is obviously smaller than that in WT (Fig. 3e-g and 3o). And the longitudinal sections of stems showed that the cell lengths of srk1-1 and srk1-2 are 77.32±18.24 μm and 74.09±15.73μm respectively, which are significantly lower than the length of 104.16±26.07 μm in WT (Fig. 3h-j and 3p). Conclusion As sessile organism, plant developed a complex system to sense and adapt to the changing environment for their survival. RLK play vital roles in plant sensing processes because it can specificity perceive ligand by ectodomain and deliver signals inside cell by kinase domain (Li et al. 2018). LecRLKs belonged to RLK family and are specifically widespread in plants. Although a large number of works showed that LecRLKs play vital roles in plant stresses, there are few works focusing on the function of LecRLKs in plant development. In this work, we identified a plasma membrane localized SRK1 as a member of LecRLK family and SRK1 had a relative higher expression in stem and internode. We showed that SRK1 is a positive regulator for plant height, revealing that the LecRLK SRK1 takes part in rice development. Moreover, plant height is closely associated with lodging resistance and grain yield. Therefore, to study the molecular functions of SRK1 will lay a solid foundation for new research direction of rice morphological formation and molecular breeding in rice. Page 7/15  Rice height are regulated by multiple factors and GA plays a crucial role in this process. The concentration of GA and GA induced responses both can affect plant height. In this work, we found that Page 7/15 there was no significant changing of CPS, KAO, KS1 and GA3ox2 expressions, which are regulator of three steps of GA biosynthesis, between the SRK1 mutants and WT. This result indicated that SRK1 may not affect the endogenous concentration. Importantly, this work evidenced that SRK1 can directly interact with GA receptor GID1, indicating that SRK1 positively regulated plant height by controlling GID1 dependent GA responses. RLK always function in a complex to deliver signals at plasma membrane. And the post transcription modification of RLK is vital for RLK mediated signal transduction. Increasing evidences shown that RLK are closely with phytohormone signals, such as auxin, gibberellin and Strigolacton. In this work, we found that SRK1 takes part in GA mediated plant height. Moreover, the localization of RLK is important for its function. For instance, the cytoplastic domain of LRR-RLK TMK4 can be cleaved and transported into nucleus to control auxin signaling. In our work, we found that the plasma localized SRK1 can directly interact with GA receptor GID1, which located in cytoplasm and nucleus. Competing interests The authors declare no competing interests. The authors declare no competing interests. Conclusion Therefore, to uncover where and how SRK1 interacted with GID1 will provide more information on the mechanism by which RLK functions. Funding This work was supported by grants from the National Natural Science Foundation of China (No. 31901530) This work was supported by grants from the National Natural Science Foundation of China (No. 31901530) Acknowledgements We thank National Natural Science Foundation of China (No. 31901530) for funding support. This article is original. Author contribution Li L. and Chong H. conceived the project; Bin L. and Yi L. performed the experiments with the help of Xiu L., Hao D. and Mu Q.; Y. L. and B. L. analyzed the sequencing data; Bin L. and Xuan L. designed the experiments and interpreted the results; Li L. and Bin L. wrote the manuscript. References 1. 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References Zhou YB, Liu H, Zhou XC, Yan YZ, Du CQ, Li YX, Liu DR, Zhang CS, Deng XL, Tang DY, Zhao XY, Zhu YH, Lin JZ (2014) Over-expression of a fungal NADP(H)-dependent glutamate dehydrogenase PcGDH improves nitrogen assimilation and growth quality in rice. Molecular Breeding 34:335-349. 23. Zhou YB, Liu H, Zhou XC, Yan YZ, Du CQ, Li YX, Liu DR, Zhang CS, Deng XL, Tang DY, Zhao XY, Zhu YH, Lin JZ (2014) Over-expression of a fungal NADP(H)-dependent glutamate dehydrogenase PcGDH improves nitrogen assimilation and growth quality in rice. Molecular Breeding 34:335-349. Figures Page 10/15 gure 1 olutionary relationship and subcellular localization of SKR1.a Phylogram of SRK1. b Schematic ructure of the SRK1 and homologous gene. Yellow is lectin domain purple is transmembrane domain d blue is kinase domain. c SRK1-GFP in protoplasts. Bar= 50 μM. relationship and subcellular localization of SKR1.a Phylogram of SRK1. b S Figure 1 Evolutionary relationship and subcellular localization of SKR1.a Phylogram of SRK1. b Schematic structure of the SRK1 and homologous gene. Yellow is lectin domain purple is transmembrane domain and blue is kinase domain. c SRK1-GFP in protoplasts. Bar= 50 μM. Page 11/15 Figure 2 Expression patterns of SRK1 in Arabidopsis plants. (a–g) GUS staining of (a) 6-d-old plantlets, (b) leaf of 45-d-old plants, (c) mature root,(d)uppermost internode, (e) stem of 45-d-old plants, (f) mature leaf and (g) spikelet. h Relative expression of SRK1 in the plants tissue. Gene expression was determined by quantitative real-time PCR and was normalized against the expression of Actin1. Data are means (±SD), n=3. Page 12/15 Page 12/15 Figure 3 The phenotype analysis of the wild type (WT) and theSRK1 transgenic plants. a Analysis of mutant type of the SRK1 mutants in 9522. b Morphological character of WT and two SRK1 transgenic plants lines in heading stage. The plant height statistical analysis in (k), the number of primary branches statistical analysis in (m) and the spikelets per panicle statistical analysis in (n). c-d Comparison of length in tassel and internodes and the statistical analysis in (i). e-g Analyze the transection of stem in WT and two SRK1transgenic plants lines, the external and internal statistical analysis in (n). h-j The cell size assays, and the length statistical analysis in (p). Data represent the mean ±SD. ** is for p-value <0.01. * is for p- value <0.05. n.s. is for not significant. Figure 4 SRK1 interacts with GID1. a Y2H assays showed the association between SRK1 and GID1. Yeast cells were grown on SD/-Ade/-Leu medium with or without His. b β-galactosidase assay the interaction between SRK1 and GID1using CPRG as substrate. AD+BD as a negative control. c Analysis of the interaction between SRK1 and GID1 was carried out by GST pull-down assays. d Luciferase complementation (LUC) assay showing the interaction of SRK1 with GID1. Figure 3 The phenotype analysis of the wild type (WT) and theSRK1 transgenic plants. a Analysis of mutant type of the SRK1 mutants in 9522. b Morphological character of WT and two SRK1 transgenic plants lines in heading stage. The plant height statistical analysis in (k), the number of primary branches statistical analysis in (m) and the spikelets per panicle statistical analysis in (n). c-d Comparison of length in tassel and internodes and the statistical analysis in (i). e-g Analyze the transection of stem in WT and two SRK1transgenic plants lines, the external and internal statistical analysis in (n). h-j The cell size assays, and the length statistical analysis in (p). Data represent the mean ±SD. ** is for p-value <0.01. * is for p- value <0.05. n.s. is for not significant. Page 13/15 Page 13/15 Figure 4 SRK1 interacts with GID1. a Y2H assays showed the association between SRK1 and GID1. Yeast cells were grown on SD/-Ade/-Leu medium with or without His. b β-galactosidase assay the interaction between SRK1 and GID1using CPRG as substrate. AD+BD as a negative control. c Analysis of the interaction between SRK1 and GID1 was carried out by GST pull-down assays. d Luciferase complementation (LUC) assay showing the interaction of SRK1 with GID1. Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. Page 14/15 TableS1Primersequences.xlsx Supplementfig1And2.docx Page 14/15 TableS1Primersequences.xlsx Supplementfig1And2.docx Page 15/15
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Atmospheric Transmittance Model Validation for CSP Tower Plants
Remote sensing
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Received: 6 March 2019; Accepted: 1 May 2019; Published: 7 May 2019 Received: 6 March 2019; Accepted: 1 May 2019; Published: 7 May 2019 Abstract: In yield analysis and plant design of concentrated solar power (CSP) tower plants, increased uncertainties are caused by the mostly unknown solar attenuation between the concentrating heliostat field and the receiver on top of the tower. This attenuation is caused mainly by aerosol particles and water vapor. Various on-site measurement methods of atmospheric extinction in solar tower plants have been developed during recent years, but during resource assessment for distinct tower plant projects in-situ measurement data sets are typically not available. To overcome this lack of information, a transmittance model (TM) has been previously developed and enhanced by the authors to derive the atmospheric transmittance between a heliostat and receiver on the basis of common direct normal irradiance (DNI), temperature, relative humidity and barometric pressure measurements. Previously the model was only tested at one site. In this manuscript, the enhanced TM is validated for three sites (CIEMAT’s Plataforma Solar de Almería (PSA), Spain, Missour, Morocco (MIS) and Zagora, Morocco (ZAG)). As the strongest assumption in the TM is the vertical aerosol particle profile, three different approaches to describe the vertical profile are tested in the TM. One approach assumes a homogeneous aerosol profile up to 1 kilometer above ground, the second approach is based on LIVAS profiles obtained from Lidar measurements and the third approach uses boundary layer height (BLH) data of the European Centre for Medium-Range Weather Forecasts (ECMWF). The derived broadband transmittance for a slant range of 1 km (T1km) time series is compared with a reference data set of on-site absorption- and broadband corrected T1km derived from meteorological optical range (MOR) measurements for the temporal period between January 2015 and November 2017. The absolute mean bias error (MBE) for the TM’s T1km using the three different aerosol profiles lies below 5% except for ZAG and one profile assumption. The MBE is close to 0 for PSA and MIS assuming a homogeneous extinction coefficient up to 1 km above ground. The root mean square error (RMSE) is around 5–6% for PSA and ZAG and around 7–8% for MIS. The TM performs better during summer months, during which more data points have been evaluated. This validation proves the applicability of the transmittance model for resource assessment at various sites. remote sensing remote sensing remote sensing Article Atmospheric Transmittance Model Validation for CSP Tower Plants Natalie Hanrieder 1,*, Abdellatif Ghennioui 2, Ahmed Alami Merrouni 2, Stefan Wilbert 1 , Florian Wiesinger 1, Manajit Sengupta 3, Luis Zarzalejo 4 and Alexander Schade 5 1 German Aerospace Center (DLR), Institute of Solar Research, Plataforma Solar de Almería (PSA), Ctra. de Senés s/n km 4, Apartado 39, 04200 Tabernas, Spain; Stefan.Wilbert@dlr.de (S.W.); Florian.Wiesinger@dlr.de (F.W.) 1 German Aerospace Center (DLR), Institute of Solar Research, Plataforma Solar de Almería (PSA), Ctra. de Senés s/n km 4, Apartado 39, 04200 Tabernas, Spain; Stefan.Wilbert@dlr.de (S.W.); Florian.Wiesinger@dlr.de (F.W.) g 2 Institut de Recherche, Energie Solaire et Energies Nouvelles (IRESEN), Green Energy Park, Km 2 Route Régionale R206, Benguerir 43152, Morocco; ghennioui@iresen.org (A.G.); alami@iresen.org (A.A.M.) 3 National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401, USA; Manajit.Sengupta@nrel.gov Régionale R206, Benguerir 43152, Morocco; ghennioui@iresen.org (A.G.); alami@iresen.org (A.A.M.) 3 National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401, USA; Manajit.Sengupta@nrel.gov j g p g 4 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), División de Energías Renovables. Avda. Complutense 40, 28040 Madrid, Spain; lf.zarzalejo@ciemat.es 4 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), División de Energías Renovables. Avda. Complutense 40, 28040 Madrid, Spain; lf.zarzalejo@ciemat.es p p j 5 Institute of Physics and Meteorology, University Hohenheim, 70593 Stuttgart, Germany; alex.schade@ymail.com * Correspondence: Natalie.Hanrieder@dlr.de Received: 6 March 2019; Accepted: 1 May 2019; Published: 7 May 2019 It enables the identification of a clear site with high T1km with a high accuracy and provides an estimation of the T1km for hazy sites. Thus it facilitates the decision if on-site extinction measurements are necessary. The model can be used to improve the accuracy of yield analysis of tower plants and allows the site adapted design. Remote Sens. 2019, 11, 1083; doi:10.3390/rs11091083 www.mdpi.com/journal/remotesensing www.mdpi.com/journal/remotesensing 2 of 18 Remote Sens. 2019, 11, 1083 Keywords: atmospheric extinction; attenuation loss; transmittance model; central receiver; solar resource assessment; CSP Keywords: atmospheric extinction; attenuation loss; transmittance model; central receiver; solar resource assessment; CSP 1. Introduction CSP (concentrated solar power) will play a strong role in the Middle East and North Africa region’s electricity market and especially in Morocco in the future ([1]). In concentrated solar tower plants, the radiation which is reflected by the heliostat field is partially lost on its way to the central receiver due to atmospheric extinction. This effect on the plant yield varies with the actual aerosol and water vapor load at a certain site and the plant yield can be reduced significantly, especially at arid sites. So far, on-site measurements are performed only rarely to take this effect into account during the project planning or plant optimization phase. It is still common to choose one of two cases representing clear or hazy conditions for yield calculations. Applying standard extinction conditions can lead to an under or overestimation of several percent of the expected annual plant yield dependent on the location and plant configuration ([2]). As such errors have to be expected for most current projects, banks and engineering, procurement and construction (EPC) contractors usually include additional risk margins in their yield calculations which unnecessarily increase the price of solar tower plants. To make CSP tower plants more cost-competitive and to ideally exploit their potential, these plants have to be optimally designed for the local conditions of the plant site. For example, the total heliostat surface combined with the available direct normal irradiance (DNI) and the extinction must fit to the receiver design, the storage and the power block. Therefore, the atmospheric extinction at the plant site has to be known and considered in the applied simulation models. However, the extinction conditions and their variability at different sites are widely unknown at the moment. A review of modeling, experimental studies and measurement methods can be found in [3]. The most applied model equations to include atmospheric extinction which are implemented in different ray-tracing tools are summarized and compared in [3]. Additionally, several developed approaches to determine atmospheric extinction and different studies about the effect of atmospheric extinction on the tower plant yield are summarized and won’t be mentioned in this summary again. Recently, more studies have been published on the topic of atmospheric extinction and its influence on solar tower plant performance. 1. Introduction To measure atmospheric extinction, following works have been published: • An experimental methodology has been proposed by [4,5], based on the use of two high resolution cameras that take simultaneous images from a Lambertian target. g g • A similar system is being investigated by [6] using reflector telescopes and a photo diode array spectrometer to measure the extinction in solar tower plants. • In [7], a diffusometer is used to estimate atmospheric extinction levels at two different sites. • Ref. [8] showed, based on monochromatic ceilometer measurements, that Sahara-dust outbreak events in South-East Spain can increase the monochromatic attenuation for slant ranges of 1 km up to 25%. p • Ref. [9] derives the atmospheric extinction from remote sensing data from MODIS and AERONET for Morocco. To model radiation losses due to atmospheric extinction, the following approaches have been presented: To model radiation losses due to atmospheric extinction, the following approaches have been presented: • Ref. [10] models the atmospheric extinction for different atmospheric conditions and site elevation with the MODTRAN radiative transfer code. The simulations showed that the solar irradiance can be reduced up to 30 % under moderately turbid conditions. p y • Radiation losses caused only by water vapor are analyzed by [11]. Remote Sens. 2019, 11, 1083 3 of 18 • This relationship is also investigated in [12] using artificial neural networks to express the non-linear relationship between atmospheric extinction and water vapor content in the atmosphere. • This relationship is also investigated in [12] using artificial neural networks to express the non-linear relationship between atmospheric extinction and water vapor content in the atmosphere. • This relationship is also investigated in [12] using artificial neural networks to express the non-linear relationship between atmospheric extinction and water vapor content in the atmosphere. p • Ref. [13] models the atmospheric extinction at CIEMAT’s Plataforma Solar de Almería (PSA) with the model of [14], generating a typical meteorological year (TMY) using five years of aerosol optical depth (AOD) measurements of the AERONET network. p • Ref. [13] models the atmospheric extinction at CIEMAT’s Plataforma Solar de Almería (PSA) with the model of [14], generating a typical meteorological year (TMY) using five years of aerosol optical depth (AOD) measurements of the AERONET network. 1. Introduction A sensitivity analysis of the influence of temporal variation of atmospheric extinction has been conducted in [15,16] and showed a significant impact in the plant performance and in optical efficiency. Ref. [17] compared the vertical aerosol concentration within the lowest 300 m layer based on satellite data from CALIPSO and ECMWF-MACC data. The comparison is performed to evaluate the usage of these sources of aerosol data to improve the assessment of potential concentrated solar power (CSP) plants. Ref. [18] analyzed the inter annual variability of aerosol optical depth (AOD) and irradiance in Quarzazate (Morocco) and its influence on the characterization of extinction conditions for a certain site. In this study, meteorological optical range (MOR) measurements, the according absorption and broadband correction (ABC) method [19] and the corrected broadband extinction and transmittance results at two desert sites (Missour (MIS) and Zagora (ZAG)) in Morocco (part of the enerMENA network, [20]) and the PSA in Spain will be evaluated. The data sets are compared to each other and seasonal and inter-annual variability is discussed. The principle of the DNI measurement based transmittance model (TM) from [21] is described in Section 2. A validation of the TM with the help of ABC corrected measured transmittance data will be presented for all three sites in Section 3. The results of the validation and its discussion are presented In Sections 4 and 5 the main conclusions about the validation are summarized. 2. Transmittance Model Based on DNI Measurements The Beer–Lambert–Bouguer law describes the monocromatic extinction coefficient. For the relation between the broadband extinction coefficient βext and the DNIA and DNIB reflected by a heliostat which reaches the central receiver after traveling through an atmospheric layer between A and B, the following approximation can be used: Tx = DNIB DNIA ≈exp (−βext · x) = exp  −τAB cos(ϑ)  . (1) (1) Tx denotes the broadband transmittance for a slant range x. The term “broadband” refers to the wavelength range between 250 and 4000 nm in this work. The broadband transmittance can be expressed by βext or the broadband optical depth τAB of the layer between A and B and the incident zenith angle ϑ of the irradiance. Tx denotes the broadband transmittance for a slant range x. The term “broadband” refers to the wavelength range between 250 and 4000 nm in this work. The broadband transmittance can be expressed by βext or the broadband optical depth τAB of the layer between A and B and the incident zenith angle ϑ of the irradiance. In [22–24], an approach has been developed to derive the atmospheric transmittance in the lowest atmospheric layer above ground with the help of on-site DNI measurements. According to [22–24], the extinction coefficient can be approximated with the following formula: βext,mod = a ·  −ln  DNImeas DNIclean,sim  · cos (ϑ)  + b, (2) (2) where DNImeas is the measured DNI at ground level and DNIclean,sim is the simulated DNI for an aerosol-free atmosphere at ground level. The coefficients a and b are derived using radiative transfer calculations with the radiative transfer code libRadtran ([25,26]). The attenuation between the receiver and a heliostat could be estimated with this model, but the model has been developed only for one altitude and water vapor content in [22–24]. This approach has been further enhanced in [2,21] and the coefficients a and b and DNIclean,sim have been derived for several meteorological conditions. Remote Sens. 2019, 11, 1083 4 of 18 To derive the TM for a distinct site of interest, a theoretical clear sky DNI for an atmosphere without any aerosol particles is simulated with radiative transfer calculations. These simulations are performed for various water vapor concentrations as well as different solar zenith angle (SZA). The DNI at ground level is highly dependent on the aerosol particles and water vapor concentrations and vertical distributions. 2. Transmittance Model Based on DNI Measurements Most aerosol particles and water vapor droplets are located in the lower troposphere. The TM is based on the assumption that the aerosol height profile is known. In [21,27], different height profiles have been tested for PSA. From on-site actual DNI measurements, the extinction coefficient close to the ground can then be derived. The TM has to be derived for each site individually. To do so, an approximation of the site-dependent aerosol extinction height profile is necessary as explained in detail in [21]. The enhanced TM is able to derive the transmittance for a slant range of 1 km (T1km) from DNI as well as common meteorological measurements like ambient temperature, barometric pressure and relative humidity. The absolute uncertainty of the transmittance which has been derived with the TM is increasing for decreasing transmittances. An uncertainty between 0.033 and 0.04 for T1km equal to 0.9 have been derived for a data set with 1 minute temporal resolution For the site of PSA ([2]). 3. Transmittance Model Validation In this context, the different data sources have been inter-compared (see Sections 4.1.1–4.1.3): The LIVAS climatology ([28]), the BLH data from ECMWF ([29]) and measurements of the lowest aerosol layer (LAL) from an on-site mounted ceilometer at PSA ([30]) Figure 1 indicates the grid sizes of LIVAS as well as the ECMWF BLH grid points of all sites. In this context, the different data sources have been inter-compared (see Sections 4.1.1–4.1.3): The LIVAS climatology ([28]), the BLH data from ECMWF ([29]) and measurements of the lowest aerosol layer (LAL) from an on-site mounted ceilometer at PSA ([30]). Figure 1 indicates the grid sizes of LIVAS as well as the ECMWF BLH grid points of all sites. In this context, the different data sources have been inter-compared (see Sections 4.1.1–4.1.3): The LIVAS climatology ([28]), the BLH data from ECMWF ([29]) and measurements of the lowest aerosol layer (LAL) from an on-site mounted ceilometer at PSA ([30]). 3. Transmittance Model Validation In this study, the TM has been applied and validated at three different sites in Morocco and Spain: CIEMAT’s PSA (Spain) and IRESEN’s stations in MIS (Morocco) and ZAG (Morocco). The site locations are shown in Figure 1 and the information about the sites is summarized in Table 1. Figure 1. Location of PSA, MIS and ZAG as well as ECMWF BLH and LIVAS extinction profile grid. Figure 1. Location of PSA, MIS and ZAG as well as ECMWF BLH and LIVAS extinction profile grid. 5 of 18 Remote Sens. 2019, 11, 1083 Table 1. LibRadtran input for TM development. Table 1. LibRadtran input for TM development. Site PSA MIS ZAG Latitude [◦N] 37.091 32.860 30.272 Longitude [◦E] −2.358 −4.107 −5.852 Altitude [m a.m.s.l.] 500 1107 783 Standard aerosol type assumed in TM “H1000” continental continental continental clean clean average Standard aerosol type assumed in TM “LIVAS” default default default Standard aerosol type assumed in TM “BLH” continental continental continental clean clean average Three aerosol height profiles and the performance of the corresponding TM have been tested for each site as explained in the following subsection. The applied standard aerosol types within the libRadtran simulations for the TM development for each aerosol height profile are listed in Table 1. The following height profiles will be used in this validation approach for PSA, MIS and Z 1. An extinction profile with a constant aerosol extinction coefficient up to 1 km above the ground and no extinction above 1 km (“TM-H1000”) ( ) 2. The extinction height profile for each validation site of the LIVAS climatology of [28] (description of modification of LIVAS profile can be found in Section 4.1.1 (“TM-LIVAS”). p p 3. The constant extinction profile as in TM-H1000 of [21] is scaled accordingly to the BLH instead of 1 km. The BLH has been extracted from the ERA-Interim reanalysis data set of ECMWF ([29]). It is assumed that the total amount of aerosol particles is homogeneously distributed in the lowest layer above ground up to the site- and time-dependent BLH (“TM-BLH”). Figure 1 indicates the grid sizes of LIVAS as well as the ECMWF BLH grid points of all sites. 3.2. Reference Data Set As a reference data set ABC corrected MOR measurements are used for the three sites. The MOR is a parameter to measure the optical clearness of the atmosphere and can be measured with commercially available instruments. The MOR is defined as the length of the path in the atmosphere which is required to reduce the luminous flux in a collimated beam from an incandescent lamp, at a color temperature of 2700 K, to 5% of its original value ([31,32]). With the help of the Koschmieder approximation [31] the T1km between heliostat and receiver can be approximated from the parameter MOR: MOR ≈−ln 0.05 βext,550nm ≈ 3 βext,550nm ≈ −3 · x ln Tx,550nm , (3) (3) where βext,550nm is the monochromatic extinction coefficient at 550 nm, x is the slant range (distance between heliostat and receiver) and Tx,550 nm is the monochromatic transmittance at 550 nm for a slant range x. The spectral variation of the extinction coefficient is neglected by the Koschmieder approximation. The sensor used in this analysis to measure the MOR at the evaluated sites is the FS11 scatterometer of Vaisala ([19,33]). It emits a defined radiation signal and measures the light that is scattered towards a given angular region. Based on assumptions for the angular distribution of the scattered light and the atmospheric absorption, the MOR is derived by an internal algorithm of the FS11. Remote Sens. 2019, 11, 1083 6 of 18 The raw MOR measurements of the FS11 have to be corrected for the varying solar spectrum as well as for the absorption contribution to atmospheric extinction. A method for this correction has been developed in [19]. The raw MOR measurements of the FS11 have to be corrected for the varying solar spectrum as well as for the absorption contribution to atmospheric extinction. A method for this correction has been developed in [19]. A spectral correction has to be performed as the FS11 (as most MOR measurement instruments) does not cover the whole solar spectrum which is important for concentrated solar power (CSP). Because the measurements are performed in a narrow wavelength range around 875 nm in the infrared region which is usually not representative for the actual DNI spectrum, the correction is necessary and its effect varies with location and time. 3.2. Reference Data Set The correction due to atmospheric absorption has to be performed for this scatterometer because the FS11 only measures the scatter contribution to extinction. The absorption effect is covered to a certain extent by the instrument but extremely absorbing phenomena are not included in the internal algorithm of the FS11 ([2]). The ABC method to correct MOR data, which is described in detail in [19], is based on calculations with the radiative transfer tool libRadtran ([25,26]). The spectral correction factor is calculated by simulating the time-dependent solar spectrum and deriving the ratio between the broadband atmospheric transmittance and the monochromatic atmospheric transmittance at the wavelength of the FS11. The time-dependent absorption correction is derived by simulating the transmittance with and without considering atmospheric absorption. The absorption correction factor is then the ratio between these two simulated transmittances for each time step and the mean ratio of these transmittances as the absorption effect is to a certain extent already covered by the internal algorithm of the FS11. The ABC method has been applied on the recorded MOR data sets for three sites. FS11 scatterometers of Vaisala have been mounted at CIEMAT’s PSA as well as at IRESEN’s stations in MIS and ZAG for several years. The period between February 2015 and November 2017 has been evaluated in this work. Within the radiative transfer calculations with libRadtran, the mid-latitude summer standard atmosphere “afglms” ([34]) has been used for all three sites. For PSA the spectral AOD, the Ångström parameter as well as the ozone and water vapor column concentration are available from the co-located AERONET station ([35]). This information has been used in the ABC method (see also [19]). For MIS and ZAG standard aerosol types and distributions have been assumed due to the lack of AERONET data. The assumed standard aerosol types for the libRadtran simulations, which have been used to derive the ABC factors, are obtained from the software package OPAC (optical properties of aerosols and clouds, see [36]). For MIS the standard continental clean aerosol was chosen as the site is in a remote continental area with low anthropogenic influences. Continental average standard aerosol has been selected for ZAG. The uncertainty of the reference data set has been approximated by applying the Gauss error propagation ([2]). 3.2. Reference Data Set The absolute uncertainty is estimated to lie between 0.04 and 0.08 for T1km dependent on T1km for a data set with a temporal resolution of 1 minute. The absolute uncertainty is increasing for decreasing T1km and lies at around 0.043 for T1km equal to 0.9. For yearly averages, it can be assumed that the absolute uncertainty of T1km equal to 0.9 lies at around 0.02 ([2]). 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG Figure 2 shows the available extinction profiles for 532 nm for PSA, MIS and ZAG. The dotted lines show the original extinction profile as provided by the LIVAS climatology ([28]) for the closest grid point for all three sites. It is assumed that the lowest peak of the extinction coefficient at each site is caused by systematic errors e.g., overlap problems. Therefore, we kept the extinction coefficient constant at the level of 876 m for PSA (1235 m and 996 m for MIS and ZAG, respectively) for the layer underneath until ground level (see also [21]). These modified profiles are shown with the solid curves in Figure 2 and are used in this analysis, indicated by “LIVAS”. It can be seen that the LIVAS profiles of PSA and MIS show a similar shape with maximal extinction coefficients close to the ground. In ZAG a second maximum can be observed in about 3.5 km height above ground. Figure 2. LIVAS extinction profiles at 532 nm for PSA, MIS and ZAG. 4.1.2. Analysis of Diurnal and Annual Course of BLH from ECMWF and Ceilometer Aerosol Layer Measurements at PSA Figure 2. LIVAS extinction profiles at 532 nm for PSA, MIS and ZAG. 4.1.2. Analysis of Diurnal and Annual Course of BLH from ECMWF and Ceilometer Aerosol Layer Measurements at PSA 4.1.2. Analysis of Diurnal and Annual Course of BLH from ECMWF and Ceilometer Aerosol Layer Measurements at PSA f Diurnal and Annual Course of BLH from ECMWF and Ceilometer Aerosol Layer t PSA A CHM15k ceilometer of Lufft ([30]) is mounted at PSA since May 2013 and continuously measures the backscattered signal up to a height of 15 km above ground with a temporal resolution of 15 s. The measurements from 1 January 2014 until 31 December 2016 have been used for this analysis. The internal software of the ceilometer automatically detects the LAL within the planetary boundary layer. The aerosol layers are identified by a pre-defined gradient in the backscatter signal (see [30]). y y y p g g The BLH data of the ECMWF ERA-Interim reanalysis data set has been extracted for the three sites PSA, MIS and ZAG. 4.1. Discussion of Extinction Height Profiles The intention of testing different data sources for the extinction profile is to test which source or parameter might be the best approximation for the specific site to be used within the TM. The LIVAS profiles from the three sites are compared to detect possibly different structures in the extinction profiles (see Section 4.1.1). The BLH of ECMWF ([29,37,38]) is analyzed to evaluate if this parameter can be used to approximate the height until which the extinction coefficient is homogeneous and no aerosol particles can be found above this height. To investigate if the BLH diurnal and annual course represents the on-site conditions, the BLH is inter-compared to LAL measurement of an on-site Remote Sens. 2019, 11, 1083 7 of 18 7 of 18 ceilometer in Section 4.1.2. In Section 4.1.3 the average LAL and BLH at PSA are inter-compared with the corresponding LIVAS profile. ceilometer in Section 4.1.2. In Section 4.1.3 the average LAL and BLH at PSA are inter-compared with the corresponding LIVAS profile. 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG The BLH data is available in a three hour temporal resolution (0, 3, 6, 9, 12, 15, 18, 21 h) and is defined with the potential temperature and the Bulk Richardson number according to [39] following the conclusions of [40]. It is the depth of air next to the Earth’s surface which is most affected by the resistance to the transfer of momentum, heat or moisture across the surface [37]. The BLH typically drops to lower heights above ground during cooling at night and rises to several kilometers over desert regions on hot sunny days ([37]). Averaged values between 1999 and 2016 have been computed for this analysis. The data points have been linearly interpolated to one minute temporal resolution. Data points for solar elevation angles less than 5◦have been ignored. The BLH typically drops to lower heights above ground during cooling at night and rises to several kilometers over desert regions on hot sunny days ([37]). Averaged values between 1999 and 2016 have been computed for this analysis. The data points have been linearly interpolated to one minute temporal resolution. Data points for solar elevation angles less than 5◦have been ignored. Although the parameters LAL and BLH are defined in different ways and therefore cannot be directly compared, this inter-comparison intends to analyze if both parameters show a similar diurnal Although the parameters LAL and BLH are defined in different ways and therefore cannot be directly compared, this inter-comparison intends to analyze if both parameters show a similar diurnal and annual course at PSA. Also, both parameters might be useful for the TM. p g Figure 3 displays the mean diurnal course of the automatically detected LAL of the ceilometer between January 2014 and December 2016 at PSA. It can be seen that the diurnal course of LAL fluctuates between 1.2 km during the night and 1.4 km a.m.s.l. at 15:00. The averaged diurnal course 8 of 18 Remote Sens. 2019, 11, 1083 of BLH at PSA fluctuates between 0.7 km and 2.2 km a.m.s.l.. The daily course is more pronounced in BLH than in LAL, both maximal values can be found at 15:00. The diurnal fluctuations of BLH at MIS and ZAG are even larger: Minimal and maximal mean BLH are 1.3 km during nighttime and 3.9 km a.m.s.l. at 15:00 (0.9 km and 4.0 km for ZAG, respectively). 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG It can be noted that the average BLH is in a height of 100–200 m above the ground during nighttime at all three sites while the mean BLH increases rapidly during the morning hours to a maximum at 15:00. These rather large BLH and their effect on the assumption about the homogeneous extinction coefficient below the BLH can also be seen in the evaluation of Section 4.3.2. Figure 3. Analysis daily BLH at PSA, MIS and ZAG and comparison to ceilometer LAL at PSA. Figure 3. Analysis daily BLH at PSA, MIS and ZAG and comparison to ceilometer LAL at PSA. Figure 4 shows the averaged monthly LAL for PSA as well as the BLH for PSA, MIS and ZAG. Also for the annual course higher fluctuations in BLH can be observed in comparison to the detected LAL at PSA. While the monthly averaged LAL fluctuates between 1.1 km in January to 1.4 km in June, the BLH has its minimum in December with 0.9 m and its maximum with 1.4 km in June. A similar behavior can be observed for the average monthly BLH at MIS and ZAG where all mean values are generally higher in comparison to PSA (maximum mean BLH of 2.9 km for MIS and ZAG in July). Figure 4. Analysis mean monthly BLH at PSA, MIS and ZAG and comparison to ceilometer LAL at PSA. 4.1.3. Comparison of LIVAS Profile with Mean Ceilometer LAL and BLH of ECMWF at PSA The available BLH from ECMWF as well as the LIVAS profile for PSA have been inter-compare Figure 4. Analysis mean monthly BLH at PSA, MIS and ZAG and comparison to ceilometer LAL at PSA. 3. Comparison of LIVAS Profile with Mean Ceilometer LAL and BLH of ECMWF at PSA The available BLH from ECMWF as well as the LIVAS profile for PSA have been inter-compared to the on-site measurement data of LAL. The comparison is shown in Figure 5. The available BLH from ECMWF as well as the LIVAS profile for PSA have been inter-compared to the on-site measurement data of LAL. The comparison is shown in Figure 5. 9 of 18 Remote Sens. 2019, 11, 1083 Figure 5. Comparison of the LIVAS profile with mean LAL of ceilometer measurements and BLH of ECMWF at PSA. Figure 5. Comparison of the LIVAS profile with mean LAL of ceilometer measurements and BLH of ECMWF at PSA. 4.1.1. Comparison of Average LIVAS Extinction Profiles for PSA, MIS and ZAG The averaged detected LAL at PSA is displayed with a horizontal green solid line and lies at around 1.3 km a.m.s.l. The mean BLH for daytime (approximated as between 9:00 and 15:00, red broken curve) corresponds at PSA to about 1.8 km. It can be seen that both values lie above the largest peak in the LIVAS extinction profile which depicts a maximum of 0.081 km−1 at about 1.0 km a.m.s.l. 4.2. Comparison of Average ABC Corrected T1km for PSA, MIS and ZAG using the integral over the whole time period. using the integral over the whole time period. It can be seen that for PSA, MIS and ZAG TM-H1000 fits best in the averaged T1km as well as the DNI weighted T1km in comparison to the reference. Applying TM-LIVAS and TM-BLH on on-site DNI measurements overestimates the mean T1km at all three sites. Average T1km derived with TM-BLH are 0.92, 0.93 and 0.94 and 0.93, 0.94 and 0.95 for DNI weighted T1km for PSA, MIS and ZAG, respectively. The overestimation with TM-LIVAS is less pronounced than with TM-BLH at MIS but comparable at PSA and ZAG. The deviation of TM-LIVAS can be explained because the grid of the LIVAS extinction profiles is rather large (1 × 1◦grid) and the corresponding averaged profile does not represent the mean local conditions on site well (see also Figure 2). Figures 3 and 4 show that the BLH does not describe the aerosol height distribution well throughout the whole day and year at PSA which might also be the case at the other sites. 4.2. Comparison of Average ABC Corrected T1km for PSA, MIS and ZAG Figure 6 displays the histogram of the DNI T1km measured by the FS11 with ABC correction for all individually available data points (511,994 for PSA, 334,582 for MIS and 261,784 for ZAG from January 2015 until November 2017. Figure 6. Histogram of all available data points of ABC corrected T1km for PSA, MIS and ZAG between January 2015 and November 2017. Figure 6. Histogram of all available data points of ABC corrected T1km for PSA, MIS and ZAG between January 2015 and November 2017. The mean corrected T1km at PSA lies around 0.89 from January 2015 until November 2017, while in MIS and ZAG a lower average T1km of about 0.87 and 0.86 is found. Only considering the summer months (June, July and August) results in mean T1km of 0.88 (PSA), 0.85 (MIS) and 0.84 (ZAG). Data points with T1km lower than 0.75 occur more frequent in ZAG in comparison to the other two sites. Data points with T1km between 0.8 and 0.9 are more frequent in MIS than in ZAG. This indicates that the overall T1km level is higher in ZAG in comparison to MIS, but extreme events with higher aerosol particle loads lower the average T1km in ZAG. All sites suffer from high dust loads during the summer months and an annual variation is the consequence. It can also be seen that the frequency distribution in MIS is wider in comparison to PSA and ZAG. Remote Sens. 2019, 11, 1083 10 of 18 4.3. Transmittance Model Validation with ABC Corrected T1km for PSA, MIS and ZAG 4.3. Transmittance Model Validation with ABC Corrected T1km for PSA, MIS and ZAG The three different TMs developed using the three extinction height profiles “H1000”, “LIVAS” and “BLH” have been compared to the site-dependent reference data between January 2015 and November 2017 for the sites PSA, MIS and ZAG. 4.3.1. Average T1km of Transmittance Model Figure 7 shows the averaged T1km for all sites derived with the reference data set, as well as with the three TMs. Figure 7. The T1km of the reference data set as well as the TMs for different assumptions for the extinction height profile. The DNI weighted mean T1km is also shown. Only data points available at all sites at the same time between January 2015 and November 2017 have been evaluated. Figure 7. The T1km of the reference data set as well as the TMs for different assumptions for the extinction height profile. The DNI weighted mean T1km is also shown. Only data points available at all sites at the same time between January 2015 and November 2017 have been evaluated. Instead of considering a simple arithmetic average, the DNI weighted average of the T1km can also be considered. The DNI weighted T1km (T1km,DNIweighted) is calculated with Formula (4): Instead of considering a simple arithmetic average, the DNI weighted average of the T1km can also be considered. The DNI weighted T1km (T1km,DNIweighted) is calculated with Formula (4): T1km,DNIweighted = ΣtT1km(t) · DNI(t) ΣtDNI(t) , (4) (4) ng the integral over the whole time period. 4.3.2. Mean Bias Error and RMSE of T1km Figure 8 summarizes the absolute mean biased error (MBE) and root mean square error (RMSE) for each combination of extinction height model and site in comparison to the corresponding ABC corrected FS11 reference data set. The performance of the TM is site-dependent. This is the case as the extinction height profile, the main assumption of the TM, varies with a different extend at each site. Assuming a constant extinction profile (as in TM-H1000 and TM-LIVAS) therefore results in different deviations from the reference data set. It can be seen that the lowest MBE can be found for all sites 11 of 18 Remote Sens. 2019, 11, 1083 with the TM-H1000 that assumes a constant extinction coefficient in the first kilometer above ground (0.33, −0.11 and −2.16% for PSA, MIS and ZAG, respectively). The lowest RMSE for PSA, MIS and ZAG are found with the modified LIVAS profile (4.6%, 6.8% and 5.7%, respectively). Figure 8. Absolute MBE and RMSE of modeled T1km for the validation of the TM for different assumptions for the extinction height profile in comparison to the according ABC corrected FS11 reference data set. Only data points available at all sites at the same time between January 2015 and November 2017 have been evaluated. Figure 8. Absolute MBE and RMSE of modeled T1km for the validation of the TM for different assumptions for the extinction height profile in comparison to the according ABC corrected FS11 reference data set. Only data points available at all sites at the same time between January 2015 and November 2017 have been evaluated. MBE and RMSE are increasing if the homogeneous extinction coefficient in the lowest layer above ground is scaled with the site- and time-dependent BLH data set. This is the case as increased BLHs result in lower extinction coefficients close to the ground and therefore increased T1km. Figures 3 and 4 showed that the BLH exceeds the measured LAL during daytime as well as during the summer months at PSA. This indicates that scaling the TM with BLHs results in an overestimation of T1km in several cases especially during periods which are of interest for CSP due to high irradiation levels. 4.3.3. Annual Course of TM Performance 4.3.3. Annual Course of TM Performance 4.3.3. Annual Course of TM Performance Figures 9–11 show the averaged daily DNI-weighted T1km as well as their 30 days moving average at PSA, MIS and ZAG calculated with all three TMs and in comparison to the reference T1km derived from ABC corrected FS11 measurements. In this examination, all available data points for each site are analyzed individually. It has to be noted that the available data points are not uniformly distributed within the different sites and the days of the year. During the winter months less data points are used to calculate the DNI-weighted daily mean T1km due to clouds masking the sun. The calculation of average DNI-weighted T1km from the different models might be therefore less accurate. However, due to the higher T1km levels in winter the absolute uncertainty of the model is lower than in summer for sunny timestamps. Also less data points are available in ZAG in comparison to PSA and MIS. The numbers of averaged data points are also shown in Figures 9–11 and days with less than 100 data points are not considered in the analysis of averages and moving averages. mote Sens. 2019, 11, 1083 12 of 1 Figure 9. Average daily DNI weighted T1km for PSA from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. emote Sens. 2019, 11, 1083 12 of 1 Figure 9. Average daily DNI weighted T1km for PSA from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Remote Sens. 2019, 11, 1083 12 of 18 ote Sens. 2019, 11, 1083 12 of Figure 9. Average daily DNI weighted T1km for PSA from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 10. Average daily DNI weighted T1km for MIS from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 9. Average daily DNI weighted T1km for PSA from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 10. Average daily DNI weighted T1km for MIS from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 11. Average daily DNI weighted T1km for ZAG from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. 4.3.3. Annual Course of TM Performance For PSA 30 days moving averaged DNI weighted T between 0 87 and 0 92 are derived fro Figure 9. Average daily DNI weighted T1km for PSA from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 10. Average daily DNI weighted T1km for MIS from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Fi 10 A d il DNI i ht d T f MIS f th ABC t d T t d Figure 10. Average daily DNI weighted T1km for MIS from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. Figure 11. Average daily DNI weighted T1km for ZAG from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. F PSA 30 d i d DNI i ht d T b t 0 87 d 0 92 d i d f Fi 11 A d il DNI i ht d T f ZAG f th ABC t d T t d Figure 11. Average daily DNI weighted T1km for ZAG from the ABC corrected T1km measurements and the three different TMs and the 30 days moving average. For PSA, 30 days moving averaged DNI-weighted T1km between 0.87 and 0.92 are derived from the reference data set (Figure 9). During summer months (May to September) the T1km moving For PSA, 30 days moving averaged DNI-weighted T1km between 0.87 and 0.92 are derived from the reference data set (Figure 9). During summer months (May to September) the T1km moving For PSA, 30 days moving averaged DNI-weighted T1km between 0.87 and 0.92 are derived from the reference data set (Figure 9). During summer months (May to September) the T1km moving Remote Sens. 2019, 11, 1083 13 of 18 average derived with TM-H1000 underestimates T1km from the reference data set and during winter it overestimates it slightly. This can be expected as both BLH as well as LAL show at PSA an annual course with higher values in summer and lower values in winter (see Figure 4). TM-BLH performs better during summer months. 4.3.3. Annual Course of TM Performance This could be explained by the fact that both the constant 1 km level as well as averaged BLH data for PSA lie closer to the mean on-site LAL measurements during these months, in comparison to the winter months (see also Figure 4). The TM-LIVAS overestimates the average T1km throughout the whole year but performs better during summer months. In MIS the reference data set shows lower T1km during summer (less than 0.85) than during winter (more than 0.91) in the 30 days moving average (Figure 10). The averaged T1km of both TM-LIVAS and TM-BLH fit well the averaged T1km from the reference data set between June and August. During the remaining months of the year T1km is overestimated by TM-LIVAS. TM-BLH underestimates T1km during winter months, but is has to be noted that only few data points are available for this analysis during these months. TM-H1000 overestimates the reference T1km during winter and underestimates it during summer months. In ZAG a similar (in comparison to MIS) annual behavior of the averaged T1km from the reference data set can be observed in the 30-days moving average (less than 0.85 during summer, more than 0.91 during winter, see Figure 11). It can be seen that all three TMs overestimate the average T1km derived from the reference data set (except of TM-H1000 during summer). This indicates that the layer which includes the majority of aerosol particles and water vapor might be thicker than 1 km during these months. Also in ZAG is has to be considered that only few data points are available during winter months. The mean BLH for ZAG during July lies at around 2.860 m a.m.s.l., which is in a height of about 1.077 m above ground (see Figure 4). 5. Conclusions A model developed in [21] based on DNI measurements to derive the atmospheric transmittance in solar tower plants has been validated at three sites in Spain and Morocco. The transmittance model (TM) can be applied to the desired site during solar resource assessment as only data sets of usually available meteorological parameters like DNI, temperature, relative humidity and barometric pressure are necessary. Three different aerosol profiles have been tested to be applied as key assumption for the transmittance model development. In one approach it is assumed that all aerosol particles are homogeneously distributed within the first kilometer above ground. In a second approach, the aerosol profiles of the LIVAS database ([28]) are assumed to describe the vertical aerosol distribution. The third transmittance model uses the boundary layer height (BLH) of the ECMWF ERA-interim dataset ([29]) to scale the height above ground in which all aerosol particles are assumed to be distributed homogeneously. The resulting broadband transmittance for a slant range of 1 km (T1km) from the three TMs for the sites of PSA in Spain, Missour, Morocco (MIS) and Zagora, Morocco (ZAG) is compared to a reference data set between January 2015 and November 2017. The reference data set consists of T1km derived with on-site meteorological optical range (MOR) measurements and an applied absorption and broadband correction (ABC) according to [19]. The average T1km for the sites PSA, MIS and ZAG are 0.89, 0.87 and 0.86 if all available data points for each site individually are analyzed. T1km at the semi-desert sites of Morocco shows a more pronounced annual variation in comparison to PSA in Spain. It has to be noted that for plant yield simulations, it is recommended to include an extinction or transmittance time series instead of arithmetic averages. If averages are used, the DNI weighted average of the transmittance data should be utilized. The validation of the TM showed that the absolute mean bias error (MBE) for all three TMs and sites lies below 5% except for ZAG and the usage of the according LIVAS profile. Assuming that all aerosol particles are homogeneously distributed within the first kilometer above ground results in a reduction of MBE to almost 0 in PSA and MIS. The absolute root mean square error (RMSE) of the TM is around 5–6% except of for the site of MIS (around 7–8%). 4.4. Transmittance Model Sensitivity Analysis T1km for different aerosol layer thicknesses in which the extinction coefficient βext is considered homogeneous in TM-H1000. 4.4. Transmittance Model Sensitivity Analysis Figure 12 shows the sensitivity of TM-H1000 concerning the thickness of the homogeneous layer above ground. The assumption about the extinction height profile within the TM has one of the largest impacts on the uncertainty of the TM ([21]). It can be seen that the sensitivity of TM-H1000 concerning the thickness of the homogeneous layer above ground is smallest for T1km close to 0 and 1 (very hazy and very clear conditions). For T1km derived with TM-H1000 around 0.5, the sensitivity of the result to the assumed homogeneous aerosol layer thickness is largest. This graph also shows that the absolute deviation of T1km for different aerosol layer thicknesses larger and smaller 1 km is evenly distributed. The solid red and gray curve display T1km for TM assuming a thickness of 0.865 and 1.647, respectively. These values have been chosen as an example as they are the mean LAL and BLH at PSA at 15:00 (see Figure 3). This example shows that the range of T1km lies between 0.89 and 0.93 for T1km of 0.9 if the main contribution of aerosol particles and water vapor to extinction is in reality up to 0.865 or 1.647 km above ground at PSA instead of 1 km. Considering a maximum deviation of 0.3 km from 1 km as aerosol layer thickness (0.7–1.3 km) will result in a deviation of less than 0.05 for T1km larger 0.83. These results fit well to the uncertainty analysis from [21]. T1km of less than 0.83 derived with the TM will therefore have larger uncertainties due to the considered aerosol layer thickness and will exceed the uncertainty of the reference data set (see [19]). These considerations motivate to recommend additional site information (e.g., by on-site ABC corrected MOR measurements) for sites where the TM derives mean T1km smaller than 0.83 as the deviations from T1km might be larger than 0.05. Note however, that the uncertainty of the average T1km is smaller than the deviations indicated by Figure 12 as some errors cancel out due to the temporal averaging. Figure 12 shows the effect of an error in the aerosol layer thickness for an indivual timestamp. 14 of 18 Remote Sens. 2019, 11, 1083 Figure 12. T1km for different aerosol layer thicknesses in which the extinction coefficient βext is considered homogeneous in TM-H1000. Figure 12. 5. Conclusions An analysis of the BLH data shows strong diurnal and annual courses for all three sites. The difference between minimal and maximal BLH within a day or year is largest in ZAG. Higher BLH during midday and summer months due to higher temperatures close to the ground and the induced vertical mixing results in lower extinction coefficients close to the ground (and therefore higher T1km) derived with the TM. The performance of the TM is site-dependent as adequate site-dependent information about the aerosol height profile is the key assumption within the TM. Remote Sens. 2019, 11, 1083 15 of 18 15 of 18 It can be noted that the TM performs better during summer months than during winter, but it has to be mentioned that more data points have been available during summer for this validation. It can be noted that the TM performs better during summer months than during winter, but it has to be mentioned that more data points have been available during summer for this validation. The TM is most sensitive for the approximation of the aerosol particle distribution within the lower atmosphere. Three approaches have been compared to be applied within the TM. It can be concluded that the TM performs similarly well, assuming a homogeneous aerosol distribution in the lowest kilometer above ground or the extinction profile extracted from the LIVAS climatology. Using BLH data to describe the height under which the aerosol particles are homogeneously distributed and above which no aerosol particles can be found results in the overestimation of T1km at all sites. The validation of the TM showed its applicability at various sites. Hazy sites can be identified with the TM but additional ground measurements of T1km, e.g., ABC corrected MOR measurements, are recommended in this case. This is recommended as the increased uncertainty of the TM for lower T1km can result in an underestimation of atmospheric transmittance at a certain site. Sites with T1km of more than 0.83 can be verified with the TM and the TM can be considered as providing sufficient site information for resource assessment for clear sites. Author Contributions: Conceptualization and methodology: N.H. and S.W. Data analysis: N.H. Software: N.H., M.S. and S.W. Resources and data curation: N.H, A.G., A.A.M., F.W., L.Z. and A.S. Writing—original draft preparation: N.H. and S.W. Interpretation of results, writing—review and editing: all the authors. Supervision and project administration: S.W. 5. Conclusions Funding: The authors would like to thank the Helmholtz Association for funding the project “Impact of Desert Environment on Solar Energy Systems” (DESERGY) (PD-205). Acknowledgments: We also acknowledge the developers of libRadtran. The authors thank the Group of Atmospheric Optics, Valladolid University, for the provision of the CÆLIS tool (http://www.caelis.uva.es) used in this publication and the AERONET, PHOTONS and RIMA staff for their support. Conflicts of Interest: The authors declare no conflict of interest. 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[CrossRef] Remote Sens. 2019, 11, 1083 18 of 18 c⃝2019 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/). Remote Sens. 2019, 11, 1083 18 of 18 c⃝2019 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/). 18 of 18 Remote Sens. 2019, 11, 1083 c⃝2019 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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Mineralocorticoid Receptors Guide Spatial and Stimulus-Response Learning in Mice
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Mineralocorticoid receptors guide spatial and stimulus-response learning in mice Arp, J.M.; Horst, J.P. ter; Kanatsou, S.; Fernandez, G.S.E.; Joels, M.; Krugers, H.J.; Oitzl, M.S. 2014, Article / Letter to editor (PLoS One, 9, 1, (2014), article e86236) Doi link to publisher: https://doi.org/10.1371/journal.pone.0086236 Version of the following full text: Publisher’s version Downloaded from: http://hdl.handle.net/2066/135969 Download date: 2024-10-24 Introduction the vast majority of male C57Bl/6j mice use a spatial strategy to navigate on a CHB [17]; to acquire a stimulus-response task, male mice have to overcome their natural tendency to use the spatial strategy [22]. Brief exposure to stress causes a shift from spatial towards stimulus-response strategies, an effect which is mediated via MRs [17]. Corticosteroid hormones are secreted from the adrenals in an ultradian and circadian pattern, as well as in response to stressful experiences [1,2]. Corticosteroid hormones regulate brain func- tion via activation of high affinity mineralocorticoid receptors (MRs) and lower affinity glucocorticoid receptors (GRs) which are both expressed in brain areas which are crucial for learning and memory such as hippocampus, amygdala, prefrontal cortex and striatum [3]. Via activation of MRs and GRs, corticosteroid hormones promote behavioral adaptation to stressful experiences [1,3–5]. MRs mediate initial behavioral responses to novel situations, and are required for adequate spatial and fear learning and memory processes [6–10]. Activation of GRs is crucial for consolidation of spatial and emotional information [6,11–13]. In these studies, the CHB task was designed to allow animals to make a choice. However, it remains to be established to what extent activation of MRs determines stimulus-response and spatial strategies to solve navigational tasks per se, i.e. when animals do not have to make a choice. In the present study we therefore studied the role of MRs in spatial (hippocampus-dependent) and stimulus-response (striatum- dependent) learning separately; i.e., we used, separately, the spatial and stimulus-response learning versions of the CHB task [22]. Moreover, to gain better insight into the role of brain MRs, we did not only examine the consequences of MR deficiency [7] but also investigated the other end of the spectrum, i.e. MR overexpression [8]. We hypothesized that MR overexpression will lead to improved performance in both tasks and might ease the shift from the spatial to the acquisition of the stimulus-response task, while the opposite is expected in the MR-deficient animals. We initially focused on female MR mutants, in view of the recently Recently we demonstrated that corticosteroids are particularly important for the choice of strategies to solve navigational tasks. Different strategies such as spatial (hippocampus-dependent) or stimulus-response (striatum-dependent) strategies can be used to solve navigational tasks [14–16]. Abstract The funders had no role in study design, data collection and analysis, decision to publish, or preparati Funding: This study was supported by grant NWO-NIBC433-09-251 to MA, GF, MJ, HJK, MSO, NWO-DN-95-420 to MSO, the European Science Foundation (07- EuroSTRESS-FP-005) to JPtH. 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: h.krugers@uva.nl Competing Interests: The authors have declared that no competing interests exist. * E-mail: h.krugers@uva.nl * E-mail: h.krugers@uva.nl Abstract Adrenal corticosteroid hormones act via mineralocorticoid (MR) and glucocorticoid receptors (GR) in the brain, influencing learning and memory. MRs have been implicated in the initial behavioral response in novel situations, which includes behavioral strategies in learning tasks. Different strategies can be used to solve navigational tasks, for example hippocampus-dependent spatial or striatum-dependent stimulus-response strategies. Previous studies suggested that MRs are involved in spatial learning and induce a shift between learning strategies when animals are allowed a choice between both strategies. In the present study, we further explored the role of MRs in spatial and stimulus-response learning in two separate circular holeboard tasks using female mice with forebrain-specific MR deficiency and MR overexpression and their wildtype control littermates. In addition, we studied sex-specific effects using male and female MR-deficient mice. First, we found that MR-deficient compared to control littermates and MR-overexpressing mice display altered exploratory and searching behavior indicative of impaired acquisition of novel information. Second, female (but not male) MR-deficient mice were impaired in the spatial task, while MR-overexpressing female mice showed improved performance in the spatial task. Third, MR-deficient mice were also impaired in the stimulus-response task compared to controls and (in the case of females) MR-overexpressing mice. We conclude that MRs are important for coordinating the processing of information relevant for spatial as well as stimulus-response learning. Citation: Arp JM, ter Horst JP, Kanatsou S, Ferna´ndez G, Joe¨ls M, et al. (2014) Mineralocorticoid Receptors Guide Spatial and Stimulus-Response Learning in Mice. PLoS ONE 9(1): e86236. doi:10.1371/journal.pone.0086236 Editor: Mathias V. Schmidt, Max Planck Institute of Psychiatry, Germany Received November 6, 2013; Accepted December 10, 2013; Published January 21, 2014 Received November 6, 2013; Accepted December 10, 2013; Published January 21, 2014 Copyright:  2014 Arp 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. Copyright:  2014 Arp et al. This is an open-access article distributed under the terms of the Creative Commons Attrib use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by grant NWO-NIBC433-09-251 to MA, GF, MJ, HJK, MSO, NWO-DN-95-420 to MSO, the Europe EuroSTRESS-FP-005) to JPtH. Note: To cite this publication please use the final published version (if applicable). J. Marit Arp1, Judith P. ter Horst1, Sofia Kanatsou1, Guille´n Ferna´ndez3, Marian Joe¨ls2, Harm J. Krugers1*, Melly S. Oitzl1 1 Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands, 2 Department of Neuroscience and Pharmacology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands, 3 Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands January 2014 | Volume 9 | Issue 1 | e86236 Timeline Male and female forebrain MR-deficient (MRCaMKCre; [7]) mice and their control littermates (MR flox/flox)(n = 12 per group; males approximately 3 months and females approximately 4 months old) were bred in the animal facility of Leiden University. The MRCaMKCre mice were obtained by breeding MRflox/flox with MRflox/wtCaMKCre mice from the German Cancer Research Center, Heidelberg, Germany. The conditional MR allele was generated in embryonic stem cells of 129Ola mice and CaMKCre transgene was injected in FVB/N mice [24]. The MR flox allele and the Cre transgene were backcrossed into C57Bl/6J mice. For a detailed description of the design and breeding of the MRCaMKCre mice see [7]. In an additional experiment, female forebrain-specific MR-overexpressing transgenic (MR-Tg; [8]) mice and their control littermates were used (n = 19220 per group; approximately 4 months old) that were bred in the animal facility of the University of Amsterdam. The MR-Tg mice were obtained from the Centre for Cardiovascular Science, Edinburgh, UK. A haemagglutinin (HA) epitope tag was inserted into the N- terminus of the full-length human MR cDNA. Transgenic mice were generated by injection of a CaMKIIa-HA-MR construct in C57Bl/6J CBA embryos (Babraham Institute, Cambridge, UK). For a detailed description of the design and breeding of the MR- Tg mice see [8]. After arrival, the mice were allowed to acclimatize to the animal facility for three weeks. Male and female MR- deficient mice were derived from 7 litters (2–6 mice per litter); 5 out of 7 litters contributed both MRCaMKCre and controls (MR flox/flox). MR-overexpressing female mice were derived from 5 litters (3–4 mice per litter); we used MR-Tg mice and control littermates from all litters. The experimental design of the experiment is schematically shown in Figure 1. We tested both male and female MRCaMKCre mice, female MR-Tg mice and the control littermates of each group in two versions of the CHB task: a spatial task and a stimulus-response task. First, mice were given a free exploration trial (FET). One week later the spatial tasks started. Mice received six training trials (inter trial-interval 15 min), where only extra- maze spatial cues were available to locate the exit hole. One day after the spatial training, each mouse performed one spatial memory test trial with all holes closed. Timeline The stimulus-response task started one week after this spatial memory test and consisted of two subsequent days of each six training trials (again 15 min inter trial- interval), where an intra-maze stimulus (the bottle) marked the exit hole. Free Exploration Trial For the free exploration trial (FET) the mice were allowed to explore the CHB for 5 min. All holes were closed. At the end of the 5 min, the exit hole was opened and the animals were guided there by the experimenter. This exploration trial allowed to analyze exploratory behavior and general activity of the mice. One week before the behavioral testing started, mice were moved to the experimental room (temperature: 20uC; humidity: 55% 615), under a 12:12 hour light/dark cycle, lights on at 07:30 h) and single housed in Macrolon cages with sawdust bedding and with food and water ad libitum. Testing was carried out between 08:30 and 12:30 h. The experiments were approved by the committee on Animal Health and Care from Leiden University, The Netherlands, in accordance with the EC Council Directive of September 2010 (2010/63/EU). The Spatial Task One week after the FET, mice were given six successive training trials with a maximum of 120 s per trial. The location of the exit hole was always fixed relative to the distal extra-maze cues in the room. There were no proximal cues present, so the exit could only be found by using the extra-maze cues. This task was used to assess spatial learning. Twenty-four hours later, we tested long-term spatial memory. Stimulus-response Task In the stimulus-response (S-R) task, the position of the exit hole was marked by a bottle and varied from trial to trial in the same sequence for all mice. The position of the exit was never at the same location or a location adjacent to it within a six trial session. Furthermore, the exit hole location of the spatial task was not used as an exit hole position during the stimulus-response task. There were two subsequent days of six trials each. A trial lasted 120 s. The distal extra-maze cues were present, but only the proximal intra-maze cue (a transparent bottle filled with water; 0.5 L; 22 cm high; 5 cm diameter), located next to the exit hole, marked the Tunnel Training One week before the behavioral experiments started the mice were weighed and trained to climb through a tunnel on every second day (three times in total). This familiarized mice with the task requirements. Apparatus The mouse was placed on the CHB for two minutes with all holes closed. The behavior and movement pattern of the mouse allowed to analyze search strategy and spatial memory. The circular hole board (CHB) is a revolvable grey round plate (Plexiglas; 110 cm in diameter; situated 1 m above the floor) with twelve holes at equal distances from each other, located 10 cm from the rim of the board. Holes are 5 cm in diameter and can be closed by a lid at a depth of 5 cm. Whether a hole is open or closed can only be detected if the mouse puts its head over the edge of the hole. An S-shaped tunnel (5 cm in diameter; 15 cm long) leads from the open exit hole to the home cage of the animal. Multiple distant cues in the room allow spatial orientation on the board [17,18,22]. Mineralocorticoid Receptors in Learning Strategies Mineralocorticoid Receptors in Learning Strategies board and exit through the open tunnel. If the mouse did not find the exit hole within 120 s, it was gently guided to the exit using a grid. The board was cleaned after each trial with 1% acetic acid solution to dissipate odor cues and rotated until another hole was at the position of the exit. The home cage was placed under the board at the position of the exit hole such that the mouse could not see the cage from the board. reported clear phenotype of female (but not male) MR-deficient mice in fear conditioning and the dual-solution CHB task [18,19,23]. Since we observed significant behavioral effects of MR deficiency in females, we next also examined the effects of MR deficiency in male mutants. January 2014 | Volume 9 | Issue 1 | e86236 Introduction We designed a version of the circular hole board (CHB) task such that both spatial and stimulus- response strategies could be used to locate the exit hole (dual- solution task; [17–21]). When exposed to such a dual-solution task, 1 PLOS ONE | www.plosone.org January 2014 | Volume 9 | Issue 1 | e86236 Mineralocorticoid Receptors in Learning Strategies Spatial Learning All groups acquired the task, as reflected by decreasing exit latencies over the trials (latency of first visit to the exit hole, MR- Tg females and their controls: F(5,185) = 6.338, p,0.0001; Figure 2A; MRCaMKCre females and their controls: F(5,110) = 10.736, p,0.0001; Figure 2B; MRCaMKCre males and their controls: F(5,110) = 10.011, p,0.0001; Figure 2C). Estrous Cycle The stage of the estrous cycle was determined in female mice by vaginal cytology after each behavioral task. Using a plastic loop (inoculation loops 1 ml, Mediscan, Greiner Bio-one), a vaginal smear was obtained. The loop was dipped in water and then inserted into the vagina and gently rubbed against the vaginal wall. Cells were smeared on a glass slide in a drop of water. After air drying, the cells were stained with Giemsa (Sigma) for 10 minutes. The stage of the cycle was determined based on the presence or absence of nucleated epithelial, cornified epithelial and leukocyte cells. Proestrus: many cells with a nucleus and some epithelial cells; estrus: many epithelial cells and some cells with a nucleus; metestrus: some epithelial cells and many macrophages; diestrus: many macrophages and some cells with a nucleus. We did not encounter the metestrus stage. ( , ) , p ; g ) MRCaMKCre and MR-Tg female mice. MRCaMKCre females showed significantly impaired performance compared to their controls (exit latency: F(1,22) = 6.587, p = 0.019), while MR-Tg females out-performed the controls (F(1,37) = 4.893, p = 0.033). MRCaMKCre females stayed longer in the center (F(1,22) = 4.986, p = 0.036) and had a lower velocity (F(1,22) = 7.335, p = 0.013) than their controls (Table 1) and than the MR-Tg mice (F(1,29) = 23.072, p,0.0001; Table 1). To figure out whether the impaired performance of the MRCaMKCre compared to control females was caused by the longer time spent in the center, the exit latency was corrected for the latency to leave the center. When corrected, the MRCaMKCre females still needed significantly more time to find the exit hole compared to their controls (F(1,22) = 4.941, p = 0.037; data not shown). Conversely, the MR-Tg females had a higher velocity during the trials than their controls (F(1,37) = 7.917, p = 0.008; Table 1). Other behavioral parameters were comparable between MR-Tg females and their controls. MRCaMKCre female mice took longer to locate the exit than the MR-Tg females (F(1,29) = 16.090, p,0.0001), while controls of both groups had similar exit latencies (F(1,30) = 0.004, p = 0.949). Results Free Exploration Trial (FET) MRCaMKCre and MR-Tg female mice. MRCaMKCre (defi- cient) female mice had a significantly longer latency to leave the center of the board when compared to their controls and also when compared to MR-Tg (overexpressing) female mice (861 vs 561; p = 0.039 and vs 361; p,0.0001, respectively). Further- more, MRCaMKCre female mice showed more perseveration than MR-Tg mice (2063 vs. 1162; p = 0.007). Exploratory behavior (% perseveration, % series, latency to leave the center, rim dips, rearing, stretched attends) and general activity (velocity, distance moved and number of holes visited) were comparable between MR-Tg mice and their control littermates (data not shown). Behavioral parameters were also comparable between control littermates of MRCaMKCre and MR-Tg female mice. General Procedure Each trial started by placing the mouse in a cylinder (Plexiglas; 25 cm high; 10 cm diameter) located at the center of the CHB. After 5 s the cylinder was lifted and the mouse could explore the January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org January 2014 | Volume 9 | Issue 1 | e86236 2 Mineralocorticoid Receptors in Learning Strategies Figure 1. Experimental design of training and memory testing. doi:10.1371/journal.pone.0086236.g001 Figure 1. Experimental design of training and memory testing. doi:10.1371/journal.pone.0086236.g001 exit. Therefore, the mice had to use a stimulus-response navigation strategy to locate the exit. Analysis of Behavior Behavior was digitally recorded and analyzed with Ethovision XT 6.1 (Noldus Information Technology b.v., Wageningen, The Netherlands). This image analysis system sampled the position of the mouse 12.5 times per second. The CHB was virtually subdivided into subareas of special interest: center (start area), rim, zone of holes (area including all holes and the space between the holes, but excluding the center, middle and rim of the CHB) and four quadrants (covering three holes with the exit hole in the middle). We calculated preference values of the mice for the quadrant that contained the exit hole, and in the S-R task also for the quadrant that contained the exit hole of the previous trial. The following parameters were calculated by Ethovision: velocity (cm/ s), distanced moved (cm), latency of first visit to exit hole (exit latency, s) (and to former exit hole for the S-R task), and latency to the quadrant of the exit hole (s) and duration in quadrant of the exit hole (s). The experimenter hand scored the number of holes visited (mouse puts at least its nose in the hole), rim dips (looking over the edge of the board), stretched attends, % perseveration (visiting the same hole twice in a row or with one other hole between the two holes) and % serial hole visits (visiting at least three adjacent holes in a row). g MRCaMKCre male. MRCaMKCre males showed more persev- eration and reared less than their controls (MRCaMKCre vs g MRCaMKCre male. MRCaMKCre males showed more persev- eration and reared less than their controls (MRCaMKCre vs controls, % perseveration: 2765 vs 1064; p = 0.018; rearing: 0.0860.1 vs 1.2560.5; p = 0.034). Statistical Analysis Data are presented as mean 6 SEM. Statistical analysis included one-way ANOVA, MANOVA, T-tests and General Linear Model repeated measures. Post hoc tests (Tukey) for multiple comparisons were used when appropriate. Reported p values are two-tailed and statistical significance was accepted for p,0.05. Statistical calculations were performed with IBM SPSS Statistics (version 20; SPSS Inc.; Chicago, IL). The numbers of female mice in the different stages of the estrous cycle were too low for test-statistics per stage. Therefore, we included the stage of the estrous cycle as a covariate in the one-way ANOVA and General Linear Model repeated measures analyses. MRCaMKCre males. The performance did not differ in any respect between MRCaMKCre males and controls (Figure 2C; Table 1). MRCaMKCre and MR-Tg female mice. Both MRCaMKCre MRCaMKCre and MR-Tg female mice. Both MRCa C e female mice and control littermates spent more time in the exit (target) quadrant than in the other quadrants, but MRCaMKCre females showed a trend for longer latency to the exit quadrant compared to their controls (56615.4 vs 2169.5; p = 0.070). MRCaMKCre females spent less time in the holes zone and showed less perseveration than their controls (Table 2). Also the general activity parameters differed between MRCaMKCre females and their controls. This is clear from the lower number of holes visited, shorter distance moved and a slower walking velocity in MRCaMKCre females (Table 2). Parameters for exploration and general activity were comparable between MR-Tg mice and controls. C MKC female mice and control littermates spent more time in the exit (target) quadrant than in the other quadrants, but MRCaMKCre p g MRCaMKCre and MR-Tg female mice. MRCaMKCre mice showed impaired performance as evident from the longer latencies to the exit compared to their controls. On the first day of S-R training an interaction of genotype*trial was found (F(5,5) = 2.763, p = 0.040), with longer exit latencies in trials 3 and 5 in MRCaMKCre females than controls (trial 3: p = 0.031; trial 5: p = 0.027). On the second day the MRCaMKCre females had longer exit latencies than their controls over all trials (F(1,22) = 14.130, p = 0.001). In MR-Tg female mice exit latency was short and comparable to control littermates on both days. On the first day, exit latencies of MR-Tg and MRCaMKCre as well as their controls were comparable. On the second day MRCaMKCre females had longer latencies than MR-Tg females (F(1,29) = 8.441, p = 0.007), while their respective controls performed comparably. g MRCaMKCre and MR-Tg female mice. MRCaMKCre mice showed impaired performance as evident from the longer latencies to the exit compared to their controls. On the first day of S-R training an interaction of genotype*trial was found (F(5,5) = 2.763, p = 0.040), with longer exit latencies in trials 3 and 5 in MRCaMKCre females than controls (trial 3: p = 0.031; trial 5: p = 0.027). On the second day the MRCaMKCre females had longer exit latencies than their controls over all trials (F(1,22) = 14.130, p = 0.001). In MR-Tg female mice exit latency was short and comparable to control littermates on both days. MRCaMKCre and MR-Tg female mice. Both MRCaMKCre On the first day, exit latencies of MR-Tg and MRCaMKCre as well as their controls were comparable. On the second day MRCaMKCre females had longer latencies than MR-Tg females (F(1,29) = 8.441, p = 0.007), while their respective controls performed comparably. MRCaMKCre mice. The male MRCaMKCre mice showed a trend for longer latency to the exit quadrant compared to their controls (males: 64614.5 vs 30610.9; p = 0.080). Furthermore, searching behavior also differed between MRCaMKCre male mice and controls. MRCaMKCre males showed a more evenly distributed searching pattern while their controls spent significantly more time in the exit quadrant than in the other quadrants (Table 2). p p p y MRCaMKCre male mice. Also MRCaMKCre male mice showed impaired performance on the second day of the S-R training compared to their controls (day 2: F(1,22) = 6.981, p = 0.015). MRCaMKCre male mice. Also MRCaMKCre male mice showed impaired performance on the second day of the S-R training compared to their controls (day 2: F(1,22) = 6.981, p = 0.015). Spatial Memory Test –24 Hours Later with Closed Exit Behavioral parameters (averaged over the day) recorded during the spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. Table 1. Behavioral parameters (averaged over the day) recorded during the spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. The spatial task consisted of six trials. Data represent mean 6 SEM of all trials. For statistics a repeated measures ANOVA was used over the trials. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female control littermates of MRCaMKCre mice. doi:10 1371/journal pone 0086236 t001 The spatial task consisted of six trials. Data represent mean 6 SEM of all trials. For statistics a repeated measures ANOVA was used over the trials. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female control littermates of MRCaMKCre mice. doi:10.1371/journal.pone.0086236.t001 (Figure 2A) and between the MRCaMKCre mice and their controls (Figure 2B (females) and 2C (males)). one.0086236.t002 Spatial Memory Test –24 Hours Later with Closed Exit Spatial Memory Test –24 Hours Later with Closed Exit Spatial Memory Test –24 Hours Later with Closed Exit Latency to the exit hole was longer than in trial 6 the day before, but comparable between MR-Tg mice and their controls Latency to the exit hole was longer than in trial 6 the day before, but comparable between MR-Tg mice and their controls PLOS ONE | www.plosone.org January 2014 | Volume 9 | Issue 1 | e86236 3 Mineralocorticoid Receptors in Learning Strategies Figure 2. Spatial task: latency to the exit hole over six training trials and spatial memory test. A) Female MR-Tg mice (n = 19) take less time to find the exit hole than controls (n = 20). B) Female MRCaMKCre mice take more time to find the exit hole than controls (n = 12 per group). C) Male MRCaMKCre and control mice (n = 12 per group) have comparable latencies to locate the exit hole. Bars show mean 6 SEM. *p,0.05 over trials, vs. control littermates. n.s. = not significant. doi:10.1371/journal.pone.0086236.g002 Figure 2. Spatial task: latency to the exit hole over six training trials and spatial memory test. A) Female MR-Tg mice (n = 19) take less time to find the exit hole than controls (n = 20). B) Female MRCaMKCre mice take more time to find the exit hole than controls (n = 12 per group). C) Male MRCaMKCre and control mice (n = 12 per group) have comparable latencies to locate the exit hole. Bars show mean 6 SEM. *p,0.05 over trials, vs. control littermates. n.s. = not significant. doi:10.1371/journal.pone.0086236.g002 January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org 4 Mineralocorticoid Receptors in Learning Strategies Table 1. Behavioral parameters (averaged over the day) recorded during the spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. Females Females Males MR-Tg Control MRCaMKCre Control MRCaMKCre Control Velocity (cm/s) 860* 761 560* 661 561 560 Latency to leave center (s) 360 360 1063*# 561$ 963 963 The spatial task consisted of six trials. Data represent mean 6 SEM of all trials. For statistics a repeated measures ANOVA was used over the trials. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female control littermates of MRCaMKCre mice. doi:10.1371/journal.pone.0086236.t001 Table 1. Data represent mean 6 SEM. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female MRCaMKCre; ,duration in exit quadrant vs average duration in other quadrants. doi:10 1371/journal pone 0086236 t002 PLOS ONE | www.plosone.org 5 January 2014 | Volume 9 | Issue 1 | e86236 doi:10.1371/journal.pone.0086236.t002 (Figure 2A) and between the MRCaMKCre mice and their controls (Figure 2B (females) and 2C (males)). C C (Figure 2A) and between the MRCaMKCre mice and their controls (Figure 2B (females) and 2C (males)). All groups decreased their exit latencies over the trials (MR-Tg females and their controls: day 1: F(5,185) = 13.314, p,0.0001; day 2: F(5,110) = 3.725, p = 0.015; Figure 3A; MRCaMKCre females and their controls: day 1: F(5,110) = 28.585, p,0.0001; day 2: F(5,110) = 3.406, p = 0.030; Figure 3B; MRCaMKCre males and their controls: day 1: F(5,110) = 25.426, p,0.0001; day 2: F(5,110) = 16.049, p,0.0001; Figure 3C). (Figure 2A) and between the MRCaMKCre mice and their controls (Figure 2B (females) and 2C (males)). All groups decreased their exit latencies over the trials (MR-Tg females and their controls: day 1: F(5,185) = 13.314, p,0.0001; day 2: F(5,110) = 3.725, p = 0.015; Figure 3A; MRCaMKCre females and their controls: day 1: F(5,110) = 28.585, p,0.0001; day 2: F(5,110) = 3.406, p = 0.030; Figure 3B; MRCaMKCre males and their controls: day 1: F(5,110) = 25.426, p,0.0001; day 2: F(5,110) = 16.049, p,0.0001; Figure 3C). ( g ( ) ( )) MRCaMKCre and MR-Tg female mice. Both MRCaMKCre 236.t002 Data represent mean 6 SEM. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCa MRCaMKCre; ,duration in exit quadrant vs average duration in other quadrants. Stimulus-response Learning C) Male MRCaMKCre mice take more time to locate the exit than controls on day 2. Bars show mean 6 SEM. *p,0.05 vs. control littermates. doi:10.1371/journal.pone.0086236.g003 Figure 3. Stimulus-response (S-R) task: latency to the exit hole over six training trials on two days. A) Female MR-Tg mice and controls have short and similar latencies to the exit hole. B) Female MRCaMKCre mice take more time to locate the exit than controls in trials 3 and 5 on day 1, and in all trials on day 2. C) Male MRCaMKCre mice take more time to locate the exit than controls on day 2. Bars show mean 6 SEM. *p,0.05 vs. control littermates. doi:10.1371/journal.pone.0086236.g003 bottle. We interpret a visit to the position of the exit hole of the previous trial as an indication that a mouse applied a spatial strategy to locate the exit hole. Therefore, for every trial we measured the latency to the previous exit hole, the latency to the quadrant of the previous exit hole and the percentage of time spent in this quadrant (Table 3). Latency to the spatial exit was comparable between MR-Tg females and their control littermates. MRCaMKCre females took longer to reach the quadrant of the spatial exit (p = 0.015) and spent less time in this quadrant (p = 0.018) while the latency to the spatial exit hole was similar to their controls (Table 4). MRCaMKCre males took significantly longer to reach the quadrant of the spatial exit hole (p = 0.042), spent less time in this quadrant (p = 0.043) and showed a trend of longer latency to the spatial exit hole than their controls (p = 0.095) (Table 4). On the first day of the S-R training, the time spent in the quadrant of the previous exit was significantly shorter for MRCaMKCre males and females than for the control littermates (males: F(1,22) = 7.615, p = 0.011; females: F(1,22) = 9.356, p = 0.006; Table 3). Latency to the quadrant of the previous exit was longer for MRCaMKCre female mice than for their control littermates (F(1,22) = 7.953, p = 0.010; Table 3) with no difference between MRCaMKCre male mice and controls. On the second day, latency to the previous exit hole was comparable between the MRCaMKCre mice and controls in both males and females. Stimulus-response Learning Latency to the exit hole and exit quadrant of the previous trial were also comparable between MR-Tg females and controls. Searching strategies and general activity in S-R trials. Searching strategies were defined as a way to find the exit hole, expressed by the order of holes visited. A serial hole visit was defined as visiting at least three adjacent holes in a row. Perseveration was defined as visiting the same hole twice in a row or with one other hole between the two holes. MRCaMKCre and MR-Tg female mice. On the first day, MRCaMKCre female mice visited less holes in a serial manner than their control littermates (% series: F(1,22) = 11.509, p = 0.003), while on the second day the genotypes had similar percentages of serial hole visits (Table 5). Both MR-Tg genotypes had a similar percentage of serial hole visits (Table 5). MRCaMKCre female mice moved slower than their controls on both days (velocity; day 1: F(1,22) = 14.592, p = 0.001; day 2: F(1,22) = 6.083, p = 0.022) and visited less holes on the first day (F(1,22) = 8.691, p = 0.007; Table 3). Velocity on both days and distance walked on the first day were similar between MR-Tg female mice and controls. On MRCaMKCre and MR-Tg female mice. On the first day, MRCaMKCre female mice visited less holes in a serial manner than their control littermates (% series: F(1,22) = 11.509, p = 0.003), while on the second day the genotypes had similar percentages of serial hole visits (Table 5). Both MR-Tg genotypes had a similar percentage of serial hole visits (Table 5). MRCaMKCre female mice moved slower than their controls on both days (velocity; day 1: F(1,22) = 14.592, p = 0.001; day 2: F(1,22) = 6.083, p = 0.022) and visited less holes on the first day (F(1,22) = 8.691, p = 0.007; Table 3). Velocity on both days and distance walked on the first day were similar between MR-Tg female mice and controls. On Long-term spatial memory in the S-R task. Before training in the S-R task, mice had received spatial training, with the exit in a fixed location in relation to the extra maze cues. These cues were still available in the S-R task, however now the exit was variable marked by a bottle, irrespective of spatial cues. We expected that spatial memory might influence the acquisition of the S-R task. Stimulus-response Learning Stimulus-response Learning Short-term spatial memory in the S-R task. In every trial the exit hole was in a different position and always marked by the Short-term spatial memory in the S-R task. In every trial the exit hole was in a different position and always marked by the Performance. One week after the spatial version of the CHB task, all animals were tested for stimulus-response (S-R) learning. Table 2. Behavioral parameters recorded during the spatial memory test 24 hours after six spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. Females Females Males Behavioral parameters MR-Tg Control MRCaMKCre Control MRCaMKCre Control General activity Distance moved (cm) 741649 741665 264629*$# 527668 512690 501660 Velocity (cm/s) 661 661 2.560*$# 4.561 461 461 Total hole visits 961 961 361*$# 962 862 861 Searching Latency to exit quadrant (s) 2167 3569 56615 21610 64615 30611 Duration in exit quadrant (s) 5066, 4067 5961,$ 6967, 2968 4768, Average duration in other quadrants (s) 2162 2362 1464$ 1363 2663 2163 Duration in holes zone (s) 4165 3563 2368*$# 4968 4667 4565 % Perseveration 1663 1363 563*$# 1764 1264 1163 Data represent mean 6 SEM. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female MRCaMKCre; ,duration in exit quadrant vs average duration in other quadrants. doi:10.1371/journal.pone.0086236.t002 Table 2. Behavioral parameters recorded during the spatial memory test 24 hours after six spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. Table 2. Behavioral parameters recorded during the spatial memory test 24 hours after six spatial training trials in MR-Tg and MRCaMKCre mice and their control littermates. January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 5 Mineralocorticoid Receptors in Learning Strategies PLOS ONE | www.plosone.org 6 January 2 January 2014 | Volume 9 | Issue 1 | e86236 January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org Mineralocorticoid Receptors in Learning Strategies Figure 3. Stimulus-response (S-R) task: latency to the exit hole over six training trials on two days. A) Female MR-Tg mice and controls have short and similar latencies to the exit hole. B) Female MRCaMKCre mice take more time to locate the exit than controls in trials 3 and 5 on day 1, and in all trials on day 2. Stimulus-response Learning Therefore, we measured the latency to the exit hole of the spatial task during the first trial of the first S-R training day. Table 3. Behavioral parameters (averaged over the day) recorded during the stimulus-response task in MR-Tg and MRCaMKCre mice and their control littermates. Females Females Males MR-Tg Control MRCaMKCre Control MRCaMKCre Control Day 1 Velocity (cm/s) 860 860 561*$ 861 761 861 Distance moved (cm) 367664 380659 296647 287648 313664 253646 Total hole visits 661 661 461* 561 561 561 %Perseveration 863* 462 764 662 362 363 Latency to previous exit quadrant (s) 48612 46612 72614* 47614 58615 51615 Duration in previous exit quadrant (s) 1864 1864 1365* 2365 1462* 2163 Day 2 Velocity (cm/s) 961 961 761* 961 761 861 Distance moved (cm) 213631* 253638 249651 213649 245646 207638 Total hole visits 361 461 361 361 361 361 %Perseveration 562* 562 362 262 362 362 Latency to previous exit quadrant (s) 51612 45611 48613 48614 55616 61616 Duration in previous exit quadrant (s) 1464 1263 1765 2264$ 1462 1061 Both days of the stimulus-response task consisted of six trials. Data represent mean 6 SEM of all trials of one day. For statistics a repeated measures ANOVA was used over the trials of one day. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female MRCaMKCre. doi:10.1371/journal.pone.0086236.t003 eters (averaged over the day) recorded during the stimulus-response task in MR-Tg and MRCaMKCre mice Both days of the stimulus-response task consisted of six trials. Data represent mean 6 SEM of all trials of one day. For statistics a repeated measures ANOVA was used over the trials of one day. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg; $male vs female MRCaMKCre. January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org 7 Mineralocorticoid Receptors in Learning Strategies Table 4. Spatial exit memory during the first trial of the stimulus-response task on day 1 (one week after the spatial memory test) in MR-Tg and MRCaMKCre mice and their control littermates. Behaviour in a Novel Environment and Learning Being exposed to the CHB after a life in a small cage with conspecifics is a challenge for the mouse. Exploration is the natural response. We and others [6,18,26,27], have shown that activation or blockade of MRs in rats and mice alters the exploration pattern and behavioral flexibility but not general activity measures. We here show that MR-overexpressing female mice showed an exploration pattern comparable to their control littermates, while MR-deficient male and female mice showed different exploratory behavior compared to controls without alterations in general Behavioral parameters Data represent mean 6 SEM. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #fem doi:10.1371/journal.pone.0086236.t004 stimulus-response learning requires more training trials [22,25]. In previous studies we had tested performance and the use of memory systems of mice with manipulated MR expression in a dual-solution CHB task. Pharmacological blockade of MR as well as MR deficiency led to deterioration of performance in naı¨ve non-stressed male mice [17–19]. However, in this design the selected strategies were mutually exclusive (animals had to choose between the two strategies), so that we did not know to what extent MR expression specifically influences the two systems. Thus, the impairment in performance could have been the result of a dysfunction of the hippocampus, a dysfunction of the dorsal striatum or both, or the coordination in the behavior-controlling network. the second day, the MR-Tg female mice walked less than the controls (distance; F(1,37) = 5.000, p = 0.031; Table 3). During both days of the stimulus-response task, MR-Tg female mice showed more perseveration than the controls (day 1: F(1,37) = 4.594, p = 0.039; day 2: F(1,37) = 8.390, p = 0.006; Table 3). MRCaMKCre male mice. Searching strategies were different between the genotypes in MRCaMKCre male mice. On the first day, MRCaMKCre males visited less holes in a serial manner than their control littermates (% series: F(1,22) = 19.489, p,0.0001), while on the second day the genotypes had similar percentages of serial hole visits (Table 5). In contrast to the females, general activity was comparable between genotypes for MRCaMKCre male mice. We report here that the expression of MRs is critical for both memory systems. Thus, forebrain MR-deficient female mice showed both an impaired spatial and stimulus-response learning, while MR overexpression resulted in opposite effects, i.e. improved spatial performance while stimulus-response learning was not improved, probably due to a ceiling effect. Performance deficits in both tasks were more strongly expressed in MR-deficient female than male mice, revealing and supporting a sex-dependent effect of MR deficiency. The opposite results of MR deficiency and MR overexpression confirm and substantiate the impact of MR on acquisition of novel information, not only for spatial but also for stimulus-response learning. Behavior and the Estrous Cycle We determined the stage of the estrous cycle in female mice by vaginal cytology after each behavioral task. We did not encounter the metestrus stage. The numbers of MRCaMKCre female mice and controls in the proestrus stage in all behavioral tasks were too low for test-statistics. The numbers of MR-Tg females and controls in the proestrus stage in the FET were too low for test-statistics. The estrus stage was well represented in all behavioral tasks in all groups. Given this uneven distribution, we opted for including the stage of the estrous cycle as a covariate in the one-way ANOVA and General Linear Model repeated measures analyses. These analyses did not support a significant contribution of estrous cycle on performance. Stimulus-response Learning Females Females Males Behavioral parameters MR-Tg Control MRCaMKCre Control MRCaMKCre Control Latency to spatial exit hole (s) 68612 82611 88614 71613 96611 64615 Latency to spatial exit quadrant (s) 38612# 38611 77616* 28610 73613* 36611 Duration in spatial exit quadrant (% of time on CHB) 3466 3666 2069* 5168 2366* 4568 Data represent mean 6 SEM. Behavioral parameters that differ significantly; p,0.05: *vs same sex control littermates; #female MRCaMKCre vs MR-Tg. doi:10.1371/journal.pone.0086236.t004 Table 4. Spatial exit memory during the first trial of the stimulus-response task on day 1 (one week after the spatial memory test) in MR-Tg and MRCaMKCre mice and their control littermates. MRs Involved in Stimulus-response Learning In rodents, stimulus-response learning takes longer and requires more training than spatial learning: they have to overcome their natural tendency to use a spatial strategy [22,25]. We expected that training the mice in the spatial version of the CHB task preceding training in the stimulus-response task might even amplify the difficulty in acquiring stimulus-response learning. On the other hand, due to prior training, the environment is familiar and mice have learned that there is an exit hole. With this prior experience they now have to learn that the exit hole is marked by an intramaze cue, the bottle, positioned at a different location every trial. Thus, again, mice had to be flexible and adapt to a novel situation. Will mice express a spatial bias to the fixed location of the exit hole learned during spatial training? C MKC Overall, behavior in the absence of functional MRs might represent a restriction of behavioral flexibility [18], while selective activation of MR allows adequate explorative behavior and adaptation. We reproduced an earlier finding [19] that MRCaMKCre female mice remain longer in the center during spatial training. Conversely, MR-overexpressing mice displayed more entries into the central area of an open field and had shorter latencies entering the light compartment of a light/dark task, which was labeled by others as reduced anxiety-related behavior [8]. This suggests that staying longer in the center as reported for the MRCaMKCre mice is due to enhanced anxiety. Yet, unconditioned anxiety was not observed in MRCaMKCre mice [7,10,18,23]. The behavior of MRCaMKCre mice may therefore also point to a different coping style. g p g As expected, the control littermates of the MRCaMKCre male and female mice and the MR-Tg mice and their control littermates showed a spatial tendency (more time in the spatial exit quadrant) in the first trial of the stimulus-response task. On the first day of training, controls of the MRCaMKCre mice used more serial searches and switched to a preference of the stimulus- response strategy on the second day. MR-Tg female mice showed more perseverations but a comparable low percentage of serial searches as their control littermates. The spatial tendency was absent in MRCaMKCre male and female mice, which could e.g. be explained by their poorer earlier performance in the spatial task or by a higher propensity to switch to the stimulus-response strategy. Novel Situation of Closed Exit Hole 24 Hrs after Spatial Learning Exposing the mice 24 hrs after six spatial trials to the CHB with the exit hole closed can be compared to a probe (free exploration trial) in the water maze. Latency to the exit hole reflects retention of spatial memory, but their behavior is also the response to this novel situation with no exit available. Similar latency to exit indicates that retention is comparable between the groups. Time to leave the center was comparable between the groups. Other measures provide a wealth of information. In the water maze task, the time spent in quadrant is mainly used to demonstrate the strength of spatial memory. Earlier studies in the water maze showed that MR-overexpressing male mice spent significantly more time during the probe trial in the target quadrant than control mice [8,27]. Is this strong memory or perseveration which could be another kind of coping with novelty? In the present study, control mice of all groups, spent most time in the target quadrant as do MRCaMKCre female and MR-Tg female mice. MRCaMKCre male mice spent a comparable amount of time in all quadrants. Latency to the target quadrant was shorter in all control groups and MR-Tg mice than in MRCaMKCre mice. Moreover, MRCaMKCre female mice had the lowest number of hole visits, spent the least time in the zone with holes and moved the shortest distance compared to all groups. This may reflect a similar difference in coping style as observed on the first day. Overall, the MRCaMKCre mice seem to lack the high degree of behavioral flexibility that is required for optimal performance in the stimulus-response task. Mineralocorticoid Receptors in Learning Strategies We tentatively conclude that spatial memory - when expressed by latencies - is not affected by MR. However, coping with a novel situation seems to depend on MR. activity: persistent revisits of holes in the male mice and longer time spent in the center before exploring the CHB in the female mice. These behaviours appear to be characteristic for MRCaMKCre mice, as they are in line with behavioral responses previously seen when MR-deficient mice were exposed to conditions of novelty [7,10,18,19]. After acute pharmacological inhibition of MR in rats goal-directed search strategies in a water maze task were absent [6]. In contrast, selectively activating MRs in adrenalectomized rats normalized the exploration pattern [26]. In line with MR effects in rodents, the few studies that were done in humans with pharmacological blockade of MR reported a deficit of selective attention and impairment of working memory [28,29] indicating difficulties in the acquisition of novel informa- tion. MRs Involved in Stimulus-response Learning However, we can rule out the latter possibility because we could not detect a stimulus-response strategy on either day. The MRCaMKCre mice simply took more time to solve the task. In contrast, MR-Tg mice were as fast as their control littermates. Since mice of all control groups perform well and the latency to the exit is short, we suggest a ceiling effect in performance, which may explain why we could not detect further improvement of MR-overexpressing mice. Even when subtracting the time in center from the overall latency to the exit hole, the latencies of MRCaMKCre mice were longer than in control mice. It is likely that the different exploration pattern of MR-deficient mice seen during the initial exposure to the CHB underlies or at least contributes to their impaired performance in the spatial and stimulus-response tasks. Processing of information from the environment is depending on the MR function, as shown by behavior 24 hrs after spatial learning and during the stimulus- response task. Performance of MR-deficient mice was impaired compared to MR-overexpressing mice, but comparable to their controls during that first stimulus-response trial. As revealed by analysis over the trials of the first day of stimulus-response training, the performance of control mice appears to be guided by spatial tendency, which was absent in the MR-deficient mice. Therefore, we propose that MR deficiency exerts a more general effect on behavior by inhibiting or delaying the adaptation to novel requirements. The current behavioral set-up did not allow to distinguish between a strong spatial tendency and reduced behavioral flexibility, as both will result in long latencies in the first stimulus-response trial after spatial training. C C Discussion To further delineate the role of MRs in spatial and stimulus- response learning we subjected mice either lacking or overex- pressing MRs in the forebrain to a spatial and stimulus-response learning task. Solving these tasks requires hippocampal and dorsal striatum memory systems, respectively. Spatial learning is the predominant form of learning in male rodents; acquisition of Table 5. Percentage of serial hole visits averaged over the trials of the two days of the stimulus-response task. Females Females Males Stimulus-response task MR-Tg Control MRCaMKCre Control MRCaMKCre Control Day 1 1966 1865 1467 2768* 1867 3869* Day 2 1165 1465 1366 1666 1166 1166 Both days of the stimulus-response task consisted of six trials. Data represent mean 6 SEM of all trials of one day. For statistics a repeated measures ANOVA was used over the trials of one day. *Significantly different between genotypes of the same group over the day; p,0.05. doi:10.1371/journal.pone.0086236.t005 tage of serial hole visits averaged over the trials of the two days of the stimulus-response task. Table 5. Percentage of serial hole visits averaged over the trials of the two days of the stimulu January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org 8 Mineralocorticoid Receptors in Learning Strategies January 2014 | Volume 9 | Issue 1 | e86236 Memory Systems, Glucocorticoids and MR: Human Studies Memory Systems, Glucocorticoids and MR: Human Studies Previous research showed that glucocorticoids are involved in the stress-induced shift from hippocampus-dependent to dorsal striatum-dependent learning. In human studies, this role of glucocorticoids was extended from navigational to other forms of learning [21,36,37]. Recently, Schwabe et al. suggested that the relationship between glucocorticoid concentrations and the use of different memory systems may not be linear but more likely in the shape of an inverted u-shaped curve [37,38]. This reasoning is based on findings that humans exhibiting high stress-induced cortisol responses used more stimulus-response learning [39], while spatial learners had higher basal cortisol concentrations [40] and pharmacological elevations of cortisol led to use of more spatial learning [41]. Schwabe et al. discussed that functioning of the hippocampus and dorsal striatum may be affected differently by low, moderate and high levels of glucocorticoids, and thus, allowing different memory systems to be in control of behavior [37,38]. Also here we might deal with a differential contribution of MR and GR to the behavioral effects which have not been entangled yet. In addition to the overall sex-dependent differences, the phase of the estrous cycle may influence the behavior of female mice [19,20,34]. Recently we reported a specific interaction between MR and female sex hormones [19]. MRCaMKCre females showed impaired performance in the dual-solution CHB task specifically in the proestrus and estrus phase of the cycle. The phase of the estrous cycle had no effect on performance of C57Bl/6j and control littermates of MRCaMKCre female mice [19]. Due to the relatively low numbers per cycle stage, we could not incorporate the data on the estrus phases in the current study, which is a limitation. However, introducing the cycle stage as a co-variate in our analysis did not affect the outcome. Recently, blockade of MR was reported to prevent the stress- induced shift from hippocampal towards dorsal striatum-depen- dent learning in a classification task in humans, underlining the importance of MR for the use of multiple memory systems [42]. Furthermore, stress-induced facilitation of inhibitory control in a stop-signal task in humans was reported to depend on MR functioning, indicating that MRs are important for the balance between inhibition and excitation that underlies adaptive behavior [43]. Influence of Task-dependent Characteristics on Behaviour Previous studies using the dual-solution CHB and water maze tasks reported impaired performance, predominantly delayed learning, in MRCaMKCre male mice [7,18]. In the present study, MRCaMKCre male mice performed comparable to control mice. Task-specific characteristics might have influenced the perfor- mance in several ways. First, for mice the water maze is a more stressful task than a dry land maze task such as the CHB [30,31]. Acute stress impaired the performance of control mice in the dual- Task-specific characteristics might have influenced the perfor- mance in several ways. First, for mice the water maze is a more stressful task than a dry land maze task such as the CHB [30,31]. Acute stress impaired the performance of control mice in the dual- January 2014 | Volume 9 | Issue 1 | e86236 January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org 9 Mineralocorticoid Receptors in Learning Strategies [7,10], but also elevated basal corticosterone levels have been reported [18]. A fast increase of corticosterone in response to stress indicates the lack of MR-dependent inhibitory control of the HPA axis and apparently more efficient negative feedback can be deduced from lower corticosterone measured directly after training in a circular holeboard task [18]. Elevated basal corticosterone in MR-deficient mice might reflect the sensitivity of the HPA axis to subtle environmental changes, which are under inhibitory control of MR in control mice. MR-overexpressing mice and their control littermates had comparable basal cortico- sterone levels and showed a comparable corticosterone response to restraint stress [8]. Like previously reported, we expect that the mice in the present study also show this initial MR-dependent disinhibition the HPA axis resulting in elevated concentrations of corticosterone. solution and spatial CHB task [17,22]. Interestingly, acute stress did not further impair performance of MRCaMKCre male mice in the dual-solution CHB task [18]. Second, the dual-solution version of the CHB task provides both intramaze and spatial cues. Since more cues are available, this requires a fine tuned coordination of hippocampal and dorsal striatal memory systems. The coordina- tion of memory systems might be affected by MR deficiency, resulting in delayed learning. In contrast to the MR-deficient mice, MR-overexpressing male mice showed no difference in spatial learning in water maze and Y-maze tasks [8,27]. Influence of Task-dependent Characteristics on Behaviour Moreover, a rather selective method, namely viral-mediated overexpression of MR in the hippocampus in male rats caused no differences in spatial performance in a water maze task [32]. The findings in MR-overexpressing mice suggest that the behavioral parameters of the tasks might not be sensitive enough to measure MR effects. Alternatively, we may conclude that MR manipulations do not directly affect the memory process. If and how these different-to-control corticosterone concentra- tions in MR-mutant mice affect and act via GRs: we don’t know yet. The characteristics and action of GR (low affinity, fast feedback) indicate an involvement of GR in MR-deficient mice in a time domain different from control mice. GRs are involved in HPA axis regulation and stress effects on cognition, specifically supporting memory consolidation [6,11–13]. GR mRNA is increased in the hippocampus of MRCaMKCre mice; however their memory is not improved [18]. GR mRNA and basal corticoste- rone levels in MR-Tg mice are comparable to controls, as is their memory [8]. Therefore, we cannot exclude that deficits in spatial and stimulus-response performance in the MR-deficient mice are linked to increased circulating basal corticosterone levels that may act via GR. Are Female Mice More Sensitive than Males to Changing Environments? Male C57Bl/6j mice and control littermates of MRCaMKCre male mice solve the dual-solution CHB task by using a spatial strategy, while female C57Bl/6j and control littermates of MRCaMKCre female mice use both, spatial and stimulus-response strategies [18–21]. MR deficiency led to impaired spatial performance in MRCaMKCre female mice, while the effect was less apparent in MRCaMKCre male mice. Similar results were found in other learning tasks. For example, MRCaMKCre female mice were unable to extinguish the contextual fear memory and could not discriminate between cue and context episodes of the task, while no effects of MR ablation were found in MRCaMKCre male mice [23]. In a radial arm maze task, MRCaMKCre female mice made more errors than males [7]. Sex-dependent differences in performance were aggravated by acute stress: male mice switched from a spatial to a stimulus-response strategy, while female mice switched to a spatial strategy [17,33]. These observations are in line with our present findings and underline that using subjects of both sexes increases the likelihood to detect effects of the experimental manipulation. In general, variations in MR appear to affect females more explicitly than males. Memory Systems, Glucocorticoids and MR: Human Studies Although the use of MR (and GR antagonists) contributes to the understanding of the function of either receptor, we are still confronted by the fact that the blockade of MR (or deficiency of MR) increases corticosterone concentrations that should allow the activation of GR. January 2014 | Volume 9 | Issue 1 | e86236 References 23. ter Horst JP, Carobrez AP, van der Mark MH, de Kloet ER, Oitzl MS (2012) Sex differences in fear memory and extinction of mice with forebrain-specific disruption of the mineralocorticoid receptor. Eur J Neurosci 36: 3096–3102. 1. de Kloet ER, Joe¨ls M, Holsboer F (2005) Stress and the brain: From adaptation to disease. Nat Rev Neurosci 6: 463–47. 2. Joe¨ls M, Krugers HJ, Lucassen PJ, Karst H (2009) Corticosteroid effects on cellular physiology of limbic cells. Brain Res 1293: 91–100. p p J 24. Casanova E, Fehsenfeld S, Mantamadiotis T, Lemberger T, Greiner E, et al. (2001) A CamKIIalpha iCre BAC allows brain-specific gene inactivation. Genesis 31: 37–42. 3. Reul JM, de Kloet ER (1985) Two receptor systems for corticosterone in rat brain: Microdistribution and differential occupation. Endocrinology 117: 2505– 2511. 25. Packard MG, McGaugh JL (1996) Inactivation of hippocampus or caudate nucleus with lidocaine differentially affects expression of place and response learning. Neurobiol Learn Mem 65: 65–72. 4. de Kloet ER, Oitzl MS, Joe¨ls M (1999) Stress and cognition: Are corticosteroids good or bad guys? Trends Neurosci 22: 422–426. g 26. Oitzl MS, Fluttert M, de Kloet ER (1994) The effect of corticosterone on reactivity to spatial novelty is mediated by central mineralocorticosteroid receptors. Eur J Neurosci 6: 1072–9. 5. Joe¨ls M, Karst H, de Rijk R, de Kloet ER (2008) The coming out of the brain mineralocorticoid receptor. Trends Neurosci 31: 1–7. 5. Joe¨ls M, Karst H, de Rijk R, de Kloet ER (2008) The 6. Oitzl MS, de Kloet ER (1992) Selective corticosteroid antagonists modulate specific aspects of spatial orientation learning. Behav Neurosci 106: 62–71. p J 27. Harris AP, Holmes MC, de Kloet ER, Chapman KE, Seckl JR (2013) Mineralocorticoid and glucocorticoid receptor balance in control of HPA axis and behaviour. Psychoneuroendocrinology 38: 648–58. specific aspects of spatial orientation learning. Behav Neuro 7. Berger S, Wolfer DP, Selbach O, Alter H, Erdmann G, et al. (2006) Loss of the limbic mineralocorticoid receptor impairs behavioral plasticity. Proc Natl Acad Sci USA 103: 195–200. y gy 28. Cornelisse S, Joe¨ls M, Smeets T (2011) A randomized trial on mineralocorticoid receptor blockade in men: Effects on stress responses, selective attention, and memory. Neuropsychopharmacology 36: 2720–8. 8. Lai M, Horsburgh K, Bae S, Carter RN, Stenvers DJ, et al. (2007) Forebrain mineralocorticoid receptor overexpression enhances memory, reduces anxiety and attenuates neuronal loss in cerebral ischaemia. References Packard MG, Knowlton BJ (2002) Learning and memory functions of the basal ganglia. Annu Rev Neurosci 25: 563–593. 37. Schwabe L, Wolf OT (2013) Stress and multiple memory systems: From ‘thinking’ to ‘doing’. Trends Cogn Sci 17: 60–68. 16. Lee AS, Duman RS, Pittenger C (2008) A double dissociation revealing bidirectional competition between striatum and hippocampus during learning. Proc Natl Acad Sci 105: 17163–17168. 38. Schwabe L (2013) Stress and the engagement of multiple memory systems: integration of animal and human studies. Hippocampus 23: 1035–1043. 17. Schwabe L, Scha¨chinger H, de Kloet ER, Oitzl MS (2010) Corticosteroids operate as a switch between memory systems. J Cogn Neurosci 22: 1362–72. 39. Schwabe L, Oitzl MS, Philippsen C, Bo¨hringer A, Richter S, et al. (2007) Stress modulates the use of spatial and stimulus-response learning strategies in humans. Learn Mem 14: 109–116. 18. ter Horst JP, van der Mark MH, Arp M, Berger S, de Kloet ER, et al. (2012) Stress or no stress: Mineralocorticoid receptors in the forebrain regulate behavioral adaptation. Neurobiol Learn Mem 98: 33–40. J p g ( ) Stress or no stress: Mineralocorticoid receptors in the forebrain regulate behavioral adaptation. Neurobiol Learn Mem 98: 33–40. 40. Bohbot VD, Gupta M, Banner H, Dahmani L (2011) Caudate nucleus- dependent response strategies in a virtual navigation task are associated with lower basal cortisol and impaired episodic memory. Neurobiol Learn Mem 96: 173–180. 19. ter Horst JP, Kentrop J, Arp M, Hubens CJ, de Kloet ER, et al. (2013) Spatial learning of female mice: A role of the mineralocorticoid receptor during stress and the estrous cycle. Front Behav Neurosci. 41. Schwabe L, Oitzl MS, Richter S, Scha¨chinger H (2009) Modulation of spatial and stimulus-response learning strategies by exogenous cortisol in healthy young women. Psychoneuroendocrinology 34: 358–366. 20. ter Horst JP, Kentrop J, de Kloet ER, Oitzl MS (2013) Stress and estrous cycle affect strategy but not performance of female C57BL/6J mice. Behav Brain Res 241: 92–95. 42. Schwabe L, Tegenthoff M, Ho¨ffken O, Wolf OT (2013) Mineralocorticoid receptor blockade prevents stress-induced modulation of multiple memory systems in the human brain. Biol Psychiatry 74: 801–808. 21. Schwabe L, Dalm S, Scha¨chinger H, Oitzl MS (2008) Chronic stress modulates the use of spatial and stimulus-response learning strategies in mice and man. Neurobiol Learn Mem 90: 495–503. 43. References Eur J Neurosci 25: 1832– 1842. 29. Otte C, Moritz S, Yassouridis A, Koop M, Madrischewski AM, et al. (2007) Blockade of the mineralocorticoid receptor in healthy men: Effects on experimentally induced panic symptoms, stress hormones, and cognition. Neuropsychopharmacology 32: 232–8. 9. Zhou M, Bakker EHM, Velzing EH, Berger S, Oitzl M, et al. (2010) Both mineralocorticoid and glucocorticoid receptors regulate emotional memory in mice. Neurobiol Learn Mem 94: 530–537. 30. Dalm S, Schwabe L, Schachinger H, Oitzl MS (2009) Post-training self administration of sugar facilitates cognitive performance of male C57BL/6J mice in two spatial learning tasks. Behav Brain Res 198: 98–104. 10. Brinks V, Berger S, Gass P, de Kloet ER, Oitzl MS (2009) Mineralocorticoid receptors in control of emotional arousal and fear memory. Horm Behav 56: 232–238. 31. Whishaw IQ, Tomie J (1997) Of mice and mazes: Similarities between mice and rats on dry land but not water mazes. Physiol Behav 60: 1191–1197. D S l k R ( ) O i f i l i id d 11. Lupien SJ, McEwen BS (1997) The acute effects of corticosteroids on cognition: Integration of animal and human model studies. Brain Res Rev 24: 1–27. 32. Ferguson D, Sapolsky R (2008) Overexpression of mineralocorticoid and transdominant glucocorticoid receptor blocks the impairing effects of glucocor- ticoids on memory. Hippocampus 18: 1103–1111. 12. Sandi C, Rose SPR (1994) Corticosterone enhances long-term retention in one- day-old chicks trained in a weak passive avoidance learning paradigm. Brain Res 647: 106–112. 33. Bettis TJ, Jacobs LF (2009) Sex-specific strategies in spatial orientation in C57BL/6J mice. Behav Processes 82: 249–255. J 34. ter Horst JP, de Kloet ER, Scha¨chinger H, Oitzl MS (2012) Relevance of stress and female sex hormones for emotion and cognition. Cell Mol Neurobiol 32: 725–35. 13. Roozendaal B, McReynolds JR, Van der Zee EA, Lee S, McGaugh JL, et al. (2009) Glucocorticoid effects on memory consolidation depend on functional interactions between the medial prefrontal cortex and basolateral amygdala. J Neurosci 29: 14299–14308. 35. Oitzl MS, Champagne DL, van der Veen R, de Kloet ER (2010) Brain development under stress: Hypotheses of glucocorticoid actions revisited. Neurosci Biobehav Rev 34: 853–866. 14. White NM, McDonald RJ (2002) Multiple parallel memory systems in the brain of the rat. Neurobiol Learn Mem 77: 125–184. 36. Schwabe L, Wolf OT (2012) Stress modulates the engagement of multiple memory systems in classification learning. J Neurosci 32: 11042–11049. 15. Acknowledgments We are grateful to S. Berger and G. Schutz, German Cancer Institute, Heidelberg, Germany and A. Fitch and J. Seckl, University of Edinburgh, U.K., for providing the original breeding stock of the MR mutant mice in 2008. Two Receptors for Adaptive Behavior: MR and GR Two Receptors for Adaptive Behavior: MR and GR Adaptive behavior depends on balanced MR and GR activation [1,35]. As documented previously [6,7,10,18] and extended by our current observations, MRs modulate the behavioral response pattern in novel situations. We cannot estimate the number of MRs that is necessary to induce the changes observed in MR- overexpressing mice. Lai et al (2007) report a brain-site-dependent increase of MR mRNA of 4 to 10 times in MR-Tg mice. MR deficiency in the forebrain affects the regulation of the hypothalamic-pituitary-adrenal (HPA) axis. Basal corticosterone levels of MR-deficient mice are either comparable to controls January 2014 | Volume 9 | Issue 1 | e86236 January 2014 | Volume 9 | Issue 1 | e86236 PLOS ONE | www.plosone.org 10 Mineralocorticoid Receptors in Learning Strategies In summary: our current study demonstrates that MRs are relevant for spatial as well as stimulus-response learning. Deficits in both tasks were more strongly expressed in MR-deficient female than male mice, revealing and supporting a sex-dependent effect. We suggest that the common nominator of MR effects can be represented as behavioral flexibility which requires a critical balance between inhibitory and excitatory systems. The conse- quences of corticosteroid actions via MR can be observed at different levels, e.g., the switch between memory systems, strategies, selective attention, performance. In this manner MRs influence and coordinate the processing of information particularly under novel conditions, which is fundamental for behavioral adaptation. Author Contributions Conceived and designed the experiments: JMA JPTH MJ HJK MSO GF. Performed the experiments: JMA. Analyzed the data: JMA JPTH MSO. Contributed reagents/materials/analysis tools: JMA SK MSO. Wrote the paper: JMA JPTH MJ HJK MSO. References Schwabe L, Ho¨ffken O, Tegenthoff M, Wolf OT (2013) Stress-induced enhancement of response inhibition depends on mineralocorticoid receptor activation. Psychoneuroendocrinology 38: 2319–2326. 22. Schwabe L, Scha¨chinger H, de Kloet ER, Oitzl MS (2010) Stress impairs spatial but not early stimulus–response learning. Behav Brain Res 213: 50–55. PLOS ONE | www.plosone.org January 2014 | Volume 9 | Issue 1 | e86236 January 2014 | Volume 9 | Issue 1 | e86236 11
https://openalex.org/W3119237624
https://zenodo.org/records/1816774/files/article.pdf
English
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The Flashing Arcs
Scientific American
1,912
public-domain
2,272
The Flashing Arcs * A V olcanic Phenomenon By Frank A. Perret ON the afternoon of April 7th, 1906, the present writer, in company with Prof. Matteucci, was skirting the southern flank of Vesuvius on a trip to the main source of the lava at the Bosco Cognoli. The volcano at this time was entering one of those paroxysmal phases by which the eruption-already three days old -worked progressively up to its gre8Jt culmination, which occurred, it will be remembered, between this and the following day. The ejected detritus was of a mixed nature, viz., the fresh lava, clear red in full day­ light, being mingled with old material from the upper portions of the cone, then in process of rapid demoli­ tion. The frequency of the explosions varied from approximately one every three or four seconds to at least three per second. Although powerful, they were very sharp and sudden in their nature, and at the in­ stant of each-but before it could be sensed by the eye or ear_ thin, luminous arc flashed upward and outward from the crater and disappeared in space. Then came the sound of the explosion and the projec­ tion of gas and detritus above the lip of the crater. The motion of translati'On of the arcs, while very rapid in comparison with that of the detritus, was not above the limits of easy observation and there could be no doubt as to the reality of the phenomenon, which was repeated some hundreds of times. the viewpoint rendered them more difficult of observa­ tion than at Vesuvius. Some fifteen were clearly seen by us, all the stronger explosions producing them. h forces were thus so subdivided and distributed that no very large cones of scorire were built up, many of the craters being little more than holes in the ground. One of these, although larger ·than the average, was so perfectly free from surrounding di!bris that a post- What is the nature of this phenomenon? The only hypothesis which seems in accord with the observed characteristicLj forth a proposition which, at first thought, may seem almost startling, viz., that we have to do with vi8ible 80und wave8. According to some far from accurate measurements made on the spot the velocity of propagation of the arcs 8eemed to corre­ spond with that of sound. The Flashing Arcs * We may certainly assume the outburst to be spherical or at all events globular, as though a huge soap bubble were rapidly blown from the crater and that the edge alone is visible and therefore appears from any point of view as an arc. The movement of this visible portion will therefore be at right angles to the line of sight and the arrival of the sound-from the crater radially to the oserver­ illUSt be compared with the arrival of the arc at some point equidistant from the crater but at right aJ,lgles to this radius. As the arcs rapidly fade into invisi­ bility with increasing distance from their source the difficulty of accurate" measurement will seem to be very great. Fig. 1.-Circles Indicate the Appearance of the Arcs. But if we attack the problem by the way of ex­ clusion we shall find, I believe, that the velocity­ even assigning to it values having a considerable mar­ gin above or below that of sound-ellD be made to harmonize with no other mode of motion. Actual illass movement, L e., motion of translation of any material, solid, liquid or gaseous, is negatived by the flashing of the arcs amid the relatively slowly rising and perfectly undisturbed volutes of vapor and detritus as well as by their Jlirection of propagation, which is outward and downward as well as upward. On the other hand, any attempt at explanation on the basis of Hertzian or electromagnetic effects, due possibly to stress relief, etc., must also b.e excluded on the speed basis, which now becomes much too low. fi The writer attempted photography but without suc­ cess, the failure being due in part, perhaps, to the velocity of the arcs and their very moderate bright­ ness, but also most certainly to the extreme unlikeli­ hood of the shutter being snapped at the precise in­ stant of the apparition. One of the photographs is reproduced in Fig. The Flashing Arcs * 1, and I have permitted myself to trace upon the negative film with aniline two circles which print out in the approximllJte appearance of the arcs, assuming these to have been arrested In­ stantaneously during their up- and out-springing form the crater.' It should be stated that this illustra­ tion, because of its crud_eness and the lack of motion, conveys but a poor idea of the actual phenomenon, the beauty of which lies in the delicate luminosity, the elegance and perfection of form, and the grace and vivacity of the arcs amid the contrasting color and relatively sluggish movement of their surroundings. y Fig. 1.-Circles Indicate the Appearance of the Arcs. Fig. 2.-Bomb Thrown Out in Etna Eruption. After all is said, is there any real difficulty in ac­ counting for the flashing arcs on the basis of the pro­ posed hypothesis? Sound is propagated in air by compressional-rarefactional waves projected normally. The conditions for the production of the arcs are sudden explosions on a large scale. Given these in sufficiency, may we l\Dt imagine that in the resulting aerial condensational·rarefactional wavljr sheet of superposed waves"':"the refractive and reflective indices will be so altered as"to form in bright daylight a zone visible by contrast, NJpecially when viewed longitudin­ ally, L e., thrOUgh· tile edges of the transparent sphere? We are familiar with the visibility by contrast of the refrangibilityot bot and oold air, and it would seem that mechanicallY engendered compressional-rarefac­ tional aerials. waves should be visible in the same manner if sufficiently accentuated. It is a question of the degree of condensation and rarefaction, and this evidently depends directly on the power and inversely on the time factor. The proposition will be more truly scientific and possiblY more acceptable if stated thus: An explosion propagates normal condensational-rare­ factional waves in air-these are perceived by the ear as sound, and may also be visible by unequal refraction when sufficiently powerful. h During the extraordinary activity of Stromboli in 1007 the wrdžter did not observe the flashing arcs al­ though some of the explosions appeared to have the quaiities which should have produced them, but the place of observation was probably too near the crater. The small eruption of Etna in 1908 was not observed, but the conditions were not, in my opinion, such as to have reproduced the phenomenon. The Flashing Arcs * At Teneriffe in 19(1), although incandescent lava was still available tor research work upon my arrival, the 'explosive ef­ fects, which had been powerful, were virtually at an end, and it was therefore with the greatest delight that during the 1910 ernption of Etna I again observed the flashing arcs. are Fig. 2.-Bomb Thrown Out in Etna Eruption. erupti'On visitor might well have been pardoned for considering it the least important of the entire series. It was, however, the seat of all the heavier explosions, each of which hurled one or two bombs of stiff, in­ candescent lava to a considerable distance, but without any accompaniment of ash or other detritus. On the morning of March 30th bombs as large as a meter in diameter were ejected (Fig. 2), anLJ these explosions produced the tlashing arcs which were in all respects identical with those of Vesuvius. Until they were pointed out to him my guide did not observe them, and it is quite possible that I myself might not have seen them had I not known what to look for, as the absence of a darker setting and the lesser distance of erupti'On visitor might well have been pardoned for considering it the least important of the entire series. It was, however, the seat of all the heavier explosions, each of which hurled one or two bombs of stiff, in­ candescent lava to a considerable distance, but without any accompaniment of ash or other detritus. On the morning of March 30th bombs as large as a meter in diameter were ejected (Fig. 2), anLJ these explosions produced the tlashing arcs which were in all respects identical with those of Vesuvius. Until they were pointed out to him my guide did not observe them, and it is quite possible that I myself might not have seen them had I not known what to look for, as the absence of a darker setting and the lesser distance of lhs By a rare good fortune the explosions in this case were almost without detritus, thus forming a condition the very opposite to that at Vesuvius in 1906. It will be remembered that this eruption of Etna produced a tlssure tW'O kilometers in length over which were formed some twenty-four ,small craters. .lteproduced from the American Jovmal 01 801ef1ce. • It JII&1 be that I haTe centered the ekcJea too high aboTe the crater. SCIENTIFIGAMERlCAN SUPPLEMENT The con­ clusion reached by Sir Charles Parsons and expressed in the course of that discussion is, however, worth notice. He said: "With the geared turbine and 100 degrees of superheat the cost of running a vessel with coal at 15 shillings a ton would be the same as with the Diesel engine with oil at 23 shillings (per ton)." If this estimate is correct, and there is no reason to doubt it, then the chances of the extensive use of geared turbines in future tramp steamers should be good; because there seems no probability of an approxi­ mation being made to such a low price of oil, particu­ larly if very large quantities of oil were required for marine propulsion. As regards the necessity for or the desirability of having something in the nature of a "floating frame," it may be said that no similar arrangement has been fitted hitherto with Parsons geared turbb1es, nor has there been any evidence in these vessels that elasticity in the bearing is necessary or important for the auto­ matic elimination of unequal tooth pressures. Whether or not with very large powers some such elasticity in the bearings may prove desirable is a matter which will be decided by experience. If there should be evidence that such elasticity is c)esirable it can be provided read­ ily; but experience up' to date, and with powers much exceeding the power installed in the collier "Neptune," shows that the Parsons system of gearing has been successfully applied and worked for long periods with­ out any such feature having been found necessary. PREVENTION OF NOISE AND WEAR. Prof. Biles, in his paper on the new Southwestern Railway steamers, said that the trials of the "Nor­ mania," "proved to those who were on board that the anticipation that the noise of the gearing would be negligible was a correct . one," and it is understood SCIENTIFIGAMERlCAN SUPPLEMENT November 28, 1912 824 that subsequent experience on service has confirmed that favorable verdict. In other cases where geared turbines have been used experience has been equally favorable, and with well cut mechanical gearing run­ ning in oil there should be no trouble from this cause. c From the foregoing statement it appears that the present position in regard to the employment of quick­ running turbines in association with reduction gear is one of great interest; and it may be hoped that many questions will soon be settled by experience which are for the time being necessarily matters of opinion and estimate. Whatever system may prove the best and most efficient on the whole, the conclusion is inevitable that by the use of some reducing gear a still further step will be made possible In the association of light­ ness with the development of power in marine propell­ ing apparatus and in economy of steam and fuel con­ sumption in war fleets and in the mercantile marine. 'In the case of cargo steamers of moderate and low speed it also appears probable that geared turbines will find· employment, although the competition of the internal combustion engine, and of the Diesel engine in particular, in vessels of this class and of low power, may play an important part. It is unnecessary to en­ large on this aspect of the question because those in­ terested therein will find it fully discussed in the Proceeding8 of the Northeast Coast Institution of Engi­ neers and Shipbuilders for the current year. The con­ clusion reached by Sir Charles Parsons and expressed in the course of that discussion is, however, worth notice. He said: "With the geared turbine and 100 degrees of superheat the cost of running a vessel with coal at 15 shillings a ton would be the same as with the Diesel engine with oil at 23 shillings (per ton)." If this estimate is correct, and there is no reason to doubt it, then the chances of the extensive use of geared turbines in future tramp steamers should be good; because there seems no probability of an approxi­ mation being made to such a low price of oil, particu­ larly if very large quantities of oil were required for marine propulsion. Proceeding8 of the Northeast Coast Institution of Engi­ neers and Shipbuilders for the current year. © 1912 SCIENTIFIC AMERICAN, INC, .lteproduced from the American Jovmal 01 801ef1ce. The Flashing Arcs * The explosive As observed by the writer at Vesuvius and Etna, the flashing arcs may be considered one of the most beautiful of all volcanic phenomena. © 1912 SCIENTIFIC AMERICAN, INC,
https://openalex.org/W2614362879
https://europepmc.org/articles/pmc5465768?pdf=render
English
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Development of indirect enzyme-linked immunosorbent assay for diagnosis of canine leptospirosis
Veterinary world/Veterinary World
2,017
cc-by
4,600
Copyright: Sathiyamoorthy, 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. Veterinary World, EISSN: 2231-0916 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf Veterinary World, EISSN: 2231-0916 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf RESEARCH ARTICLE Open Access Abstract Aim: This study was taken up to develop an indirect enzyme-linked immunosorbent assay (i-ELISA) for scr against Leptospira spp. in canines. Aim: This study was taken up to develop an indirect enzyme-linked immunosorbent assay (i-ELISA) for screening antibodies against Leptospira spp. in canines. Materials and Methods: An i-ELISA was developed using outer membrane protein extracted from Leptospira interrogans serovar canicola used for coating the well with concentration of 0.5 µg/µl. A total of 250 serum samples from clinically affected and apparently healthy dogs were collected along with relevant epidemiological data at Teaching Veterinary Clinical Complex, Veterinary College and Research Institute, Namakkal, and subjected to i-ELISA. Results: Out of 250 sera samples, 140 (56.00%) were found to be positive by i-ELISA. All the sera samples were subjected to microagglutination test (MAT) with panel of 12 different serovars. A total of 71 (28.40%) sera samples were positivity to MAT excluding the sera samples positive to L. interrogans serovars canicola and icterohaemorrhagiae in vaccinated dogs. Sensitivity and specificity of i-ELISA were higher in compared with MAT was 91.54% and 58.10%, respectively. Conclusion: An indirect ELISA developed for the detection of canine antileptospiral antibodies proved to be highly sensitive, rapid and easy to perform and overcome the drawbacks of MAT. Keywords: canine leptospirosis, indirect enzyme-linked immunosorbent assay, outer membrane protein, Leptospira canicola, Triton X-114 extraction. A. Sathiyamoorthy, G. Selvaraju, K. M. Palanivel and P. Srinivasan Department of Veterinary Preventive Medicine, Veterinary College and Research Institute, Namakkal - 6 Tamil Nadu, India. erinary Preventive Medicine, Veterinary College and Research Institute, Namakkal - 637 002, Tamil Nadu, India. Corresponding author: A. Sathiyamoorthy, e-mail: sathiyavet@gmail.com, Co-authors: GS: selvabhuvana@gmail.com, KMP: drkmpalanivel@gmail.com, PS: srinipat200 Corresponding author: A. Sathiyamoorthy, e-mail: sathiyavet@gmail.com, Co-authors: GS: selvabhuvana@gmail.com, KMP: drkmpalanivel@gmail.com, PS: srinipat2004@yahoo.co Co-authors: GS: selvabhuvana@gmail.com, KMP: drkmpalanivel@gmail.com, PS: srinipat2004@yahoo.com Received: 20-10-2016, Accepted: 04-04-2017, Published online: 20-05-2017 ors: GS: selvabhuvana@gmail.com, KMP: drkmpalanivel@gmail.com, PS: srinipat2004@yahoo.com Received: 20-10-2016, Accepted: 04-04-2017, Published online: 20-05-2017 @g , p @g , p @y Received: 20-10-2016, Accepted: 04-04-2017, Published online: 20-05-2017 doi: 10.14202/vetworld.2017.530-535 How to cite this article: Sathiyamoorthy A, Selvaraju G, Palanivel KM, Srinivasan P (2017) Development of indirect enzyme-linked immunosorbent assay for diagnosis of canine leptospirosis, Veterinary World, 10(5): 530-535. Introduction serovar specific antibodies against Leptospira spp. [10] with high sensitivity and specificity. However, it has the following disadvantages: (i) Facilities for culturing and maintaining live leptospires are needed; (ii) the method is technically demanding and time consum­ ing, particularly when the panel is large; (iii) antibod­ ies may not be detectable when the causative strain is not represented in the panel or only low titer is found; (iv) the microagglutination test (MAT) can­ not be standardized because live leptospires are used as antigen [11]. Immunosorbent assay simple, safe, specific, sensitive, easily automated, and suitable for the examination of a large number of sera samples in the diagnosis of Canine leptospirosis. Indirect ELISA can detect genus specific antibody but MAT does not detect [12,13]. Leptospirosis has been recorded in dogs throughout the major continents of the world [1-8]. Leptospirosis is a widespread zoonotic disease and is a real public health concern around the world. The dis­ ease is caused by spirochetes of the genus Leptospira, which comprises more than 300 serovars classified under 25 serogroups based on agglutinating antigens and is classified into multiple genom species based on DNA studies. The diagnosis of this disease is done mainly by dark microscopic examination and by isolation of these microorganisms. The microscopic examination is done using dark-field microscopy and aids in the early diagnosis of the disease. However, it has two major drawbacks: (i) Too low concentration of lepto­ spires (<104 cells/ml) which may not be detected and (ii) artifacts such as fibrin and extrusions from cellu­ lar elements can be easily mistaken for Leptospira by inexperienced workers [9]. Microscopic agglutination test can be used as the gold standard test for screening The purpose of this study was to develop an indi­ rect ELISA to be used as an initial screening test for the detection of the genus-specific antibodies against Leptospira in canine sera. The specificity and sensi­ tivity of the indirect ELISA relative to the MAT were estimated. Characterization of OMP by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) The protein profile of OMP of L. interrogans serovar canicola was carried out using a denaturat­ ing SDS-PAGE according to the method described by Laemmli [15] in a vertical electrophoresis apparatus. Amrutha et al. [16] observed 22.5, 29, 36, 43, 77, 93 and 112 kDa as major bands of OMP of L. canicola by SDS-PAGE. Indirect ELISA A 0.5 µg antigen in carbonate and bicarbonate buffer was coated onto each well by incubating at 4°C overnight. On the next day, the plates were washed five times with PBS with 0.05% Tween 20. 100 µl of 5% skim milk powder was added to block the uncoated sites and incubated at 37°C for 1 h. The plates were washed as above and 100 µl of 1:50 diluted test serum samples was added to individual wells in duplicates followed by incubation at 37°C for 1  h. Then, the plates were washed and 100 µl of 1:10000 diluted rabbit anti-dog HRPO conjugate was added to all the Institute, Namakkal, Tamil Nadu. About 2 ml of blood was collected in a vacutainer and transported to laboratory after clot formation. The blood samples were centrifuged at 1000 × g for 15 min, and the serum was separated [14]. Sera samples were stored in screw capped vials at −20°C until further use. About 12 standard serovars of Leptospira via Leptospira interrogans serovars autumnalis, austra­ lis, ballum, canicola, hardjo, hebdomadis, javanica, pyrogen, tarassovi, icterohaemorrhagiae, pomona, and grippotyphosa are maintained at the Department of Veterinary Preventive Medicine, Veterinary College and Research Institute, Namakkal. About 2 ml of blood was collected in a vacutainer and transported to laboratory after clot formation. The blood samples were centrifuged at 1000 × g for 15 min, and the serum was separated [14]. Sera samples were stored in screw capped vials at −20°C until further use. About 12 standard serovars of Leptospira via Leptospira interrogans serovars autumnalis, austra­ lis, ballum, canicola, hardjo, hebdomadis, javanica, pyrogen, tarassovi, icterohaemorrhagiae, pomona, and grippotyphosa are maintained at the Department of Veterinary Preventive Medicine, Veterinary College and Research Institute, Namakkal. Figure-1: Quantification of Leptospira interrogans serovar canicola outer membrane proteins by Lowry’s method. Serial dilution of known positive serum sample Known positive serum sample was serially diluted from 1:10 to 1:100 by adding phosphate buffer saline (PBS). Optimization of L. canicola OMP antigen Optimization of L. canicola OMP antigen A checkerboard titration was carried out to deter­ mine the optimum single working dilution of OMP antigen to be used to coat the ELISA plates as per the protocol (Figure-2) [18]. Collection of sera samples and epidemiological data The study population was a convenience sample of 250 canine serum samples submitted to the diag­ nostic laboratory of the Department of Veterinary Preventive Medicine, Veterinary College and Research Institute, Namakkal, Tamil Nadu. Serum samples were collected from apparently healthy and clinically affected dogs (apparently healthy dogs n=78+clini­ cally affected dogs n=172) to rule out the canine lep­ tospirosis which were brought to Teaching Veterinary Clinical Complex, Veterinary College and Research Institute, Namakkal, Tamil Nadu. Serial dilution of L. interrogans serovar canicola OMP antigen Serial two-fold dilutions of L. interrogans sero­ var canicola OMP antigen were prepared in carbon­ ate - bicarbonate buffer (pH 9.6) to provide dilutions ranging from 4 to 0.0312 µg/well across the columns. Triton X-114 extraction The outer membrane proteins (OMP) from L. interrogans serovar canicola were extracted as per the method described by Cunningham et al. [11]. Briefly, leptospires were washed in phosphate-saline–5 mM, MgCl and then extracted in the presence of 1% protein-grade  Triton X-114–150 mM NaCl–10 mM Tris (pH 8)–1 mM EDTA at 4°C. The insoluble material was removed by centrifugation at 17,000 g for 10 min. After centrifugation, 20 mM CaCl was added to the supernatant. Phase separation was performed by heat­ ing the supernatant to 37°C followed by centrifugation at 1000 g for 10 min. The detergent and aqueous phases were then separated and precipitated with acetone. Figure-1: Quantification of Leptospira interrogans serovar canicola outer membrane proteins by Lowry’s method. Figure-2: Optimization of Leptospira interrogans serovar canicola outer membrane proteins by checkerboard titration. Ethical approval Lr.No.CPCSEA/CH/2001/5286 the CPCSEA indicates that research projects involving use of ani­ mal tissues such as blood, urine etc., from pet animal and farm animals, clinical cases and necropsy need 530 Veterinary World, EISSN: 2231-0916 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf not seek approval of CPCSEA. The current research work of A. Sathiyamoorthy, Department of Veterinary Preventive Medicine, Veterinary College and Research Institute, Namakkal involves only field cases of canine leptospirosis. Hence, the approval of ethical approval may not be required. However samples were collected as per standard collection procedure. Calculation of sensitivity and specificity Sensitivity and specificity of the test results for each test were calculated by 2 × 2 contingency table and compared as per the method described by Smith [21]. Quantification of L. canicola OMP Extraction of OMP was estimated by Lowry’s method and yielded as low as concentration of 1.9 µg/µl to as high as 5.2 µg/µl. This was in accordance with the result of Kumar et al. [12] who extracted an aver­ age concentration of OMP was 3.66 µg/µl. Characterization of L. canicola OMP The protein concentration of the extracted OMP of L. interrogans serovar canicola by SDS-PAGE and protein revealed prominent components of OMP of L. canicola were found to be 32, 36, 41 and 45, 112 kDa in size. Karthikeyan [14] also observed 29, 36, 43, 77, 93, and 112 kDa as major bands of OMP of L. canicola by SDS-PAGE. Microscopic agglutination test Seven days old culture of L. interrogans sero­ var canicola with a concentration of 4.0×107 organ­ isms per milliliter was used to obtain OMPs that could be used as source of antigen. Kumar et al. [12] and Souza et al. [13] were used the Triton X-114 for extraction of OMP antigen from Leptospira serovars. Leptospira OMP was considered to be a potential antigen as they are conserved within the various pathogenic serovars and such proteins and their associated molecules, selectively solubilized using Triton X-114 detergent, would be of immense diagnostic value [11]. The procedure suggested by Cole et al. [19] was carried out in round bottom 96 well microtiter plate. A volume of 50 µl of sterile PBS (pH 7.4) was added to each well. The sera samples were diluted in separate test tubes (1:25) and added to the well to make a 1:50 dilution. To these wells, constant amount of 50 µl of each antigen was added after checking the concentration of the organism under dark field mircoscopy (DFM). The final dilution after addition of antigen was ranged from 1:100 to 6400. Positive and negative controls were included in the study. The content of the microtiter plates was incu­ bated at room temperature (37°C) for 2 h. At the end of the incubation, a loopful of sample was taken on a clean glass slide beginning from highest dilution and examined under DFM without cover glass. The end point of an agglutination reaction was taken as the highest dilution at which 50% of leptospires had agglutinated. The reciprocal of end point formed the titer. Titer of 1:100 was considered as positive titer by MAT (Figure-3) [20]. Estimation of OMP extracted from L. interrogans serovar canicola Figure-2: Optimization of Leptospira interrogans serovar canicola outer membrane proteins by checkerboard titration. The protein content in the extracted samples was estimated by Lowry’s method (Figure-1) [17]. The protein content in the extracted samples was estimated by Lowry’s method (Figure-1) [17]. Veterinary World, EISSN: 2231-0916 531 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf wells and again incubated at 37°C for 1 h. Then, the plates were final washed and 100 µl of freshly pre­ pared chromogen - substrate solution containing OPD and urea H2O as substrate was added to each well and the plate was kept at room temperature for 10 min at dark. The enzyme-substrate reaction was stopped by adding 50 μl of 1M H2 SO4. The optical density of each of the samples was recorded at 492 nm by ELISA reader (Biorad). agglutination test which can detect the serovar spe­ cific antibodies but it has several disadvantages such as handling of live culture and time consuming when serovars panel is too large. Due to complexity and drawback of MAT, the search for new ELISA type of diagnostic test is essential. Hence, an indirect-ELISA was developed to screen canine anti-leptospiral anti­ bodies in sera samples, and the results were compared with those obtained by MAT. Seropositivity of canine leptospirosis by MAT p y p p y The MAT is the gold standard test with good specificity recommended by OIE [20] widely accepted test for diagnosis, screening of animals for international trade, and epidemiological investiga­ tions. MAT was performed in paired sera samples. Paired sera, which showed rising MAT titers that was indication of a current leptospirosis infection. Low level of titers most likely indicates vaccination reac­ tions. In this study, overall seropositivity by MAT was 28.40% at a titer of 1:100 and above. Which was almost equal to the report of Senthil et al. [23] and lower than the report of Karthikeyan [14], they reported a seropositivity of 28.80% and 36.27%, respectively, in Namakkal. Several authors reported varying rate of seropositivity by MAT ranging from 11.00% [24], 71.12% [25] at different geographical areas. Seropositivity of canine leptospirosis by i-ELISA In this study, overall seropositivity was 56.00% by developed i-ELISA. This was higher than the ear­ lier report of Ribotta et al. [1], Kumar et al. [12], and Iwamoto et al. [22] who reported a seropositivity of 17.00%, 53.00%, and 3.60%, respectively. Determination of cutoff OD value for leptospirosis studies The mean OD value of control negative serum samples at 1:50 dilution was 0.276 and positive serum samples (1:50 dilution) as 1.816 using OMP concentration of 0.5  µg/well. Based on these OD values, twice the mean OD values of the negative control serum were considered as a cutoff OD value to screen the test serum samples. Therefore, any serum sample showed the OD of 0.552 and above was considered as positive for leptospirosis. Twice the mean OD values of the negative control serum were considered as a cutoff OD value to screen the test serum samples as reported by Kumar et al. [12]. In this study, serum sample showed the OD of 0.552 and above was considered as positive for leptospirosis. Sera samples were collected from 172 clinically affected dogs (Table-1). Sera were tested by MAT using a panel of 12 Leptospira antigens. Out of 172 sera samples, 66 (38.37%) samples were found pos­ itive for MAT. This was higher than report of Lau et al. [26], they reported 15.8%. Sera samples were collected from 172 clinically affected dogs. Sera samples were submitted to OMP of L. interrogans serovar canicola coated i-ELISA. Out of 172 sera samples, 127 (73.83%) samples were found positive in i-ELISA. Observed seropositivity was higher than who reported 68.67% [18]. Hence, ELISA can replace MAT effectively particularly in laboratories where MAT is difficult to perform. Comparison of i-ELISA with MAT In this study, sensitivity and specificity of i-ELISA compared with MAT were 91.54% and 58.10%, respectively. Observed rate of sensitivity was almost equal to the reports of Kumar et al. [12], Surujballi et al. [28], and Surujballi and Mallory [29] who reported the sensitivity of 94.94%, 95.30%, and 93.00%, respectively. Observed rate of specificity was very low when compared with the reports of Ribotta et al. [1], Kumar et al. [12], Souza et al. [13], Surujballi et al. [28], Surujballi and Mallory [29] who reported the specificity of 95.6%, 67.66%, 100%, and 94.70%, respectively. Lower specificity of i-ELISA might be due to the presence of non-agglutinating Leptospira antibodies that were detectable by ELISA but not by MAT, which can only detect agglutinating antibod­ ies [30]. All the sera turned out to be MAT-negative may not actually be negative as only 12 Leptospira serovars were used as antigens for detection of anti­ body [16]. Result and Discussion i-ELISA was standardized by optimization of L. canicola OMP OD values of different antigen concentrations and serum dilution. In 1:10, 1:50 and 1:60 serum dilutions, OD value was increased from the antigen concentration of 4.0 to 1  µg/well, and thereafter OD values were declined gradually. Followed by 1:20, 1:30 and 1:40 serum dilutions, OD value was increased from the antigen concentration of 4.0 to 0.5 µg/well and thereafter OD values were declined gradually. In 1:70 serum dilution, OD value was increased from the antigen concentration of 4.0 to 2 µg/well and thereafter OD values was declined gradually and in 1:80 and above serum dilution high­ est OD value was observed in antigen concentration of 4.0 µg/well and followed by declined. The result revealed that antigen concentration of 0.5 µg/well at 1:30 serum dilution is suitable to screen the test serum samples. It was observed that antigen concentration of 0.5 µg/well was suitable to screen the test serum samples. Kumar et al. [12] also reported that antigen Confirmatory serological diagnosis of lep­ tospirosis is usually made using the microscopic Veterinary World EISSN: 2231-0916 Figure-3: 100% agglutination in microagglutination test. Figure-3: 100% agglutination in microagglutination test. Veterinary World, EISSN: 2231-0916 Veterinary World, EISSN: 2231-0916 532 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf reported 2.6%. Since agglutinins to MAT tend to remain in the body for a prolonged period following infection, detectable MAT titers may be present even in healthy animals [27]. Sera samples were collected from 78 healthy dogs. Sera samples were submitted to OMP of L. interrogans serovar canicola coated i-ELISA. Out of 78 sera samples, 13 (16.66%) sam­ ples were found positive in i-ELISA. Kumar et al. [12] also reported seropositive. concentration of 0.4575 µg/well was taken as optimal antigen concentration to coat the ELISA plates for screening of test sera samples. reported 2.6%. Since agglutinins to MAT tend to remain in the body for a prolonged period following infection, detectable MAT titers may be present even in healthy animals [27]. Sera samples were collected from 78 healthy dogs. Sera samples were submitted to OMP of L. interrogans serovar canicola coated i-ELISA. Out of 78 sera samples, 13 (16.66%) sam­ ples were found positive in i-ELISA. Kumar et al. [12] also reported seropositive. Seropositivity in healthy and clinically affected dogs In conclusion, i-ELISA developed for the detec­ tion of canine anti-leptospiral antibodies proved to be highly sensitive, rapid and easy to perform. This assay was performed with non-hazardous, highly purified and reproducible antigenic preparation which can be prepared in large quantity and could be stored for long Sera samples were collected from 78 healthy dogs (Table-1). Sera were tested by MAT using a panel of 12 Leptospira antigens. Out of 78 sera sam­ ples, 5 (6.41%) samples were found positive for MAT. This was higher than report of Lau et al. [26], they Veterinary World, EISSN: 2231-0916 533 Table-1: Seropositive of leptospira in healthy and clinically affected dogs both MAT and i‑ELISA. S.No. Categories No. of animal tested No. of positive in MAT No. of positive in i‑ELISA (%) 1. Healthy dogs 78 5 (6.41) 66 (38.37) 2. Clinically affected dogs 172 13 (16.66) 127 (73.83) MAT=Microagglutination test, i‑ELISA=Indirect enzyme‑linked immunosorbent assay Veterinary World, EISSN: 2231-0916 533 Table-1: Seropositive of leptospira in healthy and clinically affected dogs both MAT and i‑ELISA. S.No. Categories No. of animal tested No. of positive in MAT No. of positive in i‑ELISA (%) 1. Healthy dogs 78 5 (6.41) 66 (38.37) 2. Clinically affected dogs 172 13 (16.66) 127 (73.83) MAT=Microagglutination test, i‑ELISA=Indirect enzyme‑linked immunosorbent assay 533 Veterinary World, EISSN: 2231-0916 Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf WHO Offset Publication, World Health Organization, Geneva. periods. This does not require the maintenance of a constant supply of live leptospiral cultures of differ­ ent serovars as in the case of MAT. This assay could be objectively interpreted and also has repeatabil­ ity. Therefore, it can be recommended as a valuable screening test in routine diagnostic laboratories that do not have the facilities or expertise to perform MAT. This study revealed that age, sex, health status, and work-related activities were significantly associated with the occurrence of canine leptospirosis in this region. 10. Safiullah, S.A., Saleh, A.A. and Munwar, S. (2009) Laboratory methods for diagnosing leptospirosis: A review. Bangladesh J. Med. Microbiol., 3(1): 39-43. 11. 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Ch. 2.1.12. World Organization for Animal Health, Paris. 21. Smith, R.D. (1995) Veterinary Clinical Epidemiology: A Problem Oriented Approach. 2nd ed. CRC Press Inc., Boca Raton. p33. g ( ) 2. Andrea, M., Ariane, S. and Thierry, F. (2014) Increasing incidence of canine leptospirosis in Switzerland. Int. J. Environ. Res. Public Health, 11: 7242-7260. 22. Iwamoto, E., Wada, Y., Fujisaki, Y., Umeki, S., Jones, M.Y., Mizuno, T., Itamoto, K., Maeda, K., Iwata, H. and Okuda, M. (2009) Nationwide survey of Leptospira anti­ bodies in dogs in Japan: Results from microscopic aggluti­ nation test and enzyme-linked immunosorbent assay. J. Vet. Med. Sci., 71(9): 1191-1199. 3. Richard, B.F. (2014) (Still) an emerging infection? Canine leptospirosis. T.V.P. J., 5: 2. 3. Richard, B.F. (2014) (Still) an emerging infection? Canine leptospirosis. T.V.P. J., 5: 2. 4. Martin, L.E.R., Wiggans, K.T. and Wennogle, S.A. (2014) Vaccine-associated Leptospira antibodies in client-owned dogs. J. Vet. Int. 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Ambily, R., Mini, M., Joseph, S., Vamshi Krishna, S. and Abhinay, G. (2013) Canine leptospirosis - A seroprevalence study from Kerala, India. Vet. World, 6(1): 42-44. 26. Acknowledgments 16. Amrutha, R., Chaudhuri, P., Amar, P., Cheema, P.S. and Srivastava, S.K. (2006) Immunoreactive outer membrane proteins of Leptospira interrogans serovar Canicola strain Hond Utrecht IV. Indian J. Med. Res., 124(5): 569-574. We are thankful to the Department of Clinics, VC&RI, Namakkal, for sample collection. The authors are grateful to Tamil Nadu Veterinary and Animal Sciences University, Chennai, for contribution of the fund for this study under the Department of Veterinary Preventive Medicine, VC&RI, Namakkal. 17. Lowry, O.H., Rosenbrough, N.J., Farrn, A.I. and Randall, R.J. (1951) Protein measurement with folin-phenol reagent. J. Biol. Chem., 193(1): 265-275. 18. Kumar, A., Sinha, D.K., Chaudhury, P., Shankar, H. and Srivastava, S.K. (2009) Comparative studies on seroepide­ miology of canine leptospirosis by micro agglutination test (MAT) and recombinant Lip L32 ELISA. Indian J. Anim. Sci., 79(11): 1089-1094. Seropositivity in healthy and clinically affected dogs Souza, C.D.S., Castro, J.R., Tavares, T.C.F., Soares, P.M., Santos, M.P., Ganda, M.R., Gomes, D.O. and Lima-Ribeiro, A.M.C. (2014) Comparison of microscopic agglutination test and indirect ELISA in the diagnosis of bovine leptospirosis. Biosci. J., 30(2): 833-838. Competing Interests The authors declare that they have no competing interests. 19. Cole, J.R., Sulzer, J. and Pursell, R. (1973) Improved micro technique for the leptospiral microscopic agglutination test. Appl. Microbiol., 25(6): 976-980. Authors’ Contributions GS designed the research work, give the idea, share as well as supervise on practical work. AS carried out the research, collected the samples, carried out the laboratory work, and analyzed the data. KMP and PS drafted and revised the manu­ script. All authors have read and approved the final manuscript. p p ( ) 14. Karthikeyan, D. (2004) Incidence of Leptospirosis in Animal and its Public Health Significance. M.V. Sc., Thesis Submitted to Tamil Nadu Veterinary and Animal Sciences University, Chennai. 15. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227(5259): 680-685. , ( ) 29. Surujballi, O.M.P. and Mallory, M. (2004) An indirect Sugden, E.A. (1997) Development and initial evaluation of an indirect enzyme - linked immunosorbent assay for the detection of Leptospira interrogans serovar hardjo antibod­ ies in bovine sera. Can. J. Vet. Res., 61(4): 260-266. Veterinary World, EISSN: 2231-0916 References Lau, S.F., Low, K.N., Khor, K.H., Roslan, M.A., Bejo, S.K., Radzi, R. and Bahaman, A.R. (2016) Prevalence of lepto­ spirosis in healthy dogs and dogs with kidney disease in Klang Valley, Malaysia. Trop. Biomed., 33(3): 469-475. 7. Aedo, L. and Monti, A.G. (2015) Meta-analyses of factors associated with leptospirosis in domestic dogs. Zoonoses Public Health, 63(4): 328-336. 8. Manju, S., Jayaprakasan, V. and Mini, M. (2014) Epidemiological study on human and canine leptospirosis in central and north Kerala. Vet. World, 7: 1. 27. Soman, M., Jayaprakasan, V. and Mini, M. (2014) Epidemiological study on human and canine leptospirosis in Central and North Kerala. Vet. World, 7(10): 759-764. , ( ) 28. Surujballi, O.M.P., Marenger, R.M., Eaglesome, M.D. and 9. Faine, S. (1982) Guidelines for the Control of Leptospirosis. Veterinary World, EISSN: 2231-0916 534 p p ( ) 30. Agunloye, C.A., Alabi, F.O., Odemuyiwa, S.O. and Olaleye, O.D. (2001) Leptospirosis in Nigerians: A seroepi­ demiological survey. Indian Vet. J., 78(5): 371-375. Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf ******** Sugden, E.A. (1997) Development and initial evaluation of an indirect enzyme - linked immunosorbent assay for the detection of Leptospira interrogans serovar hardjo antibod­ ies in bovine sera. Can. J. Vet. Res., 61(4): 260-266. 29. Surujballi, O.M.P. and Mallory, M. (2004) An indirect ELISA for the detection of bovine antibodies to multiple Leptospira serovars. Can. J. Vet. Res., 68(1): 1-6. 30. Agunloye, C.A., Alabi, F.O., Odemuyiwa, S.O. and Olaleye, O.D. (2001) Leptospirosis in Nigerians: A seroepi­ demiological survey. Indian Vet. J., 78(5): 371-375. ELISA for the detection of bovine antibodies to multiple Leptospira serovars. Can. J. Vet. Res., 68(1): 1-6. Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf Available at www.veterinaryworld.org/Vol.10/May-2017/11.pdf Veterinary World, EISSN: 2231-0916 535 535
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1Institute of Physical Geography and Environmental Planning, Adam Mickiewicz University, Pozna, Poland; e-mails: darwrze@amu.edu.pl, choinski@amu.edu.pl, marp114@wp.pl (corresponding author) 2Department of Hydrology and Water Management, Nicolaus Copernicus University, Toru, Poland; e-mail: rskowron@umk.pl 1Institute of Physical Geography and Environmental Planning, Adam Mickiewicz University, Pozna, Poland; e-mails: darwrze@amu.edu.pl, choinski@amu.edu.pl, marp114@wp.pl (corresponding author) 2Department of Hydrology and Water Management, Nicolaus Copernicus University, Toru, Poland; e-mail: rskowron@umk.pl 1Institute of Physical Geography and Environmental Planning, Adam Mickiewicz University, Pozna, Poland; e-mails: darwrze@amu.edu.pl, choinski@amu.edu.pl, marp114@wp.pl (corresponding author) 2Department of Hydrology and Water Management, Nicolaus Copernicus University, Toru, Poland; e-mail: rskowron@umk.pl Ownership: Institute of Geophysics, Polish Academy of Sciences; © 2015 Wrzesiski et al. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivs license, http://creativecommons.org/licenses/by-nc-nd/3.0/. Acta Geophysica vol. 63, no. 6, Dec. 2015, pp. 1664-1684 DOI: 10.1515/acgeo-2015-0055 Acta Geophysica vol. 63, no. 6, Dec. 2015, pp. 1664-1684 DOI: 10.1515/acgeo-2015-0055 Key words: climate change, ice cover, teleconnections. Effect of the North Atlantic Oscillation on the Pattern of Lake Ice Phenology in Poland Dariusz WRZESISKI1, Adam CHOISKI1, Mariusz PTAK1, and Rajmund SKOWRON2 Dariusz WRZESISKI1, Adam CHOISKI1, Mariusz PTAK1, and Rajmund SKOWRON2 1. INTRODUCTION Of key significance for the operation of lakes in the middle and high geo- graphical latitudes is thermal seasonality connected with ice phenology. The process of ice formation itself is well known and follows from an exchange of heat between a water mass and the surroundings. Its rate and scale are de- termined by many factors, among which Majewski (2007) lists air tempera- ture, water temperature, water depth, etc. As a result of the appearance of ice, considerable changes take place in the operation of lake ecosystems that follow from the isolation of water from external factors (no waving, reduced light, etc.). Those issues are discussed in many works, a survey of which has been made by Gerten and Adrian (2000). An effect of the observed changes in climatic conditions is a shift in thermal seasons of the year (Thomson 2009) leading, among other things, to disturbances in the ice regime of lakes. Long-term observations show that the ice season tends to shorten and the thickness of ice cover to diminish (Futter 2003, Korhonen 2006, Jensen et al. 2007, Leppäranta 2014). The interpretation of the observed trends should ac- commodate the cyclicity of macro-scale factors embracing atmospheric and oceanic circulation (Brown and Duguay 2010). What exerts a strong influ- ence on the climatic conditions in Europe is the North Atlantic Oscillation (NAO). Its effect is visible in the pattern of climatic and hydrological char- acteristics, and has been documented in several works on precipitation (Bed- norz 2011, Castro et al. 2011), air temperature (Scaife et al. 2008, Heape et al. 2013), and river runoff (Pociask-Karteczka 2006, Wrzesiski and Palusz- kiewicz 2011). The effect of the NAO has also been proved with reference to lake ice phenology (Maher et al. 2005, George 2007, Weyhenmeyer 2009, Soja et al. 2014, Sharov et al. 2014). j ) This paper seeks to establish spatial differences in the parameters of lake ice phenology in Poland in average conditions and under the influence of the variable intensity of atmospheric circulation in the North Atlantic sector. The research conducted was designed to show that the level of intensity of the North Atlantic Oscillation caused significant differences in the ice phenolo- gy of lakes in Poland. The study was carried out on the lakes of northern Po- land, i.e., a lakeland area embraced by the last Scandinavian glaciation. A b s t r a c t This paper presents an analysis of the influence of the North Atlan- tic Oscillation on the pattern of lake ice phenology in Poland. The re- search embraced 22 lakes in Poland over the period 1961-2010. Strong relations were found to hold between NAO and individual characteristics of ice phenology. In a negative NAO phase, one can observe a later ap- pearance of ice phenomena and ice cover compared with the average values, ice cover persisting even 30 days longer and being thicker even by more than 10 cm. In turn, in a positive NAO phase the duration of ice phenomena and ice cover is shorter, the cover being less thick and solid. The observed spatial differences in the effect of NAO on the pattern of ice phenomena in Poland show this matter to be fairly complex. The most significant factor changes in climatic conditions, which manifest themselves in the continentality of the climate growing eastwards. Key words: climate change, ice cover, teleconnections. EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1665 2. MATERIAL AND METHODS Observations of ice phenomena on lakes in Poland started as early as the 19th century. They mostly focused on the thickness of ice cover, more rarely on the start and end of its occurrence. Such measurements were performed for the purposes of fishing trade, but this material was scattered and non- systematic, hence of little scientific worth (Skowron 2011). Constant obser- vations of ice phenomena are conducted by the Institute of Meteorology and Water Management (IMGW). Records are made of the dates of appearance of ice phenomena (the presence of ice in water in any form: shore ice, frazil ice), the appearance of ice cover, its breakup, the disappearance of ice phe- nomena, and the thickness of ice cover. At present, observations of the char- acteristics of ice phenology are conducted on 22 out of the country’s 7000 lakes (of 1 ha and more in area) (Fig. 1), the morphometric parameters of which are presented in Table 1. This paper offers an analysis of the pattern of ice phenomena on those lakes in the period 1961-2010. Observations of ice phenomena on lakes in Poland started as early as the 19th century. They mostly focused on the thickness of ice cover, more rarely on the start and end of its occurrence. Such measurements were performed for the purposes of fishing trade, but this material was scattered and non- systematic, hence of little scientific worth (Skowron 2011). Constant obser- vations of ice phenomena are conducted by the Institute of Meteorology and Observations of ice phenomena on lakes in Poland started as early as the 19th century. They mostly focused on the thickness of ice cover, more rarely on the start and end of its occurrence. Such measurements were performed for the purposes of fishing trade, but this material was scattered and non- systematic, hence of little scientific worth (Skowron 2011). Constant obser- vations of ice phenomena are conducted by the Institute of Meteorology and Water Management (IMGW). 1. INTRODUCTION No detailed analysis of this issue has so far been made for such a large set of lakes in this part of Europe and for a 50-year-long observation period. Earli- er studies of the effect of the North Atlantic Oscillation on the parameters of lake ice phenology in Poland only focused on small groups of lakes (Girjatowicz 2003, Wrzesiski et al. 2013), four and three, respectively. The results obtained in those works reveal a strong link between this circulation and lake ice phenology, and encourage making such an analysis for a larger set of lakes. 1666 D. WRZESISKI et al. 2. MATERIAL AND METHODS Records are made of the dates of appearance of ice phenomena (the presence of ice in water in any form: shore ice, frazil ice), the appearance of ice cover, its breakup, the disappearance of ice phe- nomena and the thickness of ice cover At present observations of the char- An analysis was made of ten parameters of lake ice phenology: the start and the end of ice phenomena (the first and the last day when any form of ice in water, identified with shore ice, was recorded) the start and the end of ice cover (the first and the last day when the lake surface in the observer’s arc of visibility was completely covered with ice), the duration of ice phe- nomena and ice cover (the dates when shore ice and ice cover were observed for the first and the last time), ice cover thickness measured every five days, and the date of its maximum thickness (in the case of five lakes, no informa- Fig. 1. Location of the studied lakes (numbering in accordance with Table 1), marked area is that of Last Glaciation; A – Pomeranian Lakeland, B – Mazurian Lakeland, C – Wielkopolska–Kujavia Lakeland. Fig. 1. Location of the studied lakes (numbering in accordance with Table 1), marked area is that of Last Glaciation; A – Pomeranian Lakeland, B – Mazurian Lakeland, C – Wielkopolska–Kujavia Lakeland. EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1667 Table 1 Morphometric data of the studied lakes No. 2. MATERIAL AND METHODS Lake Area [ha] Volume [thous.m3] Depth average [m] Altitude [m a.s.l.] 1 Sawskie 822.5 42664.8 5.2 56.9 2 Osiek 514.0 50065.0 9.3 51.4 3 Lubie 1487.5 169880.5 11.6 95.4 4 Jamno 2231.5 31528 1.4 0.1 5 Gardno 2337.5 30950.5 1.3 0.3 6 ebsko 7080.0 117521 1.6 0.2 7 Raduskie Górne 362.5 60158.7 15.5 161.6 8 Ostrzyckie 296.0 20785.2 6.7 160.1 9 Charzykowskie 1336.0 134533.2 9.8 120 10 Spoleskie 157.5 7501.6 4.8 112.8 11 ninskie Due 420.5 29492.6 6.8 77.7 12 Biskupiskie 107.0 6397.2 5.5 78.6 13 Gopo 2121.5 78497.0 3.6 77.0 14 Jeziorak 3152.5 141594.2 4.1 99.2 15 Drwckie 780.0 50140.1 5.7 94.8 16 Nidzkie 1750.0 113872.3 6.2 117.9 17 Mikoajskie 424.0 55739.7 11.2 115.7 18 Orzysz 1012.5 75326.2 6.6 120.0 19 Eckie 385.0 57420.3 15.0 119.9 20 Studzieniczne 244.0 22073.6 8.7 123.4 21 Serwy 438.5 67181.5 14.1 126.8 22 Hacza 291.5 120364.1 38.7 227.3 tion was obtained about appearance of maximum ice thickness). On the basis of those observations it was possible to determine ice cover durability, un- derstood as the proportion of the number of days with ice cover to the num- ber of days between the first and the last day with ice cover [%], and its duration, which means the proportion of the number of days with ice cover in the entire period of ice phenomena, i.e., from the first to the last day when those phenomena could be observed (e.g., shore ice, ice floe, etc.) [%]. In order to determine the dependence of changes in the ice phenology pa- rameters on the intensity of the North Atlantic Oscillation, Pearson’s coeffi- cient of linear correlation was calculated (r), the correlation holding between the ice phenology parameters under study and Hurrell’s winter NAODJFM in- dex. In the case of the start of ice phenomena and the formation of ice cover, also calculated were coefficients of correlation with seasonal NAO indices from the periods September-November (NAOSON), October-December (NAOOND), and November-January (NAONDJ). 1668 D. WRZESISKI et al. Changes in the parameters of ice phenomena on the examined lakes in a positive and a negative NAODJFM phase were determined on the basis of how those parameters differed from the average values from the years 1961-2010. The average values of those parameters were calculated for years with high (NAODJFM > 1.63) and low (NAODJFM < –1.09) values of the winter NAODJFM index. 2. MATERIAL AND METHODS Those figures correspond to the first and third quartiles from the en- tire set of NAODJFM indices in the years 1961-2010. The statistical signifi- cance of those differences was examined using the T-test for stratified samples. Each time the hypothesis tested was H0: = 0 of the equality of the expected values against H1:  0. The rejection of the hypothesis al- lowed a conclusion about there being significant differences between the mean parameters of ice phenomena observed in the different NAODJFM phas- es and the average values. To verify the hypothesis, use was made of a test for a small sample based on Student’s t-distribution, with n – 1 degrees of freedom: 0 , x t n     (1) (1) where n is the sample size,  the standard deviation, x the mean of the sam- ple, and 0 the mean of the population. where n is the sample size,  the standard deviation, x the mean of the sam- ple, and 0 the mean of the population. In this paper use was made of the winter NAO index (NAODJFM) and sea- sonal NAO indices worked out by Hurrell (1995). To present spatial differences in changes in the parameters of lake ice phenology, the Surfer 10 Program (GoldenSoftware) was employed, and isolines were drawn using the kriging procedure. 3.1 Average parameters of lake ice phenology in Poland in the years 1961-2010 On the lakes under study, ice phenomena begin in mid-December. The earli- est ones start in the first half on the lakes in the Wielkopolska–Kujavia Lake- land, the western part of the Mazurian Lakeland, and the coastal lakes ebsko and Gardno (Fig. 2a). On most lakes of the Pomeranian and Mazu- rian Lakelands, ice phenomena begin in the last decade of December, and in the case of Lake Lubie, in the first decade of January. The spatial distribution of the dates of ice cover formation is similar, but about 10 days later (Fig. 2b). On the lakes of the central part of the lakeland zone and on the coast, ice cover appears on average in the last decade of De- cember, and on most lakes of the Pomeranian and Mazurian Lakelands, in the first decade of January, appearing the latest on Lake Lubie (11 January). EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1669 Fig. 2. Spatial differences in the dates of the start of: (a) ice phenomena, and (b) ice cover. Fig. 2. Spatial differences in the dates of the start of: (a) ice phenomena, and (b) ice cover. Fig. 3. Spatial differences in the dates of the end of: (a) ice phenomena, and (b) ice cover. Fig. 3. Spatial differences in the dates of the end of: (a) ice phenomena, and (b) ice cover. What is highly characteristic is the spatial distribution of the date of the end of ice phenomena and ice cover. Those ice phenomenology parameters are the earliest on lakes in the western part of the study area: in the case of ice cover, in late February and early March (Fig. 3b), and in case of ice phe- nomena, in the first decade of March (Fig. 3a). Those dates are ever later in the easterly direction. In the eastern part of the Mazurian Lakeland, ice cover usually disappears in the third decade of March, and ice phenomena in the first decade of April. The spatial distributions of the duration of ice phenomena and ice cover are similar. Ice phenomena last the shortest (under 70 days) on lakes in the western part of the area and near the sea, and the longest (over 100 days) in the east; cf. Fig. 4a. 3.1 Average parameters of lake ice phenology in Poland in the years 1961-2010 As to the ice cover, it persists for less than 60 days on the lakes in the west, and over 80 days in the east; cf. Fig. 4b. Also the mean maximum thickness of ice cover on lakes grows east- wards, from about 20 cm in the western part of the area to over 30 cm in the east; cf. Fig. 5a. Spatial differences are wider in the case of the date when it attains its maximum thickness. This occurs the earliest on the lakes of the Wielkopolska–Kujavia Lakeland and on coastal lakes (late January and early February); cf. Fig. 5b. For most lakes this date falls in mid-February, and for those in the eastern part of the area, in the third decade of February. D. WRZESISKI et al. 1670 Fig. 4. Spatial differences in the duration of: (a) ice phenomena, and (b) ice cover. Fig. 5. Spatial differences in: (a) the thickness of ice cover, and (b) the date of occur- rence of the maximum thickness of ice cover. Fig. 4. Spatial differences in the duration of: (a) ice phenomena, and (b) ice cover. Fig. 4. Spatial differences in the duration of: (a) ice phenomena, and (b) ice cover Fig. 5. Spatial differences in: (a) the thickness of ice cover, and (b) the date of occur- rence of the maximum thickness of ice cover. Fig. 5. Spatial differences in: (a) the thickness of ice cover, and (b) the date of occu rence of the maximum thickness of ice cover. Fig. 5. Spatial differences in: (a) the thickness of ice cover, and (b) the date of occur- rence of the maximum thickness of ice cover. Fig. 6. Spatial differences in: (a) the degree of durability of ice cover, and (b) dura- tion of ice cover divided by total period of phenomena. Fig. 6. Spatial differences in: (a) the degree of durability of ice cover, and (b) dura- tion of ice cover divided by total period of phenomena. The durability of ice cover is the shortest in the case of coastal lakes (about 80%) and grows markedly eastwards to over 90%; cf. Fig. 6a. There is no such regularity in the spatial variability of the share of ice cover in ice phenomena. 3.1 Average parameters of lake ice phenology in Poland in the years 1961-2010 In the case of the coastal lakes, it is under 80%, and over 85% for the lakes in the central part of the Pomeranian Lakeland and the western part of the Mazurian Lakeland (Fig. 6b). 3.2 Relations between lake ice phenology and the NAO The results obtained show that the intensity of the North Atlantic Oscillation in the winter season strongly affects the pattern of ice phenomena on Polish EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1671 lakes. This is corroborated by both, the correlation of the NAODJFM index with the parameters of ice phenomena (Table 2), and the calculated differ- ences between those parameters in the different NAODJFM phases and the av- erage values (Figs. 7-14). In a positive NAODJFM phase, the dates of the end of ice phenomena and ice cover on the lakes under study are usually about 15 days later than the average, and the calculated differences in the dates are statistically signifi- cant (p < 0.05); cf. Figs. 7 and 8. The date of the end of those phases of ice phenology is even over 20 days later on lakes in the direct neighbourhood of the Baltic (coastal lakes). In a negative NAODJFM phase, the ending dates come earlier than average, and statistically significant differences (p < 0.05) range from under 15 days in the west and east of the lakeland belt to over 20 days in the case of the coastal lakes. The deviations of the ending dates of ice phenomena and ice cover in the different NAODJFM phases from the average values cause also their duration Fig. 7. Differences between the dates of the end of ice phenomena in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 8. Differences between the dates of the end of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 7. Differences between the dates of the end of ice phenomena in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. g. 7. Differences between the dates of the end of ice phenomena in a negative NAO-) and a positive (NAO+) NAO phase, and the average values from the years 961-2010; results of the test of the significance of the differences. Fig. 7. 3.2 Relations between lake ice phenology and the NAO Differences between the dates of the end of ice phenomena in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 8. Differences between the dates of the end of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 8. Differences between the dates of the end of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 8. Differences between the dates of the end of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. D. WRZESISKI et al. 1672 Table 2 Coefficients of correlation between the parameters of ice phenomena and NAODJFM EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1673 in those phases to differ markedly, and statistically significantly (p < 0.05), from the means. In a positive NAODJFM phase, the duration of those charac- teristics is clearly shorter than the average, by more than 30 days in the case of the coastal lakes and those located in the western part of the country, dropping to under 20 days in the east. In a negative NAODJFM phase, the du- ration of ice phenomena, as well as of ice cover, is markedly longer than the average, from under 20 to over 30 days. The observed differences are statis- tically significant (p < 0.05), but more diversified spatially, although still greater in the case of the lakes in the west (especially the coastal ones) and smaller in the east under 20 days; cf. Figs. 9 and 10. Changes in the intensity of the North Atlantic Oscillation also affect the maximum thickness of ice cover and the date of its appearance. In a positive NAODJFM phase, the thickness is smaller, from under 10 cm on the lakes in the west of the country to over 10 cm in the eastern part of the lakeland zone; cf. Fig. 11. In a negative NAODJFM phase, the maximum thickness fig- Fig. 9. 3.2 Relations between lake ice phenology and the NAO Differences between the duration of ice phenomena in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 10. Differences between the duration of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; re- sults of the test of the significance of the differences. Fig. 9. Differences between the duration of ice phenomena in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 9. Differences between the duration of ice phenomena in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961- 2010; results of the test of the significance of the differences. Fig. 10. Differences between the duration of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; re- sults of the test of the significance of the differences. Fig. 10. Differences between the duration of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; re- sults of the test of the significance of the differences. D. WRZESISKI et al. 1674 D. WRZESISKI et al. 1674 Fig. 11. Differences between the maximum thickness of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 12. Differences between the dates of occurrence of the maximum thickness of ice cover in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differ- ences. Fig. 11. Differences between the maximum thickness of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 11. Differences between the maximum thickness of ice cover in a negati (NAO-) and a positive (NAO+) NAO phase, and the average values from the yea 1961-2010; results of the test of the significance of the differences. Fig. 11. 3.2 Relations between lake ice phenology and the NAO Differences between the maximum thickness of ice cover in a negative (NAO-) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 12. Differences between the dates of occurrence of the maximum thickness of ice cover in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differ- ences. Fig. 12. Differences between the dates of occurrence of the maximum thickness of ice cover in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differ- ences. Fig. 12. Differences between the dates of occurrence of the maximum thickness of ice cover in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differ- ences. ures are greater, in the western part of the lakeland by about 5 cm, although the observed differences from the average values are not statistically signifcant (p > 0.01). By contrast, the maximum thickness of ice cover on the lakes in the eastern part of the study area differs then in a statistically significant way (p < 0.05), by more than 10 cm; cf. Fig. 11. Also the date of the appearance of the maximum thickness of ice cover changes significantly depending on the NAODJFM phase. In a positive phase it comes from under 10 to over 15 days earlier than the average, and in a negative phase, later; cf. Fig. 12. The smallest deviations from average val- ues, statistically not significant, can be observed on the lakes in the western and eastern parts of the lakeland belt, while the greatest, statistically signifi- cant (p < 0.05), differences occur on those in the central belt embracing the coastal lakes in the north and those of the Kujavia Lakeland in the south. In a negative NAODJFM phase, the date of the maximum thickness of ice cover on EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1675 the coastal lakes is later than the average even by more than 20 days, and the observed differences are statistically significant (p < 0.01). 3.2 Relations between lake ice phenology and the NAO the coastal lakes is later than the average even by more than 20 days, and the observed differences are statistically significant (p < 0.01). The durability of ice cover in a positive NAODJFM phase is from less than 5% to over 10% smaller than the average, and the observed differences are usually not statistically significant; cf. Fig. 13. In a negative NAODJFM phase the durability is greater. On the lakes in Poland’s western part, however, this increase is not statistically significant, while in the central and eastern parts it is significant at p < 0.001. Also smaller in a positive NAODJFM phase is the share of the duration of ice cover in the entire period of occurrence of ice phenomena; cf. Fig. 14. The drop in this proportion observed then against average values varies from under 5 to over 15%, only the greatest differences being statistically signifi- cant (p < 0.05). In turn, in a negative NAODJFM phase this proportion grows and is 5-10% higher than the average. Fig. 13. Differences between the level of degree of durability of ice cover in a nega- tive (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 13. Differences between the level of degree of durability of ice cover in a neg tive (NAO–) and a positive (NAO+) NAO phase, and the average values from t years 1961-2010; results of the test of the significance of the differences. Fig. 13. Differences between the level of degree of durability of ice cover in a nega- tive (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 14. Differences between the proportion of ice cover duration in the duration of ice phenomena in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. Fig. 14. Differences between the proportion of ice cover duration in the duration of ice phenomena in a negative (NAO–) and a positive (NAO+) NAO phase, and the average values from the years 1961-2010; results of the test of the significance of the differences. 1676 D. WRZESISKI et al. 3.2 Relations between lake ice phenology and the NAO EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1677 It is statistically significant (p < 0.05) for all the lakes with the exception of Drwckie (Table 3). Twelve of the examined lakes also show statistically significant relations between the dates of appearance of ice phenomena and ice cover and the NAOSON index for the September-November period (p = 0.05). It is statistically significant (p < 0.05) for all the lakes with the exception of Drwckie (Table 3). Twelve of the examined lakes also show statistically significant relations between the dates of appearance of ice phenomena and ice cover and the NAOSON index for the September-November period (p = 0.05). In the study period, the lowest value of the NAODJFM index was recorded in 1969 (–4.89), and the highest in 1989 (5.08). In those years extremely dif- ferent parameters of ice phenomena were observed on the lakes. In 1969 the average duration of ice cover was 113 days (the longest one, 136 days, per- sisting on Lake Spoleskie), as against a mere 16 days in 1989, while on niskie Due, Sawskie, and Gopo it was not recorded at all that year. The mean thickness of maximum ice cover in 1969 was 43.4 cm as against a mere 10.2 cm in 1989. It should be emphasized that in the entire multi-year period under analysis the year 1969 was the one when the maximum thick- ness of ice was recorded; in two cases (Lakes Studziennicze and Miko- ajskie) it reached 65 cm. 3.2 Relations between lake ice phenology and the NAO Table 3 Coefficients of the correlation between the starting dates of ice phenomena and ice cover and the seasonal NAO indices Index NAO NAOSON NAOOND NAONDJ NAODJF Lake Beginning of Beginning of Beginning of Beginning of ice phenom- ena ice cover ice phenom- ena ice cover ice phenom- ena ice cover ice phenom- ena ice cover Sawskie 0.284 0.344 0.322 0.408 0.355 0.397 0.132 0.145 Osiek 0.335 0.238 0.452 0.369 0.447 0.481 0.225 0.171 Lubie 0.106 0.085 0.418 0.342 0.684 0.547 0.546 0.291 Jamno 0.231 0.257 0.313 0.298 0.319 0.367 0.105 0.231 Gardno 0.256 0.167 0.275 0.291 0.334 0.421 0.109 0.205 ebsko 0.264 0.179 0.356 0.239 0.374 0.316 0.176 0.133 Raduskie Górne 0.181 0.176 0.231 0.270 0.371 0.458 0.176 0.303 Ostrzyckie 0.290 0.316 0.258 0.294 0.225 0.252 –0.008 0.022 Charzykowskie 0.323 0.305 0.409 0.436 0.424 0.545 0.122 0.247 Spoleskie 0.279 0.279 0.376 0.343 0.308 0.242 0.023 –0.024 niskie Due 0.152 0.214 0.235 0.346 0.229 0.420 0.152 0.215 Biskupiskie 0.253 0.285 0.373 0.349 0.353 0.295 0.112 0.073 Gopo 0.290 0.269 0.385 0.356 0.370 0.409 0.056 0.158 Jeziorak 0.160 0.291 0.166 0.368 0.074 0.247 –0.053 0.035 Drwckie 0.016 0.242 0.120 0.262 0.154 0.275 0.066 0.046 Nidzkie 0.246 0.242 0.377 0.349 0.429 0.358 0.230 0.145 Mikoajskie 0.215 0.264 0.294 0.345 0.355 0.373 0.129 0.173 Orzysz 0.318 0.346 0.277 0.430 0.197 0.478 –0.012 0.241 Eckie 0.330 0.326 0.344 0.375 0.292 0.349 0.112 0.128 Studzieniczne 0.282 0.337 0.270 0.348 0.255 0.318 0.106 0.111 Serwy 0.304 0.355 0.261 0.304 0.182 0.260 –0.007 –0.032 Hacza 0.291 0.216 0.362 0.283 0.326 0.271 0.122 0.055 Note: Significance of correlation coefficients at the levels: p < 0.05, p < 0.01, p < 0 001 Coefficients of the correlation between the starting dates of ice phenomena and ice cover and the seasonal NAO indices Out of the parameters under study, only the starting dates of ice phenom- ena and ice cover do not show any relation with the intensity of the North Atlantic Oscillation as expressed by the NAODJFM index. Those dates usually fall in December; hence, the lack of a relation with the index determined for a later period is understandable. However, an analysis showed there to be a connection between the starting dates of ice phenomena and ice cover and NAO indices calculated for earlier seasons, especially NAOOND and NAONDJ. 4. DISCUSSION The duration of ice phenology in midland water bodies basically grows with the geographical latitude (Livingstone et al. 2009). However, this depend- ence can be modified by macro-scale circulation (which variously affects climatic conditions in different parts of the world, depending on its type), and by individual characteristics of lakes (Choiski and Ptak 2012), their surroundings (Choiski et al. 2013), and the local circulation (Blenckner et al. 2004). Ice phenology is directly connected with the thermal balance of a lake. Over the last decades, there has been a more rapid increase in air temperature in the spring period (Benson et al. 2012). This translates into higher tem- peratures of lake water. In the case of Polish lakes, it is precisely in spring that it grows the fastest, 0.2-0.5°C decade–1 (Skowron 2011). A consequence has been a quicker disappearance of ice cover, and thus its shorter duration. As a result, the tendencies of change in the pattern of ice phenology recorded for Polish lakes in the second half of the 20th century are mostly downward ones (Pasawski 1982, Marszelewski and Skowron 2006, Choiski et al. 2014). The relations between the temperatures of air and water are closely asso- ciated regionally with the macro-scale circulation of the atmosphere (D bro- wski et al. 2004, Livingstone et al. 2010). The analysis of NAO-related changes in the thermal conditions of lakes in Poland conducted by Wrzesi- ski et al. (2015) showed considerable deviations from mean values (both 1°C lower and higher, depending on the circulation phase), and those deviations were readily visible in spring, i.e., in the period of ice cover destruction. 1678 D. WRZESISKI et al. In the case of European lakes, also their ice regime shows strong rela- tions with the NAO circulation (Dokulil 2013). When analysing the pattern of ice phenomena on the largest lake in England (Windermere), George (2007) found that this circulation type had greatly influenced ice formation on it for over 30 years, and the link between this phenomenon and the NAO accounted for 50% of inter-year changes. In the case of Lake Erken located in the east of Sweden, an earlier decay of its ice cover was closely related with a high NAO index (Blenckner and Chen 2003). In turn, Maher et al. 4. DISCUSSION (2005) analysed two winter seasons in the different NAO phases on Lake Vendyurskoe in the northern part of Russia and noted that ice cover tended to be thicker in a negative phase, while its duration did not differ significant- ly in the two periods analysed. The relations between lake ice phenology and the NAO have also been documented for other regions of the Northern Hem- isphere, e.g., in Siberia (Livingstone 1999) or North America (Livingstone 2000). The ice cover of the North American Great Lakes has a linear connec- tion with the NAO and is thicker or thinner depending on its phase (Bai et al. 2012). In the case of Polish lakes, all the examined characteristics of ice phe- nology respond to variations in the pattern of macro-scale circulation by de- viating from the mean values. This is especially significant for the duration of ice cover, which isolates a lake from the influence of external factors, and this, as has been mentioned in the Introduction, completely changes the op- eration of the given ecosystem. The inter-year variability of this characteris- tic in Poland is considerable and amounts to over a month, depending on the phase and intensity of the NAO. The NAO is an essential but not the only element responsible for the pat- tern of lake ice phenology in this part of Europe. This is indicated by the spatial differences in conditions of lake ice phenology in Poland reported in this paper. Karetnikov and Naumenko (2008) came to similar conclusions in the case of Lake Ladoga; they found a connection between the NAO and ice phenology which was absent when ice cover exhibited extreme characteris- tics. In principle, the severity of ice phenomena on Polish lakes grows east- wards. This has been observed by, e.g., Girjatowicz (2003) for four coastal lakes. Thus, what should be taken as the basic feature influencing the length of the ice season on the lakes under study is their location. Departures from this rule are connected with morphometric characteristics of individual lakes and local conditions. Of key significance for lakes located in the lowland zone are the former, and the effect of the surroundings on the pattern of lake ice phenology is especially readily visible in mountain lakes, as corroborated by the research conducted, among others, by Novikmec et al. (2013). 4. DISCUSSION The most important morphometric feature of lakes in terms of ice phe- nology is their depth, because it decides about the amount of accumulated EFFECT OF THE NAO ON LAKE ICE PHENOLOGY IN POLAND 1679 warmth and hence about the time needed for cooling and freezing (Korhonen 2006). However, in the case of the lakes analysed here, this feature is not readily visible. A later start of the appearance of ice cover was recorded in both, one of the deepest lakes (e.g., Raduskie Górne) and one of the shal- lowest ones (e.g., Gopo). This situation illustrates the complexity of over- lapping processes and environmental features, the resultants of which are the formation and disappearance of ice in lakes. The transformation occurring in the conditions of the ice phenology of lakes affects their operation throughout the year, not only in winter. There are many works that connect the physico-chemical conditions of lakes (Lep- päranta et al. 2003, Witek and Jarosiewicz 2010, Mihu-Pintilie et al. 2014) and biological ones (Pettersson 1990, Hurst 2007, Vehmaa and Salonen 2009) with their ice phenology. The effect (or its absence) of ice phenology on living conditions is also observed with reference to lakes in Poland (Toporowska et al. 2010, Wojciechowska and Lenard 2014, Sienkiewicz and G siorowski 2014, Messyasz et al. 2015, Peechata et al. 2015). The consid- erable differences in the duration of ice cover may change the species com- position of both flora and fauna, which in consequence can lead to the replacement of present species by other organisms. As has been observed by Ptak (2013), the disappearance of the most endangered species would be es- pecially detrimental. 5. CONCLUSIONS The results presented in this paper concerning the pattern of lake ice phenol- ogy in Poland against changes in the intensity of the North Atlantic Oscilla- tion are similar to those established earlier for lakes of the Northern Hemi- sphere. In the different NAO phases, wide, statistically significant differ- ences can be observed between the values of ice phenology parameters (e.g., those concerning shore ice, ice cover, its thickness, etc.) and the mean fig- ures. Of special importance are the considerable deviations from the duration of ice cover an element which, by isolating water masses from external factors and processes, has the strongest influence on the operation of lakes. Also established were spatial differences in the scale of the effect of the NAO on the conditions of ice phenology of individual lakes. Like the studies by other authors cited here, it is a proof of the complexity of this issue. The effect of the NAO circulation can be stronger or weaker, depending on indi- vidual morphometric characteristics of lakes. The results obtained can be a valuable starting point for further research on lake ice phenology. In the future it might be advisable to build models de- scribing variations in the characteristics (both chemical-physical and biolog- ical) of lake ecosystems by accommodating changes in their ice regimes. With detailed multi-year information on the pattern of lake ice phenology for 1680 D. 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The cost of associating with males for Bornean and Sumatran female orangutans: a hidden form of sexual conflict?
Behavioral ecology and sociobiology
2,020
cc-by
20,336
ERROR: type should be string, got "https://doi.org/10.1007/s00265-020-02948-4\nBehavioral Ecology and Sociobiology (2021) 75: 6 https://doi.org/10.1007/s00265-020-02948-4\nBehavioral Ecology and Sociobiology (2021) 75: 6 ORIGINAL ARTICLE * Julia A. Kunz\njuliaandrea.kunz@uzh.ch The cost of associating with males for Bornean and Sumatran\nfemale orangutans: a hidden form of sexual conflict? Julia A. Kunz1\n& Guilhem J. Duvot1 & Maria A. van Noordwijk1 & Erik P. Willems1 & Manuela Townsend1 &\nNeneng Mardianah2 & Sri Suci Utami Atmoko2 & Erin R. Vogel3 & Taufiq Purna Nugraha4,5 & Michael Heistermann6 &\nMuhammad Agil5 & Tony Weingrill1 & Carel P. van Schaik1 Julia A. Kunz1\n& Guilhem J. Duvot1 & Maria A. van Noordwijk1 & Erik P. Willems1 & Manuela Townsend1 &\nNeneng Mardianah2 & Sri Suci Utami Atmoko2 & Erin R. Vogel3 & Taufiq Purna Nugraha4,5 & Michael Heistermann6 &\nMuhammad Agil5 & Tony Weingrill1 & Carel P. van Schaik1 Received: 3 August 2020 /Revised: 2 December 2020 /Accepted: 9 December 2020\n# The Author(s) 2020\n/ Published online: 30 December 2020 Abstract Sexual coercion, in the form of forced copulations, is relatively frequently observed in orangutans and generally attributed to their\nsemi-solitary lifestyle. High ecological costs of association for females may be responsible for this lifestyle and may have\nprevented the evolution of morphological fertility indicators (e.g., sexual swellings), which would attract (male) associates. Therefore, sexual conflict may arise not only about mating per se but also about associations, because males may benefit from\nassociations with females to monitor their reproductive state and attempt to monopolize their sexual activities. Here, we evaluate\nassociation patterns and costs for females when associating with both males and females of two different orangutan species at two\nstudy sites: Suaq, Sumatra (Pongo abelii), and Tuanan, Borneo (Pongo pygmaeus wurmbii). Female association frequency with\nboth males and females was higher in the Sumatran population, living in more productive habitat. Accordingly, we found that the\ncost of association, in terms of reduced feeding to moving ratio and increased time being active, is higher in the less sociable\nBornean population. Males generally initiated and maintained such costly associations with females, and prolonged associations\nwith males led to increased female fecal cortisol metabolite (FCM) levels at Tuanan, the Bornean population. We conclude that\nmale-maintained associations are an expression of sexual conflict in orangutans, at least at Tuanan. For females, this cost of\nassociation may be responsible for the lack of sexual signaling, while needing to confuse paternity. 1\nDepartment of Anthropology, University of Zurich,\nZurich, Switzerland 3\nDepartment of Anthropology, Rutgers The State University of New\nJersey, New Brunswick, NJ, USA\n4\nResearch Center for Biology, Indonesian Institute of Sciences (LIPI),\nCibinong, Indonesia\n5\nFaculty of Veterinary Medicine, Bogor Agriculture University,\nBogor, Indonesia\n6\nEndocrinology Laboratory, German Primate Center, Leibniz-Institute\nfor Primate Research, Göttingen, Germany 2\nFaculty of Biology and Primates Research Center, Universitas\nNasional, Jakarta, Indonesia 3\nDepartment of Anthropology, Rutgers The State University of New\nJersey, New Brunswick, NJ, USA Introduction troglodytes]: Emery Thompson and Georgiev 2014;\nGeorgiev et al. 2014). Therefore, males likely benefit from\nassociations with females, as this presumably facilitates mon-\nitoring their reproductive status and sexual activities and may\nbe attempts to mate guard females, even if females are often\nunlikely to be fertile. As a result, females and males may\nexperience a conflict about associating with each other. In\nfact, females may attempt to reduce time spent in associations\nbecause of potential foraging costs (e.g., Knott et al. 2018),\nwhereas males often attempt to prevent them from leaving\n(van Noordwijk and van Schaik 2009). If this is indeed the\ncase, male-female associations in orangutans can be consid-\nered an expression of sexual conflict, and male-maintained\nassociations could be seen as an indirect form of sexual coer-\ncion (cf. Muller et al. 2009). In most mammals, female reproductive success is limited by\naccess to food resources, while that of males is mainly limited\nby access to females (Darwin 1871; Emlen and Oring 1977). Hence, males and females have different behavioral strategies\nto optimize their lifetime fitness, which may lead to sexual\nconflict (Trivers 1972; Parker 1979). The high male-biased\noperational sex ratios in species with long lactational infertil-\nity and no paternal care may exacerbate sexual conflict\n(Clutton-Brock and Parker 1992; van Schaik 2016). Orangutan (Pongo spp.) females exhibit the longest inter-\nbirth intervals in primates of 6 to 9 years (van Noordwijk\net al. 2018), males do not provide direct paternal care for\ninfants (Rijksen 1978; Utami Atmoko et al. 2009), and males\nare not territorial (Spillmann et al. 2017). Hence, male-male\ncompetition for receptive females is high, which carries a high\npotential for sexual conflict (Trivers 1972; Parker 1979). However, the relative importance of male-male competition,\nfemale choice, and sexual conflict in orangutans remains in-\ncompletely understood (Nadler 1981; Fox 1998, 2002; Knott\n2009; Utami Atmoko et al. 2009; Knott et al. 2010; Spillmann\net al. 2010, 2017). There is evidence, however, for the behav-\nioral expression of sexual conflict, in the form of frequent\nforced copulations (Galdikas 1985a; Mitani 1985;\nSchürmann and van Hooff 1986; Knott et al. 2010). Females\nare vulnerable to this form of sexual coercion because of the\npronounced sexual dimorphism (Smuts and Smuts 1993), the\nsemi-solitary lifestyle (Rijksen 1978; van Schaik 1999), and\nthe absence of morphological fertility advertisements, such as\nsexual swellings (Nunn 1999; Zinner et al. 2004). Introduction Interestingly, apparent physical injuries resulting from forced\ncopulations have not been reported, and males seem to use\nonly as much force as is necessary to achieve intromission\n(Knott 2009). Significance statement Socioecological theory predicts a trade-off between the benefits of sociality and the ecological costs of increased feeding\ncompetition. Orangutans’ semi-solitary lifestyle has been attributed to the combination of high association costs and low\npredation risk. Previous work revealed a positive correlation between association frequencies and habitat productivity, but did\nnot measure the costs of association. In this comparative study, we show that females likely incur costs from involuntary, male-\nmaintained associations, especially when they last for several days and particularly in the population characterized by lower\nassociation frequencies. Association maintenance therefore qualifies as another expression of sexual conflict in orangutans, and\nespecially prolonged, male-maintained associations may qualify as an indirect form of sexual coercion. Keywords Concealed ovulation . Cost-of-sexual-attraction hypothesis . Fecal cortisol . Socioecology . Sexu Keywords Concealed ovulation . Cost-of-sexual-attraction hypothesis . Fecal cortisol . Socioecology . Sexual coercion . Pongo spp. Communicated by K. Langergraber Communicated by K. Langergraber Communicated by K. Langergraber * Julia A. Kunz\njuliaandrea.kunz@uzh.ch\n1\nDepartment of Anthropology, University of Zurich,\nZurich, Switzerland\n2\nFaculty of Biology and Primates Research Center, Universitas\nNasional, Jakarta, Indonesia\n3\nDepartment of Anthropology, Rutgers The State University of New\nJersey, New Brunswick, NJ, USA\n4\nResearch Center for Biology, Indonesian Institute of Sciences (LIPI),\nCibinong, Indonesia\n5\nFaculty of Veterinary Medicine, Bogor Agriculture University,\nBogor, Indonesia\n6\nEndocrinology Laboratory, German Primate Center, Leibniz-Institute\nfor Primate Research, Göttingen, Germany 4\nResearch Center for Biology, Indonesian Institute of Sciences (LIPI),\nCibinong, Indonesia 1\nDepartment of Anthropology, University of Zurich,\nZurich, Switzerland 5\nFaculty of Veterinary Medicine, Bogor Agriculture University,\nBogor, Indonesia 6\nEndocrinology Laboratory, German Primate Center, Leibniz-Institute\nfor Primate Research, Göttingen, Germany 6\nEndocrinology Laboratory, German Primate Center, Leibniz-Institute\nfor Primate Research, Göttingen, Germany 6\nEndocrinology Laboratory, German Primate Center, Leibniz-Institute\nfor Primate Research, Göttingen, Germany 6 Page 2 of 22 Behav Ecol Sociobiol (2021) 75: 6 Absence of fertility advertisement and the cost-of-\nsexual-attraction hypothesis Female orangutans do not exhibit any apparent graded, mor-\nphological signals advertising fertility (e.g., sexual swellings;\nNunn 1999; Zinner et al. 2004). Although rare observations of\nfemale proceptive copulations with dominant males have been\nlinked to the peri-ovulatory period (Fox 1998; Knott et al. 2010), ovulation appears largely concealed, as males initiate\ncopulations independent of the females’ reproductive state\nand during periods of lactational infertility (Nadler 1981;\nKnott et al. 2010; Kunz 2020). Unpredictable ovulation in\nother catarrhine primates has been linked to the need to coun-\nteract male monopolization and serves to confuse paternity\nand so offset the risk of infanticide (Hrdy 1979; van\nNoordwijk and van Schaik 2000; van Schaik et al. 2000,\n2004). However, signaling fertility bears costs for females\n(Matsumoto-Oda 1998; Archie et al. 2014). Particularly, the\nenergetic costs of grouping may have prevented females from\nevolving signals that advertise prolonged fertility and attract\nmale associates (Slater et al. 2008; Emery Thompson et al. 2014), thereby achieving such paternity confusion. Accordingly, Wrangham (2002) developed the “cost-of-sexu-\nal-attraction” hypothesis to explain the variation in morpho-\nlogical fertility advertisement in the genus Pan. Indeed, the\ncost of association for females (i) is negatively correlated with\nthe number of swelling cycles to conception (Deschner et al. 2004; Emery Thompson 2005; Douglas et al. 2016) and (ii) is\npositively correlated with the rate of sexual coercion and in-\nfanticide (Wilson et al. 2014). In a high-quality habitat, both\nthe immediate and delayed benefits to associate with males\nand to signal fertility over an extended period may outweigh\nthe costs for females. Bonobos (Pan paniscus) are at this low\ncost of association end (Furuichi 2011; Clay et al. 2016;\nNurmi et al. 2018) and have very prolonged periods of sexual\nattractivity (Douglas et al. 2016), and sexual coercion by\nmales is virtually absent (male aggression: Hohmann and Sexual conflict over associations Sexual conflict may arise not only about actual mating but\nalso about association maintenance. Female orangutans are\nat the solitary end of the fission-fusion spectrum (i.e., females\nspend on average 50–80% of their time with only their own\ndependent offspring; van Schaik 1999; van Noordwijk et al. 2009). The low association frequency suggests that the costs\nof association, in terms of increased scramble feeding compe-\ntition and hence reduced energy acquisition, are substantial for\nboth males and females (Galdikas 1988; van Schaik and Fox\n1996; Utami Atmoko et al. 1997). Yet, associations occur\nnevertheless, even if only one partner benefits. Specifically,\nbecause of the rare siring opportunities, male association de-\ncisions may be less cost-sensitive (van Schaik 1999), and\nmales may accept foraging costs due to increased copulation\nopportunities (orangutans: Mitani 1989; chimpanzees [Pan Page 3 of 22 Behav Ecol Sociobiol (2021) 75: 6 ge 3 of 22 6 Fruth 2003; Paoli 2009; infanticide: Hohmann et al. 2019). The cost of association for chimpanzee females varies geo-\ngraphically. In a more gregarious West African chimpanzee\npopulation (P. troglodytes verus; Boesch and Boesch-\nAchermann 2000; Riedel et al. 2011), rates of sexual coercion\nare low (Stumpf and Boesch 2010) and females may even\ndirectly profit from signaling prolonged sexual attractiveness\n(“Social Passport Hypothesis”; Deschner and Boesch 2007). In contrast, in an East African chimpanzee population\n(P. troglodytes schweinfurthii), females’ foraging effort is\ncompromised and their energy balance decreases with an in-\ncreasing number of males in association (Emery Thompson\net al. 2014). Consistent with the cost-of-sexual-attraction hy-\npothesis, East African chimpanzees have fewer swelling cy-\ncles per conception (Emery Thompson 2005; Deschner et al. 2004; but see Deschner and Boesch 2007), more male sexual\ncoercion (Muller et al. 2007, 2011), and more infanticide\n(Wilson et al. 2014) than West African chimpanzees. Harrison et al. 2010; Vogel et al. 2017). In previous studies,\nit has been shown that day journey length increases with in-\ncreasing association size, indicative of increased scramble\ncompetition both in Sumatran and Bornean populations (Fox\n1998; van Schaik 1999; Wartmann et al. 2010). In some respects, it appears that the orangutan species have\nadapted to their distinct conditions, and even under similar\nfood availability in captivity they show a different response\nto increased sociability. Male bimaturism and sexual conflict Orangutans exhibit a uniquely pronounced male bimaturism,\nwhich has been associated with alternative male reproductive\nstrategies (MacKinnon 1974; Utami Atmoko and van Hooff\n2004; Pradhan et al. 2012; Dunkel et al. 2013). Unflanged\nmales, who lack secondary sexual characteristics, reportedly\nassociate, copulate, and coerce copulations more frequently\nthan flanged males in the majority of study populations\n(MacKinnon 1974; Galdikas 1985b; Sugardjito et al. 1987;\nKnott 2009; Mitra Setia et al. 2009; Utami Atmoko et al. 2009; JAK et al., unpubl. data). Flanged males, who have fully\ndeveloped secondary sexual characteristics, emit long calls\nand are reported to rely largely on female choice around con-\nception (Fox 2002; Mitra Setia and van Schaik 2007;\nSpillmann et al. 2010). Although there is evidence for varia-\ntion among populations and species in the reproductive strat-\negies of the male morphs (Delgado and van Schaik 2000;\nKnott and Kahlenberg 2007; Mitra Setia and van Schaik\n2007; Utami Atmoko et al. 2009; Spillmann et al. 2017), sex-\nual conflict over associations is likely more pronounced with\nunflanged males than with flanged males, because the former\nassociate more frequently with females and cannot rely on\nfemale choice. Sexual conflict over associations In zoos, Bornean orangutans perma-\nnently housed with up to 5 adults exhibited overall higher\nfecal cortisol metabolite (FCM) levels than the more gregari-\nous Sumatran orangutans living in groups with up to 8 adults,\nwhich was attributed to species differences in the sensitivity to\nsocial stress (Weingrill et al. 2011). Moreover, captive\nBornean orangutans that were kept in fission-fusion like hous-\ning systems exhibited lower FCM levels than those kept in a\nstable group (Amrein et al. 2014). Taken together, these re-\nsults indicate that social factors, especially extended sociality,\nlead to a stronger physiological stress response in the less\nsociable Bornean orangutans, suggesting that they will also\nprefer lower association rates in the wild. Following the idea of the cost-of-sexual-attraction hypoth-\nesis, the absence of morphological fertility advertisement in\nthe genus Pongo may reflect the prohibitively high costs of\nassociation to repeatedly signal fertility, while still needing to\navoid male monopolization and thus confuse paternity. Here,\nwe evaluate the costs of association in orangutans; future stud-\nies will investigate how those relate to the frequency of sexual\ncoercion. Geographic variation in sociability in orangutans In the absence of high predation pressure due to their arboreal\nlife style (van Schaik and van Hooff 1983), food abundance is\nthe major constraint to population density and sociality in\norangutans (van Schaik 1999; Hardus et al. 2013; Vogel\net al. 2015). Fruit availability is not only thought to be respon-\nsible for the higher association frequency in West Sumatran\n(Pongo abelii) (average daily party size ranging from 1.6 to\n1.9 individuals) compared to both Eastern Sumatran\n(P. abelii) as well as Bornean orangutans (Pongo pygmaeus)\n(average daily party size ranging from 1.05 to 1.3 individuals)\n(van Schaik 1999; Mitra Setia et al. 2009; Wich et al. 2011;\nRoth et al. 2020), it also likely constrains associations within\npopulations over time (van Schaik and Fox 1996; Fox 1998;\nWich et al. 2006; Roth et al. 2020; J.Meric de Bellefon et al.,\nunpublished data). A high degree of scramble competition has\nbeen held responsible for the low female sociability, and direct\nfemale-female contest competition has also been reported\n(Utami Atmoko et al. 1997; Knott et al. 2008; van\nNoordwijk et al. 2012; Marzec et al. 2016). The ecological\neffect on association frequency, however, would be expected\nto be most prominent in associations between males and fe-\nmales because of the sex differences in ranging patterns and\nactivity budgets connected to their distinct energetic demands\n(Morrogh-Bernard et al. 2009; van Schaik et al. 2009; Aim of the study Associations and their maintenance may present another,\nmore subtle, context of sexual conflict in addition to forced\ncopulations in orangutans. Following the “cost-of-sexual- Behav Ecol Sociobiol (2021) 75: 6 6 Page 4 of 22 attraction” hypothesis (Wrangham 2002), high costs of asso-\nciation may be responsible for the absence of morphological\nfertility advertisements in female orangutans. Here, we evalu-\nate the costs of association for female orangutans with both\nfemales and males at two study sites, Suaq (P. abelii, Sumatra)\nand Tuanan (P. pygmaeus, Borneo) using behavioral and en-\ndocrine data. Because of large within-species variation in\nterms of their socioecology (e.g., Vogel et al. 2015; Roth\net al. 2020) and little evidence for life history differences be-\ntween species (van Noordwijk et al. 2018), we refer to study\nsite rather than species differences, as we evaluate only one\nstudy site per species. We included female-female associa-\ntions as a comparative category with the assumption that fe-\nmales have similar incentives to associate with each other (van\nNoordwijk et al. 2012) as opposed to male-female associa-\ntions and that these therefore are likely cost-sensitive (sensu\nvan Schaik 1999). We measured behavioral changes (i.e.,\nchanges in the daily activity budget) and variation in fecal\ncortisol metabolite (FCM) levels of parous females in relation\nto different types of association and social interactions. We\nhypothesized that (1) if males benefit from monitoring a fe-\nmale’s reproductive state and potentially attempt to monopo-\nlize a female’s sexual activities, they likely initiate and main-\ntain such associations with females; (2) social interactions\nbetween males and females are rare and therefore females\nlikely do not gain direct social benefits from associations with\nmales (for an exception see Marzec et al. 2016), whereas as-\nsociations with other females may provide social benefits for\ntheir infants (e.g., play opportunities; van Noordwijk et al. 2012); (3) associations with both males and females lead to\nhigher foraging costs, i.e., increased moving and reduced\nfeeding time, for females of the less sociable population,\nTuanan, than females of the more sociable population, Suaq;\nand (4) besides scramble competition, costs of grouping fe-\nmales may bear additional costs from agonistic interactions,\nespecially the occurrence of forced copulations, during asso-\nciations with males. In Table 1, we provide a detailed over-\nview of hypotheses and predictions. multiple years (van Noordwijk et al. Aim of the study 2013), both asso-\nciation patterns and the cost-benefit balances incurred\nby sociability are likely different from nulliparous\n(adolescent) females (van Schaik et al. 2009; Ashbury\net al. 2020). Therefore, only data on parous females\nwith a dependent offspring were included in this study\n(N = 20 females [Suaq: 6; Tuanan: 14]). Similarly, fe-\nmales who had lost their infants due to unknown rea-\nsons (Marzec et al. 2016; MAvN et al. unpubl. data)\nwere excluded from the analyses after the loss of their\ninfants, until they had given birth to a new infant. Infant loss is an extremely rare event (van Noordwijk\net al. 2018), and insufficient data were available to add\nthem as a separate category. The age of the dependent\noffspring of females was taken as a proxy for their\nreproductive state and included in all the analyses\n(Table 2). Infant ages were either known because the\nbirth was directly observed or estimated from the first\ntime an infant was observed (Table 2; cf. van\nNoordwijk et al. 2018). Activity budget Behavioral data were collected according to an established,\nstandardized protocol (https://www.aim.uzh.ch/de/\norangutannetwork/sfm.html). We collected 2-min instanta-\nneous data during full-day female focal follows on their activ-\nities (feeding, moving, resting, and social interactions). We\nrecorded all occurrences of any individual in association\n(within 50-m distance) per 2-min interval and ad libitum social\ninteractions with the focal individual. Social partners included\nthe female’s own dependent and independent offspring, ado-\nlescent individuals, and adult females and males (unflanged\nand flanged). We subdivided social interactions into sexual,\naffiliative, and aggressive interactions. Sexual interactions\ncomprised genital investigations by males, copulations, and\ncopulation attempts. Copulations were labelled as either\nforced, if the female showed any resistance behavior\n(e.g., repeated attempt to move away, struggling against\nthe males attempt to intromit), or unforced (following the\ndefinition of Fox 1998). We grouped aggression between\nfemales and both males and other females (excluding\nforced copulations) into non-physical (displays, short\nchases) and physical aggression (fights or coercive hand\nholding by males (van Schaik et al. 2006)). Affiliative\ninteractions comprised allo-grooming, touching another\nindividual, sitting in body contact, and begging for and\nsharing food. Because focal animals were individually\nrecognized, we could not collect blinded data. Only data\nfrom well-trained observers with high inter-observer reli-\nability were included in the analyses. Study sites and study subjects Behavioral focal data on individually recognized adult\nfemales were collected at the long-term field sites of\nTuanan, Mawas Reserve, Central Kalimantan,\nIndonesia (02° 15′ S; 114° 44′ E) and Suaq, Gunung\nLeuser National Park, South Aceh, Indonesia (03° 02′\nN; 97° 25′ E) between July 2003–July 2018 and June\n2007–March 2018, respectively. Because parous females\nare in continued association with their dependent off-\nspring (van Noordwijk et al. 2009) and lactate over Page 5 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 2 6 Table 1\nOverview of the two main hypotheses evaluated in this study with the corresponding predictions\nHypotheses and predictions\nAdditional variables\nTested in\nSite†\nMale morph‡\nTab.$\nFig.$\nMain hypothesis: Associations are a context of sexual conflict in orangutans and may therefore\nqualify as a form of indirect sexual coercion. T > S\nUFM > FLM\nPart 1: Male direct benefits to associate with females exceeds those of females\nAssociation and social\ninteractions (benefits)\nPrediction 1.1: Male-female associations are more frequent than\nfemale-female associations.E\nT > SE\nUFM > FLME\nS 1\nS 1\nPrediction 1.2: Associations are male-initiated and\nmale-maintained.E\nT > SNE\nUFM > FLMNE\nS 2\n1–2\nPrediction 1.3: Male-female associations last longer than\nfemale-female associations, indicating that males benefit from\nprolonged associations.E Tuanan\nT > SE\nUFM > FLMNE\n3\n3\nPrediction 1.4: Affiliative social interactions are rare during\nmale-female associations, indicating near-absence of direct\nsocial benefits to females from associations with males.E\nT < SE\nUFM > FLME\nBuilding up\nrelationship? S 5\nS 2\nPrediction 1.5: Agonistic social interactions outside of the sexual\ncontext are rare during male-female associations, indicating\nnear-absence of direct coercive mate guarding by males.E\nNA\nUFM > FLMO\nS 6\nS 2\nPrediction 1.6: Sexual interactions (particularly forced\ncopulations) and genital investigations by males are frequently\nobserved in associations with females, indicating reproductive\nbenefits for males from associations.E\nT < SE,O\nUFM > FLME\nS 7–8\nS 3\nPart 2: Females incur costs from associations with males as a result of both increased feeding competition and the social interactions meanwhile. Cost of association to females\nPrediction 2.1: Females’ activity budget changes reflect increased\nscramble competition when in association with males. Study sites and study subjects Active\ntime increases and the F:M ratio decreases when in association\nwith males.E\nT > SE\nNot tested (but P1.1:\nUFM > FLME)\n4\nS 9–12\n4\nS 4\nPrediction 2.1.1: Females’ activity budget changes reflect\nincreased scramble competition when in association with any\nadult individual: Active time increases and the F:M ratio\ndecreases when in association with females.E\nT > SE\nNA\n4\nS 9–12\n4\nS 4\nPrediction 2.2: Aggression by males imposes further costs on\nfemales. Female F:M ratio decreases on days when they\nexperience male aggression (either sexual or non-sexual\naggression).NE (E copulation occurrence at Tuanan)\nT = SNE\nNot tested\n(UFM > FLM)\n4\nS 9–12\n5\nS 5\nPrediction 2.2.1: Aggression by other females also imposes costs\non females and therefore, female F:M ratio decreases also on\ndays when they experience aggression from other females,\nindicating that social stressors affect females’ activity budget.NE\nT = SNE\nNA\n4\nS 9–12\nNA\nPrediction 2.3: Female FCM levels are higher on days when in\nassociation with males than on days when females are alone\nwith their dependent offspring or in association with other\nfemales. Male associates therefore are a social stressor to\nfemales.NE\nT = SUnk\nNot tested (but P1.1)\n5\nNA\nPrediction 2.3.1: Female FCM levels are also higher on days\nwhen females are in association with other adult females than\nwhen alone with their dependent offspring. Any adult\nassociation partner may qualify as a social stressor to\nfemales.NE\nT = SUnk\nNA\n5\nNA\nPrediction 2.4: Female FCM levels increase with an increasing\nnumber of days spent in association with any association\npartner as a result of the accumulating negative energy balance,\nindicating energetic stress.E\nT > SUnk\nNA\n5\n6\nPrediction 2.5: Female FCM levels are higher on days when they\nexperience forced copulations, indicating either social (Soc.) or\nenergetic (Eco.) costs.NE\nSoc. T = S\nEco. Study sites and study subjects Observed cost-benefit balances and thus, predictions may vary with both study site († ) and male morph (‡ ). The\ntwo right columns indicate where the corresponding test (table with model output and figure) can be found † Association frequency is reportedly higher at Suaq (S) than at Tuanan (T), indicating generally lower costs of association at Suaq than at Tuanan. Accordingly, each prediction may vary with the socioecological background of the study site (“T > S”: prediction is more pronounced at Tuanan than\nSuaq; “T < S”: prediction more pronounced at Suaq than at Tuanan; “T = S”: no site difference expected) ‡ The two male morphs follow different reproductive tactics. While flanged males (FLM) are reportedly preferred by females, associate, and copulate\nmore selectively, unflanged males (UFM) associate, copulate, and coerce more frequently at Suaq and Tuanan (Kunz 2020). Both the extent of social\nbenefit and the cost of association inflicted on females may therefore vary with male morph and their reproductive tactic ‡ The two male morphs follow different reproductive tactics. While flanged males (FLM) are reportedly preferred by females, associate, and copulate\nmore selectively, unflanged males (UFM) associate, copulate, and coerce more frequently at Suaq and Tuanan (Kunz 2020). Study sites and study subjects T > S\nNot tested\n(UFM > FLM)\n5\n7\nMain hypothesis 2: Female orangutans do not exhibit any apparent morphological fertility advertisements because of the prohibitively high costs of Overview of the two main hypotheses evaluated in this study with the corresponding predictions Hypotheses and predictions Association and social\ninteractions (benefits) Prediction 2.2.1: Aggression by other females also imposes costs\non females and therefore, female F:M ratio decreases also on\ndays when they experience aggression from other females,\nindicating that social stressors affect females’ activity budget.NE\nT = SNE\nNA\n4\nS 9–12\nNA\ndi i\nl\nl\nl\nhi h\nd\nh\ni\nUnk\nd b Prediction 2.3: Female FCM levels are higher on days when in\nassociation with males than on days when females are alone\nwith their dependent offspring or in association with other\nfemales. Male associates therefore are a social stressor to\nfemales.NE\nT = SUnk\nNot tested (but P1.1)\n5\nNA Prediction 2.3.1: Female FCM levels are also higher on days\nwhen females are in association with other adult females than\nwhen alone with their dependent offspring. Any adult\nassociation partner may qualify as a social stressor to\nfemales.NE\nT = SUnk\nNA\n5\nNA Prediction 2.4: Female FCM levels increase with an increasing\nnumber of days spent in association with any association\npartner as a result of the accumulating negative energy balance,\nindicating energetic stress.E\nT > SUnk\nNA\n5\n6 Prediction 2.5: Female FCM levels are higher on days when they\nexperience forced copulations, indicating either social (Soc.) or\nenergetic (Eco.) costs.NE\nSoc. T = S\nEco. T > S\nNot tested\n(UFM > FLM)\n5\n7 g\nMain hypothesis 2: Female orangutans do not exhibit any apparent morphological fertility advertisements, because of the prohibitively high costs of\nassociation (cost-of-sexual-attraction hypothesis prediction 1), while needing to confuse paternity. Study sites and study subjects Observed cost-benefit balances and thus, predictions may vary with both study site († ) and male morph (‡ ). The\ntwo right columns indicate where the corresponding test (table with model output and figure) can be found\n† Association frequency is reportedly higher at Suaq (S) than at Tuanan (T), indicating generally lower costs of association at Suaq than at Tuanan. Accordingly, each prediction may vary with the socioecological background of the study site (“T > S”: prediction is more pronounced at Tuanan than\nSuaq; “T < S”: prediction more pronounced at Suaq than at Tuanan; “T = S”: no site difference expected)\n‡ The two male morphs follow different reproductive tactics. While flanged males (FLM) are reportedly preferred by females, associate, and copulate\nmore selectively, unflanged males (UFM) associate, copulate, and coerce more frequently at Suaq and Tuanan (Kunz 2020). Both the extent of social\nbenefit and the cost of association inflicted on females may therefore vary with male morph and their reproductive tactic\n$ The “S” in front of the number indicates that the table or figure, respectively, can be found in the supplementary materials\nE, evidence for this prediction was found in the current study; NE, no evidence was found for this prediction in the current study; Unk, not enough\nevidence to either support or disapprove the prediction, often because of limited data sets; O, evidence for the opposite pattern (for study site and male\nmorph comparison) (\n)\nHypotheses and predictions\nAdditional variables\nTested in\nSite†\nMale morph‡\nTab.$\nFig.$\nPrediction 3.2: The frequency of male-female associations in-\ncreases with the age of the dependent offspring indicating some\nreproductive benefits (conception and paternity manipulation),\nwhile female-female association remains constant over the age\nof the dependent offspring (indicating socializing benefits).E\nNA\nNA\nS 1\nS 1 Predictions include the evaluation of social benefits (P1.1–1.6) and costs resulting from both associations and social interactions (P2.1–2.5) during\nassociations between males and females. Observed cost-benefit balances and thus, predictions may vary with both study site († ) and male morph (‡ ). The\ntwo right columns indicate where the corresponding test (table with model output and figure) can be found Predictions include the evaluation of social benefits (P1.1–1.6) and costs resulting from both associations and social interactions (P2.1–2.5) during\nassociations between males and females. Table 2 Overview of the data\navailable to assess the cost of\nassociation for parous females at\nTuanan and Suaq § Number of days included in the analyses *Number of samples included in analyses\n§ Number of days included in the analyses Study sites and study subjects Prediction 3.1: Females incur costs from associations with males,\nwhich are consistent with scramble competition of grouping\n(predictions 2.1, 2.4).E\nT > S E\nNA\n4, 5\n4, 6 Table 1 (continued)\nHypotheses and predictions\nAdditional variables\nTested in\nSite†\nMale morph‡\nTab.$\nFig.$\nPrediction 3.2: The frequency of male-female associations in-\ncreases with the age of the dependent offspring indicating some\nreproductive benefits (conception and paternity manipulation),\nwhile female-female association remains constant over the age\nof the dependent offspring (indicating socializing benefits).E\nNA\nNA\nS 1\nS 1\n6 Page 6 of 22\nBehav Ecol Sociobiol (2021) 75: 6 Behav Ecol Sociobiol (2021) 75: 6 Table 1 (continued)\nHypotheses and predictions\nAdditional variables\nTested in\nSite†\nMale morph‡\nTab.$\nFig.$\nPrediction 3.2: The frequency of male-female associations in-\ncreases with the age of the dependent offspring indicating some\nreproductive benefits (conception and paternity manipulation),\nwhile female-female association remains constant over the age\nof the dependent offspring (indicating socializing benefits).E\nNA\nNA\nS 1\nS 1\nPredictions include the evaluation of social benefits (P1.1–1.6) and costs resulting from both associations and social interactions (P2.1–2.5) during\nassociations between males and females. Observed cost-benefit balances and thus, predictions may vary with both study site († ) and male morph (‡ ). The\ntwo right columns indicate where the corresponding test (table with model output and figure) can be found\n† Association frequency is reportedly higher at Suaq (S) than at Tuanan (T), indicating generally lower costs of association at Suaq than at Tuanan. Accordingly, each prediction may vary with the socioecological background of the study site (“T > S”: prediction is more pronounced at Tuanan than\nSuaq; “T < S”: prediction more pronounced at Suaq than at Tuanan; “T = S”: no site difference expected)\n‡ The two male morphs follow different reproductive tactics. While flanged males (FLM) are reportedly preferred by females, associate, and copulate\nmore selectively, unflanged males (UFM) associate, copulate, and coerce more frequently at Suaq and Tuanan (Kunz 2020). Study sites and study subjects Both the extent of social\nbenefit and the cost of association inflicted on females may therefore vary with male morph and their reproductive tactic\n$ The “S” in front of the number indicates that the table or figure, respectively, can be found in the supplementary materials\nE, evidence for this prediction was found in the current study; NE, no evidence was found for this prediction in the current study; Unk, not enough\nevidence to either support or disapprove the prediction, often because of limited data sets; O, evidence for the opposite pattern (for study site and male\nmorph comparison)\nTable 2 Overview of the data\navailable to assess the cost of\nassociation for parous females at\nTuanan and Suaq\nStudy\nsite\nName of\nparous\nfemale\nDependent infant\nActivity budget\nHormone samples\nMinimum\nage of\ninfant\n(years)\nMaximum\nage of infant\n(years)\nNumber\nof follow\nperiods\nNumber of\nfull-day focal\nfollows§\nTotal\nsamples\navailable\nWith\nbehavioral\nreference*\nSuaq\nCissy\n1.6\n5.2\n4\n35\n42\n13\nSuaq\nEllie\n0.3\n2.7\n4\n37\n32\n14\nSuaq\nFriska\n0.9\n4.9\n8\n51\n33\n10\nSuaq\nLisa\n0.5\n7.7\n11\n77\n60\n15\nSuaq\nRaffi\n0.8\n1.7\n1\n6\n12\n0\nSuaq\nSarabi\n0.6\n0.9\n2\n15\n4\n0\nTuanan\nCikipos\n3.2\n3.2\n1\n5\n6\n0\nTuanan\nCinta\n0.9\n2.7\n3\n17\n12\n5\nTuanan\nDesy\n0.0\n5.8\n13\n105\n54\n37\nTuanan\nInul\n0.1\n3.3\n12\n77\n44\n24\nTuanan\nJinak\n0.3\n7.1\n45\n365\n66\n39\nTuanan\nJuni\n0.0\n6.6\n33\n255\n88\n51\nTuanan\nKerry\n0.0\n7.5\n40\n280\n65\n38\nTuanan\nKondor\n0.0\n1.9\n10\n64\n23\n12\nTuanan\nMilo\n0.1\n1.1\n3\n20\n9\n6\nTuanan\nMindy\n0.1\n6.9\n52\n390\n95\n65\nTuanan\nPinky\n0.0\n7.5\n6\n39\n25\n7\nTuanan\nSidony\n0.0\n6.1\n6\n58\n45\n25 Table 1 (continued)\nHypotheses and predictions\nAdditional variables\nTested in\nSite†\nMale morph‡\nTab.$\nFig.$\nPrediction 3.2: The frequency of male-female associations in-\ncreases with the age of the dependent offspring indicating some\nreproductive benefits (conception and paternity manipulation),\nwhile female-female association remains constant over the age\nof the dependent offspring (indicating socializing benefits).E\nNA\nNA\nS 1\nS 1\nPredictions include the evaluation of social benefits (P1.1–1.6) and costs resulting from both associations and social interactions (P2.1–2.5) during\nassociations between males and females. *Number of samples included in analyses Collection, preservation, and extraction of fecal samples We measured fecal cortisol metabolite (FCM) levels for fe-\nmales during association and non-association days. Fecal ma-\nterial was collected non-invasively, when individuals defecat-\ned naturally. Because there is an excretion lag time of 24–72 h\nfor fecal cortisol metabolites (Weingrill et al. 2011), samples\nwere collected on at least 5 consecutive days, once a day,\npreferably in the morning. Due to individual ranging patterns\nin orangutans, samples could only be taken during focal fol-\nlows lasting 5–10 days with at least 5 weeks between succes-\nsive sample periods, because individuals were not followed\nduring this time. The methods to preserve and extract fecal\nsamples from orangutans for hormone analyses have been\nestablished and validated (Weingrill et al. 2011; Amrein\net al. 2014; Marty et al. 2015; Nugraha et al. 2016). Because\nof logistic constraints and varying infrastructures at the two\nfield sites, different preservation and extraction methods had\nto be used. Generally, the fresh feces were homogenized using\na stick and a 2–5-g aliquot was collected for analysis. Only\nsamples not contaminated with urine were taken. When elec-\ntricity from solar power was available, the fresh feces were\ncollected into a polypropylene tube and frozen at −18 °C\nupon return to the field station in the evening. All samples\nremained frozen until transported to the endocrinology labo-\nratory at Bogor Agricultural University where samples were\nlyophilized, pulverized and subsequently extracted with 80%\nmethanol in water as described in detail elsewhere (Weingrill\net al. 2011; Nugraha et al. 2016). At Suaq and when electricity\nsupply was not guaranteed at Tuanan, fecal samples were\nplaced in a tube containing 5 ml of 80% ethanol in water for\npreservation upon collection. Samples were extracted upon\nreturn to the field station using a field-friendly, previously\nvalidated extraction method (Nugraha et al. 2016). Although\nthese extraction methods have been shown to produce results\nwhich are strongly correlated (Nugraha et al. 2016), we con-\ntrolled for potential extraction method differences by normal-\nizing all FCM measurements within individual and method\nusing z-transformations in the statistical analyses (van de Pol\nand Wright 2009; for details see data analysis section). Study sites and study subjects Both the extent of social\nbenefit and the cost of association inflicted on females may therefore vary with male morph and their reproductive tactic The S in front of the number indicates that the table or figure, respectively, can be found in the supplementary materials\nE, evidence for this prediction was found in the current study; NE, no evidence was found for this prediction in the current study; Unk, not enough\nevidence to either support or disapprove the prediction, often because of limited data sets; O, evidence for the opposite pattern (for study site and male\nmorph comparison) E, evidence for this prediction was found in the current study; NE, no evidence was found for this prediction in the current study; Unk, not enough\nevidence to either support or disapprove the prediction, often because of limited data sets; O, evidence for the opposite pattern (for study site and male\nmorph comparison) Study\nsite\nName of\nparous\nfemale\nDependent infant\nActivity budget\nHormone samples\nMinimum\nage of\ninfant\n(years)\nMaximum\nage of infant\n(years)\nNumber\nof follow\nperiods\nNumber of\nfull-day focal\nfollows§\nTotal\nsamples\navailable\nWith\nbehavioral\nreference*\nSuaq\nCissy\n1.6\n5.2\n4\n35\n42\n13\nSuaq\nEllie\n0.3\n2.7\n4\n37\n32\n14\nSuaq\nFriska\n0.9\n4.9\n8\n51\n33\n10\nSuaq\nLisa\n0.5\n7.7\n11\n77\n60\n15\nSuaq\nRaffi\n0.8\n1.7\n1\n6\n12\n0\nSuaq\nSarabi\n0.6\n0.9\n2\n15\n4\n0\nTuanan\nCikipos\n3.2\n3.2\n1\n5\n6\n0\nTuanan\nCinta\n0.9\n2.7\n3\n17\n12\n5\nTuanan\nDesy\n0.0\n5.8\n13\n105\n54\n37\nTuanan\nInul\n0.1\n3.3\n12\n77\n44\n24\nTuanan\nJinak\n0.3\n7.1\n45\n365\n66\n39\nTuanan\nJuni\n0.0\n6.6\n33\n255\n88\n51\nTuanan\nKerry\n0.0\n7.5\n40\n280\n65\n38\nTuanan\nKondor\n0.0\n1.9\n10\n64\n23\n12\nTuanan\nMilo\n0.1\n1.1\n3\n20\n9\n6\nTuanan\nMindy\n0.1\n6.9\n52\n390\n95\n65\nTuanan\nPinky\n0.0\n7.5\n6\n39\n25\n7\nTuanan\nSidony\n0.0\n6.1\n6\n58\n45\n25\nTuanan\nSumi\n0.4\n3.4\n20\n154\n0\n0\nTuanan\nTina\n3.7\n5.5\n5\n36\n27\n9\n*Number of samples included in analyses\n§ Number of days included in the analyses Page 7 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 (Vogel et al. 2017), and can thus be taken as a proxy for forest\nproductivity (Vogel et al. 2015). Association patterns and social interactions Male focal follows collected with the same methods as the\nfemale focal follows were used to enhance the data set on\nthe duration of associations and a fuller record of male-\nfemale dyadic interactions resulting in 960 male-female asso-\nciations (Suaq: 292; Tuanan: 668) with known start and end\ntimes. An association between two individuals could last for\nmultiple days and contain breaks, i.e., the association partners\nwere at a distance of more than 50 m. Orangutans most likely\nperceive the presence of other individuals at distances of more\nthan 50 m better than humans on the ground (van Noordwijk\net al. 2009, 2012), and therefore, brief “separations” (> 50-m\ndistance) likely are not relevant to them. If breaks lasted for\nlonger than one full-day focal follow, we considered it as two\nseparate association units. We recorded the individual respon-\nsible for any distance changes (in distance classes: contact, no\ncontact < 2 m, 2–5 m, 5–10 m, 10–50 m) during the associa-\ntion, as well as the initiator (first approach to < 50 m) and\nterminator (who left to > 50 m) of associations. We calculated\nthe Female Hinde Index (FHI) for female-male associations\nbased on these approaches and leaves as follows: Collection, preservation, and extraction of fecal samples Female Hinde Index FHI\nð\nÞ\n¼\napproaches by female\napproaches by female þ approaches by male\n\u0001\n\u0003\n−\nleaves by female\nleaves by female þ leaves by male\n\u0001\n\u0003 Female Hinde Index FHI\nð\nÞ A positive FHI indicates that the female was on average\nresponsible for the maintenance of the association, while a\nnegative FHI stands for a male-maintained association\n(Hinde and Atkinson 1970). The FHIs were calculated over\nall known approach and leave events and distance classes per\nassociation. Detailed approach and leave data throughout the\nassociation for the FHIs is available for 665 male-female as-\nsociations (Suaq: 223; Tuanan: 442). Ecological data The monthly Fruit Availability Index (FAI; percentage of\ntrees with fruits over all surveyed trees) was obtained from\nmonthly phenology surveys of ~ 1500 trees at Tuanan and ~\n1000 trees at Suaq (Harrison et al. 2010; Vogel et al. 2015)\n(Table 3). Because the FAI is generally higher at Suaq than at\nTuanan (Wich et al. 2011), we z-transformed all the FAIs\nwithin study site prior to the analyses (zFAI) to assess local\nFAI effects rather than between site comparisons. Although\nthe FAI does not include fruits from lianas, which are compo-\nnents of orangutan diet, it corresponds well to the total pro-\nportion of fruits, i.e., high-quality food items, in their diet Hormone measurement Fecal cortisol metabolite levels were measured in a total of\n745 samples (Table 2) using a microtiter plate enzyme immu-\nnoassay (EIA) for 11ß-hydroxyetiocholanolone (Ganswindt\net al. 2003), a major metabolite of cortisol in primate feces\n(Heistermann et al. 2006). The assay has been previously Behav Ecol Sociobiol (2021) 75: 6 6 Page 8 of 22 Table 3\nDefinition of fixed factors included in the activity budget analyses based on female full-day focal follows (z, continuous variables were z-\ntransformed prior to analyses)\nType\nFactor\nDefinition\nSocial\nz Cumulative male\nassociation hours\nThe sum of all association time spent with males during a full-day focal follow, e.g., if a female was 1 h in\nassociation with male A and 5 h with male B on a full-day focal follow, it would result in 6 cumulative\nmale association hours$\nz Cumulative female\nassociation hours\nThe sum of all association time spent with females during a full-day focal follow$\nNumber of consecutive days\nwith males\nThe number of (known) days a female focal animal was in association with males, independent of the\nmales’ identity, e.g., the female may have been in association with male A for 2 days and with male B\nthe next day, which would be 3 consecutive days with males\nNumber of consecutive days\nwith females\nThe number of (known) days a female focal animal was in association with females, independent of the\nfemale partner’s identity\nNumber of copulations\nNumber of observed copulations during the female full-day focal follow\nMale-female cumulative\naggression index\nWe combined the occurrence of forced copulations and other male aggression to a daily male-female\ncumulative aggression index, coded for severity (0 = no aggression; 1 = aggression not directly in a\nsexual context and no physical contact, such as displays, chases and displacements; 2 = forced sexual\ninteractions)\nFemale-female agonistic\ninteractions\nDays with female-female aggression were rare (N = 2 [Suaq], 16 [Tuanan]), and could only be included as\npresence/absence data, and not coded for the severity\nSocial interaction time (h)\nThe total time spent in social interactions with any partner (including own dependent infant and\nassociation partners) during a full-day focal follow (social interactions account for ~ 0.5% of the total\nactive time [Tuanan: 0.4%; Suaq: 1.1%])\nSite (Suaq vs. Tuanan)\nPopulation differences may be the result of either species or ecological differences between the two study\npopulations. did not exceed 15%. All FCM concentrations are expressed\nin ng/g dry fecal weight. did not exceed 15%. All FCM concentrations are expressed\nin ng/g dry fecal weight. did not exceed 15%. All FCM concentrations are expressed\nin ng/g dry fecal weight. validated and successfully applied for assessing adrenocorti-\ncal activity in numerous primate species (e.g., Heistermann\net al. 2006) including captive and wild orangutans\n(Weingrill et al. 2011; Amrein et al. 2014; Marty et al. 2015). Samples used for this study were analyzed in different\ncohorts at two different laboratories (German Primate Center,\nDPZ, by A. Heistermann and Bogor Agricultural University,\nIPB, by JAK), with the locality of analysis for each sample\nincluded as a fixed effect in the statistical analyses (results\nremain the same if we standardize by both laboratory, method\nand individual, and are not shown below). EIAs were per-\nformed as previously described (Heistermann et al. 2004). Samples from the same individual were analyzed on the same\nmicrotiter plate, whenever possible. Each sample was ana-\nlyzed in duplicate. We remeasured samples with a coefficient\nof variation (CV) > 7% between duplicates. Moreover, we\nreran any microtiter plate for which the intra-assay CV of\nthe internal high- and low-value quality controls exceeded\n10%. For the samples analyzed at both IPB and DPZ, the\nintra-assay CVs were below 10%, and the inter-assay CVs Hormone measurement Forest productivity is generally higher at Suaq (Sumatra, P. abelii) than at Tuanan\n(Borneo, P. pygmaeus wurmbii) (Wich et al. 2011). Ecological\nz Fruit Availability Index\nMonthly percentage of trees with fruits over all surveyed trees based on monthly surveys (~ 1500 trees at\nTuanan and ~ 1000 trees at Suaq)\nPhysiological z Age of dependent offspring\n(years)\nInfant ages were either known because the birth was directly observed, or estimated from the first time an\ninfant was observed (Table 2) Table 3\nDefinition of fixed factors included in the activity budget analyses based on female full-day focal follows (z, continuous variables were z-\ntransformed prior to analyses) The total time spent in social interactions with any partner (including own dependent infant and\nassociation partners) during a full-day focal follow (social interactions account for ~ 0.5% of the total\nactive time [Tuanan: 0.4%; Suaq: 1.1%]) Population differences may be the result of either species or ecological differences between the two study\npopulations. Forest productivity is generally higher at Suaq (Sumatra, P. abelii) than at Tuanan\n(Borneo, P. pygmaeus wurmbii) (Wich et al. 2011). Population differences may be the result of either species or ecological differences between the two study\npopulations. Forest productivity is generally higher at Suaq (Sumatra, P. abelii) than at Tuanan\n(Borneo, P. pygmaeus wurmbii) (Wich et al. 2011). Index\nMonthly percentage of trees with fruits over all surveyed trees based on monthly surveys (~ 1500 trees at\nTuanan and ~ 1000 trees at Suaq) Physiological z Age of dependent offspring\n(years)\nInfant ages were either known because the birth was directly observed, or estimated from the first time an\ninfant was observed (Table 2) $ We chose to include the daily cumulative hours spent with either adult females or males to account for multiple individuals in association and the\nduration spent with each of them (including both association time and the number of individuals as separate variables would have led to multi-collinearity\nissues) Behavioral data—association patterns and maintenance We evaluated the time (average daily hours) females spent in\nassociation with either other females or unflanged and flanged\nmales during follow periods in separate analyses (LMM) and\nwith the study site, zFAI, and the age of the dependent off-\nspring as fixed effects. Individual identity was added as a\nrandom intercept. We assessed when associations were male-maintained by\nsetting up a binomial GLMM based on the FHI values (male-\nmaintained when FHI < 0). We added study site, male morph,\nthe age of the dependent offspring of the female (years), local\nfruit availability (zFAI), the occurrence of copulations (both\nunforced and forced), and association duration as fixed ef-\nfects. To account for having the same individuals in several\nassociation dyads, both female and male identities were added\nas crossed random intercepts. p\nWe formulated a Cox proportional hazard mixed\nmodel (survival analysis) using the package “coxme”\n(Therneau 2018) to evaluate if male-female associations\nlasted over more consecutive days than female-female\nassociations based on the female focal follow data. We\nused right-censored data to account for unknown asso-\nciation endings, because females were no longer follow-\ned despite still being in association (N = 625 associa-\ntions [Suaq: 61 associations with females, 53 with\nflanged males and 173 with unflanged males; Tuanan:\n81 with females, 96 with flanged males, 161 with\nunflanged males] during 167 female FPs and of 21 fe-\nmales). We included both associations with known and\nunknown start times, because excluding associations\nwith unknown start times (~ 40% of association dyads)\nwould have introduced a bias against long associations\nin the analysis (for further details on this issue and for\nthe results excluding associations with unknown start\ntime, see supplementary mat). Besides the type of adult\nassociation partners (female, unflanged and flanged\nmale), we added study site, zFAI, and the age of the\ndependent offspring (years) as fixed effects in the mod-\nel. We set contrasts for the association partner type to\nfirst compare association maintenance between male and\nfemale association partners and then the two male\nmorphs. Further, we included the follow period nested\nin the female identity as a random intercept to avoid\npseudo-replication. pp\ny\n(\n)\nAs social factors, we included the total cumulative time\nspent with either males or females and any agonistic and sex-\nual interaction recorded as fixed effects (details in Table 3). Behavioral data—activity budget changes Behavioral data—activity budget changes ecological, and physiological factors) and their possible 2nd-\norder interactions (if applicable) were set up, and com-\npared to the control model, containing all the random\nand control (ecological and physiological) factors, using\nlikelihood ratio tests. All figures were generated using\nthe “ggplot2” (Wickham 2016) and “cowplot” (Wilke\n2019) packages. The daily activity budget was calculated from the 2-min in-\nstantaneous data taken during full-day female focal follows\n(N = 2086; Suaq: 221; Tuanan: 1865), and thus, (1) it includes\nthe association record over the entire day, and (2) it accounts\nfor activity budget variation over daytime. To account for\nvariation in activity budgets (van Noordwijk et al. 2012), we\nonly included female follow periods (FP) that contained at\nleast 5 full-day focal follows (mean = 8.3 ± SE 0.1) within\n40 days (on average within 9 days) in the analyses. First, we\nevaluated the variability of the total active time, which com-\nprised the total hours from leaving the morning nest to enter-\ning the evening nest. Second, we evaluated if female foraging\nbehavior changed on days with associations and social inter-\nactions by analyzing variation in daily feeding time while\ncontrolling for moving time (offset term) (henceforth referred\nto as F:M ratio). Daily moving hours correlate strongly with\nday journey length (DJL) (Pearson correlation for available\nTuanan data: R2 = 0.76, t769 = 32.66, P < 0.0001, N = 771 fe-\nmale full-day follows). We analyzed daily moving hours rath-\ner than DJL, because it is a proxy for daily travel, but also\nincludes moves within feeding patches, with no net displace-\nment in space, which are likely not accurately reflected in\nDJL. We tested for the effects of social, physiological and\necological factors on active time and F:M ratio in linear mixed\nmodels. We built in the female follow period (FP) nested in\nfemale identity as random intercepts to avoid pseudo-replica-\ntion. The separate analyses on the changes of all activity bud-\nget components (feeding, resting, and moving hours) includ-\ning separate analyses for each study site are reported in the\nsupplementary materials (STable 11–14). Statistical analyses All the statistical analyses were conducted in R version 3.5.2\n(R Core Team 2018). We ran (generalized) linear mixed effect\nmodels ([G]LMM) using the “lme4” and “lmerTest” packages\n(Bates et al. 2015; Kuznetsova et al. 2017). Model assump-\ntions (normality [for LMMs], homoscedasticity) were\nchecked by the visual inspection of residual plots. Variance\nInflation Factors (VIF) were calculated to examine potential\nmulti-collinearity issues using the “car” package (VIF < 2, for\nthe full model without interaction terms included and VIF < 4\nfor the full model with interaction terms) (Fox and Weisberg\n2018). Further, we checked all the models for influential cases\nand outliers (Cook’s distance from the package\n“influence.ME” by Nieuwenhuis et al. 2012). The P value of\n0.05 was used as a cutoff value for significance. For all statis-\ntical analyses, full models including all variables (social, Page 9 of 22 Behav Ecol Sociobiol (2021) 75: 6 9 of 22 6 6 Initiation and maintenance of associations The behavioral reference day corresponding to the measured\nFCM level was obtained by backdating 3 days from the date\nof collection of morning fecal samples and 2 days for samples\ncollected after 2 pm (Cadilek 2009; Weingrill et al. 2011;\nAmrein et al. 2014; Nugraha et al. 2016). If there were several\nfecal samples for one behavioral reference day, only the morn-\ning sample was included in the final analysis. FCM levels with\nthe same behavioral reference day were strongly correlated\n(r = 0.73, CI = [0.60, 0.83], P < 0.0001, N = 78). To control\nfor any sample hour bias, the time of sample collection (i.e.,\ntime of defecation) was included in the statistical analyses as a\ncontrol factor although previous data on captive-housed ani-\nmals showed no time-of-day effect (Weingrill et al. 2011). FCM levels were ln-transformed to normalize their distribu-\ntion. Subsequently, the values were standardized within indi-\nvidual and extraction method used, to be able to assess FCM\nlevel changes caused by social and ecological stressors within\nindividuals rather than between individuals (method described\nin van de Pol and Wright 2009). Because such z-transforma-\ntions may be sample size dependent, we only included those\nindividuals in the analyses for which more than 10 samples\nand at least 5 known behavioral reference days for a given\nextraction method were available. The within-individual\ntransformations were done including all available samples,\nincluding the samples without behavioral reference (N =\n745). The analysis included only the samples with a known\nbehavioral reference day (N = 370). The number of total sam-\nples available (per method and individual) was included in the\nanalysis as a control factor. A linear mixed effect model\n(LMM) was set up to test for the effect of social factors on\nfemale FCM levels. The same social factor categories as de-\nscribed in the activity budget analyses were tested. The time to\nsample extraction (days), the total number of days an individ-\nual was followed, the age of the dependent infant (years), an\nactivity budget parameter (feeding proportion), and the Fruit\nAvailability Index (FAI) were included in the full model to\ncontrol for possible confounding factors leading to FCM\nchanges. The female follow period was added as a random\nintercept to avoid pseudo-replication. Initiation and maintenance of associations Because the FCM levels\nwere standardized within individual and method, these two\nfactors were not included as random intercepts in the analysis\nto keep the models as parsimonious as possible. The analyses\nwithout the standardization procedure and including individ-\nual identity and extraction method as random intercepts\nyielded the same patterns and are reported in the supplemen-\ntary materials. The control model with all the potential con-\nfounding factors did not improve the model fit of the null Behavioral data—association patterns and maintenance Because consecutive association days are likely inter-\ndependent and there may be compensatory effects, we also\nincluded the total number of (known) consecutive days in\nassociation with either males or females in the full model. Further, we controlled for potential confounding physiologi-\ncal and ecological factors, overarching site differences\n(Tuanan, Suaq), and the total time spent in social interactions\nwith any partner (Table 3). We tested for interaction terms\nbetween study site and social factors to check for population\ndifferences. Interaction terms were only included in the final\nmodel if they improved the model fit based on likelihood ratio\ntests. Both control models – including study site, zFAI, age of\nthe dependent offspring and total social interaction time –\nsignificantly improved the null models, containing only the\nrandom intercepts (and the offset term) (active time: χ2\n4,8 =\n51.75, P < 0.001; F:M ratio: χ2\n4,8 = 53.08, P < 0.001). We ex-\ncluded 16 days when females fed less than 1 h and their active\ntime was below 6 h because of serious health issues or lack of 6 Page 10 of 22 Behav Ecol Sociobiol (2021) 75: 6 model containing the random intercept term only (χ2\n3,12 =\n6.96, P = 0.64, ΔAIC = 11.04). habituation, as these days revealed to be influential cases and\nthe model assumptions were violated (for one context of these\noutliers see Marzec et al. 2016). habituation, as these days revealed to be influential cases and\nthe model assumptions were violated (for one context of these\noutliers see Marzec et al. 2016). Association frequency Despite substantial day-to-day variation, females spent on av-\nerage (mean) 30.0 ± SE 0.1 min per day in association with\nother females (Suaq: 82.6 ± SE 13.6 min; Tuanan: 23.7 ± SE\n2.4 min), 53 ± SE 0.1 min with unflanged males (Suaq: 200.1\n± SE 20.0 min; Tuanan: 35.1 ± SE 3.1 min), and 20 ± SE\n0.0 min with flanged males (Suaq: 29.1 ± SE 6.8 min;\nTuanan: 19.2 ± SE 2.3 min) (SFig. 1). The time females spent\nin association with both flanged and unflanged males in-\ncreased as the age of their dependent offspring increased\n(flanged: β = 0.448 ± 0.090, t = 5.001, P < 0.001; unflanged:\nβ = 0.606 ± 0.126, t = 4.799, P < 0.001; STable 1; SFig. 1),\nwhile the association time with other parous females remained\nconstant with offspring age (β = 0.067 ± 0.063, t = 1.066, P =\n0.29; STable 1; SFig. 1). Time spent in association with other\nparous females and unflanged males was generally higher at\nSuaq than at Tuanan (females: β = −1.058 ± 0.360, t = −\n2.939, P = 0.008; unflanged: β = −1.821 ± 0.556, t = −\n3.273, P = 0.003; STable 1; SFig. 1), but not with flanged\nmales (β = 0.228 ± 0.332, t = 0.688, P = 0.5). To sum up, fe-\nmales were more frequently in association with unflanged\nmales than with adult females or flanged males, partly\nsupporting prediction 1.1 (Table 1), and time in association\nwith both male morphs increased with the age of the depen-\ndent offspring of females (Table 1: prediction 3.2). Association initiation and maintenance Both flanged males (Tuanan: 82.1%; Suaq: 73.9%) and\nunflanged males (Tuanan: 84.0%; Suaq: 80.7%) initiated as-\nsociations with females more frequently than the females\nthemselves (Fig. 1). Moreover, both flanged males (Suaq:\nmean[FHI] = −0.25 ± SE 0.06 [N = 63 associations];\nTuanan: −0.38 ± SE 0.03 [N = 205]) and unflanged males\n(Suaq: −0.16 ± SE 0.03 [N = 160]; Tuanan: −0.12 ± SE 0.03\n[N = 237]) maintained these associations (Fig. 2). The full\nmodel for the probability that associations were male-\nmaintained explained significantly more variability than the\nnull model (χ2\n3,9 = 72.53, P < 0.0001, N = 665 of 30 female\nand 140 male identities; STable 2). First, especially long as-\nsociations were more likely male-maintained (β = 1.226 ±\n0.255, OR = 3.40, z = 4.804, P < 0.001). Second, flanged\nmales were more likely to maintain associations with females\nthan unflanged males (β = 0.653 ± 0.201, OR = 1.92, z = Fig. 1 Proportion of association\ninitiations by either both, female\nor male by study site (a Suaq, b\nTuanan) and male morph. Only\nassociations with a known\ninitiator are included (N = 957\n[Suaq: 279; Tuanan: 678])\nFig. 2 Female Hinde Index of\nassociations with unflanged males\n(left) and flanged males (right) by\nstudy site (Suaq: top; Tuanan:\nbottom) by the age of the depen-\ndent offspring (year), as a proxy\nfor female reproductive status. The black crosses indicate the\nweighted mean FHI (by the num-\nber of known approaches and\nleaves) and their transparency is\nrelative to the number of associa-\ntions included. Data points (Suaq:\norange; Tuanan: blue) represent\nindividual association units and\nonly include known approaches\nand leaves (N = 665). The data\npoint size is relative to the asso-\nciation duration and a horizontal\njitter function was applied to the\ndata points to make overlapping\ndata points more visible\nPage 11 of 22 6\nBehav Ecol Sociobiol (2021) 75: 6 Page 11 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 Fig. 1 Proportion of association\ninitiations by either both, female\nor male by study site (a Suaq, b\nTuanan) and male morph. Only\nassociations with a known\ninitiator are included (N = 957\n[Suaq: 279; Tuanan: 678]) Fig. Fig. 1 Proportion of association\ninitiations by either both, female\nor male by study site (a Suaq, b\nTuanan) and male morph. Only\nassociations with a known\ninitiator are included (N = 957\n[Suaq: 279; Tuanan: 678]) Association maintenance over multiple days Association maintenance over multiple days\nMale-female associations were maintained over more co\nutive days at Tuanan (maximum 8 days) than female-f\nassociations (maximum 4 days), whereas at Suaq this d\nence between the maintenance of male-female (max\n11 days) and that of female-female (maximum 7 days)\nciations was less pronounced (Fig. 3; Table 4). Accord\nthe survival analysis on the probability of ending an as\ntion was significantly better when including the intera\nbetween study site and partner type (β = −0.234 ± 0\nHR = 0.79, P = 0.009): Female-female associations e\nsooner at Tuanan than male-female associations; at Sua\ndifference was less pronounced (Fig. 3). We could no\nany difference in association maintenance probability be\nthe two male morphs (unflanged vs. flanged) (Tab\nAssociations were maintained over more consecutive\nwith the increasing age of the dependent offspring of a f\n(β = −0.169 ± 0.066, HR = 0.84, P = 0.01). The intera\nbetween the age of the dependent infant and partner typ\nnot improve the model fit (χ2\n2 = 0.83, P = 0.66). Local\ndid not have an effect on the association mainten\n(Table 4). All in all, both unflanged and flanged males\ntained associations with females over more consecutive\nTable 4\nProbability of ending an association: output of th\nproportional hazard mixed model for the total number of (known\nin association by the type of association partner, study site, age\nβ\nSite (Suaq vs. Tuanan)\n0.5\nAssociation partner\nSex (male vs. female)\n0.2\nMale morph (unflanged vs. flanged)\n−0.0\nAge of dependent offspring (years)\n−0. z Fruit Availability Index\n−0.0\nSite: association partner sex (male vs. female)\n−0.2\nSite: partner male morph (unflanged vs. flanged)\n−0.0 Male-female associations were maintained over more consec-\nutive days at Tuanan (maximum 8 days) than female-female\nassociations (maximum 4 days), whereas at Suaq this differ-\nence between the maintenance of male-female (maximum\n11 days) and that of female-female (maximum 7 days) asso-\nciations was less pronounced (Fig. 3; Table 4). Accordingly,\nthe survival analysis on the probability of ending an associa-\ntion was significantly better when including the interaction\nbetween study site and partner type (β = −0.234 ± 0.089,\nHR = 0.79, P = 0.009): Female-female associations ended\nsooner at Tuanan than male-female associations; at Suaq this\ndifference was less pronounced (Fig. 3). Association initiation and maintenance 2 Female Hinde Index of\nassociations with unflanged males\n(left) and flanged males (right) by\nstudy site (Suaq: top; Tuanan:\nbottom) by the age of the depen-\ndent offspring (year), as a proxy\nfor female reproductive status. The black crosses indicate the\nweighted mean FHI (by the num-\nber of known approaches and\nleaves) and their transparency is\nrelative to the number of associa-\ntions included. Data points (Suaq:\norange; Tuanan: blue) represent\nindividual association units and\nonly include known approaches\nand leaves (N = 665). The data\npoint size is relative to the asso-\nciation duration and a horizontal\njitter function was applied to the\ndata points to make overlapping\ndata points more visible 6 Page 12 of 22 Behav Ecol Sociobiol (2021) 75: 6 3.244, P = 0.001), whereas this difference between male\nmorphs was more pronounced at Tuanan than at Suaq, as\nthe model fit marginally improved when adding this interac-\ntion term (χ2\n9,10 = 4.12, P = 0.04). Association maintenance\nby males was independent of the female’s dependent off-\nspring’s age (β = 0.089 ± 0.100, OR = 1.09, z = 0.891, P =\n0.37), the local zFAI (β = −0.019 ± 0.089, OR = 0.98, z = −\n0.215, P = 0.83), and the occurrence of sexual interactions\n(β = 0.556 ± 0.298, OR = 1.74, z = 1.866, P = 0.06). In sum,\nprediction 1.2 (Table 1) was supported, as associations were\nmale-initiated and male-maintained independent of the female\nreproductive state, whereas this was the case at both study\nsites and by both male morphs. than females did with other females at Tuanan, the less socia-\nble population, whereas we find no such difference at Suaq,\nthe more sociable population, supporting prediction 1.3\n(Table 1) and its site difference but not the male morph\ncomponent. Social interactions between males and females Affiliative social interactions occurred in 6.0 ± SE 0.8% of all\nmale-female associations (STable 5), always once or twice\n(mean 1.45 ± SE 0.11 occurrences) during the entire associa-\ntion (female-unflanged: 0.022−h [interactions per association\nhour] [Suaq]; 0.025−h [Tuanan]; female-flanged: 0.016−h\n[Suaq]; 0.011−h [Tuanan]). Male aggression towards females\noutside of the sexual context was observed in 7.4 ± SE 0.9%\nof all dyadic male-female associations. Physical aggression by\nmales directed at females was rare (Suaq: in 1 out of 393\nassociations; Tuanan: 9 of 521 associations) and consisted\nexclusively of coercive hand holding (van Schaik et al. 2006). Flanged males were significantly more likely to direct\nnon-physical aggression in the form of displays, displace-\nments, or short chases towards females both at Tuanan\n(14.0 ± SE 2.2% [0.091−h]) and at Suaq (9.0 ± SE 2.6%\n[0.025−h]) than unflanged males (Tuanan: 6.6 ± SE 1.5%\n[0.030−h]; Suaq: 6.6 ± SE 1.5% [0.013−h]) (STable 6). At\nSuaq and Tuanan both forced and unforced copulations were\nmore frequent during associations involving unflanged males\n(Suaq: 23.5 ± SE 2.6% [0.075−h] [forced: 17.3 ± SE 2.3%\n(0.052−h)]; Tuanan: 15.0 ± SE 2.1% [0.041−h] [forced: 7.3 ±\nSE 1.5% (0.021−h)]) than flanged males (Suaq: 5.7 ± SE 2.1%\n[0.014−h] [forced: 4.1 ± SE 1.8% (0.011−h)]; Tuanan: 6.2 ± SE\n1.5% [0.018−h] [forced: 1.2 ± SE 0.7% (0.005−h)]) (for more\ndetails: Kunz 2020). Moreover, especially unflanged males at\nTuanan frequently investigated the genitals of females during\nassociations (female-unflanged associations: 27.4 ± SE 2.4%\n[Tuanan], 7.7 ± SE 1.9% [Suaq]; female-flanged associations:\n1.3 ± SE 0.7% [Tuanan], 4.2 ± SE 2.1% [Suaq]). These genital\ninvestigations occurred independent of the female’s offspring Active time Female active time on days without any association partners\nexcept for her dependent offspring was on average 10.8 ± SD\n1.0 h (min 6.1 and max 13.1), whereas on days with female\nassociates it increased to 11.4 ± SD 1.0 h (Suaq: 11.6 ± SD\n0.8; Tuanan: 11.3 ± SD 1.0) and on days with males in asso-\nciation (independent of association duration) to 11.4 ± SD\n1.0 h (Suaq: 11.5 ± SD 0.8; Tuanan: 11.3 ± SD 1.0) (suppl. mat. STable 9). Accordingly, in both study populations, fe-\nmale active time increased significantly with increased time in\nassociation with females (β = 0.084 ± 0.025, t = 3.428, P =\n0.001) and with males (β = 0.068 ± 0.034, t = 2.004, P =\n0.045) (Fig. 4a+d). Moreover, at Tuanan a female’s active\ntime increased significantly on days with copulations whereas Association maintenance over multiple days 3 Kaplan-Meier survival curve for the maintenance of associations\nover consecutive days at Suaq (a) and Tuanan (b) by the association\npartner type (color). The survival curve is based on the female focal\ndata from follow periods also including the non-full-day focal follows (e.g., days when an individual was found) (N = 625 [Suaq: 287; Tuanan:\n338] associations of 21 females and 168 different FPs). The left-censored\ndata is indicated in crosses it did not at Suaq (suppl. mat. STable 10), as the significant\ninteraction between study site and days with copulations indi-\ncates (β = 0.387 ± 0.158, t = 2.444, P = 0.02) (Fig. 5a). Active\ntime further increased with increased number of consecutive\ndays with males (β = 0.056 ± 0.024, t = 2.385, P = 0.02), the\ntotal time spent in social interactions with any social partner\n(β = 0.556 ± 0.155, t = 3.587, P < 0.001), and the local fruit\navailability (β = 0.095 ± 0.039, t = 2.427, P = 0.02). Interaction terms between site and any other social factors,\nexcept copulation occurrence, did not significantly improve\nthe model fit. In sum, daily active time increased in both\npopulations for females in associations, and at Tuanan on days\nwith copulations, and accordingly, the model fit significantly\nimproved when including social factors (χ2\n8,16 = 56.27,\nP < 0.001, ΔAIC = 40.27; N = 2086 of 20 females and 279\nFP; for the full model suppl. mat. STable 10). age (for details see suppl. mat. STable 7; SFig. 3). In summa-\nry, both affiliative and agonistic social interactions were rare\nduring male-female associations (predictions 1.4 + 1.5,\nTable 1), indicating that costs of association to females likely\nresult from increased feeding competition rather than the ac-\ncompanying social interactions. However, sexual interactions\nwere on average the most frequent social interactions during\nmale-female associations indicating male mating effort, thus\nsupporting prediction 1.6 and 3.2 (Table 1). Association maintenance over multiple days We could not find\nany difference in association maintenance probability between\nthe two male morphs (unflanged vs. flanged) (Table 4). Associations were maintained over more consecutive days\nwith the increasing age of the dependent offspring of a female\n(β = −0.169 ± 0.066, HR = 0.84, P = 0.01). The interaction\nbetween the age of the dependent infant and partner type did\nnot improve the model fit (χ2\n2 = 0.83, P = 0.66). Local zFAI\ndid not have an effect on the association maintenance\n(Table 4). All in all, both unflanged and flanged males main-\ntained associations with females over more consecutive days Table 4\nProbability of ending an association: output of the Cox\nproportional hazard mixed model for the total number of (known) days\nin association by the type of association partner, study site, age of the dependent offspring (years), and zFAI (χ2\n7 = 28.80, P = 0.0002, N = 625\nassociations of which 426 with known end, of 21 female identities and\n167 FPs). All fixed effects with P < 0.05 are indicated in bold β\nSE\nHazard ratio\nz\nP\nSite (Suaq vs. Tuanan)\n0.551\n0.146\n1.74\n-\n-\nAssociation partner\nSex (male vs. female)\n0.233\n0.071\n1.26\n-\n-\nMale morph (unflanged vs. flanged)\n−0.029\n0.103\n0.97\n-\n-\nAge of dependent offspring (years)\n−0.169\n0.066\n0.84\n−2.560\n0.010\nz Fruit Availability Index\n−0.023\n0.063\n0.98\n−0.360\n0.720\nSite: association partner sex (male vs. female)\n−0.234\n0.089\n0.79\n−2.620\n0.009\nSite: partner male morph (unflanged vs. flanged)\n−0.019\n0.130\n0.98\n−0.150\n0.880 Page 13 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 Fig. 3 Kaplan-Meier survival curve for the maintenance of associations\nover consecutive days at Suaq (a) and Tuanan (b) by the association\npartner type (color). The survival curve is based on the female focal\ndata from follow periods also including the non-full-day focal follows\n(e.g., days when an individual was found) (N = 625 [Suaq: 287; Tuanan:\n338] associations of 21 females and 168 different FPs). The left-censored\ndata is indicated in crosses Fig. 3 Kaplan-Meier survival curve for the maintenance of associations\nover consecutive days at Suaq (a) and Tuanan (b) by the association\npartner type (color). The survival curve is based on the female focal\ndata from follow periods also including the non-full-day focal follows Fig. Foraging behavior Overall daily feeding time (F) decreased with both males and\nfemales in association, whereas moving (M) and resting time\nincreased (Fig. 4; for detailed analyses see suppl. mat. STable 9, 11, 12). At both study sites, the F:M ratio (time\nspent feeding per unit moving time) of females decreased with\nincreased association time with males (β = −0.250 ± 0.053,\nt = −4.698, P < 0.001), whereas it decreased significantly\nmore at Tuanan with increased time with females in Behav Ecol Sociobiol (2021) 75: 6 6 Page 14 of 22 Fig. 4 Daily female activity budget changes (from left to right: active\ntime (a, d), feeding (b, e), and moving (c, f) hours) depending on\ncumulative hours spent with males (a–c) and females (d–f) and by\nstudy site (round, orange: Suaq; triangles, blue: Tuanan). Each data\npoint represents one full-day focal follow (N = 2086), the regression lines\nare the correlations between hours spent with males/females and activity\nhours and do not show model predictions. The shaded areas display 95%\nconfidence intervals point represents one full-day focal follow (N = 2086), the regression lines\nare the correlations between hours spent with males/females and activity\nhours and do not show model predictions. The shaded areas display 95%\nconfidence intervals Fig. 4 Daily female activity budget changes (from left to right: active\ntime (a, d), feeding (b, e), and moving (c, f) hours) depending on\ncumulative hours spent with males (a–c) and females (d–f) and by\nstudy site (round, orange: Suaq; triangles, blue: Tuanan). Each data association compared to Suaq (β = −0.333 ± 0.070, t = −\n4.763, P < 0.001). Only consecutive days with females, but\nnot with males, led to a further decrease in a female’s daily\nF:M ratio (Table 5). Furthermore, on days with copulations,\nthe F:M ratio decreased significantly more at Tuanan than at\nSuaq (β = −0.630 ± 0.246, t = −2.557, P = 0.01). The full\nmodel for the F:M ratio including social factors was signifi-\ncantly better than the control model including ecological and physiological factors only (χ2\n8,17 = 80.47, P < 0.001,\nΔAIC = 62.47; N = 2086 of 20 females and 279 FP)\n(Table 5). Foraging behavior In sum, female foraging behavior was negatively\naffected by associations with both females and males, with the\neffects being more pronounced for the Tuanan population,\nsupporting predictions 2.1 and 2.1.1 (Table 1) that costs of\nassociation arise from scramble competition of grouping. Less support was found for predictions 2.2 and 2.2.1 Fig. 5 Daily female activity budget changes (from left to right: active\ntime (a), feeding (b), and moving (c) hours) depending on the\noccurrence of copulations and by study site (orange Suaq, blue\nTuanan). The boxplots are based on median values of full-day focal\nfollows (N = 2086) and do not show model predictions (the hinges extend\nto the first and third quantiles and the whiskers to the largest value, and\nlowest, respectively, at most 1.5*inter-quartile range. Data points beyond\nthe end of whiskers are plotted individually [Wickham 2016]) follows (N = 2086) and do not show model predictions (the hinges extend\nto the first and third quantiles and the whiskers to the largest value, and\nlowest, respectively, at most 1.5*inter-quartile range. Data points beyond\nthe end of whiskers are plotted individually [Wickham 2016]) Fig. 5 Daily female activity budget changes (from left to right: active\ntime (a), feeding (b), and moving (c) hours) depending on the\noccurrence of copulations and by study site (orange Suaq, blue\nTuanan). The boxplots are based on median values of full-day focal Page 15 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 22 6 Table 5 LMM output of the full\nmodel for daily feeding hours\n(F:M ratio) (N = 2086 full-day\nfollows of 20 parous females and\n279 follow periods; χ2\n8,17 =\n80.47, P < 0.001, ΔAIC = 62.47). All fixed and control effects with\nP < 0.05 are indicated in bold. z,\nfixed effect variable was z-trans-\nformed prior to analysis; O, offset\nterm; C, control factor; F, fixed\neffect Estimate\nSE\nt\nP\nIntercept\n4.908\n0.240\n-\n-\nMoving time (h)\nOffset\nSite (Suaq vs. Tuanan)\nC\n−0.142\n0.262\n-\n-\nz Cumulative female association hours\nF\n0.181\n0.063\n-\n-\nz Cumulative male association hours\nF\n−0.250\n0.053\n−4.698\n< 0.001\nNumber of consecutive days with females\nF\n−0.167\n0.070\n−2.376\n0.018\nNumber of consecutive days with males\nF\n0.037\n0.037\n0.993\n0.321\nNumber of copulations\nF\n0.193\n0.206\n-\n-\nMale-female cumulative aggression index\nF\n−0.052\n0.140\n−0.371\n0.710\nFemale-female agonistic interactions (no vs. Foraging behavior yes)\nF\n−0.549\n0.312\n−1.762\n0.078\nz Fruit Availability Index\nC\n−0.150\n0.063\n−2.387\n0.018\nz Age of dependent offspring (years)\nC\n−0.047\n0.069\n−0.678\n0.498\nSocial interaction time (h)\nC\n−1.045\n0.241\n−4.330\n< 0.001\nSite (Suaq vs. Tuanan): z cumulative female\nassociation hours\nF\n−0.333\n0.070\n−4.763\n< 0.001\nSite (Suaq vs. Tuanan): number of copulations\nF\n−0.630\n0.246\n−2.557\n0.011 when adding the number of consecutive days with males\n(χ2\n12,13 = 7.30, P = 0.007, ΔAIC = 5.30). Although one par-\nticular female (Desy), who had male associations over a\ncourse of 9 days, appeared to be the main driver for this result,\nthere still was a trend for consecutive days with males leading\nto elevated FCM levels when this female was excluded (β =\n0.106 ± 0.056, P = 0.06, N = 333 of 89 follow periods; com-\nparison to control model: χ2\n12,13 = 3.47, P = 0.06). proposing additional costs caused by (agonistic) social inter-\nactions (Table 1). Table 6 LMM output for female\nFCM level changes [z-ln (FCM\nconcentration (ng/g))] in response\nto various ecological,\nphysiological and social factors\n(comparison to control model\n[containing only ecological and\nphysiological factors]: χ2\n12,16 =\n9.13, P = 0.06, ΔAIC = 1.13, N =\n370 of 96 FPs; comparison to null\nmodel: χ2\n3,16 = 16.09, P = 0.24,\nΔAIC = 9.91). All fixed and\ncontrol effects with P < 0.05 are\nindicated in bold. z, fixed effect\nvariable was z-transformed prior\nto analysis; C, control factor; F,\nfixed effect Table 5 LMM output of the full\nmodel for daily feeding hours\n(F:M ratio) (N = 2086 full-day\nfollows of 20 parous females and\n279 follow periods; χ2\n8,17 =\n80.47, P < 0.001, ΔAIC = 62.47).\nAll fixed and control effects with\nP < 0.05 are indicated in bold. z,\nfixed effect variable was z-trans-\nformed prior to analysis; O, offset\nterm; C, control factor; F, fixed\neffect FCM levels 6 Standardized FCM levels (z-ln [FCM concentration (ng/g)]) (y-\naxis) of females in response to consecutive association days with adult\nmales (a) and to consecutive association days with adult females (b). A\njitter function was added to the plot to visualize the overlapping data\npoints (consecutive days are only integers). The black diamond-shaped\npoints indicate the mean FCM levels with the error bar (SE) in black. Study sites indicated by round, orange: Suaq; triangles, blue: Tuanan points (consecutive days are only integers). The black diamond-shaped\npoints indicate the mean FCM levels with the error bar (SE) in black. Study sites indicated by round, orange: Suaq; triangles, blue: Tuanan Fig. 6 Standardized FCM levels (z-ln [FCM concentration (ng/g)]) (y-\naxis) of females in response to consecutive association days with adult\nmales (a) and to consecutive association days with adult females (b). A\njitter function was added to the plot to visualize the overlapping data points (consecutive days are only integers). The black diamond-shaped\npoints indicate the mean FCM levels with the error bar (SE) in black. Study sites indicated by round, orange: Suaq; triangles, blue: Tuanan levels was no longer significant (β = 0.083 ± 0.061, P = 0.18,\nN = 361 of 96 follow periods). In sum, it appears that only\nprolonged male-female associations over more than four con-\nsecutive days lead to increased female FCM levels. directly assess the energetic costs of sociality in orangutans,\nour measure of F:M ratio should be complemented by more\naccurate measures of actual energy intake and measures of\nenergy balance, such as analysis of urinary C-peptide concen-\ntrations (e.g., Emery Thompson and Knott 2008). Orangutan females likely do not gain direct benefits from\nassociations with males, whereas males need associations with\nfemales to monitor their reproductive status. First, genital in-\nvestigations by males and male-initiated sexual interactions\nwere the most frequent social interactions observed during\nmale-female associations, whereas affiliative social interac-\ntions were extremely rare. However, benefits for females by\nassociating with certain (flanged) males, such as protection\nfrom harassing males, cannot conclusively be ruled out\n(Mesnick 1997; Fox 2002). Second, most associations were\nboth male-initiated and male-maintained, regardless of female\nreproductive state, i.e., the age of the female’s dependent off-\nspring, and females likely incurred costs from those involun-\ntary associations as discussed above. FCM levels Female FCM levels increased with the number of consecutive\ndays in association with a male (β = 0.136 ± 0.047, t = 2.870,\nP = 0.004; Fig. 6; Table 6), but not with females (β = −0.082\n± 0.085, t = −0.960, P = 0.34). None of the other social fac-\ntors, including daily association time with either females or\nmales and the occurrence of aggression, further improved the\nmodel fit. Accordingly, the control model containing all phys-\niological and ecological factors was improved significantly Because our FCM data set only contained data for at most 4\nconsecutive days of female-female associations, we restricted\nthe data set to sample days of at most 4 consecutive male-\nfemale association days in a further analysis. Then, the effect\nof consecutive days in association with males on female FCM Type\nEstimate\nSE\nt\nP\nIntercept\n−0.193\n0.390\nSite (Suaq vs. Tuanan)\nC\n−0.021\n0.281\n−0.077\n0.939\nConsecutive days in association with female(s)\nF\n−0.082\n0.085\n−0.960\n0.338\nConsecutive days in association with male(s)\nF\n0.136\n0.047\n2.870\n0.004\nMale-female cumulative aggression index\nF\n−0.110\n0.118\n−0.932\n0.352\nFemale-female agonistic interactions (no vs. yes)\nF\n0.063\n0.443\n0.142\n0.887\nNumber of days followed\nC\n−0.002\n0.018\n−0.141\n0.888\nz Daily feeding proportion\nC\n−0.072\n0.054\n−1.325\n0.186\nz Age of dependent infant (years)\nC\n0.007\n0.121\n0.059\n0.953\nz Fruit Availability Index\nC\n0.057\n0.076\n0.739\n0.462\nHour of sample collection\nC\n0.004\n0.025\n0.151\n0.880\nz Days to sample extraction\nC\n0.067\n0.082\n0.812\n0.419\nLaboratory (DPZ vs. IPB)\nC\n0.027\n0.202\n0.133\n0.894\nTotal samples available with behavioral reference\nC\n0.005\n0.008\n0.560\n0.577 Table 6 LMM output for female\nFCM level changes [z-ln (FCM\nconcentration (ng/g))] in response\nto various ecological,\nphysiological and social factors\n(comparison to control model\n[containing only ecological and\nphysiological factors]: χ2\n12,16 =\n9.13, P = 0.06, ΔAIC = 1.13, N =\n370 of 96 FPs; comparison to null\nmodel: χ2\n3,16 = 16.09, P = 0.24,\nΔAIC = 9.91). All fixed and\ncontrol effects with P < 0.05 are\nindicated in bold. z, fixed effect\nvariable was z-transformed prior\nto analysis; C, control factor; F,\nfixed effect 6 Page 16 of 22 Behav Ecol Sociobiol (2021) 75: 6 Fig. FCM levels When females are ready\nto conceive, however, they may actively seek the association\nwith (dominant) flanged males (Fox 1998, 2002; Spillmann\net al. 2010). With our analyses, we did not capture this short\nwindow around conception. We conclude that females and\nmales are likely at odds about association maintenance. Accordingly, orangutan females have been reported to active-\nly avoid male associates or try to end associations as rapidly as\npossible (Fox 2002; Mitra Setia and van Schaik 2007; Utami\nAtmoko et al. 2009; van Noordwijk and van Schaik 2009;\nSpillmann et al. 2010; Knott et al. 2018). Further investiga-\ntions to understand how and if females attempt to avoid male\nassociates have to be conducted, including the analysis of\nsimultaneous ranging data. In sum, our study indicates that\nfemales incur costs from male-maintained associations, but\nno clear immediate benefits (albeit perhaps indirect ones:\nKunz 2020), especially during the period of lactational Stress and association Female FCM levels increased as they spent more days in\nassociation with males, but not with females. This social factor\nwas the best and only predictor for FCM level changes. Thus,\nrepeated days of increased active time and reduced F:M ratio\nled to a physiological stress response. Interestingly, this was\nnot the case when in association with other females, because\nfemales can avoid lengthy associations with other females\nbefore associations become too costly. Conversely, males ap-\npear to profit from associations with females and they main-\ntain associations over a longer time period than a female\nwould. The behavioral data available support this conclusion:\nFemale-female associations never lasted more than 4 consec-\nutive days at Tuanan, where the F:M ratio decreased signifi-\ncantly more when in association with other females than at\nSuaq, while male-female associations could last up to 8 days. The elevated FCM levels of captive orangutan females when\nartificially confined to permanent association with males\n(Amrein et al. 2014) further support our hypothesis that in-\ncreased sociality over an extended time period leads to a phys-\niological stress response, especially in Bornean orangutans. The findings in captivity suggest that Bornean females show\nstress reactions to extended sociality even in the absence of\nreduced net energy intake, suggesting that in captivity in-\ncreased FCM levels in females associated with males more\nlikely reflect social rather than energetic stress. Although our\nendocrine data set is very limited, especially for the extended\nconsecutive association days with males, we propose that only\nextended association periods with males lead to increased\nFCM levels as seen in captivity. However, whether these\nFCM elevations observed in our wild females are a response\nto the association itself or, alternatively, reflect energetic con-\nstraints due to the association-related decrease in feeding time\nand increase in active time is unclear. Future studies should\ngenerally aim at obtaining a more conclusive endocrine data\nset including larger sample sizes linked to consecutive associ-\nation days. We found no evidence for differences in female FCM\nlevels on days with any agonistic interaction with either males\nor females in the two populations. Even though days with\ncopulations were characterized by increased active time and\nreduced F:M ratio at Tuanan, we found no evidence that male\naggression, in particular sexual coercion (SFig. 7), imposed\nany additional costs, either as reduced feeding time or in ele-\nvated FCM levels. Foraging costs of association Because female reproductive success is generally directly\nlinked to access to resources (chimpanzees: Emery\nThompson et al. 2007; apes: Emery Thompson et al. 2008;\nStumpf et al. 2008; orangutans: Knott et al. 2009), the ener-\ngetic costs of association with conspecifics have been held\nresponsible for the varying degrees of gregariousness across\nthe orangutan geographic distribution (van Schaik 1999). The\nfemales in our study likely suffer energetically from associa-\ntions (with both males and adult females): In both study pop-\nulations, females increased the length of their active day, but\ntheir feeding time decreased, both absolutely (suppl. mat. STable 12) and relative to moving time. This reduction is\nnot only a trade-off directly resulting from increased time\nspent in social interactions, because (1) we controlled for time\nspent in social interactions, and (2) in the more sociable\nSumatran population with higher forest productivity, feeding\ntime was less affected by time spent in association with fe-\nmales. Hence, the reduced F:M ratio and the increased active\ntime can be taken as direct evidence for elevated scramble\ncompetition, indicating that associations incur energetic costs\nto females, whereas we only found limited evidence for costs\nresulting from (agonistic) social interactions. We can conclude\nthat females modify their activity budgets when in association\nwith both males and females, in patterns that are congruent\nwith increased scramble competition. However, to more Page 17 of 22 Behav Ecol Sociobiol (2021) 75: 6 6 the future. A difference in the physiological response to social\nstressors, including energy balances, may be expected in the\nlight of the socioecological theory, because the degree of so-\nciability between the two populations differs (this study; van\nSchaik 1999). Since our activity and feeding data indicate that\nboth associations (with females) and social interactions are\ncostlier to Tuanan females than to Suaq females, where fruit\navailability is generally higher (Wich et al. 2011), a stronger\nphysiological stress response would be expected at Tuanan. Future studies are, however, needed to test this hypothesis and\nthus to evaluate whether females of the more sociable\nSumatran orangutan may be more “stress-resistant” which\ncould explain why there is less need for either behavioral or\nphysiological mechanisms to avoid associations. infertility (~ 6.5 years [van Noordwijk et al. 2018]). These\ncosts of involuntary associations may be relevant, because\norangutan females’ reproductive success highly depends on\nthe availability of resources (Knott et al. Foraging costs of association 2009), particularly\nin a less productive habitat (Wich et al. 2011). The male perspective male-maintained associations, especially if those associations\nlast multiple days. The costs include reduced feeding time and\nincreased moving and resting time, which adds up to longer\nactivity per day and thus shorter night rest. Furthermore,\nprolonged associations with males were associated with ele-\nvated FCM levels, whereas this was not the case for female-\nfemale associations which were usually much shorter. We\nsuggest that the absence of morphological fertility advertise-\nment in female orangutans may be explained by these costs of\nassociation, thus supporting the first prediction of the “cost-of-\nsexual-attraction” hypothesis (Wrangham 2002) for orangu-\ntans. The length of sexual attractivity negatively correlates\nwith the cost of association for females in the genus Pan\n(Wrangham 2002). Orangutans fit into this fission-fusion con-\ntinuum at the solitary end: They do not exhibit any morpho-\nlogical signal of fertility, arguably because this would attract\ntoo many competing males at once leading to a prolonged\nperiod of unacceptably high energetic costs for the females,\nin addition to the mere physiological costs associated with the\nswelling itself (for a review: Nunn 1999). On the contrary,\nfemale orangutans advertise non-availability with small labial\nswellings during pregnancy (Schultz 1938; Galdikas 1981),\nlikely to reduce the costs of association as males refrain from\nmaintaining associations and copulating with pregnant fe-\nmales exhibiting the labial swelling (only 2 out of 34 pregnan-\ncy matings were observed when females exhibited a pregnan-\ncy swelling, JAK et al. unpubl. data). Both unflanged and flanged males are responsible for maintain-\ning associations, independent of the females’ dependent off-\nspring age (as a proxy for reproductive state), which supports\nthe hypothesis that the males’ interest to associate exceeds that\nof the females (Table 1). Besides mating opportunities, these\nassociations may be an attempt to monitor a female’s reproduc-\ntive state and sexual activities. In the absence of any apparent\nsignal of fertility (Nunn 1999), it remains uncertain how males\nassess female reproductive state, if at all. The genital investiga-\ntions reported here may provide some olfactory information to\nmales (cf. chimpanzee: Matsumoto-Oda et al. 2003; review:\nDrea 2015), but data are insufficient to know how and if these\nrelate to sexual interactions (suppl. mat. STable 8). It is likely\nthat males also incur energetic costs from associations and in-\nteractions with females (cf. East African chimpanzees\n[P. troglodytes schweinfurthii]; Emery Thompson and\nGeorgiev 2014; Georgiev et al. The male perspective 2014), and our unpublished data\nsuggest this, too, for orangutan males. Thus, males may have a\nset of decision rules when and for how long to associate with\ncertain females. Accordingly, the time in association with males\nincreases with the increasing age of the dependent offspring of\nfemales (this study; van Schaik 1999), suggesting some type of\nreproductive benefits for males. More detailed analyses on the\nsocial context of associations will provide further insight into\nhow males benefit from sociality with females. Yet, females of both Pan spp. and Pongo spp. exhibit un-\npredictable ovulation, albeit to varying extent (Nadler 1981;\nDeschner et al. 2004; Douglas et al. 2016), which has been\nlinked to paternity confusion serving infanticide avoidance\nstrategies (Hrdy 1979; Hrdy and Whitten 1987; van Schaik\net al. 2004). The concealed ovulation in orangutans (Nadler\n1981) may therefore also serve to reduce the risk of infanticide\nas it does in most other primates (Hrdy 1979; van Schaik et al. 2004). Female orangutans seem to vary their mate preferences\nwith their reproductive status accordingly (Knott et al. 2010). However, evidence for infanticidal attacks by males remains\nindirect (Beaudrot et al. 2009; Knott et al. 2019; Scott et al. 2019) and infant mortality is generally extremely low (van\nNoordwijk et al. 2018), suggesting that male infanticide in\norangutans is extremely rare compared to chimpanzees and\nthat females employ efficient counterstrategies. It remains to be investigated if prolonged male-maintained\nassociations should be labelled as a separate indirect form of\nsexual coercion or may even function as coercive mate guarding,\ni.e., “to constrain female promiscuity” (Muller et al. 2009). First,\ndirect non-sexual aggression towards females by males is rare in\norangutans (STable 6; SFig. 2) providing little evidence for any\nherding, punishment or sequestration (apart from the ten cases of\ncoercive hand holding). However, anecdotal data suggest subtle\nsequestration attempts, in that males may try to influence fe-\nmales’ travel direction away from other males during associa-\ntions (MAvN et al., unpubl. data). Second, copulations regularly\noccur in the presence of other, even more dominant, males (Fox\n2002). (Coercive) mate guarding by males therefore appears to\nbe an inefficient strategy, especially for subordinate, unflanged\nmales. Third, although we found evidence for direct costs for\nfemales resulting from male-maintained associations, which in-\ndicates male coercion, we cannot rule out that females ultimately\nbenefit indirectly from paternity confusion through those male-\ndriven association patterns. The male perspective Future studies are needed to evaluate\nthe social contexts of associations. In a dispersed mating system with high costs of association,\nand where males generally drive association patterns as found\nhere for orangutans, the lack of morphological fertility adver-\ntisement can be explained by the selection on the total conceal-\nment of ovulation. Given a risk of infanticide (Knott et al. 2010,\n2019), females must achieve an optimum distribution of pater-\nnity assessments (van Schaik and Janson 2000; van Schaik et al. 2004) by removing as much information on female fertility sta-\ntus as possible. Accordingly, the absence of morphological fer-\ntility advertisement combined with the concealed ovulation in Stress and association Thus, the com-\nparison should be repeated with a more extensive data set in 6 Page 18 of 22 Behav Ecol Sociobiol (2021) 75: 6 Stress and association If these forced copulations are cost insen-\nsitive, they would not qualify as sexual coercion by the defi-\nnition of Smuts and Smuts (1993) (“use by a male of force, or\nthreat of force, that functions to increase the chances that a\nfemale will mate with him at a time when she is likely to be\nfertile, and to decrease the chances that she will mate with\nother males, at some cost to the female”), while prolonged,\nmale-maintained associations would. However, the absence of\na stress response does not exclude other costs of forced cop-\nulations, such as the limitation to the expression of female\nmating preferences. Indeed, the consistent attempts by females\nto escape from involuntary mating initiations (Fox 2002;\nKnott et al. 2010) suggest that females perceive resisted cop-\nulations as undesired rather than as a way to assess mate qual-\nity. For now, therefore, interpreting forced copulations as sex-\nual coercion remains the most plausible explanation. Since fecal cortisol metabolite levels represent an integra-\ntive measure of pooled endocrine activity over several hours\nor days (Hodges and Heistermann 2011), it is likely unsuited\nto detect short-term stress responses to a specific behavioral\nevent. Forced copulations lasted on average 8.8 ±SD 7.2 min\n(Kunz 2020), and any stress response associated with this\nbehavior is likely to be too short to be detected by our FCM\nmeasure. Urinary cortisol levels may thus be a more appropri-\nate measure to assess whether particular social interactions\ninduce more immediate elevations in cortisol production\n(e.g., Silk et al. 2013) as has been shown for chimpanzees\n(Muller et al. 2007; Emery Thompson et al. 2010). Further\ndetailed studies, with a larger sample size and more immediate\nmeasures of cortisol levels from urine, are needed to examine\nwhether female orangutans do indeed not show stress re-\nsponses to forced copulations. Following the same line of argument, one would expect to\nfind more pronounced FCM level changes in the less sociable\nBornean orangutans in response to involuntary associations\ncompared to Sumatran orangutans. Although we could not\nfind any evidence for differences in FCM level changes be-\ntween Suaq and Tuanan, our data set was very small for the\nSuaq population (N = 52 samples, a maximum of 6 [known]\nconsecutive days in male-female association). Conclusion Here, we report evidence for sexual conflict over associations\nin orangutans. We conclude that females incur costs from Page 19 of 22 6 Behav Ecol Sociobiol (2021) 75: 6 Informed consent\nNot applicable orangutans appears to be the result of a trade-off between the\ncosts of association and the necessity for paternity confusion\n(van Schaik et al. 2004; Knott et al. 2010, 2019). Future work\nwill have to elaborate on the details of this hypothesis. 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/. Supplementary Information The online version contains supplementary\nmaterial available at https://doi.org/10.1007/s00265-020-02948-4. Acknowledgments We thank our local field teams at Suaq and Tuanan\nand all the local and foreign students and researchers for their contribution\nin the long-term data collection. Particularly, we express our gratitude to Dr. Alison Ashbury, Rebecca Brittain, Manon Bodin, Lynda P. Dunkel,\nCaroline Fryns, Dr. Anna Marzec, Dr. Caroline Schuppli, Dr. Brigitte\nSpillmann, and Sofia Vileila. We thank Universitas Nasional (UNAS) for\nsupport and collaboration and particularly Dr. Tatang Mitra Setia, Astri\nZulfa, Misdi bin Abdullah, and Kristana P. Makur. We thank the\nIndonesian State Ministry for Research and Technology (RISTEK), the\nIndonesian Institute of Sciences (LIPI), the Ministry of Environment and\nForestry (KLHK), the Ministry of Internal Affairs, Indonesia, the local\ngovernment in Central Kalimantan, the BKSDA Palangkaraya, the\nBornean Orangutan Survival Foundation (BOSF), MAWAS in\nPalangkaraya, the Sumatran orangutan conservation Program (SOCP),\nand Balai Besar Taman Nasional Gunung Leuser (BBTNGL) in Medan\nfor their permission and support to conduct this study. We are grateful to\nAndrea Heistermann, Dr. Gholib, and Joshua Reukauf for their support\nduring fecal sample analyses. Fecal sample collection was conducted ac-\ncording to Indonesian and international regulations and with the kind per-\nmission of the Indonesian Ministry of Environment and Forestry (KLHK)\n(permit numbers: 17256/IV/SA TS-LN/2012, SK.49/KSDAE/SET/KSA.2/\n1/2017). We thank Kevin Langergraber and two anonymous reviewers for\nhelpful comments. References Amrein M, Heistermann M, Weingrill T (2014) The effect of fission–\nfusion zoo housing on hormonal and behavioral indicators of stress\nin Bornean orangutans (Pongo pygmaeus). Int J Primatol 35:509–\n528 Archie EA, Altmann J, Alberts SC (2014) Costs of reproduction in a\nlong-lived female primate: injury risk and wound healing. Behav\nEcol Sociobiol 68:1183–1193 Ashbury AM, Willems EP, Utami Atmoko SS, Saputra F, van Schaik CP,\nvan Noordwijk MA (2020) Home range establishment and the\nmechanisms of philopatry among female Bornean orangutans\n(Pongo pygmaeus wurmbii) at Tuanan. Behav Ecol Sociobiol 74:42 go pygmaeus wurmbii) at Tuanan. 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Observers did not interact with the wild focal\nindividuals in any way and kept a minimum distance of 10 m in order to\nminimize any effect on their natural behavior. The data collection proto-\ncol for this study adheres to legal requirements of Indonesia and was\napproved by the Indonesian State Ministry for Research and\nTechnology (RISTEK) (permit number 66/SIP/FRP/E5/Dit.KI/III/\n2016), the Directorate General of Natural Resources and Ecosystem\nConservation- Ministry of Environment and Forestry of Indonesia\n(KSDAE-KLHK), the Ministry of Internal Affairs, Indonesia, the\nNature Conservation Agency of Central Kalimantan (BKSDA) and\nBalai Besar Taman Nasional Gunung Leuser (BBTNGL). Fecal sample\ncollection was conducted according to Indonesian and international reg-\nulations and with the permission of the Indonesian Ministry of\nEnvironment and Forestry (KLHK) (permit numbers: 17256/IV/SA TS-\nLN/2012, SK.49/KSDAE/SET/KSA.2/1/2017). 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Early stage evaluation of colon cancer using tungsten disulfide quantum dots and bacteriophage nano-biocomposite as an efficient electrochemical platform
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The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​mmons.​org/​publi​ cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Pourakbari et al. Cancer Nanotechnology (2022) 13:7 https://doi.org/10.1186/s12645-022-00113-2 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 https://doi.org/10.1186/s12645-022-00113-2 Cancer Nanotechnology Cancer Nanotechnology Early stage evaluation of colon cancer using tungsten disulfide quantum dots and bacteriophage nano‑biocomposite as an efficient electrochemical platform Ramin Pourakbari1,2,3, Mehdi Yousefi3*, Balal Khalilzadeh2*  , Mahsa Haddad Irani‑nezhad4, Alireza Khataee4,5, Leili Aghebati‑Maleki6, Alireza Soleimanian7, Amin Kamrani2, Forough Chakari‑Khiavi7, Rozita Abolhasan2, Morteza Motallebnezhad8, Farhad Jadidi‑Niaragh9, Bahman Yousefi10, Hossein Samadi Kafil10, Mohammad Hojjat‑Farsangi11 and Mohammad‑Reza Rashidi7 Abstract Background:  Recently, biosensors have become popular analytical tools for small analytes due to their high sensitivity and wide analytical range. In the present work, development of a novel biosensing method based on tungsten disulfide quantum dots ­(WS2 QDs)-Au for rapidly and selectively detecting c-Met protein is introduced. As a proof of concept, M13 bacteriophage-based biosensors were used for the electro‑ chemical detection of c-Met protein as a colon cancer biomarker. Method:  The M13 bacteriophage (virus), as the biorecognition element, was immo‑ bilized on glassy carbon electrodes which were modified by ­WS2 QDs-functionalized gold nanoparticles. The stepwise presence of the ­WS2 QDs, gold nanoparticles, and immobilized phage on glassy carbon electrodes were confirmed by scanning electron microscope (SEM) and square wave voltammetry (SWV) technique. Results:  The designed biosensor was applied to measure the amount of c-Met protein n standard solutions, and consequently the desirable detection limit of 1 pg was obtained. Finally, as a proof of concept, the developed platform was used for the evalu‑ ation of c-Met protein in serum samples of colon cancer-suffering patients and the results were compared with the results of the common Elisa kit. Results:  The designed biosensor was applied to measure the amount of c-Met protein in standard solutions, and consequently the desirable detection limit of 1 pg was obtained. Finally, as a proof of concept, the developed platform was used for the evalu‑ ation of c-Met protein in serum samples of colon cancer-suffering patients and the results were compared with the results of the common Elisa kit. Conclusions:  As an interesting part of this study, some concentrations of the c-Met protein in colon cancer serum samples which could not be determined by Elisa, were easily analyzed by the developed bioassay system. The developed bioassay system has great potential to application in biomedical laboratories. Conclusions:  As an interesting part of this study, some concentrations of the c-Met protein in colon cancer serum samples which could not be determined by Elisa, were easily analyzed by the developed bioassay system. The developed bioassay system has great potential to application in biomedical laboratories. Keywords:  Electrochemical, Biosensor, Cancer marker, Phage, Gold nano-layer, WS2 QDs Keywords:  Electrochemical, Biosensor, Cancer marker, Phage, Gold nano-layer, WS2 QDs Page 2 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Graphical Abstract Introduction According to reports of the WHO, approximately 9 million people died in 2015 from a variety of cancers (Pourakbari et  al. 2020). In recent decades, the rates of death from cancer malignancies have sharply increased. However, by improving the early stage detection processes, the cancer mortality rates could be reduced significantly (Fitzgerald 2020). The most routinely employed methods for colon cancer diagno- sis, including colonoscopy, fecal immunochemical test (FIT) (Gupta et al. 2013), and sigmoidoscopy (Winawer et  al. 1993), are based on tissue sampling, imaging, etc. (Rathore et al. 2013). These approaches have several disadvantages, such as invasive nature, time-consuming processes, high cost, and especially insufficient sensitivity for early detection of malignancies (Grossman et al. 1989). On the other hand, the appli- cation of biosensors (as new detection devices), and their combination with advanced nanomaterials (Jaymand 2011; Jafarizad et  al. 2018) and biomaterials (Massoumi et al. 2020) for early stage and precise diagnosis of cancers has increased nowadays in the biomedical research areas (Pourakbari et al. 2019; Isildak et al. 2020; Khalilza- deh et al. 2019, 2017). Biosensors offer some benefits including; ultrahigh sensitivity, desirable selectivity, cost-effectiveness, real-time monitoring, and fast response time. These features make biosensors potent, on-desk, and ready-to-use devices for clini- cal analyses, which also have a robust capacity for both in vitro and in vivo applica- tions for routine clinical laboratory tests (Soleymani and Li 2017; Hasanzadeh et al. 2018; Manzoori et al. 2012; Soleymani et al. 2017). The lack of sufficient sensitivity to low concentrations of cancer biomarkers in unprocessed blood or serum in the past decades has forced the development of new strategies, such as the merging of nano- technology and electrochemical biosensors that can partially overcome this problem. The upgrading of electrochemical nano-biosensors seems to be a problem-solving Graphical Abstract Graphical Abstract Graphical Abstract Introduction According to reports of the WHO, approximately 9 million people died in 2015 from a variety of cancers (Pourakbari et  al. 2020). In recent decades, the rates of death from cancer malignancies have sharply increased. However, by improving the early stage detection processes, the cancer mortality rates could be reduced significantly (Fitzgerald 2020). The most routinely employed methods for colon cancer diagno- sis, including colonoscopy, fecal immunochemical test (FIT) (Gupta et al. 2013), and sigmoidoscopy (Winawer et  al. 1993), are based on tissue sampling, imaging, etc. (Rathore et al. 2013). These approaches have several disadvantages, such as invasive nature, time-consuming processes, high cost, and especially insufficient sensitivity for early detection of malignancies (Grossman et al. 1989). On the other hand, the appli- cation of biosensors (as new detection devices), and their combination with advanced nanomaterials (Jaymand 2011; Jafarizad et  al. 2018) and biomaterials (Massoumi et al. 2020) for early stage and precise diagnosis of cancers has increased nowadays in the biomedical research areas (Pourakbari et al. 2019; Isildak et al. 2020; Khalilza- deh et al. 2019, 2017). Biosensors offer some benefits including; ultrahigh sensitivity, desirable selectivity, cost-effectiveness, real-time monitoring, and fast response time. These features make biosensors potent, on-desk, and ready-to-use devices for clini- cal analyses, which also have a robust capacity for both in vitro and in vivo applica- tions for routine clinical laboratory tests (Soleymani and Li 2017; Hasanzadeh et al. 2018; Manzoori et al. 2012; Soleymani et al. 2017). The lack of sufficient sensitivity to low concentrations of cancer biomarkers in unprocessed blood or serum in the past decades has forced the development of new strategies, such as the merging of nano- technology and electrochemical biosensors that can partially overcome this problem. The upgrading of electrochemical nano-biosensors seems to be a problem-solving Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Page 3 of 17 approach with regards to sensitivity, speed, and selectivity (Wang et al. 2013). In addi- tion, electrochemical sensors and biosensors have significant role in biomedical and pharmaceutical analysis (Saghatforoush et al. 2009; Khalilzadeh et al. 2011, 2015). Quantum dots are a subcategory of semiconductors, in which, they have been used as electrochemical modifiers for improving the sensitivity of sensors and specially biosensors (Bera et al. 2010; Jalili and Khataee 2019). Introduction Tungsten (W), as an electroac- tive metal, and its combination with sulfide compounds make an advanced material with high surface area and acceptable electrical conductivity for application as modi- fier in electrochemical-based biosensors (Pumera and Loo 2014). The electrical con- ductivity feature of ­WS2 could be further improved by merging ­WS2 with conductive compounds, such as metallic nanoparticles, such as gold, silver, and platinum via one- step or sequential electrodeposition processes (Polyakov et  al. 2014; Khataee et  al. 2018). In this study, we applied AuNPs, which were used as a bi-proposed layer. First, they were used for improving the electrical conductivity of the developed platform, and second, they were applied for bioconjugation of bioreceptors on the designed electrochemical platform. 2018). In this study, we applied AuNPs, which were used as a bi-proposed layer. First, they were used for improving the electrical conductivity of the developed platform, and second, they were applied for bioconjugation of bioreceptors on the designed electrochemical platform. Some receptor tyrosine kinases (RTKs) are proto-oncogenes that are involved in the activation process of downstream signaling molecules, which play a part in cell prolif- eration, migration, and survival (Safaie Qamsari et al. 2017). Among the most important receptors of the RTKs are c-Kit (also known as tyrosine–protein kinase KIT), Ephrin receptor, Platelet-derived growth factor (PDGF), fms-like tyrosine kinase 3 (Flt3; which in fact belongs to the receptor tyrosine kinase class III), and tyrosine–protein kinase Met (c-Met) (Ma et al. 2003). Binding of c-Met to its ligand, namely, the hepatocyte growth factor (HGF) receptor, initiates a chain of intracellular signaling pathways that interfere with the embryogenesis as well as the process of wound healing in normal cells. Never- theless, the aberrant HGF/c-Met signaling in malignant cells, which is almost attributed to the mutations, overexpression, and amplification of the c-Met gene, results in the pro- gression of the tumor through the stimulation of PI3K/AKT, MAPK/ERK, JAK/STAT, Wnt/β-catenin, as well as some other signaling pathways (Birchmeier et al. 2003). Fun- damental roles of the c-Met (mesenchymal epithelial transition factor) have been inves- tigated in numerous researches involving the spreading and metastasis of many various malignancies in humans, such as pancreas, colon, stomach, breast, prostate, bones, liver, and ovary (Ma et al. 2003). Recently, some unique features, such as high specificity for target molecules, temper- ature stability, and easy production procedures, have led to the increased use of bac- teriophages in various fields. Apparatus and procedures Autolab potentiostat/galvanostat was utilized to perform electrochemical measure- ments including electrochemical impedance spectroscopy (EIS), differential pulse vol- tammetry (DPV), square wave voltammetry (SWV), and cyclic voltammetry (CV), for all of which the NOVA 1.8 software was used for data processing. Shimadzu 8101 M FTIR spectrophotometer (Shimadzu, Kyoto, Japan) was employed to perform Fourier transform infrared (FTIR) experiments. Preparation of the FTIR discs was performed by grinding appropriate sample contents with KBr salt. A VEGA TESCAN (Czech Republic) instrument was utilized to take the scanning electron microscopy (SEM) images illustrating the stepwise modifications on glassy carbon electrode (GCE). Ini- tially, exposure of the samples to the electron bombardment with gold atoms was per- formed under vacuum condition, and then the samples were moved to SEM chamber for taking the images. The absorbance was measured with a spectrophotometer (Shimadzu UV-2550, Kyto, Japan), and fluorescence intensity was analyzed by the spectrofluorophotometer (Shimadzu RF-5301PC, Kyoto, Japan). Materials and methods Materials Gold (III) chloride trihydrate ­(HAuCl4, 99.9%), ­KNO3, NaCl, ­Na2HPO4, ­KH2PO4, KCl, ­K4 [Fe (CN)6].3H2O, ampicillin, and kanamycin were acquired from Sigma (St. Louis, MO). European bacteriological agar, extract of yeast, and Tryptone were obtained from Laboratorios Conda (Madrid, Spain). The c-Met protein, was bought from JPT (Berlin, Germany). Re-suspension of the peptide was performed in deionized water (at 0.2 mg/mL), following which it was aliquoted and stored at − 20 °C. ­WS2, dimeth- ylformamide (DMF), ethanol, acetone, and ­H2SO4 (98%) were supplied from Sinop- harm Chemical Reagent Co. Ltd. (Shanghai, China). Introduction The application of bacteriophages in biotechnology and biosensors has increased during the last decades (Gervais et al. 2007). Because of the declared top features of bacteriophages, we used these bioreceptors on ­WS2–AuNPs platform for the detection of c-Met protein. In this project, ­WS2 QDs were cast-dried on the GCE, and then the AuNPs were electrochemically deposited on the modified electrode. Following, the c-Met bacterio- phage, as the biorecognition element was immobilized on the modified electrode, and was finally applied for electrochemical evaluation of c-Met protein as a colon cancer bio- marker. As far as we are aware, this is the first report on the application of nanocomposi- tion of ­WS2 QDs, AuNPs, and bacteriophage for early stage evaluation of colon cancer. Page 4 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Phage biopaning and amplification In this study, 500 mL of phagemid library was added to cultured media containing 200 mL of 2XYT medium and ampicillin (120 mg/mL), by the time the optical den- sity of the suspension at 600 nm (i.e., OD 600) achieved ≈ 0.4–0.5. Then, approxi- mately 5 × ­1011 plaque-forming units (PFU) from the helper phage M13K07 were supplemented to each milliliter of the bacterial culture, where they were incubated for 30 min at 37 °C, and later for another 30 min at 37 °C on a shaker (at 100 rpm). Consequently, the bacteria were centrifuged (10 min, 4 °C, at 4000 rpm) and dis- persed in 100 mL of fresh 2XYT, which contained both ampicillin (120 mg/mL) and kanamycin (50 mg/mL). Next, incubation at 30 °C was performed for 16 h with shak- ing (200 rpm). Afterwards, purification of the phage was performed in line with the PEG/NaCl precipitation procedure (Qamsari et al. 2017). Preparation of ­WS2 QDs and AuNPs To this end, 1 g from tungsten disulfide powder was added to 100 mL of DMF, fol- lowing which a solution was prepared and sonicated for 3  h. Later, stirring of the collected suspension was performed in a sealed container for 6  h at 140  °C. Proof of the successful production of the ­WS2 QDs was the observed yellow solution over the sediments. The supernatant was vaporized under vacuum condition at a specific temperature and the debris was re-suspended in double distillated water for further applications (Xu et al. 2015). Consequently, the yellowish tungsten sulfide nanosheets were obtained and confirmed by FTIR. i The AuNPs were prepared using in  situ electrodeposition process (Chiang et  al. 2019). In brief, a solution of 0.005 M of ­HAuCl4 and 0.1 M of KCl in deionized water was prepared. A portion of the obtained suspension was transferred onto the electro- chemical cell and CV technique was applied for electrosynthesis process (the poten- tial was swiped between − 0.5 and 0 V, scan rate 0.05 V/S, for 25 cycles). Page 5 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Electrode preparation steps and sequential modificationsh The GCE was polished with alumina powder followed by electrochemical cleaning, which was processed in 0.5 M ­H2SO4 using CV technique, where the potential range was 0.0–1.5 V versus Ag/AgCl reference electrode at scan rate of 100 ­mVs−1 for 10 cycles and finally dried with nitrogen stream. i The electrochemical performance of each immobilization step was studied via CV technique in the electrochemical cells containing the modified working electrode, an Ag/AgCl as a reference electrode, and a platinum wire as counter electrode in ­K4[Fe(CN6)0.3H2O] solution. At first, the ­WS2 QDs were drop casted on pre-cleaned GCE. Then, AuNPs were electrochemically deposited on the ­WS2 QDs via CV technique. Next, the modified electrode was incubated with M13 phage solution as the biorecognition element. Finally, the unbound phages were removed by immersing the modified electrode in phosphate buffer solution (PBS, pH = 7) for 1 min. Characterization of ­WS2 QDs FTIR The FTIR absorption peaks are illustrated in (Additional file 1: Figure S1). Based on the obtained FTIR peaks, ­WS2 QDs have two characteristic absorption peaks, where the first one approximately appeared at 659 ­cm−1, which was associated to the wolf- ram–sulfur (W–S) bond. The second one occurred at about 866  ­cm−1, which was related to the disulfide (S–S) bond. Broad peaks, which appeared at 3527 ­cm−1 (OH bond stretching), 2933 ­cm−1 (methylene asymmetric stretching), 1674 ­cm−1 (C = O vibration), 1394 ­cm−1 (C–NH–C or C = N–C stretching vibration), 1257 ­cm−1 (C–N stretching) and 1097 ­cm−1 (C–NH–C or C–N stretching), showed that the ­WS2 QDs were correctly synthesized. In addition, the good water solubility of the ­WS2 QDs was regarded to the presence of carboxyl and hydroxyl groups (Xu et al. 2019). Page 6 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Fluorescence The photoluminescence (PL) activity of the synthesized ­W in 100-fold diluted samples at different excitation wavele increasing the excitation wavelengths, the PL activity i spectra are shown in (Additional file 1: Figure S2). The that the prepared ­WS2 QDS were synthesized proper obtained by others (Haddad Irani-nezhad et al. 2019). SEM The topography of the modified electrode surface, nanopar position of the deposited nanomaterials were successfully regard, the stepwise modifications on the working electro SEM images were taken. The SEM images are illustrated in in the different panels, the size of the ­WS2 QDs are approxi and the average size of the electrodeposited AuNPs are in t casting bacteriophage as biorecognition element on the mo morphology was changed. Because of the small size of the tures weren’t specified by SEM. However, through the chan istics, it could be concluded that the bacteriophages were modified electrode via N–Au and S–Au bonds. Furthermor dated via the Energy-Dispersive X-Ray Analysis (EDX). Fig. 1  SEM images of A ­WS2 QDs; B AuNPs–WS2 QDs; C c-Met–phage–Au images of D W and S; E S and Au and F N and Au which were extracted fro Fluorescence The photoluminescence (PL) activity of the synthesized ­WS2 QDs was characterized in 100-fold diluted samples at different excitation wavelengths (300 and 350 nm). By increasing the excitation wavelengths, the PL activity increased. The fluorescence spectra are shown in (Additional file 1: Figure S2). The obtained spectra confirmed that the prepared ­WS2 QDS were synthesized properly. The same spectra were obtained by others (Haddad Irani-nezhad et al. 2019). SEM The topography of the modified electrode surface, nanoparticles’ morphology, and com- position of the deposited nanomaterials were successfully evaluated by SEM. In this regard, the stepwise modifications on the working electrode were prepared and their SEM images were taken. The SEM images are illustrated in Fig. 1A–C. As demonstrated in the different panels, the size of the ­WS2 QDs are approximately in the range of 25 nm and the average size of the electrodeposited AuNPs are in the range of 25–45 nm. After casting bacteriophage as biorecognition element on the modified electrode, the surface morphology was changed. Because of the small size of the phages, their unique struc- tures weren’t specified by SEM. However, through the changes in the surface character- istics, it could be concluded that the bacteriophages were desirably conjugated on the modified electrode via N–Au and S–Au bonds. Furthermore, the SEM images were vali- dated via the Energy-Dispersive X-Ray Analysis (EDX). Fig. 1  SEM images of A ­WS2 QDs; B AuNPs–WS2 QDs; C c-Met–phage–AuNPs–WS2 QDs and dot mapping images of D W and S; E S and Au and F N and Au, which were extracted from Energy-Dispersive X-Ray Analysis (EDX) from the same samples Fig. 1  SEM images of A ­WS2 QDs; B AuNPs–WS2 QDs; C c-Met–phage–AuNPs–WS2 QDs and dot mapping images of D W and S; E S and Au and F N and Au, which were extracted from Energy-Dispersive X-Ray Analysis (EDX) from the same samples Page 7 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Optimization of ­WS2 QDs thickness on GCE Optimization of ­WS2 QDs thickness on GCE The first step of optimization is to optimize the concentration or thickness of nanomate- rials on the working electrode surface. In this regard, different volumes (1, 2, 3, 4, 5 and 10 µL, as a function of concentration) of the initial prepared suspension of ­WS2 QDs were drop casted on the pre-cleaned GCE. Then, the ­WS2 QDs modified electrodes were incubated at room temperature for 1 h. Following, the electrocatalytic activity of the ­WS2 QDs modified electrodes were evaluated in ­K4 [Fe (CN)6] as standard electrochemi- cal solution via CV technique in the potential range of − 0.5 to 1.0 V as well as scan rate of 100 mV (5 cycles were recorded). The results of the voltammograms relevant to this study are shown in Fig. 3A. The average of the recorded peak heights corresponding to each volume are calculated and the histogram of average peak heights versus applied dif- ferent volumes of ­WS2 QDs are presented in Fig. 3B. According to the obtained voltam- mograms and corresponding histogram, the volume of 3 µL was selected as the optimal volume of ­WS2 QDs for further studies. Previous studies have shown that after optimiz- ing the nanomaterial concentration or thickness on the electrode surface, any increasing of the nanomaterials’ concentration or resulted thick layers could prevent redox reaction on the modified electrode or act as a semiconductor or insulating agent (Tonelli et al. 2019). Then, the incubation temperature of the ­WS2 QDs on the electrode was optimized for better binding of the ­WS2 QDs. For this purpose, the modified electrodes were studied at different temperatures of 37 °C, Room Temperature (RT), and 4 °C for 1 h as constant incubation time. To investigate this step, the CV technique was applied, such as the pre- vious optimization. The obtained voltammograms are shown in (Additional file 1: Fig- ure S3A). In addition, the average of 5 replicates of peak heights are calculated and the related histogram is depicted in (Additional file 1: Figure S3B). Based on the obtained voltammogram and linked histogram, the temperature of 37 °C was selected as the opti- mum temperature for further studies. Finally, the incubation time of the ­WS2 QDs on the working electrode was optimized. For this purpose, the prepared electrodes were incubated at 37 °C for 30, 60, 90, 120, and 140 min as different incubation timepoints. EDX The presence of tungsten (W), sulfur (S), gold (Au) and carbon (C) with W:S ratio of 1:2 was revealed by EDX patterns of WS2 QDs, as shown in Fig. 1D, E. The presence of ‘C’ is due to carbonic based working electrode (GCE), while the presence of gold is mostly because of gold sputtering process during sample preparation for EDX and SEM. On top of that, the correct positioning of nanoparticles (WS2 QDs and AuNPs) and biomaterials (bacteriophage) involved in the step by step modifications was approved by EDX. The EDX results are depicted in Fig. 1F. According to the results of dot mapping, W and S are next to each other, meaning that ­WS2 is properly arranged. Likewise, Au is next to S, which means that the gold nanoparticles are immobilized on S. Besides, from the combination of N and Au, it can be concluded that the phages are mostly connected to gold through the amino groups. A B Fig. 2  A Square wave voltammograms. B The histograms of all electrode preparation steps in the standard electrochemical solution A A B Fig. 2  A Square wave voltammograms. B The histograms of all electrode preparation steps in the standard electrochemical solution Page 8 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Characterization of electrode preparation steps All of the electrode preparation steps were approved by square wave voltammetry (SWV) technique and are presented in Fig. 2. In this regard, at first, the bare GCE was put in the electrochemical cell containing potassium ferrocyanide (2 M) and potassium chloride (5 M) solution. Then, ­WS2 QDs were immobilized on the electrode by a drop- casting method, following which the modified electrode surface was again modified via gold nanoparticles through electrosynthesis. Next, the phage solution was poured onto the modified electrode with optimized concentration. Optimization of ­WS2 QDs thickness on GCE Again, the CV technique, such as previous optimizations, was applied for the evaluation of different incubation times. The recorded voltammograms and related histogram relevant to this study are shown in (Additional file 1: Figure S4). According to the obtained voltammograms and corresponding histo- gram, 60 min was determined as the optimal incubation time for further studies. Page 9 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Page 9 of 17 A B Fig. 3  A Cyclic voltammograms B The histograms of ­WS2 QDs concentration at different amounts (1, 2, 3, 4 and 10 µL) from the same source sample A B Fig. 3  A Cyclic voltammograms B The histograms of ­WS2 QDs concentration at different amounts (1, 2, 3, 4 and 10 µL) from the same source sample Fig. 3  A Cyclic voltammograms B The histograms of ­WS2 QDs concentration at different amounts (1, 2, 3, 4 and 10 µL) from the same source sample Fig. 3  A Cyclic voltammograms B The histograms of ­WS2 QDs concentration at different amounts (1, 2, 3, 4 and 10 µL) from the same source sample It was observed after 60 min of incubation that by increasing the incubation time, the redox peak currents did not change significantly. Optimization of Phage immobilization conditions After culturing and propagating the phages, 10 µL of homogenous phage solution with the concentration of ­106, which is stated by the previous studies (Ertürk and Lood 2018), was dropped on the final modified electrode (AuNPs–WS2 QDs–GCE). To optimize better binding between phage and gold, we examined the incubation temperature and time of phage binding. To optimize the incubation temperature of phage immobilized electrodes, different temperatures of 37 °C, RT, and 4 °C, were examined for 1 h. To investigate this step, CV techniques were applied (5 electrochemical cycles were performed). The voltammo- grams and histogram relevant to this study are presented in (Additional file 1: Figure S6). According to the obtained voltammograms and histogram, the temperature of 4 °C was selected as the optimum temperature for the subsequent steps. Based on the acquired results, the chemical bonding between the bioreceptor and gold nano-layer was more strong and stable at 4 °C. Next, the incubation time of phage was optimized at different timepoints of 30, 60, 120 and 180 min at 4 °C. The corresponding voltammograms and histogram are illustrated in (Additional file 1: Figure S7). Based on the calculated results, 60 min was chosen as the optimal incubation time. The lowest interaction of phages occurred at 30 and 300 min. According to the results obtained after 60 min of incubation, increasing the incubation time did not affect the interactions between the bioreceptor and gold nano-layer. Optimization of AuNPs on the ­WS2 QDs modified GCE To increase the conductivity, stabilize the ­WS2 QDs, and achieve the most obtainable and stable binding of phages (as bioreceptor) on the surface of the modified electrode, we used gold nanoparticles. For this purpose, a solution of KCl at a concentration of 0.1 M and ­HAuCl4 at a concentration of 0.005 M was prepared and transferred to the electrochemical cell. The modified electrode ­(WS2 QDs–GCE) was inserted into the electrochemical cell, which contained the gold solution. To optimize the thickness and morphology of the gold nanoparticles on the modified electrode, CV technique was per- formed in various cycle numbers (10, 15, 20, 25 and 30) in the range of − 0.5 to 0.0 V, where the scanning rate was set in 0.05 V/S. Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Page 10 of 17 Pourakbari et al. Cancer Nanotechnology To investigate the electrocatalytic properties of the modified electrodes (AuNPs–WS2 QDs–GCE), the CV technique was used in the range of 0–0.3 V. The recorded voltam- mograms relevant to this study are shown in (Additional file 1: Figure S5A). The aver- age of peak heights of the five replicates are calculated and the associated histogram is shown in (Additional file 1: Figure S5B). According to the obtained voltammograms and linked histogram, 25 cycles was chosen as an optimal cycle number for the electroprepa- ration of Au layer for additional studies. Optimization of the target protein capturing conditionsh The last step of optimization is optimizing the target protein capturing conditions on the final modified electrode (phage–AuNPs–WS2 QDs–GCE). In this regard, 10 µL of 1000 pg/mL concentration of target protein (c-Met) was immobilized on the final modi- fied electrode, and optimization of its incubation temperature and time was performed. i Temperatures of the incubation for the final modified electrodes carrying c-Met pro- tein were monitored at 37 °C, RT, and 4 °C for 1 h, and related voltammograms and his- togram are presented in (Additional file 1: Figure S8). The incubation temperature of 37 °C was selected as the optimum temperature. According to published articles, usually the bioconjugation between protein and phage occurs at a higher temperature as com- pared to phage and nanomaterial binding (Singh et al. 2009). To optimize the incubation time of the target protein, different timepoints of 30, 60, 120 and 180 min at 37 °C were applied. The resulted voltammograms and histogram are presented in (Additional file 1: Figure S9). Based on the achieved results, 60 min was applied as the optimal incubation time. It is expected that over 60 min of incubation time, damages to the protein structure may occur. Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Page 11 of 17 Pourakbari et al. Cancer Nanotechnology Calibration curve After optimization of all experimental factors, the optimized system was used to inves- tigate the different concentrations of target protein (1, 250, 500, 750 and 1000 pg/mL). To evaluate this step, the SWV technique was applied in the standard electrochemical solution in the range of − 0.1 to 0.6 V (SWV voltammograms were repeated 3 times for each concentration). The results of SWV voltammograms and histogram corresponding to the calibration curve are shown in Fig. 4. According to the calculated results, the limit of detection of the c-Met protein as a colon cancer biomarker for the designed biosensor was 1 pg/mL as well as a linear range of 1–1000 pg/mL. Repeatability To evaluate the repeatability of the developed biosensor (in the presence of 1 ng/mL of protein), the average peak height of the 10 replicates was calculated. Based on the recorded electrical signals, the desirable relative standard deviation (RSD) was obtained as 6.37% for repeatability measurements. Stability and specificity To evaluate the stability of the designed biosensor, after all preparation steps (c-Met– phage–AuNPs–WS2 QDs–GCE) (protein concentration, 1  ng/mL), the SWV was applied as same as the calibration curve condition and its voltammogram was recorded for 3 times. Then it was transferred to a refrigerator (4 °C) by placing the cap on the final modified electrode. Four days later, three SWV voltammograms were recorded again under the same conditions, and the results were finally compared. The results indicated A B Fig. 4  A Square wave voltammograms B The histograms of calibration curve A A B ammograms B The histograms of calibration curve B Fig. 4  A Square wave voltammograms B The histograms of calibration curve Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Page 12 of 17 Pourakbari et al. Cancer Nanotechnology that the average peak height of the fifth day SWV voltammograms had increased by almost 15%, as compared to the first day, proposing that by increasing the storage period some attachments related to different electrode preparation steps may be separated and detached from the GCE surface, and consequently the electrical signals increase. According to the obtained stability outcomes, the designed biosensor is sufficiently sta- ble to be used as a commercial biosensor. The specificity of the designed biosensor was successfully tested in the presence of two proteins (BSA, 0.05% and ROR1, 1 ng/mL concentrations). These two proteins are generally present in human serum samples. On the other hand, previous studies have shown that the BSA protein could react with gold, silver, and platinum, which reduces the sensitivity of the designed biosensors (Saptarshi et al. 2013). For this reason, both proteins (BSA and ROR1) were immobilized on the final modified electrode (c-Met– phage–AuNPs–WS2 QDs–GCE) in the presence of 1 ng/mL of the target protein and were incubated at room temperature for 1 h. Then, the SWV voltammograms were recorded as same as the calibration curve conditions. The resulted voltammograms and histograms for BSA and ROR1 are presented in Fig. 5. Real samples analysis by the developed biosensor and commercial Elisa Kit Lastly, the optimized bioassay was used for the quantification of c-Met protein in the serum samples of the patients with colon cancer at different stages. For this purpose, 9 patients and 1 healthy person as negative control were examined and their serum sam- ples were collected and diluted (1:1000) with PBS. Then, 10 µL of the diluted serum sam- ples were placed on the modified electrodes (instead of target protein in the calibration curve), and their SWV voltammograms were recorded as same as the calibration curve. The results of this real sample analysis are shown in Fig. 6A. The histogram of the aver- age peak height of the three replicates was calculated and is shown in Fig. 6B. Also, the c-Met protein of the same samples were evaluated by the Elisa protocol (as a positive control of this study) and their results are presented in Fig. 6C. Based on the obtained results of the reals samples, there is no difference between the healthy individual samples and the electrical signal of the modified electrode (phage– AuNPs–WS2 QDs–GCE) without target protein. In other words, there is no c-Met protein in the serum sample of the healthy person to react with or be captured by the developed biosensor. Approximately the electrical signal of four patients were in the range of 250–500 pg, while five patients were in the range of 750–1000 pg in the obtained calibration curve. In some samples, Elisa was unable to respond (samples 1, 2, 3, 4, and 8). This is a sign of the inability of Elisa and the sensitivity of the designed biosensor. Reproducibility To investigate the reproducibility of the designed bioassay, the two concentrations of target protein were selected as 1000 and 750  pg/mL. Two separated GCEs were identically modified for 1000 and 750  pg/mL, individually. The corresponding SWV Fig. 5  Interfering agents Page 13 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Page 13 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology A B C Fig. 6  Real sample analysis with designed biosensor for serum samples of different human colon cancer suffering patients at different stages. A SWV voltammograms; B corresponding histogram and C results of ELISA as a positive conventional method for the same samples A A A B C Fig. 6  Real sample analysis with designed biosensor for serum samples of different human colon cancer suffering patients at different stages. A SWV voltammograms; B corresponding histogram and C results of ELISA as a positive conventional method for the same samples Fig. 6  Real sample analysis with designed biosensor for serum samples of different human colon cancer suffering patients at different stages. A SWV voltammograms; B corresponding histogram and C results of ELISA as a positive conventional method for the same samples Page 14 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology voltammograms were recorded 3 times at the same experimental conditions. The results showed that the proposed biosensor had adequate reproducibility for clinical and com- mercial approaches. Conclusion In conclusion, a novel biosensor based on nanomaterials and with facile fabrication pro- cedure was developed using non-lytic bacteriophage M13 (as bioreceptor) for measuring the c-Met protein. A great detection limit was exhibited by the sensor (1 pg/mL). This excellent limit of detection could be contributed to the high surface area of ­WS2 QDs and phage specificity, as well as to the effective chemical binding between M13 and the surface of well-dispersed gold nanoparticles. The specificity of the phage-based biosen- sor was successfully examined in the presence of ROR1 and BSA proteins, where the introduced biosensor exhibited good response with neglectable interferences. Therefore, this biosensor could be introduced as a prospective analytical tool to monitor the desired protein in real samples. Moreover, good stability is displayed by the biosensor over an extensive range of temperatures and time. In addition, high sensitivity and selectivity are observed in the reported phage-based biosensor. As a proof of concept, the constructed bioassay was effectively applied for the detection of target protein in the colon cancer suffering patients. Interestingly, the results of the developed biosensor are more precise and sensitive as compared to commercial kits. Page 15 of 17 Pourakbari et al. Cancer Nanotechnology (2022) 13:7 Pourakbari et al. Cancer Nanotechnology Availability of data and materials Not applicable. Acknowledgements Th k Acknowledgements This work was supported by the Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, Tabriz, Iran (Grant Number: 60976). Supplementary Information The online version contains supplementary material available at https://​doi.​org/​10.​1186/​s12645-​022-​00113-2. Additional file 1: Figure S1. ­WS2 QDs FTIR. Figure S2. ­WS2 QDs fluorescence. Figure S3. A Cyclic voltammograms. B The histograms of 3 µL ­WS2 QDs at different incubation temperatures (RT, 37 °C and 4 °C). Figure S4. A Cyclic voltammograms. B The histograms of 3 µL ­WS2 QDs at different incubation times (30, 60, 90, 120 and 240 min) in RT incubation temperature. Figure S5. A Cyclic voltammograms. B The histograms of AuNPs deposition process at different cycles numbers (10, 15, 20, 25 and 30 cycles) in the range of − 0.5 to 0 V and the scanning rate of 0.05 V/S. Figure S6. A Cyclic voltammograms. B The histograms of immobilization of bacteriophage at different incuba‑ tion temperatures (RT, 37 °C and 4 °C). Figure S7. A Cyclic voltammograms. B The histograms of phage at different incubation times (30, 60, 120, 180 and 300 min) at 4 °C. Figure S8. A Cyclic voltammograms. B The histograms of target protein incubation temperature at RT, 37 °C and 4 °C. Figure S9. A Cyclic voltammograms. B The histograms of incubation time of protein at 30, 60, 120 and 180 min in 37 °C. Received: 30 September 2021 Accepted: 3 February 2022 Received: 30 September 2021 Accepted: 3 February 2022 Consent for publication Not applicable. Consent for publication Not applicable. Authors’ contributions RP was contributed in all experimental analysis and preparing of first draft. MY was the supervised the study and assisted ELISA data interpretations. MHI-n and AK were helped in synthesis and characterization of the nanomaterials. LA-M, MM and FJ-N were participated in preparation of phage library and culture. BY, HSK, MH-F were contributed in data inter‑ pretations. AS, AK, FC-K and RA were assisted in experimental analysis. BK was supervised the study and participated in idea, development of the method, validation of data and editing. M-RR was helped in research design, data analysis and method development. All authors read and approved the final manuscript. Funding g Tabriz University of Medical Sciences, Tabriz, Iran (Grant Number: 60976). Availability of data and materials Not applicable Bera D, Qian L, Tseng T-K, Holloway PH (2010) Quantum dots and their multimodal applications: a review. Materials 3(4):2260–2345 Birchmeier C, Birchmeier W, Gherardi E, Woude GFV (2003) Met, metastasis, motility and more. Nat Rev Mol Cell Biol 4(12):915–925 Chiang H-C, Wang Y, Zhang Q, Levon K (2019) Optimization of the electrodeposition of gold nanoparticles for the appli‑ cation of highly sensitive. Label Free Biosens Biosens 9(2):50 Author details 1 1 Student’s Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran. 2 Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, 51664‑14766 Tabriz, Iran. 3 Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. 4 Research Laboratory of Advanced Water and Wastewater Treatment Processes, Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, 51666‑16471 Tabriz, Iran. 5 Depart‑ ment of Environmental Engineering, Gebze Technical University, 41400 Gebze, Turkey. 6 Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. 7 Pharmaceutical Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. 8 Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran. 9 Molecular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. 10 Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. 11 Department of Oncology‑Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institute, Stockholm, Sweden. Ethics approval and consent to participate pp p p All phases of this study were approved by National Committee for Ethics in Biomedical Research (IR.TBZMED.VCR. REC.1397.286). Prior to sampling, all patients were request to fill informed consent. References RSC Adv 5(72):58316–58326 Khalilzadeh B, Shadjou N, Charoudeh HN, Rashidi M-R (2017) Recent advances in electrochemical and electrochemilumi‑ nescence based determination of the activity of caspase-3 Microchim Acta 184(10):3651–3662 p y p p Khalilzadeh B, Shadjou N, Charoudeh HN, Rashidi M-R (2017) Recent advances in electrochemical and electrochemilumi‑ nescence based determination of the activity of caspase-3. Microchim Acta 184(10):3651–3662 Khalilzadeh B, Rashidi M, Soleimanian A, Tajalli H, Kanberoglu GS, Baradaran B, Rashidi M-R (2019) Development of a reliable microRNA based electrochemical genosensor for monitoring of miR-146a, as key regulatory agent of neuro‑ degenerative disease. 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The impact of textual elements on the comprehensibility of drug label instructions (DLIs): A systematic review
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PLOS ONE RESEARCH ARTICLE OPEN ACCESS Citation: Maghroudi E, van Hooijdonk CMJ, van de Bruinhorst H, van Dijk L, Rademakers J, Borgsteede SD (2021) The impact of textual elements on the comprehensibility of drug label instructions (DLIs): A systematic review. PLoS ONE 16(5): e0250238. https://doi.org/10.1371/ journal.pone.0250238 Citation: Maghroudi E, van Hooijdonk CMJ, van de Bruinhorst H, van Dijk L, Rademakers J, Borgsteede SD (2021) The impact of textual elements on the comprehensibility of drug label instructions (DLIs): A systematic review. PLoS ONE 16(5): e0250238. https://doi.org/10.1371/ journal.pone.0250238 Method Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0250238 A systematic search was performed in PubMed, EMBASE, PsychINFO, and Smartcat (until April 2019) to identify studies investigating textual elements that facilitate or hinder the cor- rect interpretation of DLIs in relation to patients’ health literacy. Ekram MaghroudiID1,2☯*, Charlotte Miriam Joyce van Hooijdonk3☯, Heidi van de Bruinhorst1,4, Liset van Dijk5,6, Jany Rademakers2,5, Sander Diederik Borgsteede1 Ekram MaghroudiID1,2☯*, Charlotte Miriam Joyce van Hooijdonk3☯, Heidi van de Bruinhorst1,4, Liset van Dijk5,6, Jany Rademakers2,5, Sander Diederik Borgsteede1 1 Department of Clinical Decision Support, Health Base Foundation, Houten, The Netherlands, 2 Department of Family Medicine, Maastricht University, CAPHRI, Maastricht, The Netherlands, 3 Faculty of Humanities, Department of Languages, Literature & Communication, Universiteit Utrecht, Utrecht, The Netherlands, 4 Universiteit Utrecht, Pharmacy, Utrecht, The Netherlands, 5 Nivel, Netherlands Institute for Health Services Research, Utrecht, The Netherlands, 6 Faculty of Mathematics and Natural Sciences, Department of PharmacoTherapy, -Epidemiology & -Economics (PTEE), Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 * Ekram.maghroudi@healthbase.nl Introduction Correct interpretation of drug labels instructions (DLIs) is needed for safe use and better adherence to prescribed drugs. DLIs are often too difficult for patients, especially for those with limited health literacy. What is yet unknown, is how specific textual elements in DLIs (e.g., the presentation of numbers, or use of medical jargon) and patients’ health literacy skills are related to the comprehension of DLIs. In order to provide concrete directions for health professionals on how to optimize drug prescriptions, we performed a systematic review to summarize the available research findings on which textual elements facilitate or hinder the correct interpretation of DLIs in relation to patients’ health literacy. Editor: Yen-Ming Huang, National Taiwan University College of Medicine, TAIWAN Received: December 31, 2019 Accepted: April 4, 2021 Published: May 19, 2021 Received: December 31, 2019 Accepted: April 4, 2021 Published: May 19, 2021 ☯These authors contributed equally to this work. * Ekram.maghroudi@healthbase.nl ☯These authors contributed equally to this work. * Ekram.maghroudi@healthbase.nl PLOS ONE PLOS ONE Introduction Instructions on how to use drugs are an essential part of patients’ drug management. Patients’ adherence to drug instructions influences the effectiveness of their therapy [1]. Patients receive information about their drug therapy from different sources, including information from the prescriber, information in the patient leaflet, and instructions on drug labels. Understanding and remembering treatment regimens are prerequisites for drug adherence [2]. However, approximately 40 to 80 per cent of the information during patient-physician encounters is for- gotten or remembered inaccurately [2–4] and information in patient leaflets is often consid- ered as too complex [5–7]. Therefore, patients would benefit from drug instructions that are easily read, understood, and remembered during their drug therapy. In this context, compre- hensible drug label instructions (DLIs) may contribute to drug adherence. As drug labels are physically attached to each unit dispensed to patients, it is likely to be the last information source patients read before taking their drugs [8]. Therefore, DLIs should serve as an indepen- dent, comprehensible information source supporting patients’ correct drug use which in turn facilitates their drug therapy [9]. The information on drug labels consists of the name of the patient, the name of the phar- macy, the name of the drug as well as the strength and the amount of the active substance in the drug [10]. Besides this information, drug labels consist of dosage instructions and auxiliary labels. Dosage instructions describe how patients should use the drugs, the intake frequency, and the number of units per intake (e.g., ‘take two capsules twice daily’). Auxiliary labels consist of warnings (e.g., ‘do not drink alcoholic beverages’) and advices (e.g., ‘take with food or milk’). The size and design of drug packages limit the amount of available space for DLIs, i.e., only the most essential instructions are presented in a concise way. This presentation might imply DLIs are easy to read and understand. However, research shows patients often misunderstand DLIs: patients misread label instructions, patients make errors when restating the instructions in their own words, and patients are unable to demonstrate a functional understanding (i.e., demonstrating when, how, and how many tablets they would take) [11–14]. Research shows patients’ health literacy skills play a vital role in understanding DLIs and correct drug use [9,12,15–18]. Conclusion Funding: This work was supported by ZonMw, under Grant 848022004. Based on our findings, we provide an overview of textual elements that contribute to the cor- rect interpretation of DLIs. Optimizing the textual instruction on drug labels may increase the safety and adherence to prescribed drugs, taking into account that a significant proportion of patients has low health literacy. Competing interests: The authors have declared that no competing interests exist. Results Copyright: © 2021 Maghroudi 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. A total of 434 studies were identified of which 28 studies met our inclusion criteria. We found that textual elements contributing to the correct interpretation of DLIs were: using explicit time periods in dosage instructions, using plain language, presenting numbers in a numerical for- mat, and providing DLIs in patients’ native language. Multistep instructions per instruction line, using abbreviations and medical jargon seem to hinder the correct interpretation of DLIs. Although health literacy was taken into account in a majority of the studies, none of them assessed the effectiveness of specific textual elements on patients’ comprehensibility of DLIs. Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files. 1 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Funding: This work was supported by ZonMw, under Grant 848022004. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Introduction The construct of health literacy deals with literacy skills in the context of health care, whereas literacy can be defined as basic skills in reading, writing, and numeracy [19]. Historically, health literacy was first used to describe the relation of patients’ literacy level and their adherence to therapeutic regimens [20]. Gradually, the construct evolved to patients’ skills to obtain, understand, and use health information in order to enhance health, well-being, and active involvement in medical decision making [21]. Different levels of health literacy can be distinguished: (1) functional health literacy: basic skills in read- ing and writing to be able to function effectively in everyday life, (2) interactive health literacy: advanced literacy skills and social skills are used to extract health information from different forms of communication and apply this information to changing circumstances, and (3) criti- cal health literacy: advanced cognitive skills and social skills are used to critically analyse and 2 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions apply health information to exert greater control over life events and situations [20]. In sum, this classification shows functional health literacy is part of the broader construct of health lit- eracy. Moreover, the levels of health literacy progressively allow for greater patient autonomy and empowerment [20,21]. Many different instruments have been developed to assess patients’ health literacy which vary in adopted method and purpose [22]. For example, the Rapid Estimate of Adult Literacy in Med- icine (REALM), Test of Functional Health Literacy in Adults (TOFHLA), and the Newest Vital Sign (NVS) all focus on functional health literacy, but differ in adopted method. The REALM tests the ability to read and pronounce 66 medical terms [23] whereas the TOFHLA consists of a 50-item reading comprehension and 17-item numerical ability test [24]. The NVS, on the other hand, consists of a reading comprehension and numerical ability test in which patients answer 6 questions about the information in a nutritional label for ice cream [25]. Other instruments, such as the Functional Communicative Critical Health Literacy (FCCHL) and the Set of Brief Screening Questions (SBSQ) assess patients’ perceived health literacy skills, but differ in purpose and adopted method. For example, the FCCHL focuses on functional, interactive, and critical health literacy skills. It consists of 14 statements using 4-point Likert scales as response options [19]. Introduction The SBSQ only focuses on functional health literacy skills and consists of 3 statements using a 5-point Likert scale as response options [23] In sum, most instruments focus on functional health literacy skills, but the variation between the instruments in adopted method and purpose makes it hard to compare the results from health literacy interventions. Patients with limited health literacy skills often experience difficulties in reading, under- standing, and applying DLIs compared to patients with adequate health literacy [12,14,26]. Therefore, it is important to take health literacy into account when evaluating the compre- hensibility of DLI’s (cf., [27]). Especially as research shows 46 per cent of the Europeans have limited health literacy skills, varying from 29 per cent in the Netherlands to 62 per cent in Bul- garia [28]. Also, 14 per cent of the American population have limited health literacy skills [29]. As the processing of textual instructions poses a challenge for patients with limited health liter- acy, much research has been conducted on how visual elements, such as icons, pictograms, and graphics, can be used to improve the comprehensibility of DLIs [7,8,30]. However, mixed results have been found regarding their effectiveness. Wolf et al. [13] found simplified textual DLI with icons were more likely to be interpreted correctly by patients with marginal and lim- ited health literacy compared to simplified textual DLIs alone. However, other studies report that icons on drug labels were frequently misunderstood by patients with limited health liter- acy [7,8,30]. As far as we know, in most countries the DLI attached on medication packages does not contain pictograms or graphics. Therefore, it is relevant to know how the textual instructions on drug labels are comprehended. What is yet unknown, is how specific textual elements in DLIs (e.g., the presentation of num- bers, or use of medical jargon) and patients’ health literacy skills are related to (improved) com- prehension of DLIs. While Samaranayake et al. [31] conducted a narrative review on the impact of patient-related factors, such as age and health literacy, and drug label-related factors, such as the use of icons and the format of the label, on the comprehensibility of DLIs, they did not pro- vide an overview of specific textual elements associated with better comprehension of DLIs. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Search strategy We conducted a literature search in PubMed, Embase, PsychINFO, and Smartcat to identify studies that examined the relation between textual elements and comprehensibility of DLIs. The search was limited to studies published in English or Dutch, up to April 2019. We searched these databases using various synonyms for ‘drug labeling’ and ‘drug label compre- hension’. Reference lists of relevant studies were manually checked, and relevant studies were included. The detailed search strategies are presented in Table 1. Study selection Two reviewers (EM and HB) extracted data from the identified records, with one reviewer (EM) extracting data, and the other reviewer (HB) checking the information for accuracy. Duplicate publications listed in multiple databases were removed. Publications were eligible for inclusion if they met the following criteria: (1) studies which dealt with the comprehensibil- ity of DLIs, and (2) studies which addressed textual elements of DLIs. Hence, articles focussing solely on the comprehensibility of DLIs in relation to icons, font, format, the way of printing, or other graphical elements were excluded. Also, articles about the comprehensibility of other health information sources than DLIs were excluded (reported as ‘other information source’ in Fig 1). Furthermore, only actual studies were included, which implies editorials, letters to the editor, or reviews were excluded (reported as ‘no study’ in Fig 1). Two reviewers (EM and HB) assessed whether studies had to be excluded based on titles and abstracts. To validate the assessment, twenty per cent of the identified titles and abstracts were independently annotated by the two reviewers (EM and HB) after which Cohen’s kappas were calculated. The results showed the inter-rater reliability was good (κ = 0.78) [32]. After excluding studies based on titles and abstracts, both reviewers (EM and HB) read the full texts and assessed whether the study should be excluded, based on the eligibility criteria. Both reviewers had to agree on the eliminated studies. Differences in assessment were resolved by discussion or with assistance from a third reviewer (CVH or SB). Multiple publications reporting different analyses of data collected in the same study were counted as a single study with two separate research questions (see also data extraction). Introduction Knowledge of which textual elements facilitates patients’ comprehension of DLIs, especially those with limited health literacy, will provide concrete directions for health professionals, such as physicians and pharmacists, on how to optimize their drug prescriptions. In summary, the research question is: how are specific textual elements of DLI’s and patients’ health literacy related to the correct interpretation of DLIs? To answer this research question a systematic review was conducted of studies investigating the relation between the presence of specific tex- tual elements in DLIs and patients’ health literacy skills on the comprehensibility of DLIs. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 3 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions https://doi.org/10.1371/journal.pone.0250238.t001 Data extraction Data from all included articles were extracted using a data extraction sheet in Excel. The data extraction was reviewed by a second author (HB) for 33 per cent of the studies. As Table 1. Search strategy in electronic databases. Database Search components Search PubMed Comprehension AND drug labeling OR prescription label ((comprehension[MeSH Terms]) AND drug labeling[MeSH Terms]) OR prescription label[Title] PubMed Comprehension OR misunderstanding AND prescription label OR medication label "Comprehension" (Mesh) OR misunderstanding (tiab)) AND (prescription label (tiab) OR instruction label (tiab) OR medication label (tiab) Field: Title SmartCat Comprehension OR misunderstanding AND medication label OR prescription label su: comprehension OR su:misunderstanding) AND (kw:medication label OR kw: prescription label PsychINFO Comprehension OR misunderstanding AND prescription label OR medication label OR instruction label comprehension OR misunderstanding) AND (prescription label OR medication label OR instruction label Embase Comprehension OR misunderstanding AND prescription AND label OR medication AND label OR instruction AND label (’comprehension’/exp OR misunderstanding:ti,ab) AND (prescription:ti,ab AND label:ti,ab OR (medication:ti,ab AND label:ti,ab) OR (instruction:ti,ab AND label: ti,ab)) Table 1. Search strategy in electronic databases. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 4 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Fig 1. Flow chart of the selection of studies about DLIs included in the review. https://doi.org/10.1371/journal.pone.0250238.g001 Fig 1. Flow chart of the selection of studies about DLIs included in the review. https://doi.org/10.1371/journal.pone.0250238.g001 there were no major differences between the reviewers, the remaining studies were only extracted by the first author (EM). Data extraction included: study type and setting, popula- tion, methods, primary outcome, textual elements, and conclusions. If the study compared an intervention and a control group, the intervention and the primary outcome was expressed as an effect of the intervention compared to the control group. If present, quanti- tative data were extracted concerning the impact of optimized DLIs compared to standard DLIs and differences between patients with limited health literacy and adequate health liter- acy on the primary outcome. Instruments measuring participants’ health literacy were extracted to explore health literacy as explaining factor for differences in DLI comprehen- sion. Missing information was scored as ‘not reported’. PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions PLOS ONE Table 2. Assessment of the methodological quality of the included publications using the JBI critical appraisal checklists. PLOS ONE Risk of Bias Tools Reference Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12 Q13 JBI Critical Appraisal Checklist for Cross-sectional studies Alburikan et al., 2018 [36] Yes Yes Yes Yes No NA Yes Yes Davis et al., 2006 [26] Yes Yes Yes Yes No NA Yes Yes Koster et al., 2014 [41] Yes Yes Yes Yes Yes Yes Yes Yes Locke et al., 2014 [42] Yes Yes Yes Yes No NA Yes Yes Muluneh et al., 2018 [43] Yes Yes Yes Yes Yes Unclear Yes Yes Davis et al., 2006 [12] Yes Yes Yes Yes Yes Yes Yes Yes Shiyanbola et al., 2016 [35] Yes Yes Yes Yes No NA Yes Yes Shiyanbola et al., 2017 [34] Yes Yes Yes Yes No NA Yes Yes Wolf et al., 2006 [14] Yes Yes Yes Yes No NA Yes Yes Wolf et al., 2010 [13] Yes Yes Yes Yes Yes Yes Yes Yes You et al., 2011 [14] Yes Yes Yes Yes Yes Yes Yes Yes Bailey et al., 2009 [11] Yes Yes Yes Yes Yes Yes Yes Yes Beckman et al., 2005 [6] Unclear Unclear Unclear Unclear No NA Yes Yes Comer et al., 2011 [49] Yes Yes Yes Yes No NA Yes Yes Davis et al., 2009 [9] Yes Yes Yes Yes No NA Yes Yes Holt et al., 1992 [38] No No No No No NA Yes Unclear Kendrick & Bayne, 1982 [40] No No Yes Yes No NA Yes Unclear Lo et al., 2006 [18] Yes Yes Yes Yes No NA Yes Yes Mbuagbaw & Ndongmanji, 2012 [50] Yes Yes Yes Yes Yes Yes Yes Yes McCarthy et al., 2013 [46] Yes Yes Yes Yes Yes Yes Yes Yes Sahm et al., 2012 [37] Yes Yes Yes Yes No NA Yes Yes Wallace et al., 2012 [39] Yes Yes Yes Yes No NA Yes Yes Wolf et al., 2007 [17] Yes Yes Yes Yes No NA Yes Yes Wolf et al., 2011 [47] Yes Yes Yes Yes Yes Yes Yes Yes Hanchak et al., 1996 [53] Yes Yes Yes Yes No NA Yes Yes JBI Critical Appraisal Checklist for Experimental study Bailey et al., 2012 [5] Yes No Yes Yes NA Yes Yes Yes Yes JBI Critial Appraisal Checklist for Qualitative studies Webb et al., 2008 [8] Yes Yes Yes Yes Yes No No Yes Yes Yes Bailey et al., 2014 [45] Yes Yes Yes Yes Yes No Yes Yes Yes Yes JBI Critial Appraisal Checklist for Randomized Controlled Trials Wolf et al., 2016 [51] Yes No No NA No No Yes Yes Yes Yes Yes Yes Yes McManus et al., 2018 [48] Yes Yes Yes No No No Yes Yes Yes Yes Yes Yes Yes https://doi.org/10.1371/journal.pone.0250238.t002 sessment of the methodological quality of the included publications using the JBI critical appraisal checklists. Quality assessment of included studies Data extraction was based on the Preferred Reporting Items for Systematic and Meta-Analysis (PRISMA) guidelines. This review included observational, cross-sectional, cohort, experimen- tal, qualitative studies, and a randomized controlled trial. We used the Joanna Briggs Institute Critical Appraisal Checklists, for the cross-sectional studies, the cohort study, the experimental study, the qualitative studies and the randomized controlled trial. The checklists included 8 to 13 questions for assessing the methodological quality of the included studies (see Table 2) [33]. Two authors (EM and HvB) assessed the methodological quality of the included studies inde- pendently and the inter-rater reliability was, after discussion, 100%. 5 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Data analysis Data were synthesized by narrative and tabular methods. The included studies differed sub- stantially regarding patient population and measurements methods. The study characteristics (primary outcome, study design and sample, patient characteristics, health literacy skills, and textual elements) of the publications were classified (Table 3). The studies were grouped by DLI type. Three types were distinguished: dosage instructions, auxiliary labels, and drug labels with combined instructions. The latter category was used when a study investigated a combi- nation of auxiliary labels and dosage instructions, or when the DLI type was not specified. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 6 / 30 The impact of textual elements on the comprehensibility of drug label instructions PLOS ONE Table 3. Characteristics of included studies (author(s), primary outcome, study design and sample, and health literacy) and recommendations on composing comprehensible DLIs, stratified to type of instruction (drug label, auxiliary label instruction, or dosage instruction) and type of textual element (plain language, native language, presentation of numbers, specificity of dosage instructions, number of messages per instruction line, and abbreviations). Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements DRUG LABELS WITH COMBINED INSTRUCTIONS 1. Alburikan et al., 2018 [36] Prescription label comprehension was measured by asking patients ‘How would you take this medicine?’ for commonly prescribed drugs. A multicentre, cross-sectional observational study based on semi- structured interviews. 511 Saudi patients. HL: Arabic Single Item Literacy Screener. Arabic drug labels. TE: The hybridization of the label language between Arabic and English lead to misunderstanding. All of the label aspects were written in Arabic except the numbers, which were written in English. TE: Other causes for misunderstanding were complexity of the DLI and implicit dosage intervals HL: Patients with limited HL skills were associated with a high percentage of misunderstanding DLIs in comparison to patients with good HL skills (59.5% versus 36.0%). - Instruction in native language - Presentation of numbers - Specificity of dosage instructions - Write instructions (both text and numbers) in patients’ native language. - Instructions containing fewer numbers enhance comprehensibility (e.g., ‘Take 1 tablet by mouth 1 time a week’ vs. ‘Take 5 ml every 8 hours for 7 days’). - Provide instructions with explicit dosage intervals. 2. Data analysis Bailey et al., 2012 [5] Prescription label comprehension was measured by asking participants ‘Using this dosing tray, please show me when you would take this drug over the course of one full day.’ Prescription label regimen dosing and consolidation was measured by handing participants five medication bottles. Participants used the dosing tray to demonstrate how and when they would take all five drugs on a typical day. Randomized experimental evaluation. 202 Low English Proficiency (LEP) adult speaking 5 non-English languages. HL: not reported. ConcordantRx instructions (i.e., multilingual instructions which incorporated health literacy ‘best practices’) vs. standard instructions. TE: Participants receiving the ConcordantRx instructions demonstrated significantly greater comprehension, regimen dosing and regimen consolidation compared to those receiving standard instructions. HL: - - Specificity of dosage instructions - Plain language - Presentation of numbers - Instruction in native language - Specify dosage intervals to four distinct time periods (i.e., ‘morning, noon, evening, bedtime’). - Use simple terms (e.g. ‘pills’ vs. ‘tablets’). - Use numbers instead of letters (i.e., ‘2’ vs. ‘two’). - Translate instructions to patients’ native language. (Continued) 7 / 30 7 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 3a. Davis et al., 2006 [26] Prescription label comprehension was measured by asking patients ‘How would you take this medicine?’ Functional prescription label comprehension was measured by asking patients ‘Show me how many pills you would take of this medicine in one day’. Cross-sectional study using in- person, structured cognitive interviews. 395 adults. HL: REALM. Container label instructions and warning labels. TE: The majority (51.8%) of incorrect patient responses reflected an error in dosage (i.e., ‘tablespoon’ vs. ‘teaspoon’) and 28.2% stated the wrong dose frequency (i.e., ‘one tablet each day for seven days’ vs. ‘Take one tablet by mouth twice daily for seven days’). HL: Patients reading at or below the 6th grade level (limited literacy) were less able to understand all 5 label instructions. Prevalence of misunderstanding of one or more DLI was for patients with adequate, marginal, and limited literacy was 37.7%, 51.3%, and 62.7%, respectively. Data analysis - Presentation of numbers - Specificity of dosage instructions - Dose measurements - Instructions containing fewer numbers enhance comprehensibility (i.e., ‘Take one tablet by mouth once each day’ vs. Take one tablet by mouth twice daily for seven days’). - Explicate dosage instructions with daypart- and hour of intake (i.e., ‘Take one tablet in the morning and one at 5 p.m.’). - The formulation of dose measurements should be evaluated. 3b. Wolf et al., 2007 [17] See study 3a See study 3a. See study 3a. See study 3a. TE: Patients were better able to interpret more explicit dose frequencies, such as ‘Take one tablet in the morning and one at 5 p.m’ (90%), compared to ‘Take two tablets by mouth twice daily’ (83%), and ‘Take one teaspoonful by mouth three times daily’ (73%). TE: Patients found simpler dosing regimens easier to understand while more complex regimens resulted in more errors in their interpretation. HL: The prevalence of misunderstanding among patients with adequate, marginal and limited literacy was 38%, 51% and 63% respectively. HL: Patients with low literacy were less able to state the correct number of pills taken daily compared to those with marginal and adequate literacy (35% versus 63% versus 80) - Plain language - Specificity of dosage instructions - Avoid repetitiveness in numbers between dosage (‘two’) and frequency (‘twice’). - Words as ‘antibiotic’, ‘orally’, ‘teaspoonful’, ‘medication’, ‘prescription’ and ‘dose’ were difficult to recognize and pronounce by patients reading at 6th grade level or below. - Avoid unclarified medical jargon (‘antibiotic’) or awkward terms (‘twice’). - The amount of content to be retained (dosage, frequency and/or duration of intake) makes instructions complex. - Explicit dose frequencies were easier to interpret than implicit, vague dose frequencies (‘Take one tablet in the morning and one at 5 p.m’ vs. ‘Take two tablets by mouth twice daily’). (Continued) 8 / 30 The impact of textual elements on the comprehensibility of drug label instructions PLOS ONE Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 4. Koster et al., 2014 [41] Participants completed a survey containing multiple- choice questions about five frequently used standard drug label instructions (i.e., combination of over the counter and prescribed drugs). Cross-sectional study. Individually completed surveys. Data analysis 691 First-generation immigrants from the Antilles, Iran and Turkey. Reference group: 153 Dutch first-year pharmacy students. HL: not reported. Five DLIs. TE: Only two out of five DLI’s were interpreted correctly by the majority of all respondent groups. The instruction ‘Take with water, not with milk” was correctly interpreted by less than 25% of the participants. The warning ‘Avoid sunlight exposure’ was often misinterpreted (<8% correct). The instruction ‘Do NOT drink grapefruit juice along with this drug’ was correctly interpreted by approximately half of the participants HL: - - Plain language - Instruction in native language - Reformulate ‘Take with water, not with milk’ by mentioning dairy products should be avoided. - Reformulate the instruction ‘Do NOT drink grapefruit juice along with this drug’ by ‘Do not use grapefruit(juice) while taking this medicine’. - Instructions should be given preferably in the patients’ native language. 5. Locke et al., (2014) [42] Comprehension of new and existing prescription auxiliary labels was measured by asking patients ‘What do you think this auxiliary label is saying?’ Cross-sectional study. Semi- structured interviews. 120 Adults from minority populations (all ethnicities other than non-Hispanic white) who were currently taking or had previously taken a prescription medication and could understand English. HL: Revised REALM (REALM-R). Four existing prescription auxiliary labels. New labels were designed based on previous research. TE: All existing prescription auxiliary labels yielded less than 50% correct interpretation except for ‘Take with food’ and ‘Do not chew or crush’. The newly designed labels were better understood compared to existing labels. HL: 56.7% had a REALM-R score below 7th grade. Higher REALM-R score was associated with better interpretation of DLIs. - Number of messages per instruction line - Plain language - Newly designed DLIs were single item instructions (e.g., ‘Swallow this medication whole’). - Newly designed DLIs were written in plain language (e.g., ‘Take this medication with a full glass of water’). 6. Muluneh et al., (2018) [43] Cancer patients’ use of oral chemotherapies and comprehension of labelling directions was investigated using a 30-question survey. Survey. 93 Patients taking oral chemotherapies, adult patients (>18 years old), diagnosed with breast cancer, renal cell carcinoma (RRC), chronic myeloid leukaemia (CML) and colorectal cancer (CRC). HL: not reported. Drug labels of oral chemotherapy. TE: 15% of the patients had difficulty understanding label directions. Data analysis Patients had recommendations to help them understand textual aspects of the medication label: avoiding abbreviations (23%) and easier directions (21%). HL: - - Abbreviations - Plain language - Abbreviations should be avoided. - Uses easier label directions. However, it is not mentioned what easy directions are. AUXILIARY LABEL INSTRUCTIONS LOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 4. Koster et al., 2014 [41] Participants completed a survey containing multiple- choice questions about five frequently used standard drug label instructions (i.e., combination of over the counter and prescribed drugs). Cross-sectional study. Individually completed surveys. 691 First-generation immigrants from the Antilles, Iran and Turkey. Reference group: 153 Dutch first-year pharmacy students. HL: not reported. Five DLIs. TE: Only two out of five DLI’s were interpreted correctly by the majority of all respondent groups. The instruction ‘Take with water, not with milk” was correctly interpreted by less than 25% of the participants. The warning ‘Avoid sunlight exposure’ was often misinterpreted (<8% correct). The instruction ‘Do NOT drink grapefruit juice along with this drug’ was correctly interpreted by approximately half of the participants HL: - - Plain language - Instruction in native language - Reformulate ‘Take with water, not with milk’ by mentioning dairy products should be avoided. - Reformulate the instruction ‘Do NOT drink grapefruit juice along with this drug’ by ‘Do not use grapefruit(juice) while taking this medicine’. - Instructions should be given preferably in the patients’ native language. 5. Locke et al., (2014) [42] Comprehension of new and existing prescription auxiliary labels was measured by asking patients ‘What do you think this auxiliary label is saying?’ Cross-sectional study. Semi- structured interviews. 120 Adults from minority populations (all ethnicities other than non-Hispanic white) who were currently taking or had previously taken a prescription medication and could understand English. HL: Revised REALM (REALM-R). Four existing prescription auxiliary labels. New labels were designed based on previous research. TE: All existing prescription auxiliary labels yielded less than 50% correct interpretation except for ‘Take with food’ and ‘Do not chew or crush’. The newly designed labels were better understood compared to existing labels. HL: 56.7% had a REALM-R score below 7th grade. Higher REALM-R score was associated with better interpretation of DLIs. Data analysis - Number of messages per instruction line - Plain language - Newly designed DLIs were single item instructions (e.g., ‘Swallow this medication whole’). - Newly designed DLIs were written in plain language (e.g., ‘Take this medication with a full glass of water’). 6. Muluneh et al., (2018) [43] Cancer patients’ use of oral chemotherapies and comprehension of labelling directions was investigated using a 30-question survey. Survey. 93 Patients taking oral chemotherapies, adult patients (>18 years old), diagnosed with breast cancer, renal cell carcinoma (RRC), chronic myeloid leukaemia (CML) and colorectal cancer (CRC). HL: not reported. Drug labels of oral chemotherapy. TE: 15% of the patients had difficulty understanding label directions. Patients had recommendations to help them understand textual aspects of the medication label: avoiding abbreviations (23%) and easier directions (21%). HL: - - Abbreviations - Plain language - Abbreviations should be avoided. - Uses easier label directions. However, it is not mentioned what easy directions are. AUXILIARY LABEL INSTRUCTIONS 7. Davis et al., 2006 [12] Comprehension of commonly used prescription medication warnings was measured by asking patients ‘What does this label mean to you?’ In-person structured interviews. 251 Patients receiving primary care at a hospital clinic. HL: REALM. Warning labels. TE: The simplest label (‘Take with food’) was interpreted correctly by 84% of the patients while a label with multi-step instructions like ‘Do not take dairy products, antacids or iron preparations within 1 hour of this medication’ was interpreted correctly by 7.6% of the patients. HL: Patients with limited HL were at greater risk to misinterpret DLIs. - Number of messages per instruction line - Use single action instructions (e.g., ‘Take with food’. (Continued) 9 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 8a. Shiyanbola et al., 2016 [35] Patients’ perspectives on the words (content) of prescription warning labels were examined. Semi-structured face-to-face interviews. 21 patients. HL: NVS. Warning labels. TE: Patients wanted the warning instructions to be more specific, especially the time frame needed to adhere to the instruction. TE: For the instruction ‘Take with a full glass of water’ patients preferred more information about the meaning of ‘a full glass’. Data analysis TE: Patient preferred the inclusion of the word ‘warning’ on the PWL to create alertness. HL: The mean HL score was 2.4. Prevalence of patients with limited, marginal and adequate HL was 19%, 14% and 43% respectively. - Plain language - Specify the time frame needed to adhere to the instruction. - Specify ‘a full glass of water’. - Include the word ‘warning’ on the label and the reason for the warning. 8b. Shiyanbola et al., 2017 [34] Pharmacists’ perspectives on the words (content) of prescription warning labels were examined. See study 8a. 8 Pharmacists. See study 8a. TE: Pharmacists wanted the instructions to be more specific, especially the time frame needed to adhere to the instruction. For the instruction ‘Take with a full glass of water’ they preferred more information about the meaning of ‘a full glass’. - Plain language - Specify the time frame needed to adhere to the instruction. - Specify ‘a full glass of water’. 9. Webb et al., 2008 [8] Comprehension of prescription warning labels was investigated by showing participants a prescription pill bottle container with a prototype of a warning label asking them to interpret the label. Participants were then tested on their comprehension of 10 common warning labels by matching warning messages with the corresponding icons. Participants took part in a discussion group to solicit feedback around improving existing language and content, and revising icons of ten of the most commonly used warning labels. Patients were shown warning message in text form only and asked ‘If this message was on your prescription pill bottle, how would you take the medicine?’ Structured cognitive interviews followed by discussion groups that solicited feedback for revising text and icons. 85 adults. HL: REALM. Warning labels. TE: Most text messages were confusing and used language that was too difficult. HL: 56% of patients had limited HL. - Plain language Language should be shortened and made clear and simple. Words like ‘external’, ‘prolonged or excessive exposure’ and ‘non- prescription’ should be avoided. ‘External’ should be written as ‘on your skin’, ‘Prolonged or excessive exposure’ as ´limit your time in the sun’ and ‘non- prescription’ as ‘over-the- counter’. Data analysis (C ti d) PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 10 / 30 The impact of textual elements on the comprehensibility of drug label instructions PLOS ONE Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 10. Wolf et al., 2006 [14] Comprehension was measured by asking patients to interpret and comment on eight commonly used warning labels on prescribed drugs. Structured interviews. 74 Patients reading at 6th- grade level or below. HL: REALM. Warning labels. TE: Rates of correct interpretation of the eight prescription warning labels ranged from 0% to 78.7%. None of the patients were able to correctly interpret ‘Do not take dairy products, antacids, or iron preparations within one hour of this medication’. The causes for misunderstanding were attributed to word choice, message length, and number of steps for action. HL: patients 3rd-grade or below: 38% Patients 4th-6th grade: 62%. Patients with low literacy skills demonstrated a lower rate of correct interpretation of the eight most commonly used prescription warning labels than did those with higher literacy. - Number of messages per instruction line - Plain language - Avoid multiple-step instructions (e.g., ‘Refrigerate, shake well, discard after . . .’) - Avoid unnecessary complex (e.g., ‘You should avoid prolonged or excessive exposure to direct and/or artificial sunlight while taking this medication’) or vague formulations (e.g., ‘medication should be taken with plenty of water’). - Refrain from professional jargon (e.g., ‘iron preparations’, ‘dairy products’, ‘antacids’). 11. Wolf et al., 2010 [13] Patients’ interpretations of the nine (prescription and over-the-counter) drug warnings placed on container vials was investigated by asking ‘In your own words, what do these labels mean to you?’ Semi-structured interviews. 500 adult patients. HL: REALM. Warning labels: (1) current standard drug warning labels, or (2) drug warnings with text rewritten in plain language, or (3) plain language and icons developed with patient feedback. TE: Auxiliary warning labels with explicit, easy-to-read messages significantly improved rate of attendance and comprehension among patients. Prescription drug warning labels with simplified text and simplified text + icons were significantly more likely to be correctly interpreted compared with standard labels. HL: 20.1% were reading below 7th grade level (= limited literacy). Limited literacy was an independent predictor of misinterpretation. Data analysis - Plain language Use plain language in DLIs, such as ‘Limit your time in the sun’ 12. You et al., 2011 [44] Patients’ interpretation of prescription warning labels was examined by asking ‘In your own words, what does this mean to you?’ Structured cognitive interview. 132 Pregnant and/or breast-feeding females at reproductive age. HL: REALM. Warning labels: (1) current teratogen warning, (2) label with simplified text and (3) label with simplified text and icons. TE: Comprehension of enhanced text + icon label (94%) was significantly higher than the standard (76%) and enhanced text-only (79%) labels. HL: 18% low HL, 39% marginal HL and 42% adequate HL. Interactions on HL were not found to be significant. - Plain language Use explicit, easy-to-read messages in plain language. However, authors do not explicate what plain language and easy-to-read messages are. DOSAGEINSTRUCTIONS LOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 DOSAGEINSTRUCTIONS 11 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 13. Bailey et al., 2009 [11] Participants’ comprehension of dosage instructions of a liquid drug commonly prescribed for children was investigated. To assess participants’ understanding of the prescription labels they were asked ‘How would you give this medicine?’ Qualitative structured interviews. 373 adults. HL: REALM. Dosage instructions of liquid drugs. TE: One in three participants misunderstood dosage instructions. Common causes for misunderstanding included problems with dosage measurement (28%; i.e., ‘tablespoon’ vs. ‘teaspoon’) and frequency of use (33%; i.e., ‘every 3 hours’ vs. ‘every 6–8 hours’). HL: 43.2% of patients with limited HL misunderstood DLIs. Inadequate and marginal HL were independent predictors of misunderstanding DLIs - Dose measurements - Specificity of dosage instructions No explicit recommendation mentioned, authors mention that studies are underway to evaluate the formulation of dose measurement for liquid medication. Separate dose from interval and provide the explicit frequency of the drug (e.g., ‘Take 1 (unit) at morning, take 1 (unit) noon, and take 1 (unit) at bedtime’ vs. ‘Take one teaspoon full by mouth three times daily’). 14. Bailey et al., 2014 [45] During discussion groups, participants were shown a series of ‘standard’ and ‘improved’ prescribed drug instructions. Participants were asked to consider how the terminology and phrasing of instructions could be improved to promote comprehension. Four iterative sessions of discussion groups. 40 English speaking adults. HL: REALM. Dosage instructions: standard instructions (e.g., ‘Take one inhalation twice a day’) vs. improved instructions (e.g. ‘Take 1 puff in the morning and 1 puff in the evening every day’) which incorporated the UMS and health literacy best practices: - Easy-to-understand terms - Chunking/grouping information - Explicit dosage information - Specific time periods - Sentence format - Numbers in numeric form TE: Participants suggested using clear, concise wording and phrasing whenever possible. Words, such as ‘subcutaneously’ and ‘inhalation’, were viewed as unnecessarily difficult, by many participants. TE: Participants preferred ‘half’ over ‘0.5’ and ‘½’ TE: Participants agreed on the need detailed instructions (i.e., ‘when you are short of breath’ vs. ‘as needed’; ‘until all pills have been taken’ vs. ‘until the bottle is empty’). DOSAGEINSTRUCTIONS HL: 33% of the patients had limited HL skills. - Dose measurements - Presentation of numbers - Plain language - Authors recommend additional research on the comprehensibility of measurement formulations (‘teaspoon’ vs. ‘teaspoonful’). - Use a numeric instead of an alphanumeric presentation for numbers, except for fractions. - Avoid the term ‘as needed’. - The duration and maximum dose per day should be specified on the label for short- term drugs. - Avoid the word ‘maximum’. Use ‘Do not take more than . . . per day’. - Avoid unnecessarily difficult words, such as ‘subcutaneously’ and ‘inhalation’. Use ‘under your skin’ and ‘puff’. (Continued) 12 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions ( ) Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 15. Beckman et al., 2005 [6] Comprehension of DLIs was measured using three tests: 1) Participants were given a box of aspirin. They were asked to read the instructions and answer the question ‘What is the maximum number of times you may take this aspirin during one day? 2) Participants were given a box of penicillin with the instruction ‘2 tablets morning and evening’. They were asked how many days the pills would last. 3) Participants were given a receipt from the pharmacy with the sum of two items billed for a total of 64 crowns. They were asked to calculate how much change they would receive if they paid with a 100-crown note. Performance of three cognitive tests through direct interviews. 492 Elderlies in Sweden, aged 77 or older. HL: not reported. Dosage instructions. TE: For the first test with the aspirin container (i.e., understanding instructions), 30.7% answered incorrectly. The second test with the penicillin instruction (i.e., calculating number of days) 47.4% answered incorrectly. For the third test in which participants had to calculate their change at the pharmacy, 20% answered incorrectly. HL: - Specificity of dosage instructions The instruction ‘2 tablets morning and evening’ should be rephrased as ‘2 tablets in the morning and 2 tablets in the evening’. 16. Comer et al., 2011 [49] The variability in patients’ understanding of quantitative statements from prescription orders was investigated. DOSAGEINSTRUCTIONS Patients received a scenario and were asked to use a proved tube of cream with the instruction ‘Apply a small amount to the area’ and squeeze out what they considered as a small amount. Interviews. 100 patients. HL: not reported. Dosage instruction ‘Apply a small amount to the area’ TE: Patients showed variability in the interpretation of a small amount of topical product cream. The mean weight of a small amount was between 36 and 50 grams. HL: - Dose measurements Be specific in what is meant by phrases like ‘a small amount’. However, the authors do not provide alternative formulations. 17. Davis et al., 2009 [9] Comprehension of prescription DLIs was measured by showing patients ten prescription bottles one at a time and asking ‘How would you take this medicine?’ Cross-sectional study using in- person, structured interviews. 359 adults. HL: REALM. Dosage instructions. TE: Patients were significantly more likely to understand instructions with explicit time periods compared to instructions stating times per day or hourly intervals. Four out of five patients in this study misinterpreted one or more of the ten common DLIs. HL: 55 patients had low HL, 109 patients had marginal HL and 195 patients had adequate HL. Low and marginal literacy were significant independent predictors of misinterpreting instructions. Specificity of dosage instructions Avoid frequency in hourly intervals or the number of times of day in dosage instructions (e.g., ‘Take 1 pill by mouth every 12 hours with a meal’; ‘Take two tablets by mouth twice daily’). Instead use time periods in dosage instructions (e.g., ‘Take 2 pills in the morning and 2 pills in the evening’; ‘Take 1 pill by mouth every day’) (Continued) LOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 13 / PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 13 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions ( ) Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 18. Hanchak et al., 1996 [53] Comprehension of prescribed drug dosage instructions was investigated by asking patients ‘How many times a day do you understand that your medication is to be taken?’ Prospective cohort study. 500 patients. HL: not reported. Dosage instructions. DOSAGEINSTRUCTIONS TE: Dosage instructions specifying hourly intervals were less understood than dosage instructions specifying daily frequency. HL: - Specificity of dosage instructions Use dosage instructions in which daily frequency is specified instead of dosage instruction in which hourly intervals are specified 19. Holt et al., 1992 [38] Consumers’ interpretations of dosage instructions was investigated by asking consumers how they would take drugs. The DLIs were common and could occur on over-the-counter and prescribed drugs. Survey. 321 participants. HL: not reported. Six dosage instructions: Take 1 tablet 3 times daily. Take 1 tablet every 8 hours. Take 1 tablet daily. Take 1 tablet twice daily. Take 1 tablet every 12 hours. Take 2 tablets daily. TE: Dosage instructions elicited a higher percentage of correct responses if they specified the number of hours between doses (i.e., ‘Take 1 tablet every 8 hours’) compared to dosage instructions which did not specify the number of hours between doses (i.e., Take 1 tablet 3 times daily’). The use of specific hourly intervals is superior to more vague instructions. The use of daily terms is more frequently associated with correct comprehension than meal terms. HL: - Specificity of dosage instructions Explain specifically how medications are to be taken by using specific hourly intervals (morning, noon, evening, bedtime). 20. Kendrick & Bayne, 1982 [40] Comprehension was measured by asking patients how many of their prescribed drug they should take every day. Also, patients were asked to explain how many tablets a day they would take following the instruction: ‘Take one tablet every 6 hours’. Interviews with questions on: 1) where they kept their medicines; 2) how many pills they should be taking every day. 40 Patients, 65 years or older of age. HL: not reported Dosage instruction ‘Take one tablet every 6 hours’ TE: In 29% of the cases, participants’ understanding differed from what was written on the drug label. For the instruction ‘Take one tablet every 6 hours’, only 22% of 37 participants answered that they would take four pills in a day HL: - Specificity of dosage instructions Oral instructions should be reinforced with explicit written instructions. 21. Lo et al., 2006 [18] Comprehension of a DLI of a prescription for ferrous sulfate was investigated. Participants answered the following questions: 1) Please use the medicine dropper to show me how much medicine you should give. 2) How many times a day should you give this medicine? DOSAGEINSTRUCTIONS 3) If you give the first dose now, when should you give the next dose of medicine? An anonymous cross-sectional survey. 326 English-speaking parents who were 18 years or older, primary caretaker of a child of 5 years or younger. HL: A quantitative portion of the TOFHLA to indicate parental HL. Dosage instruction ‘Give 1 dropperful by mouth twice daily’ TE: 252 (77%) participants incorrectly dosed the medicine. The majority of errors occurred with demonstrating the amount of medicine to give (74%) and stating the time to give the next dose (67%). Participants did not understand the term ‘dropperful’. HL: No numbers reported about the HL of patients. - Dose measurements - Specificity of dosage instructions - Avoid ‘dropperful’ to indicate dose measurements. - Specify the number of hours in between doses or the hour to give each dose. (Continued) LOS ONE | https://doi org/10 1371/journal pone 0250238 May 19 2021 14 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions ( ) Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 22. Mbuagbaw & Ndongmanji, 2012 [50] Comprehension of frequently used prescriptions was measured by asking patients if they could tell how drugs should be taken. Cross-sectional study: a pilot tested questionnaire. 204 Outpatients in semi- urban Cameroon. HL: not reported. Four different DLIs: fully written out, Latin abbreviations, symbols, and pictograms Latin abbreviations were least understood (26.9%), DLIs with symbols were understood by 89.7% of participants and written-out instructions by 87.7% of participants. HL: - Abbreviations Written-out instructions are better understood. Avoid the use of Latin abbreviations. 23. McCarthy et al., 2013 [46] Comprehension was measured by presenting participants a dosing tray that contained 24 slots representing each hour of a day. Participants were given a hypothetical prescription bottle and the scenario that they had been prescribed pain medication. Participants answered the following questions: 1) Imagine that it is 8am and you are having pain. Please show me how many pills of this medicine you would take at 8am by placing the beads into the box.’ 2) If you were still in pain after taking this dose of medicine, when could you take this medicine again? DOSAGEINSTRUCTIONS (Continued) LOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 15 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 25. Wallace et al., 2012 [39] Comprehension of dosage instructions was measured by presenting participants a bottle of over-the-counter medicine. Participants answered two questions: 1) Please describe how you would give this medicine over a 24-hour period (1 day). 2) Please show me how you would give one dose of this medicine. Participants could use three oral liquid measuring devices. A structured interview. 193 English-speaking women of childbearing age. HL: SBSQ-D. Implicit dosage instruction: ‘Shake liquid well and give (child’s name) 6ml by mouth every 12 hours’ Explicit dosage instruction: ‘Shake liquid well and give (child’s name) 6 ml by mouth at 7 am and 7 pm’. TE: Approximately one third of participants (32.1%) were able to describe and measure a dose of the medication correctly. However, implicit versus explicit dosage intervals—did not result in improved patient comprehension of instructions. HL: 48,7% of the participants had inadequate HL. HL was associated with higher odds of correctly measuring a dose of the medication. The prevalence of understanding among patients with adequate, marginal and limited literacy was 82.8%, 74.1% and 55.6% respectively. Specificity of dosage instructions Specify the dosing interval 26. Wolf et al., 2011 [47] Comprehension was measured by providing patients a hypothetical drug regimen, which consisted of 7 actual prescription drug pill bottles with mock-up labels, each with a retired drug name and different dosage instructions. Patients had to demonstrate when they would take the entire regimen by dosing fake pills contained with each prescription bottle at the times of day that they would take the drugs. A structured interview. 464 adult patients. HL: REALM. Dosage instructions with implicit timing intervals (e.g., ‘Take 1 tablet by mouth 3 times daily’) and dosage instructions with explicit timing intervals (e.g., ‘Take 1 tablet by mouth at bedtime’) TE: One-third of the participants (29.3%) dosed their medications 7 or more times per day, while only 14.9% organized the regimen into 4 or fewer times a day. TE: When the drugs had variable expressions of the same dose frequency (e.g., ‘every 12 hours’ vs. DOSAGEINSTRUCTIONS 3) Show me at what time and how many pills of this medicine you would take for your next dose. In-person interviews. 87 adults. HL: REALM. Standard ‘as needed’- instructions versus a patient-centred Take- Wait-Stop label. The Take-Wait-Stop label included explicit, deconstructed instructions along with simplified text, numeric characters instead of words, and ‘carriage returns’ to place each part of the instructions on separate lines. In addition, to convey the maximum daily dosage the word ‘Stop’ was used to replace the typical wording ‘Do not exceed’. TE: 31.8% of the participants who were shown the standard label demonstrated taking in excess of 6 pills in 24 hours compared with only 14.0% of participants who were shown the Take-Wait-Stop label. TE: Of the standard label group, 20.5% of the participants demonstrated dosing intervals of fewer than 4 hours compared with 23.3% of the participants the Take- Wait-Stop label group TE: Participants who were exposed to the standard label were 2.5 times more likely to exceed the recommended maximum daily dose. HL:72,4% had adequate literacy. Study was not powered to detect such differences, large extent had adequate HL. Plain language, specificity of dosage instructions, presentation of numbers, single item instructions Use Take-Wait-Stop instructions. Example: ‘Take: 1 or 2 pills Wait: 4 hours before taking again Stop: Do not take more than 6 pills in 24 hours’ 24. Sahm et al., 2012 [37] Correct interpretation of three prescribed dosage instructions was evaluated by asking participants the following questions: 1) In your own words, how would you take this medicine? 2) How many tablets would you take of this medicine in one day? In-person interviews. 94 participants. HL: REALM. Different dosage instructions: 1) Standard prescription instructions written as times per day (usual care). 2) Patient centred instructions hat specify explicit timing with standard intervals (morning, noon, evening, bedtime) or with mealtime anchors. 3) Patient centred instructions with a graphic aid to visually depict dose and timing of the medication. TE: PCI were more likely to be correctly interpreted than the standard instructions. HL: 30.9% with limited HL. Patients with limited health literacy were more likely to correctly interpret the patient centred instructions (91%) than the standard instructions (66%). Specificity of dosage instructions Specify explicit timing with standard intervals: morning, noon, evening, bedtime or mealtime-anchors. DOSAGEINSTRUCTIONS ‘twice daily’), 79.0% of the participants did not consolidate the drugs. HL: Nearly half of the participants were identified as having either low (20.7%) or marginal (22.8%) health literacy skills. HL: Low health literacy was found to be the sole independent predictor of a greater number of times per day for dosing the 7-drug regimen. Specificity of dosage instructions Provide standard, explicit instructions. However, the authors do not provide examples of standard, explicit instructions. (Continued) 26. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 16 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Author(s), publication year Primary outcome Study design and sample Patients and Health Literacy (HL) measure Type of instructions Findings on textual elements (TE) and health literacy (HL), if reported Textual elements Recommendations concerning textual elements 27. Wolf et al., 2016 [51] Comprehension of a prescribed drug in a patient’s regimen was measured at the baseline, 3 months, and 9 months by patient’s ability to correctly report, for each medication: 1) How many pills taken per dose. 2) Times per day a medicine was to be taken, specifying the hour of each dose. 3) The total number of pills taken daily. Patients’ adherence was measured at 3 and 9 months via: 1) Self-report of missed or incorrect doses in the prior 4 days using the Patient Medication Adherence Questionnaire. 2) Pill count (for diabetes and hypertensive medicines). Two-arm, multi- site patient- randomized pragmatic trial. Interviews. 845 English- or Spanish speaking patients, 30 years of age, diagnosed with type 2 diabetes and/ or hypertension and taking 2 oral medications. HL: REALM for English speaking patients and SAHLSA for LEP Spanish speaking patients. Standard label instructions vs. patient- centred label instructions. The patient-centred label instructions incorporated evidence-based practices for format and content, including prioritized information, larger font size, and increased white space. Most notably, patient-centred instructions were conveyed with the UMS, which uses standard intervals for expressing when to take medicine (morning, noon, evening, bedtime). TE: Patients receiving the patient-centred instructions demonstrated slightly better proper use of their drug regimens at first exposure and at 9 months. However, patient-centred instructions did not improve drug adherence. HL: 37.4% limited HL and 62.6% adequate HL. The patient-centred instructions were particularly better understood by patients with limited literacy. DOSAGEINSTRUCTIONS Specificity of dosage instructions Specify dosage instructions using standard time intervals (morning, noon, evening and bedtime). 28. McManus et al., 2018 [48] Comprehension was measured by showing patients five prescription drugs. For each drug participants were asked the following questions: 1) How many tablets would you take at any one time? 2) How many tablets would you take in a day? 3) Are there any precautions you would take while taking this medicine? In addition, participants were asked to dose out the five drugs into a 24h dosette box. A pilot randomised controlled trial. 76 adult in-patients, receiving oral medicines, who spoke English fluently. HL: NVS and validated HL screening questions. Standard dosage instructions (e.g., ‘Take two twice daily’) vs. patient centred UMS labels. These labels contain simplified text, numeric characters instead of words to detail the dose, and “carriage returns” to place each dose on a separate line to clearly identify every time period a medicine is taken (e.g. ‘Take 2 tablets in the morning and 2 tablets in the evening’) TE: Patients receiving the UMS labels consolidated their medicines into more times per day than those in receiving the standard labels, but no statistically significant difference was found. HL: 44.7% of the patients had limited health literacy. Subgroup analysis did not find any additional benefit of UMS labels in those with limited health literacy (Mean score 8.56 vs. 9.06, p = 0.514), but rather in those who said that they found instructions hard to understand (mean score 10.00 vs. 8.43, p = 0.019). Specificity of dosage instruction, plain language and number of messages per instruction line Use simplified text, numeric characteristics instead of words to detail dose, place each dose on a separate line to identify every time period a medicine should be taken. Abbreviations: DLIs, drug label instructions; CI, confidence interval; HL, health literacy; NVS, Newest Vital Sign; REALM, Rapid Estimate of Adult Literacy in Medicine; RR, relative risk; SBSQ-D, Set of Brief Screening Questions in Dutch; TE, Textual Element; TOFHLA, Test Of Functional Health Literacy in Adults; UMS, Universal Medication Schedule.  Publications based on the same study. 28. 17 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Instruments measuring health literacy were also identified. We checked if they only measured functional health literacy, or whether they measured interactive and/or critical health literacy skills as well. Selection of studies A total of 434 records were identified in our literature search: PubMed (n = 177), SmartCat (n = 109), PsychINFO (n = 16), and Embase (n = 132). Records were eligible for inclusion if they met the following criteria: (1) studies which dealt with the comprehensibility of DLIs, and (2) actual studies which addressed textual elements of DLIs. A total of 60 studies remained for full-text review. Fig 1 presents a complete overview of the article search and review process. Finally, 30 publications addressing textual elements that affect the comprehension of DLIs were included in our review, of which four articles were merged into two studies in Table 3. The articles of Wolf et al. [17] and Davis et al. [26] were based on one study as well as the stud- ies of Shiyanbola [34,35]. Therefore, 28 studies are mentioned in Table 3. DOSAGEINSTRUCTIONS As the studies were heterogeneous with respect to type of intervention, primary outcome and study design, pooling of the results was considered inappropriate [36]. We aimed to give a graphical impression of the potential effects of interventions and the influence of health liter- acy on improved comprehension. Effects and certainty were expressed as presented in the original studies as Relative Risk (RR) or Odds Ratio (OR) with corresponding confidence intervals. Two figures were plotted with the main quantitative outcomes (RR/OR), confidence intervals, number of included patients, and a description of the intervention for the effects of interventions on improved comprehension (Fig 3) and influence of health literacy on compre- hension (Fig 4). The studies expressed their primary outcome differently (e.g., patients with correct understanding or misunderstanding), hence we recalculated, if necessary, the relative risks and odds ratios to the effects on improved comprehension. Similarly, we recalculated all comparisons for health literacy to the effects of higher levels of health literacy compared to lower levels of health literacy. The questions in the JBI checklists for cross-sectional studies, experimental studies, qualita- tive studies, and randomized controlled trials are specified in the critical appraisal tools avail- able on the website of the Joanna Briggs Institute [33]. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Characteristics of the included studies Table 3 presents a complete overview of the included studies. The 28 included studies used dif- ferent research methods: in-person structured interviews (n = 19), surveys (n = 4), discussion groups (n = 3), and randomized controlled experiments (n = 2). The comprehension of DLIs was measured in participant groups varying from 21 to 845 participants. Dosage instructions were most often investigated (n = 16), followed by auxiliary instructions (n = 6), and a combi- nation of instructions (n = 6). Also, most studies investigated DLIs of prescriptions (n = 22) or DLIs that could occur on both prescribed and over-the-counter drugs (n = 5). One study focused on the comprehension of over-the-counter DLIs (n = 1). The included studies used different methods to measure participants’ comprehension of DLIs. In 16 studies, participants’ comprehension was assessed by rephrasing the instructions in their own words (e.g., ‘What do you think this auxiliary label is saying?), whereas four studies asked participants to demon- strate when and how many tablets they would take on a day. Four studies used multiple meth- ods to measure participants’ DLI comprehension (i.e., rephrasing the DLI in their own words as well as demonstrating when and how many tablets they would take). In four other studies patients’ comprehension was assessed using a survey (n = 2), a discussion group (n = 1) and an PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 18 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions interview in which patients’ perspectives on the formulation of DLIs were discussed (n = 1). Finally, in 19 studies participants’ health literacy skills were assessed. Interventions and textual elements in DLIs The following textual elements were studied: the specificity of dosage instructions (implicit vs. explicit formulation), plain language, wording of dose measurements, the number of messages per instruction line, the presentation of numbers (numerical vs. alphanumerical), DLIs in patients’ native language, and the use of abbreviations. Fig 2 provides an overview of the fre- quency of textual elements in the included studies. Also, Table 4 provides an overview of the textual elements investigated in the included studies, and the quantitative data regarding the comprehensibility of DLIs. In total, seven of the 28 studies investigated the effect of textual interventions in DLIs on participants’ comprehension. Fig 3 gives an impression of these quantitative findings: four out of seven showed that interventions in DLIs significantly improved the comprehension, three studies found no effect. Specificity of dosage instructions A total of 17 studies investigated the specificity dosage instructions: using implicit dosage intervals or explicit dosage intervals. Implicit dosage intervals only mention the frequency of intake (e.g., ‘2 times daily’), whereas explicit dosage intervals mention the moment of intake specified by the hour of intake, dayparts, or mealtime anchors (e.g., ‘1 tablet in the morning and 1 tablet in the evening’). Misunderstanding was less frequent for explicit dosage instructions [9,11,36]. Correct inter- pretation of dosage instructions increased when providing dosage intervals specified by four distinct time periods (i.e., morning, noon, evening, and bedtime) [9,37,38,49] or hour of intake [36,37]. Only one study on administering liquid paediatric medication using implicit versus explicit dosage instructions concluded that there was no significant difference in patient com- prehension [39]. Two studies [36,40] recommended explicit DLIs, however, without defining what implicit and explicit dosage intervals were. https://doi.org/10.1371/journal.pone.0250238.g002 PLOS ONE he included studies, and, (if provided), an overview of the quantitative data on the effect of (combined) textual ele- = 28). Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs 1, 13, 15, 20, 21 No quantitative data presented. 2. Effects of combined textual elements were studied (ConcordantRx label). ConcordantRx label (four distinct time periods, plain language, lowercase and uppercase letters, and numeric characters) improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). 3a. Misunderstanding was less frequent for instructions with explicit dosage instructions. Drug label instruction Correct understanding according to health literacy level (%) p-value Low marginal adequate Take one tablet by mouth once each day 86.7 87.6 94.7 0.032 Take one tablet in the morning and one at 5 p.m. 82.7 91.2 91.3 0.092 Take two tablets by mouth twice daily 70.7 84.1 89.4 <0.001 Take one teaspoonful by mouth three times daily 58.7 65.5 82.6 <0.001 Take one tablet by mouth twice daily for seven days 52.0 66.4 73.0 <0.001 3b. Effects of combined elements were studied (Patient Centered Label, PCL). Better proper use at first exposure (76.9% vs. 70.1%, p = 0.06). Better proper use at 9 months (85.9% vs. 77.4%, p = 0.03). Subgroup analysis: effect significant for English-speaking patients (OR: 2.21, 95% CI: 1.13– 4.31), not for Spanish speakers (OR: 1.19, 95% CI:0.63–2.24). PCL did not improve medication adherence. 17. Rates of correct interpretation were lowest for instructions that depicted frequency in hourly intervals or the number of times of day (53% and 61%, respectively) and highest for those that used time periods (89%). 18. Only 4 (0.93%) out of 429 prescriptions specifying daily frequency of dosage were misinterpreted, whereas 55 (77%) of the 71 prescriptions specifying hourly intervals were misinterpreted (RR: 83, 95% CI: 31–200). 19. DLIs with daily terms were more frequently associated with correct comprehension than meal terms (rates of incorrect responses were 24.2% and 52.2% respectively). 23. Effects of combined elements were studied (Take-Wait-Stop label, TWS). 14% of the participants using the Take-Wait-Stop label exceeded the maximum dose. 31.8% of the participants using the Take-Wait-Stop label exceeded the maximum dose. Difference between TWS-label and standard label was significant (OR = 2.5, 95% CI 1.05– 2.70). 24. Effects of combined elements were studied (Patient Centered Label, PCL). PCLs specify explicit timing with standard intervals (morning, noon, evening, bedtime). PLOS ONE PCL labels were more likely to be correctly interpreted than the standard instructions (ARR: 1.08, 95% CI: 0.98–1.18). 25. Effects of implicit vs. explicit dosage intervals were studied Describe DLI Implicit dosage interval: 37.5% correct [OR: 1.00] Explicit dosage interval: 37.1% correct [OR: 1.01, 95% CI: 0.50–1.88] Demonstrate DLI Implicit dosage interval: 80.2% correct [OR: 1.00] Explicit dosage interval: 70.1% correct [OR: 0.53, 95% CI: 0.25–1.12] 26. Effects of combined elements were studied (Patient Centered Label, PCL). DLIs with the PCL format were significantly more likely to be correctly interpreted compared to standard instructions (ARR: 1.33, 95% CI: 1.25–1.41, p<0.001) 27 Effects of PCLs were studied. More proper use of drug regimens at first exposure (76.9% vs. 70.1%, p = 0.06) and at 9 months (85.9% vs. 77.4%, p = 0.03). 28. Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group, but this was not statistically significant. (Mean score 9.28 vs. 8.81, p = 0.135). Subgroup analysis: no additional benefit of UMS for patients with limited health literacy (mean score 8.56 vs 9.06, p = 0.514), but rather in those who said that they found instructions on tablets hard to understand (mean score 10.00 vs 8.43, p = 0.019). (Continued) Table 4. The frequency of textual elements in the included studies, and, (if provided), an overview of the quantitative data on the effect of (combined) textual ele- ments on the comprehensibility of the DLIs (n = 28). Textual elements Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs Specificity of dosage instructions, n = 17 1, 13, 15, 20, 21 No quantitative data presented. 2. Effects of combined textual elements were studied (ConcordantRx label). ConcordantRx label (four distinct time periods, plain language, lowercase and uppercase letters, and numeric characters) improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). 3a. Misunderstanding was less frequent for instructions with explicit dosage instructions. Drug label instruction Correct understanding according to health literacy level (%) p-value Low marginal adequate Take one tablet by mouth once each day 86.7 87.6 94.7 0.032 Take one tablet in the morning and one at 5 p.m. PLOS ONE 82.7 91.2 91.3 0.092 Take two tablets by mouth twice daily 70.7 84.1 89.4 <0.001 Take one teaspoonful by mouth three times daily 58.7 65.5 82.6 <0.001 Take one tablet by mouth twice daily for seven days 52.0 66.4 73.0 <0.001 3b. Effects of combined elements were studied (Patient Centered Label, PCL). Better proper use at first exposure (76.9% vs. 70.1%, p = 0.06). Better proper use at 9 months (85.9% vs. 77.4%, p = 0.03). Subgroup analysis: effect significant for English-speaking patients (OR: 2.21, 95% CI: 1.13– 4.31), not for Spanish speakers (OR: 1.19, 95% CI:0.63–2.24). PCL did not improve medication adherence. 17. Rates of correct interpretation were lowest for instructions that depicted frequency in hourly intervals or the number of times of day (53% and 61%, respectively) and highest for those that used time periods (89%). 18. Only 4 (0.93%) out of 429 prescriptions specifying daily frequency of dosage were misinterpreted, whereas 55 (77%) of the 71 prescriptions specifying hourly intervals were misinterpreted (RR: 83, 95% CI: 31–200). 19. DLIs with daily terms were more frequently associated with correct comprehension than meal terms (rates of incorrect responses were 24.2% and 52.2% respectively). 23. Effects of combined elements were studied (Take-Wait-Stop label, TWS). 14% of the participants using the Take-Wait-Stop label exceeded the maximum dose. 31.8% of the participants using the Take-Wait-Stop label exceeded the maximum dose. Difference between TWS-label and standard label was significant (OR = 2.5, 95% CI 1.05– 2.70). 24. Effects of combined elements were studied (Patient Centered Label, PCL). PCLs specify explicit timing with standard intervals (morning, noon, evening, bedtime). PCL labels were more likely to be correctly interpreted than the standard instructions (ARR: 1.08, 95% CI: 0.98–1.18). 25. Effects of implicit vs. explicit dosage intervals were studied Describe DLI Implicit dosage interval: 37.5% correct [OR: 1.00] Explicit dosage interval: 37.1% correct [OR: 1.01, 95% CI: 0.50–1.88] Demonstrate DLI Implicit dosage interval: 80.2% correct [OR: 1.00] Explicit dosage interval: 70.1% correct [OR: 0.53, 95% CI: 0.25–1.12] 26. Effects of combined elements were studied (Patient Centered Label, PCL). DLIs with the PCL format were significantly more likely to be correctly interpreted compared to standard instructions (ARR: 1.33, 95% CI: 1.25–1.41, p<0.001) 27 Effects of PCLs were studied. More proper use of drug regimens at first exposure (76.9% vs. 70.1%, p = 0.06) and at 9 months (85.9% vs. 77.4%, p = 0.03). 28. Plain language In 15 studies, plain language is acknowledged as an important factor affecting the compre- hensibility of DLIs [5,8,13,14,17,34,35,41–48]. These studies recommended instructions should be brief, clear, and concrete. Medical jargon should be avoided (e.g., ‘subcutaneously’, ‘inhalation’) and complex words (e.g., ‘prolonged or excessive exposure’, ‘tablets’) should be substituted for simpler ones (e.g., ‘under your skin’, ‘puff’, limit your time in the sun’, ‘pills’) Fig 2. The frequency of textual elements in the included studies (n), and the way in which the quantitative data were presented in the studies. https://doi org/10 1371/journal pone 0250238 g002 Fig 2. The frequency of textual elements in the included studies (n), and the way in which the quantitative data were presented in the studies. https://doi.org/10.1371/journal.pone.0250238.g002 https://doi.org/10.1371/journal.pone.0250238.g002 19 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 The impact of textual elements on the comprehensibility of drug label instructions (Continued) PLOS ONE Table 4. (Continued) Textual elements Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs Plain language, n = 15 4, 6, 8a, 8b, 9, 14 No quantitative data presented. 2 Effects of combined elements were studied (ConcordantRx label). ConcordantRx label (four distinct time periods, plain language, lowercase and uppercase letters, and numeric characters) improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). 3b. Effects of combined elements were studied (Patient Centered Label, PCL). 79% of patients could not recognize and pronounce ‘antibiotic’, 73% ‘orally’, 70% ‘teaspoonful’, 48% ‘medication’, 45% ‘prescription’, and 35% ‘dose’. Poor word recognition may have contributed to patients misreading words on labels, such as ‘tablespoon’ instead of ‘teaspoon’. This accounted for 9% of errors (n = 34). 5 According to participants’ interpretations of the newly developed labels, the labels understood best were those with the following indications: ‘Avoid excessive sun exposure’ (n = 61, 50.8%), ‘Do not drink alcohol’ (n = 49, 40.8%), and ‘Take with plenty of water’ (n = 49, 40.8%). 10 Labels were at greater risk for being misunderstood if they included multiple instructions, or included unfamiliar terms. Rates of correct interpretation of the eight patient warning labels (PWL) ranged from 0% to 78.7%. Rates of comprehension among patients were the lowest for multiple-step PWLs (8.0%, 0%, and 5.3%). Specific PWLs were not understood by most patients. For example, ‘For external use only’ proved to be difficult for 90.7% of the participants. 11 Simplified text warning labels (with and without icons) were studied. Simplified text + icon and simplified text only warnings more likely to be properly understood compared to standard warnings (92.1%, 90.6%, and 80.3% respectively; p<0.001). 12 Comprehension of the enhanced text + icon label was significantly higher compared to both standard and enhanced text-only labels (icon vs standard: RR: 1.26; 95% CI: 1.04–1.53; icon vs enhanced text: RR:1.22; 95% CI: 1.02–1.46). 23 Of the sample, 23% exceeded the maximum daily dose noted on the bottle and for this error type, there were statistically significant differences by study arm (standard label error rate = 31.8% vs. Take-Wait-Stop label error rate = 14%, p = .05). Those exposed to the standard label were 2.5 times more likely to exceed the recommended maximum daily dose (95% CI: 1.05, 7.70, p = .03). 26. Effects of combined elements were studied (Patient Centered Label, PCL). PLOS ONE Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group but this was not statistically significant (Mean score 9 28 vs (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 20 / 30 The impact of textual elements on the comprehensibility of drug label instructions Dose measurements, n = 5 PLOS ONE DLIs with tPCL format were significantly more likely to be correctly interpreted compared to standard instructions (ARR: 1.33, 95% CI: 1.25–1.41, p<0.001) 28 Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group, but this was not statistically significant. (Mean score 9.28 vs 8.81, p = 0.135). Subgroup analysis: no additional benefit of UMS for patients with limited health literacy (mean score 8.56 vs 9.06, p = 0.514), but rather in those who said that they found instructions hard to understand (mean score 10.00 vs 8.43, p = 0.019). Dose measurements, n = 5 13, 14, 16, 21  No quantitative data presented. 3a Twenty-two percent of the patients with incorrect responses to the instructions, ‘Take one teaspoonful by mouth three times daily’, misinterpreted the dose as ‘tablespoon’ rather than ‘teaspoon’. Drug label instruction Correct understanding according to health literacy level (%) p-value Low marginal adequate Take one tablet by mouth once each day 86.7 87.6 94.7 0.032 Take one tablet in the morning and one at 5 p.m. 82.7 91.2 91.3 0.092 Take two tablets by mouth twice daily 70.7 84.1 89.4 <0.001 Take one teaspoonful by mouth three times daily 58.7 65.5 82.6 <0.001 Take one tablet by mouth twice daily for seven days 52.0 66.4 73.0 <0.001 (Continued) Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs 4, 6, 8a, 8b, 9, 14 No quantitative data presented. 2 Effects of combined elements were studied (ConcordantRx label). ConcordantRx label (four distinct time periods, plain language, lowercase and uppercase letters, and numeric characters) improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). 3b. Effects of combined elements were studied (Patient Centered Label, PCL). 79% of patients could not recognize and pronounce ‘antibiotic’, 73% ‘orally’, 70% ‘teaspoonful’, 48% ‘medication’, 45% ‘prescription’, and 35% ‘dose’. Poor word recognition may have contributed to patients misreading words on labels, such as ‘tablespoon’ instead of ‘teaspoon’. This accounted for 9% of errors (n = 34). 5 According to participants’ interpretations of the newly developed labels, the labels understood best were those with the following indications: ‘Avoid excessive sun exposure’ (n = 61, 50.8%), ‘Do not drink alcohol’ (n = 49, 40.8%), and ‘Take with plenty of water’ (n = 49, 40.8%). PLOS ONE 10 Labels were at greater risk for being misunderstood if they included multiple instructions, or included unfamiliar terms. Rates of correct interpretation of the eight patient warning labels (PWL) ranged from 0% to 78.7%. Rates of comprehension among patients were the lowest for multiple-step PWLs (8.0%, 0%, and 5.3%). Specific PWLs were not understood by most patients. For example, ‘For external use only’ proved to be difficult for 90.7% of the participants. 11 Simplified text warning labels (with and without icons) were studied. Simplified text + icon and simplified text only warnings more likely to be properly understood compared to standard warnings (92.1%, 90.6%, and 80.3% respectively; p<0.001). 12 Comprehension of the enhanced text + icon label was significantly higher compared to both standard and enhanced text-only labels (icon vs standard: RR: 1.26; 95% CI: 1.04–1.53; icon vs enhanced text: RR:1.22; 95% CI: 1.02–1.46). 23 Of the sample, 23% exceeded the maximum daily dose noted on the bottle and for this error type, there were statistically significant differences by study arm (standard label error rate = 31.8% vs. Take-Wait-Stop label error rate = 14%, p = .05). Those exposed to the standard label were 2.5 times more likely to exceed the recommended maximum daily dose (95% CI: 1.05, 7.70, p = .03). 26. Effects of combined elements were studied (Patient Centered Label, PCL). DLIs with tPCL format were significantly more likely to be correctly interpreted compared to standard instructions (ARR: 1.33, 95% CI: 1.25–1.41, p<0.001) 28 Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group, but this was not statistically significant. (Mean score 9.28 vs 8.81, p = 0.135). Subgroup analysis: no additional benefit of UMS for patients with limited health literacy (mean score 8.56 vs 9.06, p = 0.514), but rather in those who said that they found instructions hard to understand (mean score 10.00 vs 8.43, p = 0.019). 13, 14, 16, 21  No quantitative data presented. 3a Twenty-two percent of the patients with incorrect responses to the instructions, ‘Take one teaspoonful by mouth three times daily’, misinterpreted the dose as ‘tablespoon’ rather than ‘teaspoon’. PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Table 4. (Continued) Textual elements Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs Number of messages per instruction line, n = 5 7 No quantitative data presented. 5 To make the new labels more comprehensible, the researchers used single-action directions, plain-language text, and explicit pictorial descriptions of the warning message. According to participants’ interpretations of the newly developed labels, the labels understood best were those with the following DLIs (single-action instructions): ‘Avoid excessive sun exposure’ (n = 61, 50.8%), ‘Do not drink alcohol’ (n = 49, 40.8%), and ‘Take with plenty of water’ (n = 49, 40.8%). 10 Understanding of DLIs for liquid medication was studied. Rates of comprehension were lowest for the three patient warning labels with multiple precautions or steps instructing proper use of medication (8.0%, 0%, and 5.3%). 23 Effects of combined elements were studied (Take-Wait-Stop label, TWS). 14% of the participants using the Take-Wait-Stop label exceeded the maximum dose. 31.8% of the participants using the Take-Wait-Stop label exceeded the maximum dose. Difference between TWS-label and standard label was significant (OR: 2.5, 95% CI 1.05– 2.70). 28 Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group, but this was not statistically significant. (Mean score 9.28 vs. 8.81, p = 0.135). Presentation of numbers, n = 7 1, 14 No quantitative data presented. 2 Effects of combined elements were studied (ConcordantRx label). ConcordantRx label (four distinct time periods, plain language, lowercase and uppercase letters, and numeric characters) improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). 3a Mistakes were more common when the instructions consisted of several components with varying numerical information. Drug label instruction Correct understanding according to health literacy level (%) p-value Low marginal adequate Take one tablet by mouth once each day 86.7 87.6 94.7 0.032 Take one tablet in the morning and one at 5 p.m. 82.7 91.2 91.3 0.092 Take two tablets by mouth twice daily 70.7 84.1 89.4 <0.001 Take one teaspoonful by mouth three times daily 58.7 65.5 82.6 <0.001 Take one tablet by mouth twice daily for seven days 52.0 66.4 73.0 <0.001 3b. Effects of combined elements were studied (Patient Centered Label, PCL). PLOS ONE Drug label instruction Correct understanding according to health literacy level (%) p-value Low marginal adequate Take one tablet by mouth once each day 86.7 87.6 94.7 0.032 Take one tablet in the morning and one at 5 p.m. 82.7 91.2 91.3 0.092 Take two tablets by mouth twice daily 70.7 84.1 89.4 <0.001 Take one teaspoonful by mouth three times daily 58.7 65.5 82.6 <0.001 Take one tablet by mouth twice daily for seven days 52.0 66.4 73.0 <0.001 (Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 21 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Table 4. (Continued) Textual elements Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs DLIs in patients’ native language, n = 3 1, 4 No quantitative data presented. 2 Effects of combined elements were studied (ConcordantRx label). Language concordantRx label improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). Abbreviations, n = 2 6 No quantitative data presented. 22 Effects of simplified text labels (with and without icons) were studied. Simplified text labels, with and without patient-centred icons were better attended to by patients than standard labels (simplified text: AOR: 1.17, 95% CI: 1.02–1.36. Table 4. (Continued) Textual elements Mentioned in: Quantitative data about the effect of (combined) textual elements on the comprehensibility of DLIs DLIs in patients’ native language, n = 3 1, 4 No quantitative data presented. 2 Effects of combined elements were studied (ConcordantRx label). Language concordantRx label improved comprehension (RR: 1.25, 95% CI: 1.06–1.48). Abbreviations, n = 2 6 No quantitative data presented. 22 Effects of simplified text labels (with and without icons) were studied. Simplified text labels, with and without patient-centred icons were better attended to by patients than standard labels (simplified text: AOR: 1.17, 95% CI: 1.02–1.36. Numbers refer to the numbers used in Table 3.  Quantitative data indicates understanding of several textual elements in DLIs.  No quantitative data on the understanding of the textual element(s) in DLIs. Abbreviations: AOR, Adjusted Odds Ratio; ARR, Adjusted Relative Risk; CI, Confidence Interval; PCL, Patient-Centred Label; PWL, Patient Warning Label; OR, Odds Ratio; TWS, Take-Wait-Stop label; RR, Relative Risk; UMS, Universal Medication Scheme. Numbers refer to the numbers used in Table 3.  Quantitative data indicates understanding of several textual elements in DLIs.  No quantitative data on the understanding of the textual element(s) in DLIs. Abbreviations: AOR, Adjusted Odds Ratio; ARR, Adjusted Relative Risk; CI, Confidence Interval; PCL, Patient-Centred Label; PWL, Patient Warning Label; OR, Odds Ratio; TWS, Take-Wait-Stop label; RR, Relative Risk; UMS, Universal Medication Scheme. [8,14,45,46]. Four studies [13,14,42,44] recommended using plain language, however, without defining what plain language entails. PLOS ONE Errors that appeared to be the result of label language were most prevalent on the instruction ‘Take two tablets by mouth twice daily’. The repetitiveness between dosage (‘two’) and frequency (‘twice’) often led to the common interpretation ‘Take a pill twice a day’, whereas dosage would go ignored. This was confirmed in the follow-up demonstration task, ‘How many pills would you take in one day’ with the common incorrect response of ‘two’ (72% of incorrect responses). 23 Effects of combined elements were studied (Take-Wait-Stop label, TWS). Of the sample, 23% exceeded the maximum daily dose noted on the bottle and for this error type, there were statistically significant differences by study arm (standard label error rate = 31.8% vs. Take-Wait-Stop label error rate = 14%, p = .05). Those exposed to the standard label were 2.5 times more likely to exceed the recommended maximum daily dose (95% CI: 1.05, 7.70, p = .03). 28 Effects of Universal Medication Scheme (UMS) were studied. Those in the UMS group displayed better understanding of the prescription regimen than those in the usual care group, but this was not statistically significant. (Mean score 9.28 vs. 8.81, p = 0.135). Subgroup analysis: no additional benefit of UMS for patients with limited health literacy (mean score 8.56 vs. 9.06, p = 0.514), but rather in those who said that they found instructions on tablets hard to understand (mean score 10.00 vs. 8.43, p = 0.019). (Continued) (Continued) 22 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Dose measurements The formulation of dose measurements should be concrete and simple. Research showed words, such as ‘teaspoon’, ‘tablespoon’, ‘dropperful’, ‘ml’, and ‘a small amount’, are often misinterpreted due to participants’ unfamiliarity with the terminology or found the terminology confusing [5,11,12,18,45,49]. However, the research did not provide recommendations for alternative for- mulations for dose measurements other than avoiding the above-mentioned examples. Fig 3. Relative risks and odds ratios of interventions in DLI on correct comprehension. https://doi org/10 1371/journal pone 0250238 g003 Fig 3. Relative risks and odds ratios of interventions in DLI on correct comprehension. Fig 3. Relative risks and odds ratios of interventions in DLI on correct comprehension. https://doi.org/10.1371/journal.pone.0250238.g003 23 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Abbreviations Only one study compared patients’ comprehension of the use of Latin abbreviations in DLIs (e.g., ‘Take one tablet TID’) versus written-out instructions (e.g., ‘Take one tablet three times day’) [50]. The Latin abbreviations were least understood compared to the written-out instruc- tions. Also, two other studies recommend to avoid abbreviations (e.g., ‘ml’) [43,45,50]. DLIs in patients’ native language Three studies recommended providing instructions in patients’ native language [5,36,41]. Patients were more likely to demonstrate the correct dosing amount when receiving instruc- tions in their native language instead of standard instructions [5,36,41]. Presentation of numbers Four studies recommend the use of numeric over alphanumeric presentation of numbers in DLIs (e.g., 1 vs. one) [5,17,45,46]. However, fractions (i.e., ½) were better understood when presented alphanumerical (i.e., half) as the former lead to more confusion [45]. Research also showed DLIs containing fewer numbers (e.g., ‘Take one tablet by mouth once each day’) were better understood compared to instructions containing multiple numbers (‘Take one tablet by mouth twice daily for seven days’). Number of messages per instruction line Five studies found multi-step instructions (e.g., ‘You should avoid prolonged or excessive expo- sure to direct and/or artificial sunlight’) while taking this medication lead to more misinterpre- tations [14,26,42,46]. Participants became confused when interpreting the multi-step instructions or did not address all messages of the drug label. Placing each part of the instruc- tion on a separate instruction line (i.e., ‘carriage returns’) was proposed as an effective way to enhance comprehensibility [26] as well as the use of single step instructions (e.g. ‘Take with food’) [14,27,44]. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Health literacy and drug label understanding Participants’ health literacy skills were measured in 19 studies, using the following measures: the REALM (n = 13), the NVS (n = 2), the revised REALM (n = 1), the Arabic Single Item Lit- eracy Screener (n = 1), the Set of Brief Screening Questions (SBSQ) (n = 1), Short Assessment of Health Literacy for Spanish Adults (SAHLSA (n = 1) and the Test Of Functional Health Lit- eracy in Adults (TOFHLA) (n = 1). One study used two measures (SAHLSA and REALM) depending on participants’ native language [51]. All instruments measured functional health literacy. In most studies the effectiveness of specific textual elements on the comprehensibility of DLIs for participants with limited health literacy skills was not measured separately, and, therefore cannot be described in this review. However, five studies compared DLI comprehen- sion between people with lower and higher levels of health literacy. In these studies, health lit- eracy was classified as low, marginal or adequate. A graphical impression of these comparisons is presented in Fig 4 (also see Table 4). For these five studies, the results showed that partici- pants with adequate health literacy comprehended DLIs better than people with limited health literacy. Two out of five studies also showed participants with adequate health literacy under- stood DLIs better compared to participants with marginal health literacy. However, the three other studies found no difference between these groups. 24 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions Fig 4. Relative risks and odds ratios of misunderstanding of patients with marginal/low health literacy compared to patients with adequate health literacy. https://doi.org/10.1371/journal.pone.0250238.g004 Fig 4. Relative risks and odds ratios of misunderstanding of patients with marginal/low health literacy compared to patients with adequate health literacy. https://doi.org/10.1371/journal.pone.0250238.g004 Fig 4. Relative risks and odds ratios of misunderstanding of patients with marginal/low health literacy compared to patients with adequate health literacy. https://doi.org/10.1371/journal.pone.0250238.g004 Two studies investigated the impact of textual DLI interventions on participants’ compre- hension and took respondents’ health literacy into account. In 2010, Wolf et al. [13] investi- gated the effects of an enhanced label for auxiliary warnings with simplified text and, in addition, simplified icons. As described in Table 4, and shown in Fig 4, in all patients simpli- fied text improved DLI comprehension. Health literacy and drug label understanding In participants with low health literacy, DLI compre- hension was improved by the combination of simplified text and icons [OR 3.22, 95% CI 1.39– 7.50]–but not for simplified text alone (see Fig 4). In 2016, Wolf et al. [38] found that the Patient Centred Label (PCL) led to slightly better use of drug regimens. The results were not significant for the entire population. However for the subgroup of participants with low health literacy, the intervention improved drug adherence (calculated by pill count) at nine months after the start of the intervention [OR = 5.08, 95% CI 1.15–22.37]. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Discussion All studies in this review conclude that standard DLIs are too complex for patients which is attributed to their wording. Explicit time periods in dosage instructions, plain language, num- bers in a numerical format, and providing DLIs in patients’ native language contributed to improved comprehension. Correct interpretation of DLIs was hindered by multistep instruc- tions per instruction line as well as using abbreviations and medical jargon. The included stud- ies differ in the adopted research methods as well as their respondent population, which suggests this is a robust conclusion. Although health literacy was taken into account in a majority of the studies, none of them assessed the effectiveness of specific textual elements on patients’ comprehension of DLIs. The reviewed research is consistent about specifying dosage instructions and using plain language. Dosage instructions indicating more times daily use without specifying the time are often misunderstood (e.g., ‘1 tablet 2 times a day’). Using dayparts or mealtime anchors to specify the moment of intake facilitates patients’ comprehension (e.g., ‘1 tablet in the morning; 1 tablet in the evening’). Future research should investigate whether dayparts are to be pre- ferred over mealtime anchors, as meals are often skipped or consumed on different moments [52]. However, using time intervals to specify the moment of intake (e.g., ‘every 8 hours’) should be avoided, as both Hanchak et al. and Davis et al. showed that about 75% of the partic- ipants misunderstood these instructions [9,53]. Regarding the use of plain language, the reviewed research recommends to avoid medical jargon and to substitute complex words for simpler ones. However, only few studies provide directions to simplify DLIs or provide an overview of alternative formulations for difficult words and/or medical jargon [5,8,13,41,45]. Moreover, the evidence on the wording of dose measurements, presentation of numbers, 25 / 30 PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions presence of abbreviations, number of messages per instruction line as well as the use of DLIs in patients’ native language is limited. Due to the heterogeneity of the included studies with respect to primary outcome and study design pooling of the results was considered inappropriate. The effect of the individual textual elements on the comprehensibility of DLIs was not always presented quantitively, and rela- tively few studies compared the effect of optimized DLIs to standard DLIs. Discussion However, the included studies that allowed a quantitative comparison showed that textual interventions in DLIs are promising: optimized DLIs seem to have a positive impact on comprehensibility, especially in patients with limited health literacy. This might be explained by the fact that patients with limited health literacy experience more problems with the comprehension of DLIs, so there is more room for improvement in this population. In 19 studies, participants’ health literacy was measured with instruments focusing on func- tional skills. For example, the REALM measures whether participants can read and pronounce medical terms. However, being able to read and pronounce medical terms does not necessarily imply that patients are able to interpret medical terms in DLIs. Moreover, the reviewed research shows patients are able to rephrase DLIs in their own words, but experience difficulty in demonstrating proper drug use [5,46,47,49,51]. Therefore, it is likely that beside functional skills, interactive and critical skills also play a role when interpreting and applying DLIs. Future research should therefore incorporate multiple health literacy measures in order to cover these aspects of health literacy as well as multiple comprehension measures (i.e., reading, interpret- ing, and demonstrating). At the start of a new drug therapy, patients usually receive DLIs combined with spoken information from prescriber and written information in patient leaflets. However, approxi- mately 40 to 80 per cent of the information during patient-physician encounters is forgotten or remembered inaccurately [2–4]. Unlike patient information leaflets, DLIs present only the most essential information on drug use and are likely to be the last information source patients read before taking their drugs [8]. Hence, DLIs should serve as an independent text which should be comprehensible for all patients. This systematic review shows specifying dosage instructions and using plain language may facilitate patients’ comprehension. PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 Strengths and limitations As far as we know, this is the first systematic review investigating the relation between textual elements in DLIs and patients’ comprehension. A strength of this review is the focus on DLIs instead of focussing on other types of health information sources. Other strengths are the focus on textual elements in DLIs and (if possible), and the inclusion of patients’ health literacy in the data analysis. A first limitation of this review is a consequence of our focus on textual elements: we did not study other elements, such as icons, that may impact DLI comprehensibility. Additional elements, such as icons or pictograms, could facilitate the comprehension of DLIs. For exam- ple, a systematic review of Sletvold et al. [54] showed pharmaceutical pictograms combined with written/oral information are useful for patients that are normally at risk for non-adher- ence. Also, Katz et al. [55] concluded a combination of pictorial aids and textual information facilitate patients’ comprehension of medication instructions compared to pictorial aids only. Therefore, future research should focus on the effectiveness of both textual and visual elements in DLIs on patients’ comprehension. Another limitation is that most studies in this review were not performed in a clinical set- ting and used hypothetical drug labels. Participants had to interpret instructions of drugs they did not use themselves. Therefore, the occurrence of misinterpreting DLIs might be PLOS ONE | https://doi.org/10.1371/journal.pone.0250238 May 19, 2021 26 / 30 PLOS ONE The impact of textual elements on the comprehensibility of drug label instructions underestimated. This especially goes for patients following multiple drugs regimens and patients with limited health literacy. Future research should therefore investigate patients’ understanding of instructions of their own medications (cf. [56]) to increase the ecological validity of research on the comprehensibility of DLIs. A final limitation is the heterogeneity of the included studies in this review and the differ- ences in data presented on the comprehension of DLIs. This makes it impossible to quantify the effectiveness of textual interventions in general, and to identify the contribution of specific textual elements. Although the data in this review illustrate that (decreased) comprehensibility of DLIs is a substantial problem, especially in patients with limited health literacy, it would be valuable to have pooled data on how (optimized) DLIs influence patients’ comprehension, and other outcomes, such as adherence to treatment regimens and even clinical outcomes. Strengths and limitations We would welcome such comparisons, however, we believe heterogeneity will also be problematic in future evaluations as interventions directed at improved drug use will always be context spe- cific, with multiple factors contributing to the primary outcome. Implications for future research Our results underline that the wording of DLIs impacts patients’ comprehension. The textual elements found in this review can be used to improve existing drug labels instructions, such as specifying dosage instructions and using plain language. Although health literacy skills are a known predictor of patients’ comprehension of DLIs, little is known about the effectiveness of specific textual interventions for patients with marginal or limited literacy skills. Therefore, future research should focus on the effectiveness of specific textual interventions and should include patients’ health literacy in the research design. Moreover, the patients’ comprehension of DLIs should be tested in a clinical setting using the DLIs of patients’ own medication. Implications for practice Based on this review, DLIs could be optimized by specifying dosage instructions and using plain language. In many countries, prescribing and dispensing is supported by healthcare information systems [55] which contains a centrally maintained table for all available dosing instructions on DLI with corresponding codes. When processing a prescription, the health care professional will use these predefined DLI codes in order to automatically print the instructions on the drug label. Depending on the health care context, optimized DLIs can be implemented by adapting the associated codes in these information systems. Also, guidelines for the composition of comprehensible DLIs can be developed to support prescribing and dis- pensing professionals. Conclusion The present systematic review documents which textual elements have been investigated to facilitate patients’ comprehension of DLIs: specifying dosage instructions and using plain lan- guage are promising ways to increase DLI comprehensibility. Especially, patients with limited health literacy might benefit from optimized DLIs. However, the heterogeneity in study design, the textual interventions, and outcomes measured, prevents us from conclusively asserting that specific textual elements are effective in improving patients’ comprehension of DLIs. S1 Checklist. PRISMA 2009 checklist. (DOC) Author Contributions Conceptualization: Charlotte Miriam Joyce van Hooijdonk. Funding acquisition: Charlotte Miriam Joyce van Hooijdonk, Liset van Dijk, Jany Rade- makers, Sander Diederik Borgsteede. Methodology: Ekram Maghroudi, Charlotte Miriam Joyce van Hooijdonk, Heidi van de Bruinhorst, Liset van Dijk, Jany Rademakers, Sander Diederik Borgsteede. Supervision: Charlotte Miriam Joyce van Hooijdonk, Sander Diederik Borgsteede. Writing – original draft: Ekram Maghroudi, Charlotte Miriam Joyce van Hooijdonk, Sander Diederik Borgsteede. Writing – review & editing: Ekram Maghroudi, Charlotte Miriam Joyce van Hooijdonk, Heidi van de Bruinhorst, Liset van Dijk, Jany Rademakers, Sander Diederik Borgsteede. We would like to thank Reza Bandraz for his contribution to the study selection. We would like to thank Reza Bandraz for his contribution to the study selection. Supporting information S1 Checklist. PRISMA 2009 checklist. 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Patients aged 80 years or older with non-ST-elevation myocardial infarction or unstable angina pectoris randomised to an invasive versus conservative strategy: angiographic and procedural results from the After Eighty study
Open heart
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To cite: Tegn N, Eek C, Abdelnoor M, et al. Patients aged 80 years or older with non-­ST-­elevation myocardial infarction or unstable angina pectoris randomised to an invasive versus conservative strategy: angiographic and procedural results from the After Eighty study. Open Heart 2020;7:e001256. doi:10.1136/ openhrt-2020-001256 What is already known about this subject?i ► ►The After Eighty study was the first randomised controlled trial specifically targeting very elderly pa- tients with non-­ST-­elevation myocardial infarction (NSTEMI) or unstable angina pectoris (UAP). The re- sults indicated that the invasive strategy was supe- rior to the conservative strategy, and that bleeding complication rates were similar between the two groups. ► ►The After Eighty study was the first randomised controlled trial specifically targeting very elderly pa- tients with non-­ST-­elevation myocardial infarction (NSTEMI) or unstable angina pectoris (UAP). The re- sults indicated that the invasive strategy was supe- rior to the conservative strategy, and that bleeding complication rates were similar between the two groups. of revascularisation. Methods  Patients of ≥80 years old with non-­ST-­elevation myocardial infarction and unstable angina pectoris were randomised to an invasive or conservative strategy. Angiographic and procedural results were recorded. Univariate and multivariate analyses were performed to explore variables predicting revascularisation. Results  Among 229 patients in the invasive group, 220 underwent immediate coronary angiography (90% performed via the radial artery). Of these patients, 48% had three-­vessel disease or left main stenosis, 18% two-­vessel disease, 16% one-­vessel disease, 17% minor coronary vessel wall changes and two patients had normal coronary arteries. Six patients (3%) underwent coronary artery bypass graft. Percutaneous coronary intervention (PCI) was performed in 107 patients (49%), with 57% treated with bare metal stents, 37% drug-­eluting stents and 6% balloon angioplasty. On average, 1.7 lesions were treated and 2 stents delivered per patient. Complications included 1 major PCI-­related bleeding (successfully treated), 2 minor access site-­related bleedings, 3 side branch occlusions during PCI and 11 periprocedural myocardial infarctions (considered end points). Sex, bundle branch block and smoking were independent predictors of revascularisation. Methods  Patients of ≥80 years old with non-­ST-­elevation myocardial infarction and unstable angina pectoris were randomised to an invasive or conservative strategy. Angiographic and procedural results were recorded. Univariate and multivariate analyses were performed to explore variables predicting revascularisation. Abstract To cite: Tegn N, Eek C, Abdelnoor M, et al. Patients aged 80 years or older with non-­ST-­elevation myocardial infarction or unstable angina pectoris randomised to an invasive versus conservative strategy: angiographic and procedural results from the After Eighty study. Open Heart 2020;7:e001256. doi:10.1136/ openhrt-2020-001256 What does this study add? Received 7 February 2020 Revised 17 April 2020 Accepted 27 May 2020 Received 7 February 2020 Revised 17 April 2020 Accepted 27 May 2020 ► ►Previous trials of considerably younger patients have not shared angiographic and procedural data. In the After Eighty study, procedural success was high and complications few despite a high propor- tion of the patients having three-­vessel and/or left main disease. How might this impact on clinical practice? How might this impact on clinical practice? ► ►The trial demonstrates that invasive management of NSTEMI or UAP can be performed in clinically stable octogenarians without compromising patient safety. ► ►The trial demonstrates that invasive management of NSTEMI or UAP can be performed in clinically stable octogenarians without compromising patient safety. that is, those aged 80 years or older. As this age group grows, the absolute prevalence of cardiovascular disease is expected to increase further.2 1Department of Cardiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway 2Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway Correspondence to Bjørn Bendz; ​bbendz@​ous-​hf.​no © Author(s) (or their employer(s)) 2020. Re-­use permitted under CC BY. Published by BMJ. Conclusions  PCI was performed in approximately half of the patients, similar to findings in younger populations. Procedural success was high, with few complications. Trial registration number  NCT01255540 In the After Eighty study, patients aged 80 years or older who presented with non-­ST-­ elevation myocardial infarction (NSTEMI) and unstable angina pectoris (UAP) were randomised to management using either an invasive or conservative approach.3 The primary end point was a composite of myocardial infarction, required urgent revas- cularisation, stroke or death. The results indi- cated that the invasive strategy was superior to the conservative strategy, and that bleeding y guest. Protected by copyright. on October 23, 2024 by guest. Protected by copyright. http://openheart.bmj.com/ lished as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Nicolai Tegn,1,2 Christian Eek,1 Michael Abdelnoor,1 Lars Aaberge,1 Knut Endresen,1 Rita Skårdal,1 Erlend Sturle Berg,1 Lars Gullestad,1,2 Bjørn Bendz ‍ ‍ 1,2 Key questions Objectives  We aimed to report the angiographic and procedural results of the After Eighty study (​ClinicalTrials.​ gov, NCT01255540), and to identify independent predictors of revascularisation. What is already known about this subject?i Open access Open access Coronary artery disease Open access Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020 on October 23, 2024 by guest http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Introduction Ischaemic heart disease is the leading cause of death among patients in the USA and Europe.1 Cardiovascular disease is particu- larly common among very elderly individuals, Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. D Methods The After Eighty study (​ClinicalTrials.​gov number NCT01255540) was an open-­label, prospective, randomised, controlled, multicentre trial. It included 457 patients admitted to 16 hospitals without percuta- neous coronary intervention (PCI) facilities in the South-­ East Health Region of Norway between 2010 and 2014. Consecutive patients were evaluated for study eligibility within 2 days after hospital admission year round. Those fulfilling the inclusion criteria were invited to partici- pate. All participants gave their written informed consent before inclusion. The protocol was approved by the rele- vant institutional review boards and the regional board of research ethics. Open Heart research data interpretation, the coronary angiograms were ultimately evaluated by four independent invasive cardiologists before consensus was made. complication rates were similar between the two groups. The superiority of the invasive strategy was diluted with increasing age, and was not reflected by changes in health-­related quality of life, as measured by the SF-36.4 When patients in the conservative group experienced reinfarction, refractory angina pectoris, malignant ventricular arrhythmias or increasing heart failure symp- toms, they were considered for urgent coronary angiog- raphy by doctors at the community hospitals (considered as end point). The low viscosity and non-­ionic iodixanol (Visipaque 320, GE Healthcare) were used as contrast medium. Contrast-­induced nephropathy (CIN) was defined as renal function impairment measured as a 25% increase in serum creatinine within 48–72 hours after contrast administration. Here, we report the angiographic and procedural results of the After Eighty study. Analysis was performed to identify independent predictors of revascularisation. Statistical analysis All values are presented as mean and SD unless other- wise stated. We performed univariate and multivariate analyses, using revascularisation as the end point, to iden- tify predictors of revascularisation in the intervention group. Univariate analysis was performed using contin- gency tables for dichotomised variables, and the Mann-­ Witney test for the continuous variables for patients with or without revascularisation. Multivariate analysis was performed using a logistic model to identify independent predictors of revascularisation. To assess the model’s predictive accuracy, we evaluated the calibration using the Hosmer and Lemeshow goodness-­of-­fit test, and the discrimination via analysis of the area under the Receiver Operating Characteristic (ROC) curve. An area under the curve of >0.7 indicates that a model has acceptable discriminatory capability.8 This substudy was underpow- ered to identify predictors of mortality and reinfarction. Enrolled patients were randomised to either an invasive or a conservative management strategy. The conservative strategy involved optimal medical therapy (OMT) admin- istered at the community hospital. The invasive strategy involved early coronary angiography with immediate evaluation for ad hoc PCI, coronary artery bypass graft (CABG) or OMT. Patients randomised to the invasive strategy were transported to Oslo University Hospital, and underwent coronary angiography 1 day after inclusion. Patients who underwent only coronary angiography were returned to their local hospital after 4–6 hours. Those requiring PCI were returned after 6–18 hours, depending on the treated segments and the travel distance. The primary end point was a composite of myocardial infarc- tion, required urgent revascularisation, stroke and death. on October 23, 202 http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Table 1  Baseline characteristics Characteristic Invasive strategy (n=220) Age in years, mean (range) 84.7 (80–93) Male, n (%) 122 (55) Medical history, n (%)   Previous myocardial infarction 103 (47)   Previous angina 122 (55)   Previous PCI 53 (24)   Previous CABG 42 (19)   Hypertension 127 (58)   Type 2 diabetes 45 (20)   Chronic obstructive pulmonary disease 23 (10)   Apoplexia cerebri 38 (17)   Peripheral vascular disease 19 (9)   Atrial fibrillation 47 (21) Smoking status, n (%)   Current 17 (8)   Previous 93 (42) EF, n (%)   EF <30% 11 (5)   EF 30%–50% 60 (27)   EF >50% 103 (47) ECG at admission, n (%)   Atrial fibrillation 49 (22)   Pathological Q-­wave 35 (16)   ST depression 40 (18)   Negative T-­wave 31 (14)   Right bundle branch block 21 (10)   Left bundle branch block 21 (10) Troponin elevation* 210 (95) Creatinine, μmol/L 102.4 Values are mean±SD unless otherwise indicated. *Troponin levels exceeding the 99th percentile of a normal population. CABG, coronary artery bypass graft; EF, left ventricular ejection fraction; PCI, percutaneous coronary intervention. Table 2  Medical treatment at discharge Characteristic Invasive strategy (n=220) Medical therapy at discharge, n (%)   Acetylsalicylic acid 211 (96)   Clopidogrel 162 (74)   Ticagrelor 8 (4)   Warfarin 47 (21)   Dabigatran 1 (0.5)   Rivaroxaban 3 (1)   Beta blocker 188 (85)   Statins 203 (92)   ACE inhibitor/ARB 117 (53)   Calcium channel blocker 53 (24)   Nitrates 76 (35) ACE, angiotensin-­converting enzyme; ARB, angiotensin receptor blocker. Table 2  Medical treatment at discharge on October 23, 2024 by guest. Protected by copyright. http://openheart.bmj.com/ eart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from ACE, angiotensin-­converting enzyme; ARB, angiotensin receptor blocker. contrast (range, 80–515 mL). No serious ventricular arrhythmias were registered during the procedures. Table 3 presents additional angiographic data. contrast (range, 80–515 mL). No serious ventricular arrhythmias were registered during the procedures. Table 3 presents additional angiographic data. In the conservative group, 56 patients (25%) were referred for coronary angiography. The median time to angiography was 38 days (range, 1–1160 days) after randomisation. Of these patients, 33 (59%) subsequently underwent PCI. Table 4 presents additional angiographic data. In the conservative group, 56 patients (25%) were referred for coronary angiography. The median time to angiography was 38 days (range, 1–1160 days) after randomisation. Of these patients, 33 (59%) subsequently underwent PCI. Table 4 presents additional angiographic data. Univariate analysis using contingency tables revealed that the incidence of revascularisation was lower among women (39.2%) than men (62.2%) (p<0.01). Results Tables 1 and 2 present the patients’ baseline character- istics and medical treatment. Among the 457 patients in the After Eighty study, 229 were randomised to the inva- sive strategy. Within 24 hours after randomisation, five patients in the invasive group dropped out of the study.3 Another four patients did not undergo coronary angi- ography due to stroke (n=1), gastrointestinal bleedings (n=2) and refractory delirium (n=1) shortly after rando- misation. Consequently, 220 patients in the invasive group underwent immediate coronary angiography. None of the 228 patients in the conservative group underwent immediate coronary angiography. However, 56 patients in the conservative group were eventually referred for coronary angiography due to need for revascularisation or acute coronary syndrome. The angiographic and procedural methods were in accordance with generally accepted guidelines and routines involving digital imaging acquisition and storage.5 6 The radial artery was the preferred access approach. Lesions were imaged in at least two different projections, preferably at 90°, especially for eccentric stenoses. A lesion was deemed significant when it reduced luminal diameter by at least 50% (ie, 75% area stenosis) based on visual assessment. The culprit lesion was identi- fied using a combination of ECG, echocardiographic and angiographic findings. Fractional flow reserve, optical coherence tomography (OCT) and intravascular ultra- sound (IVUS) were not routinely performed. r 23, 2024 by guest. Protected by copyright. uest. Protected by copyright. Of the coronary angiographies, 90% were performed via the radial artery. Among the patients in the invasive group, 48% had three-­vessel disease or left main stenosis, 18% had two-­vessel disease, 16% had one-­vessel disease, 17% had minor coronary vessel wall changes and two patients had normal coronary arteries. Thus, of the 220 patients, 180 (82%) had obstructive coronary disease. The SYNTAX score was used to grade coronary anatomy, and to guide patient selection for optimal revascularisa- tion treatment.7 The residual SYNTAX score was calcu- lated to quantify revascularisation completeness. Before deciding the revascularisation strategy for each patient, coronary angiograms were reviewed to consensus by at least two invasive cardiologists. Including the process for 2 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Coronary artery disease Coronary artery disease on October http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from In the remaining fiv (2.2%) patients, CIN could not be excluded as cause of increased creatinine. Discussion Within the invasive strategy arm of the After Eig 180 (82%) of the 220 patients had obstruc nary disease, while 17% had minor coronary v changes and 1% had normal coronary arteri patients (5%) had an acute occlusive thrombo Of these patients, 49% underwent PCI and 3 went CABG. Within the conservative study arm patients were eventually referred to a corona raphy at a median of 38 days after randomisation patients, 59% underwent PCI. The rates of p bleeding complications were low: 0.4% major minor. Eleven patients (5%) experienced perip myocardial infarctions. Patients with NSTEMI and UAP show dive graphic patterns of coronary artery disease Open Heart Table 3  Details regarding coronary angiography and intervention, at index and reintervention, in the invasive strategy group Characteristic Invasive strategy (n=220) Days from inclusion to angiography 1.4 Coronary angiographic and interventional data at index event, n (%)   Three-­vessel disease or left main 105 (48)   Two-­vessel disease 40 (18)   One-­vessel disease 35 (16)   Calcification, no significant stenosis 38 (17)   Normal 2 (1) No previous CABG, n (%)   Left main lesion 17 (8)   LAD lesion 138 (63)   CX lesion 115 (52)   RCA lesion 115 (52) Previous CABG, n (%) 41 (19)   Left main lesion 19 (46)   LAD lesion 40 (98)   CX lesion 37 (90)   RCA lesion 36 (88)   Occluded graft/LIMA 17/4 Treatment PCI 107 (49)   BMS (% of total PCI) 61 (57)   DES (% of total PCI) 40 (37)   POBA (% of total PCI) 6 (6) CABG 6 (3) Medical treatment only 107 (49) Chronic total occlusion 74 Calcified lesion 95 Thrombotic lesion 11 No. treated lesions per patient 1.7 No. stents implanted per patient 2 Total stent length per patient in mm 35 Receipt of allocated stent type 100% Segments with angiographic success 87% Syntax score, median (range) 12 (0–66) Residual Syntax score, median (range) 1 (0–66) Complications   Occluded side branch, % 3   Perforation 1 Radial/femoral access, n (%) 198 (90) Contrast (angiography) in mL, median (range) 65 (35–150) C t t ( i h PCI) i L di ( ) 180 (80 515) BMS, bare metal stent; CABG, coronary artery bypass graft; CX, ramus circumflexus; DES, drug-­eluting stent; LAD, left anterior descending artery; PCI, percutaneous coronary intervention; POBA, plain old balloon angioplasty; RCA, right coronary artery. Complications One incident of major bleeding (pericardial tamponade) occurred in relation to the PCI procedure and was successfully treated. Two minor bleeding complications occurred in relation to the access site (arteria radialis). Three patients experienced side branch occlusion during PCI. A total of 11 periprocedural myocardial infarctions occurred (considered as end points). No procedural stroke was observed, and Syntax score did not predict procedural complications. The mean overall hospital stay length was 6 days in the invasive group, and 5 days in the conservative group. A creatinine elevation of >25% occurred during the index hospital stay in seven patients (3.1%) in the invasive group, and four (1.8%) in the conservative group. Of the seven patients in the invasive group, two (0.9%) had a urinary tract infection. In the remaining five patients (2.2%) patients, CIN could not be excluded as a possible cause of increased creatinine. on October http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Open Heart Table 3  Details regarding coronary angiography and intervention, at index and reintervention, in the invasive strategy group Characteristic Invasive strategy (n=220) Days from inclusion to angiography 1.4 Coronary angiographic and interventional data at index event, n (%)   Three-­vessel disease or left main 105 (48)   Two-­vessel disease 40 (18)   One-­vessel disease 35 (16)   Calcification, no significant stenosis 38 (17)   Normal 2 (1) No previous CABG, n (%)   Left main lesion 17 (8)   LAD lesion 138 (63)   CX lesion 115 (52)   RCA lesion 115 (52) Previous CABG, n (%) 41 (19)   Left main lesion 19 (46)   LAD lesion 40 (98)   CX lesion 37 (90)   RCA lesion 36 (88)   Occluded graft/LIMA 17/4 Treatment PCI 107 (49)   BMS (% of total PCI) 61 (57)   DES (% of total PCI) 40 (37)   POBA (% of total PCI) 6 (6) CABG 6 (3) Medical treatment only 107 (49) Chronic total occlusion 74 Calcified lesion 95 Thrombotic lesion 11 No. treated lesions per patient 1.7 No. stents implanted per patient 2 Total stent length per patient in mm 35 Receipt of allocated stent type 100% Segments with angiographic success 87% Syntax score, median (range) 12 (0–66) Residual Syntax score, median (range) 1 (0–66) Complications   Occluded side branch, % 3   Perforation 1 Radial/femoral access, n (%) 198 (90) Contrast (angiography) in mL, median (range) 65 (35–150) Characteristic Inva stra (n= Coronary angiographic data and interventional data after readmission, n (%)   Number 12   Target lesion 3   Stent thrombosis 0   New lesion 4   PCI 7   No intervention 5 BMS, bare metal stent; CABG, coronary artery bypass g ramus circumflexus; DES, drug-­eluting stent; LAD, left a descending artery; PCI, percutaneous coronary interven POBA, plain old balloon angioplasty; RCA, right coronar Table 3  Continued Complications One incident of major bleeding (pericardial tam occurred in relation to the PCI procedure successfully treated. Two minor bleeding com occurred in relation to the access site (arteria Three patients experienced side branch occlusi PCI. A total of 11 periprocedural myocardial i occurred (considered as end points). No p stroke was observed, and Syntax score did n procedural complications. The mean overall hospital stay length was 6 d invasive group, and 5 days in the conservative creatinine elevation of >25% occurred during hospital stay in seven patients (3.1%) in th group, and four (1.8%) in the conservative g the seven patients in the invasive group, two (0 a urinary tract infection. on October 23, 202 http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from The inci- dence of revascularisation was lower among patients with left bundle branch block (LBBB) (16.1%) compared with the patients with right bundle branch block (60%) and no bundle branch block (54%; p=0.03). Current smokers had a lower incidence of revascularisation (23.5%) compared with previous smokers (58.6%) and non-­smokers (48.4%) (p=0.02). Multivariate analysis using a logistic model confirmed the three variables sex, bundle branch block and smoking to be significant independent predictors of revascular- isation. The model showed acceptable discrimination (0.68) and satisfactory calibration (p=0.31). Women had 65% less revascularisation than men (p=0.0001). Current smokers had a 77% lower incidence of revas- cularisation compared with previous smokers and non-­ smokers (p=0.02). Patients with LBBB had a 54% lower incidence of revascularisation compared with those with right bundle branch block and no bundle branch block (p=0.05). 3, 2024 by guest. Protected by copyright. Eleven patients (5%) had an acute occlusive thrombotic lesion. CABG was performed in six patients (3%). PCI was performed in 107 patients (49%), of whom 57% were treated with bare metal stents (BMS), 37% with drug-­ eluting stents (DES) and 6% with balloon angioplasty alone. In each patient, an average of 1.7 lesions were treated, and 2 stents were delivered. The median Syntax score was 12 (range, 0–66), with 69% having a score of ≤22, 18% a score of 23–32 and 13% a score of >32. uest. Protected by copyright. Previous angina pectoris, CABG, atrial fibrillation, hypertension, chronic obstructive pulmonary disease and type 2 diabetes were not predictors of coronary intervention. Patients who underwent angiography alone received a median of 65 mL contrast (range, 35–150 mL). Patients treated with ad hoc PCI received a median of 180 mL 3 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Characteristic Invasive strategy (n=220) Coronary angiographic data and interventional data after readmission, n (%)   Number 12 (5)   Target lesion 3   Stent thrombosis 0   New lesion 4   PCI 7   No intervention 5 BMS, bare metal stent; CABG, coronary artery bypass graft; CX, ramus circumflexus; DES, drug-­eluting stent; LAD, left anterior descending artery; PCI, percutaneous coronary intervention; POBA, plain old balloon angioplasty; RCA, right coronary artery. Table 3  Continued on October 23, 2024 by guest. Protected by copyright http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Coronary artery disease on October 23, 202 http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Table 4  Details regarding coronary angiography and intervention in the conservative group Characteristic Conservative (n=56) Days from inclusion to angiography 130 Coronary angiographic and interventional data at index event, n (%)   Three-­vessel disease or left main 19 (34)   Two-­vessel disease 20 (36)   One-­vessel disease 13 (23)   Calcification, no significant stenosis 4 (7)   Normal 0 (0) No previous CABG 51   Left main lesion 9 (18)   LAD lesion 35 (67)   CX lesion 29 (57)   RCA lesion 27 (53) Previous CABG 5   Left main lesion 4 (80)   LAD lesion 5 (100)   CX lesion 5 (100)   RCA lesion 5 (100)   Occluded graft/LIMA 4/0 Treatment   PCI 33 (59)   BMS (% of total PCI) 13 (39)   DES (% of total PCI) 19 (58)   POBA (% of total PCI) 1 (3) CABG 0 (0) Medical treatment only 23 (41) Chronic total occlusion 22 No. of treated lesions per patient 1.6 No. of stents implanted per patient 2.3 Total stent length per patient in mm 38 Receipt of allocated stent type 100% BMS, bare metal stent; CABG, coronary artery bypass graft; CX, ramus circumflexus; DES, drug-­eluting stent; LAD, left anterior descending artery; LIMA, Left Internal Mammary Artery; PCI, percutaneous coronary intervention; POBA, plain old balloon angioplasty; RCA, right coronary artery. Coronary Syndrome (ACS) study included patients of ≥75 years old,15 and its design differed from the present study, specifically regarding the fact that only medically stabilised patients were randomised in the After Eighty study. Within the early aggressive group of the Italian Elderly ACS study, 48% underwent PCI and 6% CABG during the index admission, which is comparable with the rates in our study. The two studies also showed similar lesion distributions. on October 23, 2024 by guest. Protected by copyright. http://openheart.bmj.com/ Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from The median amounts of contrast used—65 mL for diag- nostic angiography and 180 mL for angiography plus ad hoc PCI—were greater than expected. Despite this, only five patients (2.2%) exhibited a >25% rise in creatinine during the index hospital stay (6 days). Adequate hydra- tion and the type of contrast media used appear to be crit- ical factors in patients at risk of CIN. When angiography/ PCI is performed, patients are generally well hydrated and not in a fasting condition. Coronary artery disease Use of the low viscosity and non-­ionic iodixanol as the contrast medium may also offer renal protection. In the invasive group, 113 patients (51.3%) underwent angiography alone. These factors may have reduced the risk of CIN despite the age of the population. However, CIN can develop up to 1 week after contrast administration; thus, it is possible that we may have failed to detect CIN in some individuals. Most bleeding was of gastrointestinal origin and was probably due to double antiplatelet therapy. Except for one pericardial tamponade and two minor bleeding complications related to the access site, bleeding compli- cation rates were similar between the two strategy groups. Among elderly patients undergoing cardiac catheterisa- tion, the rates of major bleeding or access site complica- tions are lower with radial access compared with femoral access.16 In the After Eighty study, radial access was used in 90% of patients, and only 2 of 198 patients experi- enced minor access site-­related bleeding. Overall, the evidence supports the use of radial access among very elderly patients. y p In small studies designed and powered for composite end points, subanalysis results must be interpreted cautiously. Here, we performed a possible hypothesis generating subanalysis to explore whether we could find any possible variables predicting revascularisation, because many clinicians wonder if there are predictors that can help them to choose the right patient at the right strategy. We identified a trend towards lower intervention rates among women, patients with LBBB and smokers. The explanation for these trends remains unclear, and the present study is not powered to determine whether this may be due to non-­obstructive coronary artery disease, small vessel disease or very complex lesions. However, one may speculate if the trends are due to small coronary lumen diameter in women, extensive obstructive coro- nary artery disease in LBBB and the smokers paradox. on October 23, 2024 by guest. Protected by copyright. j.com/ BMS, bare metal stent; CABG, coronary artery bypass graft; CX, ramus circumflexus; DES, drug-­eluting stent; LAD, left anterior descending artery; LIMA, Left Internal Mammary Artery; PCI, percutaneous coronary intervention; POBA, plain old balloon angioplasty; RCA, right coronary artery. BMS, bare metal stent; CABG, coronary artery bypass graft; CX, ramus circumflexus; DES, drug-­eluting stent; LAD, left anterior descending artery; LIMA, Left Internal Mammary Artery; PCI, percutaneous coronary intervention; POBA, plain old balloon angioplasty; RCA, right coronary artery. Discussion Within the invasive strategy arm of the After Eighty study, 180 (82%) of the 220 patients had obstructive coro- nary disease, while 17% had minor coronary vessel wall changes and 1% had normal coronary arteries. Eleven patients (5%) had an acute occlusive thrombotic lesion. Of these patients, 49% underwent PCI and 3% under- went CABG. Within the conservative study arm, 25% of patients were eventually referred to a coronary angiog- raphy at a median of 38 days after randomisation. Of these patients, 59% underwent PCI. The rates of procedural bleeding complications were low: 0.4% major and 1.0% minor. Eleven patients (5%) experienced periprocedural myocardial infarctions. guest. Protected by copyright. Patients with NSTEMI and UAP show diverse angio- graphic patterns of coronary artery disease, ranging from normal epicardial coronary arteries to a severely and diffusely diseased coronary artery tree.9 Among 4 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 References Among the treated patients, 57% received BMS, 37% DES and 6% balloon angioplasty only. During the inclusion period (2010–2014), it was thought that stent thrombosis was more frequent among patients receiving DES than BMS. Dual antiplatelet therapy was manda- tory in both the invasive and conservative strategy arms. However, in the event of a serious bleeding complication (which was very likely in this very old population), a single platelet inhibitor was considered safer after implantation of a BMS compared with a DES. The same was believed for patients requiring anticoagulation (eg, atrial fibril- lation). However, during the last part of the inclusion period, there was a trend towards more frequent use of DES. It was later shown that the rates of repeat revas- cularisation and stent thrombosis are lower after DES implantation.17 1 Murray CJ, Lopez AD. Mortality by cause for eight regions of the world: global burden of disease study. Lancet 1997;349:1269–76. 1 Murray CJ, Lopez AD. Mortality by cause for eight regions of the world: global burden of disease study. Lancet 1997;349:1269–76. 2 Jaguszewski M, Ghadri J-­R, Diekmann J, et al. Acute coronary syndromes in octogenarians referred for invasive evaluation: treatment profile and outcomes. Clin Res Cardiol 2015;104:51–8. 3 Tegn N, Abdelnoor M, Aaberge L, et al. Invasive versus conservative strategy in patients aged 80 years or older with non-­ST-­elevation myocardial infarction or unstable angina pectoris (after eighty study): an open-­label randomised controlled trial. Lancet 2016;387:1057–65. 4 Tegn N, Abdelnoor M, Aaberge L, et al. Health-­Related quality of life in older patients with acute coronary syndrome randomised to an invasive or conservative strategy. The after eighty randomised controlled trial. Age Ageing 2018;47:42–7. g g g 5 Judkins MP. Selective coronary arteriography. I. A percutaneous transfemoral technic. Radiology 1967;89:815–24. 6 Windecker S, Kolh P, Alfonso F, et al. ESC/EACTS Guidelines on myocardial revascularization: The Task Force on Myocardial Revascularization of the European Society of Cardiology (ESC) and the European Association for Cardio-­Thoracic Surgery (EACTS) Developed with the special contribution of the European Association of Percutaneous Cardiovascular Interventions (EAPCI). Eur Heart J 2014;2014:2541–619. 7 Sianos G, Morel M-­A, Kappetein AP, et al. The SYNTAX score: an angiographic tool grading the complexity of coronary artery disease. EuroIntervention 2005;1:219–27. In the present trial, the invasive treatment strategy was decided based on the consensus of at least two invasive cardiologists prior to selection of the revascularisation strategy in each patient. Open Heart Acknowledgements  The authors thank the patients who participated in our trial, our coinvestigators and colleagues, the staff at the participating centres and our dedicated research nurses. artery disease (eg, three-­vessel/left main) combined with severe peripheral disease (ineligible for PCI/CABG) and severe coronary artery disease after CABG ineligible for redo surgery and PCI. Moreover, it can be challenging to detect the culprit lesion in acute coronary syndrome. The lesions may have both ruptured or intact fibrous caps and may be difficult to analyse. In the present trial, OCT and IVUS were not routinely used, but would probably have increased the precision. However, OCT and IVUS may complicate the invasive procedure in advanced disease as found in the present population. Funding  Norwegian Health Association (ExtraStiftelsen) and Ingrid and John Fredriksen Heart Foundation. Funding  Norwegian Health Association (ExtraStiftelsen) and Ingrid and John Fredriksen Heart Foundation. Competing interests  The authors declare that the paper is not under consideration elsewhere, that none of the paper’s contents have been published previously, and that all authors have read and approved the manuscript. The authors have no potential conflict of interest. http://openheart.bmj hed as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from Patient consent for publication  Not required. Patient consent for publication  Not required. Patient consent for publication  Not required. Provenance and peer review  Not commissioned; externally peer reviewed. Provenance and peer review  Not commissioned; externally peer reviewed. Data availability statement  Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. All data relevant to the study are included in the article. Data availability statement  Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. All data relevant to the study are included in the article. Within the conservative strategy arm of this study, 69 patients experienced myocardial infarction and 24 patients required urgent revascularisation (considered end points). Only 56 of these patients were referred for coronary angiography. We believe that this rather conser- vative approach was due to a lack of evidence of coronary intervention in this group, as well as the advanced age. In both strategy arms, the doctors at the community hospi- tals decided whether a patient with myocardial infarction or refractory angina pectoris should be scheduled for coronary angiography. ORCID iD ORCID iD Bjørn Bendz http://​orcid.​org/​0000-​0002-​1392-​6481 Coronary artery disease very elderly patients, treatment is often complicated by additional challenges, such as complex multivessel coro- nary calcification disease, tortuous vascular anatomy, impaired ventricular function, a higher risk profile and substantial comorbidity.10 11 Comparing the present find- ings with the results of previous trials is not straightfor- ward. In FRISC II, ICTUS and RITA-3, the median age was under 65 years,12–14 and angiographic and procedural data are difficult to obtain (personal communication with steering committees). The Italian Elderly Acute guest. Protected by copyright. Within the invasive arm of this study, approximately half of the patients with significant stenosis did not undergo PCI. The reasons included small vessel disease ineligible for revascularisation therapy, severe coronary 5 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Open Heart Open Heart Open access  This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://​creativecommons.​org/​ licenses/​by/​4.​0/. References Compared with a full revas- cularisation strategy, it was considered preferable to treat symptomatic and prognostic lesions (eg, left main and proximal left anterior descending artery), eligible subtotal stenosis and the most likely culprit lesion. This approach was favoured due to the advanced age of the patients. It is unclear whether this strategy is warranted. 8 Kleinbaum DG, Klein M. Logistic regression: a Self-­Learning text. New York, NY: Springer New York, New York, NY, 2010.i 9 Roffi M, Patrono C, Collet JP, et al. Esc guidelines for the management of acute coronary syndromes in patients presenting without persistent ST-­segment elevation: Task force for the management of acute coronary syndromes in patients presenting without persistent ST-­segment elevation of the European Society of cardiology (ESC). Eur Heart J 2015;2016:267–315. gy ( ) 10 Liistro F, Angioli P, Falsini G, et al. Early invasive strategy in elderly patients with non-­ST elevation acute coronary syndrome: comparison with younger patients regarding 30 day and long term outcome. Heart 2005;91:1284–8. ; 11 Behan M, Dixon G, Haworth P, et al. PCI in octogenarians--our centre 'real world' experience. Age Ageing 2009;38:469–73. In conclusion, the After Eighty study included octoge- narians with NSTEMI and UAP who were randomised to an invasive or conservative strategy. A high proportion of patients had three-­vessel and/or left main disease. PCI was performed in approximately half of the patients with a high procedural success and with few complications. Sex, bundle branch block and smoking were indepen- dent predictors of revascularisation. 12 Wallentin L, Lagerqvist B, Husted S, et al. Outcome at 1 year after an invasive compared with a non-­invasive strategy in unstable coronary-­artery disease: the FRISC II invasive randomised trial. FRISC II Investigators. fast revascularisation during instability in coronary artery disease. Lancet 2000;356:9–16. y y 13 de Winter RJ, Windhausen F, Cornel JH, et al. Early invasive versus selectively invasive management for acute coronary syndromes. N Engl J Med 2005;353:1095–104. g ; 14 Fox KAA, Poole-­Wilson P, Clayton TC, et al. 5-­Year outcome of an interventional strategy in non-­ST-­elevation acute coronary syndrome: g ; 14 Fox KAA, Poole-­Wilson P, Clayton TC, et al. 5-­Year outcome of an interventional strategy in non-­ST-­elevation acute coronary syndrome: 6 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Tegn N, et al. Open Heart 2020;7:e001256. doi:10.1136/openhrt-2020-001256 Coronary artery disease on October 23, 202 http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from on October 23, 2024 by guest. Protected by co http://openheart.bmj.com/ Open Heart: first published as 10.1136/openhrt-2020-001256 on 22 July 2020. Downloaded from 16 Cantor WJ, Mehta SR, Yuan F, et al. Radial versus femoral access for elderly patients with acute coronary syndrome undergoing coronary angiography and intervention: insights from the rival trial. Am Heart J 2015;170:880–6. 17 Bønaa KH, Mannsverk J, Wiseth R, et al. Drug-­Eluting or bare-­metal stents for coronary artery disease. N Engl J Med 2016;375:1242–52. 7
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Property on the Line: Life on the Frontier between Copyright and the Public Domain
Victoria University of Wellington law review
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public-domain
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1 1 * BA (Hons); LLB; LLM (VUW); LLM; JSD (Columbia). Chair in Private Law, Victoria University of Wellington. Thanks to Dean Tony Smith and Professor Jane Ginsburg for comments on an earlier draft, and to Vice-Chancellor Pat Walsh for his generous hosting of this event. 1 See for example RH Coase "The Problem of Social Cost" in RH Coase The Firm, The Market, and The Law (University of Chicago Press, Chicago, 1988) 95; reprint of RH Coase "The Problem of Social Cost" (1960) 3 J of L and Economics 1. See also Commonwealth Reserves I v Chodar [2001] 2 NZLR 374 at 384 per PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN Graeme W Austin* This article is an edited transcript of Professor Graeme W Austin's Inaugural Lecture, delivered in the Council Chamber of Victoria University of Wellington on 15 November 2012. Professor Austin was appointed Chair in Private Law in the Faculty of Law in November 2010. This lecture explores claims that in copyright law, the public domain is necessarily in opposition to proprietary rights, and suggests that in many contexts the incentives offered by copyright contribute to the vibrancy and volume of material that is available for downstream creativity and innovation. Drawing on his earlier work on the relationship between human rights law and intellectual property, Professor Austin's lecture advances the idea that cognisance of the human rights dimensions of intellectual property, including creators' human rights, should inform our understanding of the appropriate scope of the rights of copyright owners. The lecture concludes with a warning against the "Walmartization" of copyright. (2013) 44 VUWLR we are disputatious; and, second, that we are constantly striving to improve things. In the legal discipline, we're all frontiersmen and women: peering beyond the boundary of (relative) legal certainty into a much more contested territory. And sometimes, especially so in pluralistic societies, part of the challenge is that others might have got there first. This makes it harder to take tried-and- true ideas for granted. But if our minds and hearts are open, we can learn from the ways that others see things. we are disputatious; and, second, that we are constantly striving to improve things. In the legal discipline, we're all frontiersmen and women: peering beyond the boundary of (relative) legal certainty into a much more contested territory. And sometimes, especially so in pluralistic societies, part of the challenge is that others might have got there first. This makes it harder to take tried-and- true ideas for granted. But if our minds and hearts are open, we can learn from the ways that others see things. The specific boundary on which I shall focus this evening is that between property – or, more specifically, copyright (a particular, even peculiar, type of property) – and the public domain. In broad terms, copyright law concerns whether, and to what extent, creative expression can and should be privatised (that is, be made the subject of property rights). The public domain is said to be across the border, as it were, from this kind of property. The public domain is thus that area that belongs to no one and to everyone, from which we all can draw in our own creative efforts.2 Ideas about the public domain can be highly relevant to technology entrepreneurs' views about their freedom to operate – whether, for example, firms marketing distribution platforms need to factor copyright licences into their operating costs, or whether they are entitled to use others' creative outputs as seed capital.3 The boundary between copyright law and the public domain provokes vigorous debate. There is a lot at stake here. Privatise too far upstream, lock up too much of the materials of culture, and downstream we'll be left with desert – nothing with which our creative juices can mix. For the intellectual property rich – both firms and nations – there is also much to provoke anxiety. 3 This point was discussed, for example, during oral argument in the United States Supreme Court's decision in Grokster v MGM 545 US 913 (2005) (Transcript 04-480, 29 March 2005 at 36 per Justice Kennedy): … what you want to do is to say that unlawfully expropriated property can be used by the owner of the instrumentality as part of the startup capital for his product. … [J]ust from an economic standpoint and a legal standpoint, that sounds wrong to me. 2 Professors David Lange and Jessica Litman authored two of the seminal articles on the public domain. David Lange "Recognizing the Public Domain" (1981) 44 Law & Contemp Probs 147; Jessica Litman "The Public Domain" (1990) 39 Emory L J 965. 4 For an insightful survey of technological challenges to copyright, and technological and legal responses by copyright owners, see Jessica Litman Digital Copyright: protecting intellectual property on the Internet (Prometheus Books, New York, 2001) at 151–165. I INTRODUCTION The metaphors in the title of this talk – "property on the line" and "life on the frontier" – try to capture something about the craft of lawyering, and perhaps something especially salient about the work of academic lawyers. As lawyers, we are very often on the frontier. Whatever the subject area, lawyers occupy an uneasy space where claims and concepts are constantly contested – and where different normative visions, different ideas about what ought to be, vie for attention. Legal regimes of course benefit from certainty and predictability.1 But disputes over the "oughts" in the legal order reflect at least two important truths about the human condition: first, that 2 Glazebrook J: "Reliability and certainty are primary considerations of any system of property rights, and the unprovoked alteration of those rights is to be avoided where possible". 8 John Locke (Peter Laslett (ed)) Two Treatises on Government (Cambridge University Press, New York, 1988) Second Treatise at 286; William Blackstone (Robert Malcolm Kerr (ed)) Commentaries on the Laws of England in Four Books (John Murray, London, 1862) vol I at 121. In Entick v Carrington (1765) 19 How St Tr 1030, 95 ER 807 (KB) at 818, Lord Camden drew on Locke's justification for property in the following passage: "The great end, for which men entered into society, was to secure their property." (2013) 44 VUWLR Copyright owners are already labouring under technological assaults of various kinds.4 Over the border from copyright, in the public domain, there might not be dragons, but there are certainly uncompensated uses. Moving the line further toward the public domain would add legal insult to technological injury. Alternatively, some see copyright and the public domain as being locked in PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 3 3 battle. Copyright means to vanquish the public domain – but the "free culture movement" might turn out to be copyright's Achilles' heel.5 How can we improve the way that we talk about the boundary between copyright and the public domain? Or to prod the metaphor once more, how can we live better on this frontier? First, I shall frame this discussion by considering some of the justifications for copyright. Second, I'll explore some of the legal principles that are relevant to our understanding of the copyright/public domain divide. Toward the end, I'll suggest that how we think about the copyright/public domain divide says something about the kind of society to which we aspire, perhaps even about who we want to be. 11 See Jeremy Waldron Law and Disagreement (Clarendon Press, Oxford, 1999), where it is suggested that Locke's recourse to the language of natural rights was a rhetorical or persuasive device. 6 Stephen Breyer "The Uneasy Case for Copyright: A Study of Copyright in Books, Photocopies, and Computer Programs" (1970) 84 Harv L Rev 281. 9 Garrett Hardin "The Tragedy of the Commons" (1968) 162 Science 1243. 5 For a graphical representation of this metaphor, see Christopher Dombres "The Battle of Copyright" (2011) <www.christopherdombres.fr>, where the artist depicts copyright as Achilles, vanquishing Hektor (the public domain), but with an arrow in copyright's heel representing "free culture". 7 For an exploration of these ideas, see Carol M Rose "Romans, Roads, and Romantic Creators: Traditions of Public Property in the Information Age" (2003) 66 Law & Contemp Probs 89. 5 For a graphical representation of this metaphor, see Christopher Dombres "The Battle of Copyright" (2011) <www.christopherdombres.fr>, where the artist depicts copyright as Achilles, vanquishing Hektor (the public domain), but with an arrow in copyright's heel representing "free culture". (2013) 44 VUWLR 4 4 our labour (that which is peculiarly our own) with the commons. The leading example he gave was the labour expended in gathering apples.12 He also mentioned acorns and ambergris, to some alliterative effect, but we tend to remember the apples. As the utilitarian take on this story goes, our motivation to hang on to those apples (without having to rely only on force) and to find functioning markets in which to sell them, encouraged us to join together to form societies under the rule of law. our labour (that which is peculiarly our own) with the commons. The leading example he gave was the labour expended in gathering apples.12 He also mentioned acorns and ambergris, to some alliterative effect, but we tend to remember the apples. As the utilitarian take on this story goes, our motivation to hang on to those apples (without having to rely only on force) and to find functioning markets in which to sell them, encouraged us to join together to form societies under the rule of law. For intellectual property, however, utilitarian claims can really be grounded only in the second set of justifications.13 The first concern, with inefficient overuse, doesn't work. Copyright protects cultural productions that are non-rivalrous.14 My enjoyment of a digital file containing a movie can occur simultaneously with that of myriads of others. The resource survives undiminished. Hence, the utilitarians are left only with the economic incentives copyright provides to create and disseminate. So, the first English copyright statute, the Statute of Anne 1710, was an "Act for the Encouragement of Learning",15 a phrase echoed in the United States Constitution's invitation to the legislative branch to "promote the Progress of Science … by securing for limited Times to Authors … the exclusive Rights to their … Writings."16 Neither was directed at the overgrazing problem. If that's all there is, then our justifications for copyright need, at the very least, to account for the rise of amateur content. A wonderful new book on amateur media,17 co-edited by distinguished alumna Professor Megan Richardson, discusses in impressive detail the large and vibrant array of amateur content that is produced today: YouTube videos, flash mobs, blogging, pastiche audio- visual works – some of which are known as "mash ups" – even Minecraft. II COPYRIGHT JUSTIFICATIONS It is quite obvious that justifications for copyright are under siege. Figuratively and commercially the "buy in" is increasingly absent. Difficulties with copyright are nothing new, however. The case for copyright has long been characterised as "uneasy".6 Viewed through a utilitarian lens, justifications for intellectual property seem thinner than for other kinds of property.7 Justifications for the general institution of private property are ambitious indeed, explaining nothing less than society itself. The very reason people entered society, it is claimed, was to secure their property rights.8 Within the utilitarian skein, property has two intertwined justifications: first, property rights prevent overgrazing – the wasteful overuse of resources, sometimes described as the tragedy of the commons;9 second, and relatedly, property facilitates the internalisation of the investment in creating and maintaining resources.10 There is also a natural rights flavour to all of this: Locke sought to persuade us11 that the institution of private property was justified by mixing 9 Garrett Hardin "The Tragedy of the Commons" (1968) 162 Science 1243. 10 One of the classic statements on this point is Harold Demsetz "Toward a Theory of Property Rights" (1967) 57 Am Econ Rev 347. 13 Rose "Romans, Roads, and Romantic Creators", above n 7. 17 Dan Hunter and others (eds) Amateur Media: Social, Cultural and Legal Perspectives (Routledge, London, 2012). 12 Locke Two Treatises on Government, above n 8, at 287–291. 14 This observation is almost ubiquitous in intellectual property theory. For an early exposition of the theme, see Paul A Samuelson "The Pure Theory of Public Expenditure" (1954) 36 The Review of Economics and Statistics 387. For a recent iteration, see Herbert Hovencamp "Antitrust and the Movement of Technology" (2012) 19 Geo Mason L Rev 1119 at 1120. 16 Constitution of the United States of America, art I.8.8. 15 Statute of Anne 1710 (GB) 8 Ann c 19. (2013) 44 VUWLR The ready availability of the means of creation, reproduction and dissemination of cultural products, seemingly independently of copyright's traditional incentives, increases the pressure on copyright law to improve its cover story. Secondly, utilitarian justifications for copyright are just failing to capture the imagination of large sectors (and young sectors) of the population. For many kids alone in university hostel rooms, the idea that there might be property rights in the material that they are downloading for free, and the idea that doing so causes harm, must seem like a decidedly abstract concept, or just plain PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 5 5 weird.18 Equally weird is the idea that there should be legal sanctions imposed for this kind of thing. As an aside, my doctoral supervisor, renowned copyright scholar Professor Jane Ginsburg, is currently involved in a project examining papal printing privileges from the 16th century – some of which purported to extend throughout Catholic Christendom. Infringers could be punished by excommunication.19 Perhaps this puts sanctions in our current law into clearer perspective. The internationalisation of copyright seems to make things worse. Domestic copyright law is buttressed on all sides by powerful public international law demands. And there is constant pressure to up the ante even further. All of this challenges whatever might remain of the social contract that undergirds utilitarian justifications for copyright. Within a specific domestic polity, the societal bargain – granting of rights in exchange for creative output – might make some intuitive sense.20 This all gets more than a little abstract, however, when it is other nations' authors, but our legal system's rights, and our citizens' dollars. And this all seems especially troubling when the socio- economic policy calculus that gets reflected in the minutiae of our domestic copyright laws has been exported to us, even imposed upon us, from abroad. Different nations' lobbyists, different politicians, different policy compromises. With intellectual property, we might be provoked to say, with due apologies to Jean-Paul Sartre, that the "public choice hell is other peoples'". But the international trade game has a much wider playing field. The underlying exchange is not just about intellectual property. It is sometimes characterised as: "give us access for our agricultural products and we'll better protect your copyrights".21 There are immediate beneficiaries other than Viacom. Some of them live in the Waikato and South Canterbury. 18 Graeme W Austin "The Metamorphosis of Copyright in the Digital Era" (2004) 28 Colum J L & Arts 397. 19 Jane C Ginsburg "Proto-Property in Literary and Artistic Works: 16th-Century Papal Printing Privileges" (paper presented to Columbia Law School Faculty Workshop Series, Columbia, 6 September 2012). 20 Michael H Davis "Extending Copyright and the Constitution: 'Have I Stayed Too Long?'" (2002) 52 Fla L Rev 989 at 1005. But see Graeme W Austin "Does Copyright Mandate Isolationism?" (2002) 26 Colum J L & Arts 17 at 44–51 (advancing a number of critiques of bargain theory in copyright). 21 See Graeme B Dinwoodie "The Architecture of the International Intellectual Property System" (2002) 77 Chi-Kent L Rev 993 at 1004. 22 Carol M Rose "The Moral Subject of Property" (2007) 48 Wm & Mary L Rev 1897 at 1902. See also Emily Sherwin "Three Reasons Why Even Good Property Rights Cause Moral Anxiety" (2007) 48 Wm & Mary L Rev 1927. 18 Graeme W Austin "The Metamorphosis of Copyright in the Digital Era" (2004) 28 Colum J L & Arts 397. 19 Jane C Ginsburg "Proto-Property in Literary and Artistic Works: 16th-Century Papal Printing Privileges" (paper presented to Columbia Law School Faculty Workshop Series, Columbia, 6 September 2012). 21 See Graeme B Dinwoodie "The Architecture of the International Intellectual Property System" (2002) 77 Chi-Kent L Rev 993 at 1004. 20 Michael H Davis "Extending Copyright and the Constitution: 'Have I Stayed Too Long?'" (2002) 52 Fla L Rev 989 at 1005. But see Graeme W Austin "Does Copyright Mandate Isolationism?" (2002) 26 Colum J L & Arts 17 at 44–51 (advancing a number of critiques of bargain theory in copyright). (2013) 44 VUWLR 6 6 with issues surrounding rights to water.23 Reasons for this include the ambiguities and uncertainties that cluster around property questions, as well as the ubiquity of our engagement with private property. If this is true in the tangible world, it is now very much the case with copyright. As a child, I went to the movies, watched television, read books, listened to music on a state-of-the-art Phillips radiogram. But this was nothing compared to the incessant use (technically licensing) of copyright-protected material that now occurs in our daily lives. Recently, I needed to write a conference paper while visiting at another university. I had my laptop, but nobody had organised wireless Internet access for me. No JSTOR, no SSRN, no HeinOnline, no Westlaw: I didn't know quite what to do with myself. I had to go and find the library. Or consider new devices such as the Apple TV that give us seamless access to copyright- protected material throughout our homes. Or the iPhone that enables me to listen to BBC and PBS podcasts during my walk home from the office. Or technologies that enable space shifting of my music collection. As an aside, it's perhaps useful to remember the extra value for money we now get when we purchase individual copies of copyright-protected works. Once upon a time, that individual copy was a vinyl record that sat in a record rack, and could only be played on that radiogram. Many of us now wander around with our music collections in our pockets. We're often told that copyrights are expanding. But it's perhaps salutary to bear in mind that, with these kinds of space shifting technologies, consumers nowadays probably get much more bang for their copyright buck. Our incessant engagement with copyright, combined with the perception that some of the conventional economic rationales for this kind of property are pallid, if not entirely infirm, might account for the intensity in the moral discourse that now surrounds copyright.24 Moral claims are made on all sides. Two recent examples: a United Kingdom-based online "television catch up" service recently disabled its links to torrent files containing proprietary content. The site had adopted a so-called "non-commercial content" stance – it refused access to television programmes that were available commercially. 25 The 1709 Blog "C&D letter causes UKNova to take down links to television content" (27 August 2012) <http://the1709blog.blogspot.co.nz/2012/08/c-letter-causes-uknova-to-take-down.html>. (2013) 44 VUWLR But it says something about the reputational deficit with which intellectual property is currently burdened that these dots are seldom connected in populist commentaries. Whether the exchange is fair is of course a different matter – but that's a political and economic problem, not a copyright problem. All of this contributes, I think, to a cluster of current anxieties about copyright. As my former University of Arizona colleague, prominent United States property scholar Professor Carol Rose, points out, almost all property can provoke dispute and anxiety.22 Think of our current engagement 23 New Zealand Maori Council v Attorney-General [2013] NZSC 6. 24 Rose "The Moral Subject of Property", above n 22, at 1902. 24 Rose "The Moral Subject of Property", above n 22, at 1902. 23 New Zealand Maori Council v Attorney-General [2013] NZSC 6. (2013) 44 VUWLR Confronted by a cease and desist letter, it sent a message to all its subscribers:25 Whilst we believe that they are wrong both legally and morally on account of the strong 'no commercial content' stance that we have always taken, we are not in a position to be able to risk lengthy and costly court battles to prove this. PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 7 Or consider a recent observation by another alumna, Stella Duffy, now working as a London- based novelist, who was provoked to write this in her blog when she found two of her novels on a downloading site:26 … these pirates who like to see themselves as the Captain Jack Sparrow of the high seas (and seem rather more like modern-day pirate-thugs to me) have no problem paying Apple or Microsoft or Dell or whoever for the hardware. They have no problem paying the site that is hosting the theft. The ONLY person they mind paying is the originator of the work, the writer. … these pirates who like to see themselves as the Captain Jack Sparrow of the high seas (and seem rather more like modern-day pirate-thugs to me) have no problem paying Apple or Microsoft or Dell or whoever for the hardware. They have no problem paying the site that is hosting the theft. The ONLY person they mind paying is the originator of the work, the writer. She ends: "Nice going guys, that's the way to change the world." 26 Stella Duffy "Copyright Theft – Robin Hood it Ain't" (20 March 2012) Not Writing But Blogging <http://stelladuffy.wordpress.com/2012/03/20/copyright-theft-robin-hood-it-aint/>. (Emphasis in original.) 27 Jane C Ginsburg "'Une Chose Publique'? The Author's Domain and the Public Domain in Early British, French and US Copyright Law" (2006) 65 CLJ 636 at 637 (critically scrutinising these claims). 28 Copyright is sometimes likened to a new enclosure movement, whereby ordinary folk are locked out of the jus publicum. See James Boyle "The Second Enclosure Movement and the Construction of the Public Domain" (2003) 66 Law & Contemp Probs 33. 29 Lawrence Lessig "Copyright's First Amendment" (2001) 48 UCLA L Rev 1057 at 1072. 30 Most prominently: Golan v Holder 565 US (2012) (forthcoming); Eldred v Ashcroft 537 US 186 (2003). 30 Most prominently: Golan v Holder 565 US (2012) (forthcoming); Eldred v Ashcroft 537 US 186 (2003) 29 Lawrence Lessig "Copyright's First Amendment" (2001) 48 UCLA L Rev 1057 at 1072. 28 Copyright is sometimes likened to a new enclosure movement, whereby ordinary folk are locked out of the jus publicum. See James Boyle "The Second Enclosure Movement and the Construction of the Public Domain" (2003) 66 Law & Contemp Probs 33. 33 Clifford Geertz Local Knowledge: Further Essays in Interpretive Anthropology (Basic Books, New York, 1983) at 175. See also Mary Ann Glendon Abortion and Divorce in Western Law (Harvard University Press, Cambridge, 1987) at 141–142. 35 Robert Benchley Life (New York) cited in Dorothy Herrmann With Malice Toward All: The Quips, Lives and Loves of Some Celebrated 20th-Century American Wits (G P Putnam's Sons, New York, 1982) at 41. (2013) 44 VUWLR 8 strange bedfellows with constitutional originalists – or, perhaps more accurately, postulant bedfellows. For the most part, the originalists aren't signing on to these appeals to history.31 strange bedfellows with constitutional originalists – or, perhaps more accurately, postulant bedfellows. For the most part, the originalists aren't signing on to these appeals to history.31 Others take a more metaphysical turn, seeking to describe the essence of the public domain in opposition to copyright. As one leading scholar wrote: "We need to understand the delicate and subtle balance between property and the opposite of property, the role of rights, but also of the public domain and the commons."32 Grow copyright: shrink the public domain. Copyright hypertrophy: public domain atrophy – these are the yin and yang of contemporary copyright politics. 34 Nichols v Universal Pictures Corporation 45 F 2d 119 (2d Cir 1930). 32 James Boyle The Public Domain: Enclosing the Commons of the Mind (Yale University Press, Durham, 2008) at 238. 31 On this point, see generally Thomas Nachbar "Intellectual Property and Constitutional Norms" (2004) 104 Colum L Rev 272 at 344–345. III COPYRIGHT AND THE PUBLIC DOMAIN III COPYRIGHT AND THE PUBLIC DOMAIN Copyright is a huge and fascinating topic, and these issues are variously engaged right across this body of law. But one area where the debate is truly intense is in the discourse surrounding the boundary between copyright and the public domain. Those who valorise the public domain sometimes appeal to history, and seem to yearn for some kind of golden age: "In the beginning there was the public domain."27 By erecting fences in this primordial paradise, copyright represents a kind of fall from grace. Alternatively, it is suggested that the familiar narrative explaining the rise of property systems has, in the copyright context, morphed into a tragedy of the anti-commons. Too much private property, too many fences in that primordial paradise, too much acquisitiveness about those apples: with the result that the rest of us are locked out of those Arcadian fields of freely-available cultural detritus.28 One answer is said to be turning back the clock. In the United States, for instance, there has been no small amount of pining for the "framers' copyright" – that is, the modest copyright envisaged by the framing generation. In the beginning, copyrights had an initial term of 14 years; they could be forfeited for failure to comply with formalities; the adaptation right did not reach translations and so on.29 In the past decade in the United States, these general ideas catalysed a number of constitutional challenges to domestic copyright laws.30 To me, this always seemed to make for 30 Most prominently: Golan v Holder 565 US (2012) (forthcoming); Eldred v Ashcroft 537 US 186 (2003). 8 A Copyright's "Give and Take" I worry that conceiving of copyright and the public domain as having a hard-line border between them, or as being in opposition to each other, might not project the most useful vision of their relationship. As Clifford Geertz admonished us, in all legal activity, it is incumbent upon us to be attentive, intelligent, reasonable and responsible in the "stories [we] tell" and the "visions [we] project."33 For one thing, this characterisation risks overlooking copyright's ability to expand the public domain. An example of what I mean is provided by the very famous 1930 decision of Judge Learned Hand in the United States' Second Circuit Court of Appeals, Nichols v Universal Pictures Corporation.34 The plaintiff was the American playwright Ann Nichols, who penned the extraordinarily successful play Abie's Irish Rose. Set in early 20th century United States, the play concerns an Orthodox Jewish family, the patriarch of which hopes his only son will marry an Orthodox Jewish girl; and an Irish Catholic family, the daughter of which has secretly married the Jewish boy. When discovered, this situation only serves to intensify the religious animosity between the patriarchs of each family, with much Broadway-esque fun along the way. The families are reconciled when the young couple produces offspring – that tried and true passport to goodwill. Critics panned the play, one commenting that "people laugh at this every night, which explains why democracy will never be a success"35 and that the play was "[j]ust about as low as good clean fun PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 9 9 can get."36 Despite or perhaps because of this, the play was a hit. One of the longest-running plays on Broadway of its time, it spawned a radio series and two Hollywood movies. It also seemed to attract imitators. Ann Nichols brought proceedings against Universal Pictures, claiming that United's movie, the Cohens and the Kellys, which, suffice to say, also concerned a Jewish and a Catholic family whose relationship is also characterised by perpetual enmity, breached her copyright. (In the film it apparently extends to pets: neither family's dog appears to have much time for the other). But again the adult children of each house are in love. 39 Attributed to Samuel Johnson is the observation: "No man but a blockhead ever wrote except for money." James Boswell (George Birkbeck Hill (ed)) Life of Johnson: Including Boswell's Journal of a Tour to the Hebrides and Johnson's Diary of a Journey Into North Wales (Bigelow Brown & Co, New York, 1921) vol VI at 307. 38 Professor Waldron insightfully pursues a Hohfeldian analysis of copyright law, requiring simultaneous cognisance of the burdens imposed by copyrights. Jeremy Waldron "From Authors to Copiers: Individual Rights and Social Values in Intellectual Property" (1993) 68 Chi-Kent L Rev 841 at 844. 37 Nichols v Universal Pictures Corporation 34 F 2d 145 (SD NY 1929) at 150. A Copyright's "Give and Take" The Cohens and the Kellys was actually a successful series of films, including the follow-ups The Cohens and the Kellys in Scotland and The Cohens and the Kellys in Africa. The last in the series, perhaps presaging the end of the franchise, was apparently titled The Cohens and the Kellys in Trouble. Nichols lost, both in the District Court and on appeal to the Second Circuit. In the Court of Appeals, Judge Learned Hand accepted, at least for the sake of argument, that Nichols was the first to develop the theme of racially motivated disputants reconciled in the melting pot of America by the fecundity of the next generation – and that this same vein also yielded much gold for others, or, at least, successful Hollywood movies. Indeed, the District Court found that there was "a fairly strong inference that the authors of the film gained some of their ideas from Abie's Irish Rose,"37 – but the former took only ideas, and copyright does not protect ideas. So assuming that this general idea was original in some sense, copyright granted to Ms Nichols (and took from us)38 copyright in her play – Abie's Irish Rose – but, at the same time, copyright took from her (and gave to us) her apparently lucrative idea, consigning it to the public domain for others to use. Ann Nichols was a commercial playwright. She was not one of those Johnsonian blockheads: she wrote for money.39 The case illustrates how copyright's commercial motivations actually grow the area beyond copyright – the public domain adds to the raw materials of culture available for free for all of us on the non-property side. 40 Agreement on Trade-Related Aspects of Intellectual Property Rights 1869 UNTS 299 (signed 15 April 1994, entered into force 1 January 1995), art 10 (requiring that computer programs be protected as literary works under the Berne Convention for the Protection of Literary and Artistic Works 828 UNTS 221 (opened for signature 14 July 1967, entered into force 29 January 1970) [Berne Convention])). The Berne Convention dates from 9 September 1886, was revised on 24 July 1971 and amended on 28 September 1979. (2013) 44 VUWLR demands that computer programs be protected by copyright.40 But the international law obligations are vague, to say the least, as to the scope of protection required. In many jurisdictions, important parts of the intellectual input that goes into producing proprietary software are consigned to the public domain. In New Zealand, as in many other jurisdictions, there are, for instance, specific defences for copying computer programs in order to develop certain kinds of interoperable products.41 And our law, like that of a number of other nations,42 voids contracts that purport to override this provision.43 In the decisional law and policy discussion, there is also a tendency to "thin" the protection afforded by copyright to computer software. Across the Tasman, for instance, both the Full Federal Court and the High Court of Australia have restricted the scope of copyright in, for example, lists of computer commands.44 And, as early as 1995, the Australian Copyright Law Review Committee on Computer Software Protection45 cited with approval a seminal decision of the United States Court of Appeals for the Second Circuit,46 Computer Associates International Inc v Altai Inc, which significantly limited the strength of copyright in cases of non-literal infringement – again, consigning to the public domain key aspects of program architecture, especially when these aspects are dictated by the function of the program. 45 Copyright Law Review Committee Computer Software Protection (Office of Legal Information and Publishing, Attorney-General's Department, 1995) at [9.10]–[9.22]. 42 Directive 2009/24/EC on the legal protection of computer programs [2009] OJ L111/16. B Thin Copyright for Functional Works Copyright doctrines are especially solicitous of the public domain when it comes to functional works. The most useful examples involve computer programs. Rightly or wrongly, international law 10 41 Copyright Act 1994, s 80A. 44 Powerflex Services Pty Ltd v Data Access Corporation (1997) 37 IPR 436 (FCA). 46 Computer Associates International Inc v Altai Inc 982 F 2d 693 (2d Cir 1992). 41 Copyright Act 1994, s 80A. 47 Berne Convention, above n 40. 43 Copyright Act 1994, s 80D. C Copyright Duration Of course, when copyrights do eventually expire, more goes into the public domain. If one is solicitous of the public domain, therefore, one should also be a copyright enthusiast. But the objection is that copyrights last too long. Certainly, the term of "life of the author plus 70 years", the term increasingly being adopted, does seem dismayingly long. New Zealand has so far, and admirably, held the internationally-mandated line47 of life plus 50 years for many works. It has been PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 11 11 suggested that the intensity of the modern populist outrage at the copyright system seems to date from the decision in the United States in the late 1990s to increase copyright terms by 20 years.48 Greed has consequences.49 It is useful to recall, though, that even New Zealand's "life of the author plus 50 years" term does not tell the whole story. Our law significantly shortens the term of protection for a category of works that are applied in industrial contexts.50 These are often functional products. Cutting off the copyright term early in this way helps ensure that more "important" kinds of copyright-protected works are consigned to the public domain sooner. The length of protection is more or less in line with industrial designs and patents. Here, I mean "important" in a very specific sense. Works with longer terms, such as songs and movies, are "important", but they are, in a sense, more fungible than functional products. Gifted as Lady Gaga might be, there are limits to the extent to which she can leverage her copyright monopoly. If copies of her work were priced too high, consumers would move on to the next pop diva, and many are doubtless waiting in line. With functional products, however, the array of ready substitutes is smaller. Hence the determination that the copyright monopoly must end sooner for works of a functional character. Of course, it is questionable whether copyright should attach at all. In the United States, for example, copyright consigns many useful aspects of products to the public domain from the get-go.51 The viability of the United States approach is something we might consider carefully in this country. 51 In broad outline, the Copyright Act 17 USC §§ 101–810 consigns to the public domain utilitarian pictorial, graphic and sculptural works or aspects of these works that cannot be separated, conceptually or physically, from the aesthetic aspects of these works. See (3 September 1976) House Report No 94-1476, 94th Congress, 2d Session at § 105. This aspect of United States law has distilled a rich, and not entirely consistent jurisprudence. See for example Carol Barnhart Inc v Economy Cover Corp 773 F 2d 411 (2d Cir 1985); Pivot Point International Inc v Charlene Products Inc 372 F 3d 913 (7th Cir 2004). 52 Anupam Chander and Madhavi Sunder "The Romance of the Public Domain" (2004) 92 CLR 1331. 48 Jane C Ginsburg "How Copyright Got a Bad Name for Itself" (2002) 26 Colum J L & Arts 61. 50 Copyright Act 1994, s 75. 49 Ginsburg, above n 48. 57 Carol M Rose "Introduction: Property and Language, Or, The Ghost of the Fifth Panel" (2006) 18 Yale J L & Human 1. 56 Laurence R Helfer and Graeme W Austin Human Rights and Intellectual Property: Mapping the Global Interface (Cambridge University Press, New York, 2011) at 432–502. 54 For a more sceptical view, see Andrew Keen The Cult of the Amateur: How Today's Internet is Killing our Culture (Nicholas Brealey, London, 2007). 55 Waitangi Tribunal Ko Aotearoa Tēnei: A Report into Claims Concerning New Zealand Law and Policy Affecting Māori Culture and Identity (Wai 262, 2011). 53 Report of the Special Rapporteur on the promotion and protection of the right to freedom of opinion and expression, Frank La Rue A/HRC/17/27 (2011) at [61]. D Unexamined Assumptions But back to the main theme. There is, as Professors Madhavi Sunder and Anupam Chander have pointed out, a kind of "romance" about the public domain.52 Part of the normative heft accompanying the valorisation of the public domain comes from the idea that the externalities of copyright protection are more burdensome when technological developments make downstream innovation easier. The claim that copyright does not, for instance, inappropriately burden speech when it merely privatises expression and not ideas, perhaps looks a little different in the era of the mash up. New technologies facilitate creativity using protected expression, not just ideas, and to the extent that copyright prohibits this kind of activity, it intolerably burdens creativity. 12 (2013) 44 VUWLR (2013) 44 VUWLR One difficulty with the argument is that it treats the downstream creative community like a "black box" – as if everyone has equal access to technological tools of derivative creativity. But the externalities story is a hopeless description of life in many nations. Often, access to electricity cannot be taken for granted, let alone fancy digital media tools.53 Quite appropriately, people often object that our copyright laws are Eurocentric. But I worry that assumptions about the capacity to enjoy and exploit the public domain also betray a first-world bias. I don't decry the importance of amateur creativity.54 That said, we should perhaps be more attentive to the class issues that lurk below the surface of our celebrations of amateurism. Really good amateur content takes talent, to be sure. And, if the blessings of talent are not evenly distributed, the time and the money that are also required for amateur creative activity certainly are not. More empirical work is needed on this point – but I would hazard a guess that, at least in terms of sheer volume, rather more amateur content is produced by the kid in the United States college dorm room, with ready access to bandwidth, hardware and software, than by the solo mum holding down two, sometimes, three jobs to put food on the table for her family. Surplus time and money for amateur creativity probably sit somewhere near the top of the Maslovian hierarchy. Not all of us ever reach those toney heights. To champion amateur user-generated content uncritically, without interrogating these class implications, seems like an irresponsible basis for the formulation of social policy. And as for that solo mum: we do have one famous example that perhaps reminds us that if she does eke out time to write, she might appreciate the income that might one day provide her with the kind of economic freedom that some dorm-room occupiers at fancy United States universities seem already to take for granted. – but I would hazard a guess that, at least in terms of sheer volume, rather more amateur content is produced by the kid in the United States college dorm room, with ready access to bandwidth, hardware and software, than by the solo mum holding down two, sometimes, three jobs to put food on the table for her family. 53 Report of the Special Rapporteur on the promotion and protection of the right to freedom of opinion and expression, Frank La Rue A/HRC/17/27 (2011) at [61]. 54 For a more sceptical view, see Andrew Keen The Cult of the Amateur: How Today's Internet is Killing our Culture (Nicholas Brealey, London, 2007). 55 Waitangi Tribunal Ko Aotearoa Tēnei: A Report into Claims Concerning New Zealand Law and Policy Affecting Māori Culture and Identity (Wai 262, 2011). 56 Laurence R Helfer and Graeme W Austin Human Rights and Intellectual Property: Mapping the Global Interface (Cambridge University Press, New York, 2011) at 432–502. 57 Carol M Rose "Introduction: Property and Language, Or, The Ghost of the Fifth Panel" (2006) 18 Yale J L & Human 1. (2013) 44 VUWLR Surplus time and money for amateur creativity probably sit somewhere near the top of the Maslovian hierarchy. Not all of us ever reach those toney heights. To champion amateur user-generated content uncritically, without interrogating these class implications, seems like an irresponsible basis for the formulation of social policy. And as for that solo mum: we do have one famous example that perhaps reminds us that if she does eke out time to write, she might appreciate the income that might one day provide her with the kind of economic freedom that some dorm-room occupiers at fancy United States universities seem already to take for granted. – but I would hazard a guess that, at least in terms of sheer volume, rather more amateur content is produced by the kid in the United States college dorm room, with ready access to bandwidth, hardware and software, than by the solo mum holding down two, sometimes, three jobs to put food on the table for her family. Surplus time and money for amateur creativity probably sit somewhere near the top of the Maslovian hierarchy. Not all of us ever reach those toney heights. To champion amateur user-generated content uncritically, without interrogating these class implications, seems like an irresponsible basis for the formulation of social policy. And as for that solo mum: we do have one famous example that perhaps reminds us that if she does eke out time to write, she might appreciate the income that might one day provide her with the kind of economic freedom that some dorm-room occupiers at fancy United States universities seem already to take for granted. Finally, the recent Wai 262 report55 – the so-called Māori Intellectual Property claim – provides a further reminder that the ideas that mark out the boundary between property and the public domain can betray cultural biases. Many indigenous peoples are contesting the culturally-specific foundations of property rights, including in the intellectual property field.56 Property systems can be elaborate and some are highly bureaucratised, but property is also a language, a symbolic economy.57 The Wai 262 report reminds us of the importance of trying to understand different languages of property, something we've not been very good at in the past. Unthinking adoption of PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 13 other nations' ideas about the scope of copyright is certainly a problem. 60 See Graeme W Austin "The Berne Convention as a Canon of Construction: Moral Rights After Dastar" (2005) 61 NYU Ann Surv Am L 111, discussing obligations imposed by article 6bis of the Berne Convention, above n 39 (entered into force in the United States 1 March 1989). 59 "'[H]ow does the creative worker get paid?' can itself be characterized as a human rights issue." Helfer and Austin, above n 56, at 195. See also Graeme W Austin and Amy Zavidow "Copyright Law Through a Human Rights Lens" in Paul L C Torremans (ed) Intellectual Property and Human Rights (Kluwer, The Netherlands, 2008) 257. (2013) 44 VUWLR But, as indigenous peoples' claims in the intellectual property space persistently underscore, unthinking importation of foreign ideas about the public domain – about the materials of culture that should be unowned – may be similarly problematic. 61 For example: Bonito Boats Inc v Thunder Craft Boats Inc 489 US 141 (1989); Sears, Roebuck & Co v Stiffel Co 376 US 225 (1964). 58 Dastar Corp v Twentieth Century Fox Film Corporation 539 US 23 (2003). (2013) 44 VUWLR domain. This is a logic that, in seeing us only as consumers demanding cheaper stuff, obliterates the creative worker almost entirely. I believe that very similar logic underlies quite a lot of the valorisation of the public domain – which is animated by a desire to get stuff cheaply or even for free, so that the efforts of the creative worker do not need to be factored into the bottom line. These kinds of ideas also inform some strands of so-called liberal copyright scholarship, especially in the United States, which in turn is grounded on a commitment to the idea that tinkering with the ambit of property rights (which mostly means reducing their scope), dismantling those fences in that public domain paradise, points the way to salvation. In my view, the critique must be much more radical. To live well on the frontier between copyright and the public domain requires us to examine what we are like, and what we value – whether we are merely consumers wanting cheap stuff. It involves asking if protections for the creative worker have any moral or political salience, or whether the universe of concerns informing our copyright laws should only be informed by a drive to get prices down as close as possible to the marginal cost of production. I call this the "Walmartization" of copyright. This is partly why in the last few years, I've become so interested in the relationship between human rights law and intellectual property.62 Human rights certainly provide compelling reasons for being concerned about the public domain, reasons that go beyond getting more stuff more cheaply. Human rights law draws attention to a broader set of values: educational rights, environmental rights, the right to food, an adequate standard of health, indigenous peoples' rights – with which any decent intellectual property system, and any decent society, must contend. And human rights lawyers have crafted a powerful lens through which to analyse these issues. These are not just ad hoc distributive justice claims du jour. At the same time, however, human rights laws recognise the importance and the rights imperatives associated with functioning markets. 62 See Helfer and Austin, above n 56. 63 Helfer and Austin, above n 56, at 212–220. 64 Universal Declaration of Human Rights GA Res 217A (III) (1948) at art 27. 65 Committee on Economic, Social and Cultural Rights General Comment No 17: The Right of Everyone to Benefit from the Protection of the Moral and Material Interests Resulting from Any Scientific, Literary or Artistic Production of Which He Is the Author E/C12/2005 (2005) at art 15(1)(c). 66 International Covenant on Economic, Social and Cultural Rights 993 UNTS 3 (opened for signature 19 December 1966, entered into force 3 January 1976). IV LIVING WELL ON THE FRONTIER How we map this frontier says something, I believe, about the kind of society to which we aspire. A 2003 United States Supreme Court decision, Dastar Corp v Twentieth Century Fox Film Corporation,58 helps to illustrate what I mean. The Dastar case arguably expanded the public domain or, at least, shrank the rights of authors. I have long been fascinated by this decision, especially for what it says about creative labour.59 It concerned a documentary series produced by the plaintiff that was based on the wartime memoirs of President Eisenhower. Due to some peculiarities of United States copyright law that need not detain us, copyright in the films fell into the public domain. Recognising that popular interest in World War II was increasing, another production company reissued the documentaries, but this company failed to acknowledge the plaintiff's original authorship of the films. Now, under United States copyright law, this was perfectly lawful. Despite its international law obligations, the United States has never enacted a full- blooded authorial attribution right.60 To partially fill this gap, United States litigators had cleverly developed domestic trademark law, so that misinformation about authorship was often considered to be a breach of unregistered trademark rights, or, technically, a form of reverse passing off. So this case reached the Supreme Court on the issue of whether trademark law could continue to provide an attribution right. The Court said no. There is a very strong theme in Justice Scalia's opinion that creating a "mutant copyright law" out of trademark law would be contrary to a legislative policy that firms should be entitled to market public domain works free of any kind of impediments, including attribution rights. Tellingly, the Court's analysis rested heavily on a line of cases limiting the scope of trade dress protection in consumer products.61 Authors' rights were suspect, therefore, if they got in the way of lower prices. Whatever claims authors might have had, they were overridden by the imperative logic of the public 14 62 See Helfer and Austin, above n 56. 63 Helfer and Austin, above n 56, at 212–220. 66 International Covenant on Economic, Social and Cultural Rights 993 UNTS 3 (opened for signature 19 December 1966, entered into force 3 January 1976). 65 Committee on Economic, Social and Cultural Rights General Comment No 17: The Right of Everyone to Benefit from the Protection of the Moral and Material Interests Resulting from Any Scientific, Literary or Artistic Production of Which He Is the Author E/C12/2005 (2005) at art 15(1)(c). 64 Universal Declaration of Human Rights GA Res 217A (III) (1948) at art 27. 67 Helfer and Austin, above n 56, at 189 and 194–196. See also Laurence R Helfer "Toward a Human Rights Framework for Intellectual Property" (2007) 40 U C Davis L Rev 971 at 996. 68 Neil W Netanel "Copyright and a Democratic Civil Society" (1996) 106 Yale L J 283. (2013) 44 VUWLR Hence the recognition in many human rights instruments of the right of property.63 In the intellectual property context, no less venerable document than the Universal Declaration of Human Rights demands protection of the right of "[e]veryone … to the protection of the moral and material interests resulting from any scientific, literary or artistic production of which he or she is the author."64 The 2005 General Comment65 on the equivalent article in the International Covenant on Economic, Social and Cultural Rights66 emphasises the link between this right and the PROPERTY ON THE LINE: LIFE ON THE FRONTIER BETWEEN COPYRIGHT AND THE PUBLIC DOMAIN 15 idea that authors should enjoy an adequate standard of living, and that they are entitled to just remuneration. Amongst other things, the document invites us to take seriously the idea that liberty interests can be furthered by participation in functional markets for creative work. One of the many themes that Professor Larry Helfer and I develop in our book on human rights and intellectual property is that the right to participate in private markets for creative work helps to carve out for authors "a zone of personal autonomy in which authors … control their productive output, and lead independent, intellectual lives."67 These are things any free society needs, and they are nurtured by a system that enables authors to derive at least some of their income from a paying public (assuming they can find one) rather than depending entirely on political or other forms of patronage.68 In other words, if the public domain were all we had, if property in creative outputs were dispatched over the line, we risk creating a new kind of thraldom. There is, therefore, a lot at stake in these urgent, sometimes fractious, often dismayingly impolite, discussions about the future of copyright. Like all interesting legal issues, they implicate questions about the kind of society we want, and who we want to be. And the disputed terrain is quite large. Mapping the boundary between copyright and the public domain puts much that is important on the line. One might conclude by saying: "get over it". Better, I think, is to say: "live with it". Better yet: "live well with it". Thank you. (2013) 44 VUWLR 16
https://openalex.org/W2236687381
http://journals.iucr.org/e/issues/2013/03/00/rk2391/rk2391.pdf
English
null
1′-(1,3-Diphenyl-1<i>H</i>-pyrazol-4-yl)-1′′-methyl-2′,3′,5′,6′,7′,7a'-octahydro-1′<i>H</i>-dispiro[1-benzopyran-3,2′-pyrrolizine-3′,3′′-indoline]-2′′,4-dione
Acta crystallographica. Section E
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cc-by
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Related literature For the biological activity of pyrazole derivatives, see: Mahajan et al. (1991); Baraldi et al. (1998); Katayama & Oshiyama (1997); Chen & Li (1998). For a related structure, see: Fun et al. (2011). For puckering parameters, see: Cremer & Pople (1975). Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RK2391). Table 1 In the title compound C38H32N4O3, one pyrrolidine ring adopts an envelope conformation with the N atom as the flap while other pyrrolidine ring adopts an twisted conformation. The pyrrolizine ring forms dihedral angles of 79.24 (5) and 77.57 (5) with the chromene and indole rings, respectively. The carbonyl O atoms deviate from the least-square planes through the chromene and indole rings by 0.0113 (12) and 0.0247 (12) A˚ , respectively. In the crystal, non-classical C— H  O interactions link the molecules, generating an C(9) chain along the b-axis direction. Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97; molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009). The authors thank Dr Babu Varghese, SAIF, IIT, Chennai, India, for the data collection. 1000-(1,3-Diphenyl-1H-pyrazol-4-yl)-1000000- methyl-2000,3000,5000,6000,7000,7a’-octahydro-1000H- dispiro[1-benzopyran-3,2000-pyrrolizine- 3000,3000000-indoline]-2000000,4-dione 1000-(1,3-Diphenyl-1H-pyrazol-4-yl)-1000000- methyl-2000,3000,5000,6000,7000,7a’-octahydro-1000H- dispiro[1-benzopyran-3,2000-pyrrolizine- 3000,3000000-indoline]-2000000,4-dione organic compounds Experimental Crystal data C38H32N4O3 Mr = 592.68 Triclinic, P1 a = 10.8240 (3) A˚ b = 10.8382 (3) A˚ c = 13.9127 (4) A˚  = 70.290 (1)  = 88.946 (2)  = 73.578 (1) V = 1468.47 (7) A˚ 3 Z = 2 Mo K radiation  = 0.09 mm1 T = 295 K 0.30  0.25  0.20 mm Data collection Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008) Tmin = 0.975, Tmax = 0.983 35301 measured reflections 9340 independent reflections 5865 reflections with I > 2(I) Rint = 0.032 Refinement R[F 2 > 2(F 2)] = 0.055 wR(F 2) = 0.166 S = 1.06 9340 reflections 406 parameters H-atom parameters constrained max = 0.35 e A˚ 3 min = 0.25 e A˚ 3 Acta Crystallographica Section E Structure Reports Online ISSN 1600-5368 Acta Crystallographica Section E Structure Reports ISSN 1600-5368 G. Jagadeesan,a K. Sethusankar,b* D. Kathirvelan,c J. Haribabuc and B. S. R. Reddyc aDepartment of Physics, Meenakshi College of Engineering, West K.K. Nagar, Chennai 600 078, India, bDepartment of Physics, RKM Vivekananda College (Autonomous), Chennai 600 004, India, and cIndustrial Chemistry Lab, Central Leather Research Institute, Adyar, Chennai 600 020, India Correspondence e-mail: ksethusankar@yahoo.co.in 406 parameters H-atom parameters constrained max = 0.35 e A˚ 3 min = 0.25 e A˚ 3 Received 18 December 2012; accepted 21 January 2013 Table 1 Hydrogen-bond geometry (A˚ , ). D—H  A D—H H  A D  A D—H  A C34—H33  O3i 0.93 2.59 3.523 (3) 178 Symmetry code: (i) x; y þ 1; z. Key indicators: single-crystal X-ray study; T = 295 K; mean (C–C) = 0.002 A˚; R factor = 0.055; wR factor = 0.166; data-to-parameter ratio = 23.0. S1. Comment Pyrazole derivatives in general are well known nitrogen containing heterocyclic compounds and these derivatives have been the subject of enormous research due to their importance in various applications and their widespread potential biological and pharmacological activities such as antimicrobial (Mahajan et al., 1991), antiviral (Baraldi et al., 1998), antitumor (Katayama & Oshiyama, 1997), antifungal activities (Chen & Li, 1998). The molecular structure of the title compound C38H32N4O3, is shown in Fig. 1. The phenyl rings (C1-C6) and (C8-C13) attached with the pyrazole ring (C7/C14/C15/N4/N5) form a dihedral angle of 52.60 (6)° between them. The pyrazole ring (C7/C14/C15/N4/N5) forms dihedral angles of 41.24 (6)° and 12.85 (5)° with the two phenyl rings (C1-C6) and (C8- C13), respectively. The pyrrolizine ring (C16-C21/C30/N1) forms dihedral angles of 79.24 (5)° and 77.57 (5)° with the chromene ring (C30-C38/O1) and indole ring (C21-C27/C29/N3), respectively. The atoms C28, O3 and O2 deviate from the l.s. planes of the indole ring (C21-C27/C29/N3) and chromene ring (C30-C38/O1) by 0.020 (2)Å, 0.0247 (12)Å and 0.0113 (12)Å, respectively. The title compound exhibits the structural similarities with the already reported related structure (Fun et al., 2011). The sum of angles around the N1 atom (340°) indicates sp3 hybridization. The pyrrolidine ring (C16/C17/C21/C30/N1) adopts an envelope conformation on N1 with puckering parameters (Cremer & Pople, 1975) of q2 = 0.3225 (15)Å and φ2= 186.4 (3)°. Also, the atom N1 deviates from the mean planes of the remaining ring atoms by -0.2027 (14)Å. The other pyrrolidine ring (C17-C20/N1) adopts a twisted conformation on C17 and C18 with puckering parameters of q2 = 0.294 (2)Å and φ2 = 236.2 (4)°. Also, the atoms C17 and C18 deviate from the mean planes of the remaining ring atoms by 0.1743 (17)Å and -0.179 (2)Å. The crystal packing is stabilized by non-classical C–H···O interactions (Table 1). The C34-H33···O3i interaction generates a C(9) chain along the b axis. The symmetry code: (i) x, y+1, z. The packing view of the compound is shown in Fig. 2. S2. Experimental A mixture of methyl isatin (1.05 mmol), sarcosine (1.1 mmol), dipolarophile (1.0 mmol) in ethanol was refluxed for 85 min and cooled to room temperature. Then the mixture was poured into crushed ice breaker and the solid formed in the mixture was filtered, dried, and recrystallized from ethanol to obtain the pure product in good yield 93%. Acta Cryst. (2013). E69, o317 [doi:10.1107/S1600536813002043] Acta Cryst. (2013). E69, o317 [doi:10.1107/S1600536813002043] 1′-(1,3-Diphenyl-1H-pyrazol-4-yl)-1′′-methyl-2′,3′,5′,6′,7′,7a′-octahydro-1′H-di- spiro[1-benzopyran-3,2′-pyrrolizine-3′,3′′-indoline]-2′′,4-dione G. Jagadeesan, K. Sethusankar, D. Kathirvelan, J. Haribabu and B. S. R. Reddy G. Jagadeesan, K. Sethusankar, D. Kathirvelan, J. Haribabu and B. S. R. Reddy References Baraldi, P. G., Manfredini, S., Romagnoli, R., Stevanato, L., Zaid, A. N. & Manservigi, R. (1998). Nucleosides Nucleotides, 17, 2165–2171. Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Chen, H. S. & Li, Z. M. (1998). Chem. J. Chin. Univ. 19, 572–576. Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358. Chen, H. S. & Li, Z. M. (1998). Chem. J. Chin. Univ. 19, 572 576. Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358. p ( ) Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Fun, H.-K., Chia, T. S., Malladi, S., Isloor, A. M. & Shivananda, K. N. (2011). Acta Cryst. E67, o2822–o2823. y Katayama, H. & Oshiyama, T. (1997). Can. J. Chem. 75, 913–919. Mahajan, R. N., Havaldar, F. H. & Fernandes, P. S. (1991). J. Indian Chem. Soc. 68, 245–249. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Spek, A. L. (2009). Acta Cryst. D65, 148–155. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Spek, A. L. (2009). Acta Cryst. D65, 148–155. Acta Cryst. (2013). E69, o317 Jagadeesan et al. o317 o317 Jagadeesan et al. doi:10.1107/S1600536813002043 supporting information supporting information Acta Cryst. (2013). E69, o317 [doi:10.1107/S1600536813002043] S3. Refinement Hydrogen atoms were placed in calculated positions with C–H = 0.93-0.98Å and refined in the riding model with fixed isotropic displacement parameters: Uiso(H) = 1.5Ueq(C) for methyl group and Uiso(H) = 1.2Ueq(C) for other groups. Acta Cryst. (2013). E69, o317 sup-1 supporting information Fi 1 Figure 1 Figure 1 g The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at 30% probability level. H atoms are presented as a small spheres of arbitrary radius. sup-2 Acta Cryst. (2013). E69, o317 supporting information Figure 2 The crystal packing of the title compound viewed down a axis, dashed lines indicates C–H···O interactions. H atoms not involved in hydrogen bonds have been excluded for clarity. Figure 2 The crystal packing of the title compound viewed down a axis, dashed lines indicates C–H···O interactions. H atoms not involved in hydrogen bonds have been excluded for clarity. The crystal packing of the title compound viewed down a axis, dashed lines indicates C–H···O interactions. H atoms no involved in hydrogen bonds have been excluded for clarity. supporting information Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.055 wR(F2) = 0.166 S = 1.06 9340 reflections 406 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0793P)2 + 0.1729P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.35 e Å−3 Δρmin = −0.25 e Å−3 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.055 wR(F2) = 0.166 S = 1.06 9340 reflections 406 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0793P)2 + 0.1729P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.35 e Å−3 Δρmin = −0.25 e Å−3 Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0793P)2 + 0.1729P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.35 e Å−3 Δρmin = −0.25 e Å−3 1′-(1,3-Diphenyl-1H-pyrazol-4-yl)-1′′-methyl-2′,3′,5′,6′,7′,7a′-octahydro-1′H-dispiro[1-benzopyran-3,2′- pyrrolizine-3′ 3′′-indoline]-2′′ 4-dione 1′-(1,3-Diphenyl-1H-pyrazol-4-yl)-1′′-methyl-2′,3′,5′,6′,7′,7a′-octahydro-1′H-dispiro[1-benzopyran-3,2′- pyrrolizine-3′,3′′-indoline]-2′′,4-dione Crystal data C38H32N4O3 Mr = 592.68 Triclinic, P1 Hall symbol: -P 1 a = 10.8240 (3) Å b = 10.8382 (3) Å c = 13.9127 (4) Å α = 70.290 (1)° β = 88.946 (2)° γ = 73.578 (1)° V = 1468.47 (7) Å3 Z = 2 F(000) = 624 Dx = 1.340 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 9340 reflections θ = 2.1–31.2° µ = 0.09 mm−1 T = 295 K Block, colourless 0.30 × 0.25 × 0.20 mm Data collection Bruker Kappa APEXII CCD diffractometer Radiation source: fine-focus sealed tube Graphite monochromator ω scans Absorption correction: multi-scan (SADABS; Bruker, 2008) Tmin = 0.975, Tmax = 0.983 35301 measured reflections 9340 independent reflections 5865 reflections with I > 2σ(I) Rint = 0.032 θmax = 31.2°, θmin = 2.1° h = −15→15 k = −15→15 l = −20→19 sup-3 Acta Cryst. (2013). E69, o317 supporting information Special details Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes. Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq C1 1.20015 (16) 0.45544 (16) 0.12448 (12) 0.0447 (4) H1 1.1229 0.5038 0.1421 0.054* C2 1.3123 (2) 0.4889 (2) 0.13459 (15) 0.0582 (5) H2 1.3102 0.5594 0.1589 0.070* C3 1.4264 (2) 0.4182 (2) 0.10881 (18) 0.0723 (6) H3 1.5022 0.4389 0.1174 0.087* C4 1.42844 (19) 0.3164 (2) 0.07008 (19) 0.0758 (6) H4 1.5054 0.2702 0.0507 0.091* C5 1.31727 (17) 0.28249 (19) 0.05992 (15) 0.0543 (4) H5 1.3197 0.2134 0.0338 0.065* C6 1.20183 (14) 0.35058 (14) 0.08829 (11) 0.0365 (3) C7 1.08498 (13) 0.30861 (14) 0.08134 (11) 0.0335 (3) C8 0.90446 (14) 0.17479 (14) −0.03996 (11) 0.0372 (3) C9 0.94126 (19) 0.19600 (19) −0.13752 (13) 0.0521 (4) H9 1.0018 0.2431 −0.1609 0.063* C10 0.8874 (2) 0.1466 (2) −0.20098 (16) 0.0649 (5) H10 0.9118 0.1614 −0.2674 0.078* C11 0.7992 (2) 0.0766 (2) −0.16741 (17) 0.0626 (5) H11 0.7643 0.0429 −0.2103 0.075* C12 0.76284 (19) 0.05675 (19) −0.07089 (16) 0.0587 (5) H12 0.7018 0.0101 −0.0482 0.070* C13 0.81477 (17) 0.10454 (17) −0.00578 (14) 0.0489 (4) H13 0.7896 0.0896 0.0605 0.059* C14 0.91574 (14) 0.23330 (15) 0.11587 (11) 0.0380 (3) H14 0.8460 0.2064 0.1464 0.046* Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq omic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) sup-4 Acta Cryst. (2013). Special details E69, o317 supporting information C15 0.99309 (13) 0.28870 (14) 0.15423 (11) 0.0338 (3) C16 0.98987 (13) 0.30356 (13) 0.25733 (10) 0.0319 (3) H16 1.0618 0.3383 0.2658 0.038* C17 1.01160 (14) 0.16187 (14) 0.34315 (11) 0.0374 (3) H17 0.9760 0.1025 0.3194 0.045* C18 1.15159 (16) 0.08961 (18) 0.38548 (13) 0.0510 (4) H18A 1.1669 −0.0088 0.4150 0.061* H18B 1.2098 0.1090 0.3323 0.061* C19 1.16913 (18) 0.1481 (2) 0.46624 (16) 0.0677 (6) H19A 1.2281 0.0789 0.5229 0.081* H19B 1.2041 0.2248 0.4380 0.081* C20 1.03935 (16) 0.1942 (2) 0.50153 (13) 0.0508 (4) H20A 1.0344 0.1345 0.5705 0.061* H20B 1.0223 0.2870 0.5015 0.061* C21 0.82823 (13) 0.30387 (14) 0.38591 (10) 0.0322 (3) C22 0.76483 (14) 0.36324 (14) 0.46523 (11) 0.0347 (3) C23 0.79918 (15) 0.43927 (16) 0.51647 (11) 0.0407 (3) H23 0.8702 0.4719 0.4990 0.049* C24 0.72698 (17) 0.46666 (18) 0.59423 (12) 0.0474 (4) H24 0.7498 0.5180 0.6288 0.057* C25 0.62210 (17) 0.41859 (19) 0.62049 (13) 0.0529 (4) H25 0.5754 0.4368 0.6734 0.063* C26 0.58482 (16) 0.34373 (19) 0.56975 (13) 0.0502 (4) H26 0.5133 0.3119 0.5873 0.060* C28 0.53123 (18) 0.1847 (2) 0.43800 (18) 0.0645 (5) H27A 0.4777 0.2036 0.4901 0.097* H27B 0.5660 0.0874 0.4550 0.097* H27C 0.4805 0.2233 0.3733 0.097* C29 0.72848 (14) 0.23509 (14) 0.36510 (11) 0.0368 (3) C30 0.86386 (13) 0.39982 (13) 0.28047 (10) 0.0294 (3) C31 0.89175 (14) 0.52146 (14) 0.29848 (10) 0.0341 (3) C32 0.78405 (15) 0.64959 (14) 0.27149 (11) 0.0378 (3) C33 0.7986 (2) 0.76442 (17) 0.28913 (14) 0.0514 (4) H32 0.8775 0.7606 0.3172 0.062* C34 0.6973 (2) 0.88303 (19) 0.26547 (16) 0.0662 (6) H33 0.7080 0.9590 0.2773 0.079* C35 0.5800 (2) 0.88894 (19) 0.22412 (17) 0.0663 (5) H34 0.5120 0.9694 0.2080 0.080* C36 0.56248 (19) 0.77743 (18) 0.20650 (15) 0.0551 (4) H35 0.4831 0.7819 0.1789 0.066* C37 0.66482 (15) 0.65802 (15) 0.23050 (12) 0.0396 (3) C38 0.75803 (14) 0.45991 (14) 0.19302 (11) 0.0352 (3) H37A 0.7906 0.5106 0.1314 0.042* H37B 0.7363 0.3856 0.1802 0.042* N1 0.94466 (12) 0.18845 (12) 0.42931 (9) 0.0362 (3) C27 0.65651 (14) 0.31774 (15) 0.49263 (11) 0.0384 (3) N3 0.63590 (12) 0.24491 (13) 0.43134 (10) 0.0424 (3) N4 0.95794 (12) 0.22443 (12) 0.02610 (9) 0.0359 (3) sup-5 Acta Cryst. (2013). Special details E69, o317 supporting information N5 1.06305 (12) 0.27041 (12) 0.00305 (9) 0.0372 (3) O1 0.64346 (10) 0.54909 (10) 0.21348 (8) 0.0419 (3) O2 0.99610 (11) 0.51308 (12) 0.33489 (9) 0.0505 (3) O3 0.73360 (11) 0.17644 (12) 0.30382 (9) 0.0491 (3) Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 C1 0.0454 (9) 0.0474 (8) 0.0443 (9) −0.0211 (7) 0.0063 (7) −0.0136 (7) C2 0.0624 (12) 0.0633 (11) 0.0570 (11) −0.0352 (9) 0.0015 (9) −0.0170 (9) C3 0.0483 (11) 0.0859 (15) 0.0876 (16) −0.0369 (11) −0.0011 (10) −0.0214 (12) C4 0.0356 (10) 0.0840 (15) 0.1056 (18) −0.0183 (10) 0.0170 (10) −0.0299 (13) C5 0.0407 (9) 0.0576 (10) 0.0662 (12) −0.0152 (8) 0.0131 (8) −0.0233 (9) C6 0.0354 (7) 0.0395 (7) 0.0319 (7) −0.0149 (6) 0.0040 (6) −0.0059 (6) C7 0.0336 (7) 0.0340 (6) 0.0315 (7) −0.0102 (5) 0.0043 (5) −0.0094 (5) C8 0.0376 (8) 0.0343 (7) 0.0388 (8) −0.0065 (6) −0.0005 (6) −0.0147 (6) C9 0.0602 (11) 0.0633 (10) 0.0443 (9) −0.0247 (9) 0.0102 (8) −0.0278 (8) C10 0.0746 (14) 0.0794 (13) 0.0519 (11) −0.0200 (11) 0.0041 (10) −0.0388 (10) C11 0.0603 (12) 0.0649 (11) 0.0723 (13) −0.0111 (9) −0.0119 (10) −0.0410 (10) C12 0.0560 (11) 0.0580 (10) 0.0727 (13) −0.0235 (9) −0.0015 (9) −0.0300 (10) C13 0.0513 (10) 0.0517 (9) 0.0503 (10) −0.0212 (8) 0.0037 (8) −0.0209 (8) C14 0.0378 (8) 0.0451 (8) 0.0369 (8) −0.0175 (6) 0.0097 (6) −0.0175 (6) C15 0.0335 (7) 0.0363 (7) 0.0324 (7) −0.0112 (5) 0.0047 (5) −0.0121 (5) C16 0.0298 (7) 0.0378 (7) 0.0308 (7) −0.0131 (5) 0.0043 (5) −0.0125 (5) C17 0.0396 (8) 0.0373 (7) 0.0332 (7) −0.0105 (6) 0.0049 (6) −0.0102 (6) C18 0.0431 (9) 0.0510 (9) 0.0440 (9) 0.0003 (7) 0.0036 (7) −0.0093 (7) C19 0.0425 (10) 0.0907 (15) 0.0651 (13) −0.0051 (10) −0.0079 (9) −0.0323 (11) C20 0.0420 (9) 0.0666 (10) 0.0425 (9) −0.0129 (8) −0.0028 (7) −0.0194 (8) C21 0.0319 (7) 0.0362 (6) 0.0319 (7) −0.0157 (5) 0.0054 (5) −0.0115 (5) C22 0.0335 (7) 0.0408 (7) 0.0304 (7) −0.0140 (6) 0.0072 (5) −0.0109 (6) C23 0.0402 (8) 0.0508 (8) 0.0359 (8) −0.0182 (7) 0.0062 (6) −0.0172 (7) C24 0.0468 (9) 0.0586 (9) 0.0398 (8) −0.0131 (7) 0.0049 (7) −0.0229 (7) C25 0.0457 (9) 0.0708 (11) 0.0418 (9) −0.0125 (8) 0.0141 (7) −0.0235 (8) C26 0.0375 (8) 0.0648 (10) 0.0470 (9) −0.0184 (7) 0.0146 (7) −0.0156 (8) C28 0.0468 (10) 0.0686 (12) 0.0983 (16) −0.0378 (9) 0.0225 (10) −0.0377 (11) C29 0.0372 (8) 0.0363 (7) 0.0389 (8) −0.0172 (6) 0.0054 (6) −0.0102 (6) C30 0.0294 (6) 0.0337 (6) 0.0285 (6) −0.0139 (5) 0.0031 (5) −0.0110 (5) C31 0.0369 (7) 0.0426 (7) 0.0304 (7) −0.0215 (6) 0.0078 (6) −0.0140 (6) C32 0.0470 (9) 0.0370 (7) 0.0350 (7) −0.0196 (6) 0.0121 (6) −0.0140 (6) C33 0.0688 (12) 0.0483 (9) 0.0525 (10) −0.0307 (8) 0.0178 (9) −0.0259 (8) C34 0.0953 (17) 0.0428 (9) 0.0710 (13) −0.0274 (10) 0.0283 (12) −0.0281 (9) C35 0.0771 (15) 0.0425 (9) 0.0727 (13) −0.0060 (9) 0.0175 (11) −0.0218 (9) C36 0.0497 (10) 0.0483 (9) 0.0594 (11) −0.0049 (7) 0.0085 (8) −0.0166 (8) C37 0.0438 (8) 0.0382 (7) 0.0377 (8) −0.0134 (6) 0.0097 (6) −0.0134 (6) C38 0.0348 (7) 0.0377 (7) 0.0344 (7) −0.0112 (6) 0.0011 (6) −0.0135 (6) N1 0.0357 (6) 0.0400 (6) 0.0302 (6) −0.0121 (5) 0.0037 (5) −0.0081 (5) C27 0.0336 (7) 0.0423 (7) 0.0378 (8) −0.0137 (6) 0.0059 (6) −0.0102 (6) N3 0.0360 (7) 0.0476 (7) 0.0512 (8) −0.0237 (6) 0.0116 (6) −0.0176 (6) Atomic displacement parameters (Å2) Acta Cryst. supporting information supporting informa 0.9700 C27—N3 1.400 (2) 0.9700 N4—N5 1.3582 (16) 1.476 (2) 120.59 (17) N1—C21—C29 103.59 (11) 119.7 C22—C21—C29 101.45 (11) 119.7 N1—C21—C30 106.50 (11) 120.08 (18) C22—C21—C30 121.01 (11) 120.0 C29—C21—C30 110.50 (11) 120.0 C23—C22—C27 118.57 (13) 119.79 (18) C23—C22—C21 133.02 (13) 120.1 C27—C22—C21 108.19 (12) 120.1 C22—C23—C24 119.54 (14) 120.40 (19) C22—C23—H23 120.2 119.8 C24—C23—H23 120.2 119.8 C25—C24—C23 120.49 (16) 120.44 (18) C25—C24—H24 119.8 119.8 C23—C24—H24 119.8 119.8 C24—C25—C26 121.14 (15) 118.64 (14) C24—C25—H25 119.4 119.68 (14) C26—C25—H25 119.4 121.67 (14) C27—C26—C25 117.91 (15) 111.59 (12) C27—C26—H26 121.0 119.80 (13) C25—C26—H26 121.0 128.29 (13) N3—C28—H27A 109.5 119.92 (15) N3—C28—H27B 109.5 120.33 (14) H27A—C28—H27B 109.5 119.74 (14) N3—C28—H27C 109.5 119.34 (18) H27A—C28—H27C 109.5 120.3 H27B—C28—H27C 109.5 120.3 O3—C29—N3 124.73 (14) 120.95 (19) O3—C29—C21 126.96 (13) 119.5 N3—C29—C21 108.23 (12) 119.5 C38—C30—C31 106.51 (11) 119.30 (17) C38—C30—C16 112.90 (11) 120.4 C31—C30—C16 110.79 (11) 120.4 C38—C30—C21 115.00 (11) 121.15 (18) C31—C30—C21 108.62 (10) 119.4 C16—C30—C21 103.01 (10) 119.4 O2—C31—C32 121.27 (13) 119.34 (17) O2—C31—C30 122.10 (13) 120.3 C32—C31—C30 116.62 (12) 120.3 C37—C32—C33 118.30 (15) 108.14 (13) C37—C32—C31 120.90 (13) 125.9 C33—C32—C31 120.78 (15) 125.9 C34—C33—C32 120.66 (19) 104.05 (12) C34—C33—H32 119.7 126.24 (13) C32—C33—H32 119.7 C19—H19A 0.9700 C27—N3 1.400 (2) C19—H19B 0.9700 N4—N5 1.3582 (16) C20—N1 1.476 (2) C2—C1—C6 120.59 (17) N1—C21—C29 103.59 (11) C2—C1—H1 119.7 C22—C21—C29 101.45 (11) C6—C1—H1 119.7 N1—C21—C30 106.50 (11) C3—C2—C1 120.08 (18) C22—C21—C30 121.01 (11) C3—C2—H2 120.0 C29—C21—C30 110.50 (11) C1—C2—H2 120.0 C23—C22—C27 118.57 (13) C2—C3—C4 119.79 (18) C23—C22—C21 133.02 (13) C2—C3—H3 120.1 C27—C22—C21 108.19 (12) C4—C3—H3 120.1 C22—C23—C24 119.54 (14) C5—C4—C3 120.40 (19) C22—C23—H23 120.2 C5—C4—H4 119.8 C24—C23—H23 120.2 C3—C4—H4 119.8 C25—C24—C23 120.49 (16) C4—C5—C6 120.44 (18) C25—C24—H24 119.8 C4—C5—H5 119.8 C23—C24—H24 119.8 C6—C5—H5 119.8 C24—C25—C26 121.14 (15) C5—C6—C1 118.64 (14) C24—C25—H25 119.4 C5—C6—C7 119.68 (14) C26—C25—H25 119.4 C1—C6—C7 121.67 (14) C27—C26—C25 117.91 (15) N5—C7—C15 111.59 (12) C27—C26—H26 121.0 N5—C7—C6 119.80 (13) C25—C26—H26 121.0 C15—C7—C6 128.29 (13) N3—C28—H27A 109.5 C9—C8—C13 119.92 (15) N3—C28—H27B 109.5 C9—C8—N4 120.33 (14) H27A—C28—H27B 109.5 C13—C8—N4 119.74 (14) N3—C28—H27C 109.5 C8—C9—C10 119.34 (18) H27A—C28—H27C 109.5 C8—C9—H9 120.3 H27B—C28—H27C 109.5 C10—C9—H9 120.3 O3—C29—N3 124.73 (14) C11—C10—C9 120.95 (19) O3—C29—C21 126.96 (13) C11—C10—H10 119.5 N3—C29—C21 108.23 (12) C9—C10—H10 119.5 C38—C30—C31 106.51 (11) C12—C11—C10 119.30 (17) C38—C30—C16 112.90 (11) C12—C11—H11 120.4 C31—C30—C16 110.79 (11) C10—C11—H11 120.4 C38—C30—C21 115.00 (11) C11—C12—C13 121.15 (18) C31—C30—C21 108.62 (10) C11—C12—H12 119.4 C16—C30—C21 103.01 (10) C13—C12—H12 119.4 O2—C31—C32 121.27 (13) C12—C13—C8 119.34 (17) O2—C31—C30 122.10 (13) C12—C13—H13 120.3 C32—C31—C30 116.62 (12) C8—C13—H13 120.3 C37—C32—C33 118.30 (15) N4—C14—C15 108.14 (13) C37—C32—C31 120.90 (13) N4—C14—H14 125.9 C33—C32—C31 120.78 (15) C15—C14—H14 125.9 C34—C33—C32 120.66 (19) C14—C15—C7 104.05 (12) C34—C33—H32 119.7 C14—C15—C16 126.24 (13) C32—C33—H32 119.7 sup-8 Acta Cryst. Special details (2013). E69, o317 sup-6 supporting information N4 0.0362 (6) 0.0417 (6) 0.0339 (6) −0.0146 (5) 0.0054 (5) −0.0159 (5) N5 0.0361 (6) 0.0444 (6) 0.0343 (6) −0.0156 (5) 0.0079 (5) −0.0150 (5) O1 0.0319 (5) 0.0426 (5) 0.0525 (6) −0.0097 (4) 0.0006 (5) −0.0188 (5) O2 0.0417 (6) 0.0613 (7) 0.0626 (8) −0.0254 (5) 0.0011 (5) −0.0304 (6) O3 0.0546 (7) 0.0542 (6) 0.0554 (7) −0.0307 (6) 0.0112 (6) −0.0284 (6) Geometric parameters (Å, º) C1—C2 1.383 (2) C20—H20A 0.9700 C1—C6 1.385 (2) C20—H20B 0.9700 C1—H1 0.9300 C21—N1 1.4645 (18) C2—C3 1.369 (3) C21—C22 1.518 (2) C2—H2 0.9300 C21—C29 1.5548 (19) C3—C4 1.377 (3) C21—C30 1.5998 (18) C3—H3 0.9300 C22—C23 1.380 (2) C4—C5 1.376 (3) C22—C27 1.395 (2) C4—H4 0.9300 C23—C24 1.387 (2) C5—C6 1.385 (2) C23—H23 0.9300 C5—H5 0.9300 C24—C25 1.373 (2) C6—C7 1.475 (2) C24—H24 0.9300 C7—N5 1.3354 (18) C25—C26 1.379 (3) C7—C15 1.4146 (19) C25—H25 0.9300 C8—C9 1.369 (2) C26—C27 1.372 (2) C8—C13 1.380 (2) C26—H26 0.9300 C8—N4 1.4137 (18) C28—N3 1.446 (2) C9—C10 1.385 (2) C28—H27A 0.9600 C9—H9 0.9300 C28—H27B 0.9600 C10—C11 1.364 (3) C28—H27C 0.9600 C10—H10 0.9300 C29—O3 1.2157 (18) C11—C12 1.356 (3) C29—N3 1.3553 (19) C11—H11 0.9300 C30—C38 1.5204 (19) C12—C13 1.380 (2) C30—C31 1.5305 (18) C12—H12 0.9300 C31—O2 1.2136 (17) C13—H13 0.9300 C31—C32 1.476 (2) C14—N4 1.3465 (18) C32—C37 1.387 (2) C14—C15 1.365 (2) C32—C33 1.397 (2) C14—H14 0.9300 C33—C34 1.376 (3) C15—C16 1.4952 (19) C33—H32 0.9300 C16—C17 1.5519 (19) C34—C35 1.380 (3) C16—C30 1.5678 (18) C34—H33 0.9300 C16—H16 0.9800 C35—C36 1.374 (3) C17—N1 1.4587 (19) C35—H34 0.9300 C17—C18 1.519 (2) C36—C37 1.387 (2) C17—H17 0.9800 C36—H35 0.9300 C18—C19 1.502 (3) C37—O1 1.3595 (17) C18—H18A 0.9700 C38—O1 1.4311 (17) C18—H18B 0.9700 C38—H37A 0.9700 C19—C20 1.486 (3) C38—H37B 0.9700 N4 0.0362 (6) 0.0417 (6) 0.0339 (6) −0.0146 (5) 0.0054 (5) −0.0159 (5) N5 0.0361 (6) 0.0444 (6) 0.0343 (6) −0.0156 (5) 0.0079 (5) −0.0150 (5) O1 0.0319 (5) 0.0426 (5) 0.0525 (6) −0.0097 (4) 0.0006 (5) −0.0188 (5) O2 0.0417 (6) 0.0613 (7) 0.0626 (8) −0.0254 (5) 0.0011 (5) −0.0304 (6) O3 0.0546 (7) 0.0542 (6) 0.0554 (7) −0.0307 (6) 0.0112 (6) −0.0284 (6) sup-7 Acta Cryst. (2013). E69, o317 supporting information supporting information (2013). E69, o317 supporting information supporting information pp g C7—C15—C16 129.14 (13) C33—C34—C35 119.85 (17) C15—C16—C17 110.44 (11) C33—C34—H33 120.1 C15—C16—C30 117.73 (11) C35—C34—H33 120.1 C17—C16—C30 105.55 (10) C36—C35—C34 120.85 (18) C15—C16—H16 107.6 C36—C35—H34 119.6 C17—C16—H16 107.6 C34—C35—H34 119.6 C30—C16—H16 107.6 C35—C36—C37 119.11 (19) N1—C17—C18 104.84 (12) C35—C36—H35 120.4 N1—C17—C16 106.34 (11) C37—C36—H35 120.4 C18—C17—C16 114.24 (13) O1—C37—C32 121.25 (13) N1—C17—H17 110.4 O1—C37—C36 117.52 (15) C18—C17—H17 110.4 C32—C37—C36 121.23 (15) C16—C17—H17 110.4 O1—C38—C30 113.00 (11) C19—C18—C17 103.82 (13) O1—C38—H37A 109.0 C19—C18—H18A 111.0 C30—C38—H37A 109.0 C17—C18—H18A 111.0 O1—C38—H37B 109.0 C19—C18—H18B 111.0 C30—C38—H37B 109.0 C17—C18—H18B 111.0 H37A—C38—H37B 107.8 H18A—C18—H18B 109.0 C17—N1—C21 106.82 (11) C20—C19—C18 106.76 (15) C17—N1—C20 108.47 (12) C20—C19—H19A 110.4 C21—N1—C20 120.70 (12) C18—C19—H19A 110.4 C26—C27—C22 122.34 (15) C20—C19—H19B 110.4 C26—C27—N3 127.43 (14) C18—C19—H19B 110.4 C22—C27—N3 110.23 (13) H19A—C19—H19B 108.6 C29—N3—C27 111.44 (12) N1—C20—C19 106.76 (14) C29—N3—C28 123.50 (14) N1—C20—H20A 110.4 C27—N3—C28 125.06 (14) C19—C20—H20A 110.4 C14—N4—N5 111.74 (11) N1—C20—H20B 110.4 C14—N4—C8 126.92 (12) C19—C20—H20B 110.4 N5—N4—C8 121.34 (12) H20A—C20—H20B 108.6 C7—N5—N4 104.48 (11) N1—C21—C22 112.43 (11) C37—O1—C38 112.91 (11) C6—C1—C2—C3 0.0 (3) N1—C21—C30—C16 16.80 (13) C1—C2—C3—C4 1.8 (3) C22—C21—C30—C16 146.76 (12) C2—C3—C4—C5 −1.9 (4) C29—C21—C30—C16 −95.07 (12) C3—C4—C5—C6 0.2 (3) C38—C30—C31—O2 −153.47 (14) C4—C5—C6—C1 1.6 (3) C16—C30—C31—O2 −30.33 (18) C4—C5—C6—C7 −177.19 (17) C21—C30—C31—O2 82.13 (16) C2—C1—C6—C5 −1.7 (2) C38—C30—C31—C32 27.90 (16) C2—C1—C6—C7 177.10 (15) C16—C30—C31—C32 151.04 (12) C5—C6—C7—N5 −37.9 (2) C21—C30—C31—C32 −96.50 (13) C1—C6—C7—N5 143.31 (14) O2—C31—C32—C37 −179.59 (14) C5—C6—C7—C15 134.98 (17) C30—C31—C32—C37 −0.94 (19) C1—C6—C7—C15 −43.8 (2) O2—C31—C32—C33 −1.3 (2) C13—C8—C9—C10 0.1 (3) C30—C31—C32—C33 177.34 (13) N4—C8—C9—C10 −179.90 (16) C37—C32—C33—C34 −0.6 (2) C8—C9—C10—C11 −0.4 (3) C31—C32—C33—C34 −178.92 (16) sup-9 Acta Cryst. (2013). supporting information E69, o317 supporting information pp g C9—C10—C11—C12 0.8 (3) C32—C33—C34—C35 0.2 (3) C10—C11—C12—C13 −0.8 (3) C33—C34—C35—C36 0.3 (3) C11—C12—C13—C8 0.5 (3) C34—C35—C36—C37 −0.3 (3) C9—C8—C13—C12 −0.2 (2) C33—C32—C37—O1 −178.60 (13) N4—C8—C13—C12 179.84 (15) C31—C32—C37—O1 −0.3 (2) N4—C14—C15—C7 −1.22 (15) C33—C32—C37—C36 0.6 (2) N4—C14—C15—C16 −173.21 (13) C31—C32—C37—C36 178.93 (14) N5—C7—C15—C14 1.20 (16) C35—C36—C37—O1 179.05 (16) C6—C7—C15—C14 −172.17 (14) C35—C36—C37—C32 −0.2 (3) N5—C7—C15—C16 172.87 (13) C31—C30—C38—O1 −57.50 (14) C6—C7—C15—C16 −0.5 (2) C16—C30—C38—O1 −179.31 (10) C14—C15—C16—C17 57.39 (18) C21—C30—C38—O1 62.87 (15) C7—C15—C16—C17 −112.57 (15) C18—C17—N1—C21 156.51 (12) C14—C15—C16—C30 −63.88 (18) C16—C17—N1—C21 35.16 (14) C7—C15—C16—C30 126.16 (15) C18—C17—N1—C20 24.96 (16) C15—C16—C17—N1 −151.63 (12) C16—C17—N1—C20 −96.39 (14) C30—C16—C17—N1 −23.37 (14) C22—C21—N1—C17 −167.23 (11) C15—C16—C17—C18 93.24 (15) C29—C21—N1—C17 84.06 (13) C30—C16—C17—C18 −138.51 (13) C30—C21—N1—C17 −32.52 (13) N1—C17—C18—C19 −30.83 (17) C22—C21—N1—C20 −42.87 (17) C16—C17—C18—C19 85.18 (17) C29—C21—N1—C20 −151.58 (13) C17—C18—C19—C20 25.5 (2) C30—C21—N1—C20 91.84 (14) C18—C19—C20—N1 −10.8 (2) C19—C20—N1—C17 −9.05 (19) N1—C21—C22—C23 71.02 (19) C19—C20—N1—C21 −132.63 (16) C29—C21—C22—C23 −178.92 (15) C25—C26—C27—C22 0.5 (2) C30—C21—C22—C23 −56.3 (2) C25—C26—C27—N3 −179.74 (15) N1—C21—C22—C27 −103.33 (14) C23—C22—C27—C26 −1.3 (2) C29—C21—C22—C27 6.73 (14) C21—C22—C27—C26 174.04 (14) C30—C21—C22—C27 129.33 (13) C23—C22—C27—N3 178.97 (13) C27—C22—C23—C24 0.9 (2) C21—C22—C27—N3 −5.73 (16) C21—C22—C23—C24 −172.97 (15) O3—C29—N3—C27 179.58 (14) C22—C23—C24—C25 0.1 (2) C21—C29—N3—C27 2.63 (16) C23—C24—C25—C26 −0.8 (3) O3—C29—N3—C28 0.7 (3) C24—C25—C26—C27 0.5 (3) C21—C29—N3—C28 −176.27 (15) N1—C21—C29—O3 −65.80 (18) C26—C27—N3—C29 −177.82 (16) C22—C21—C29—O3 177.48 (15) C22—C27—N3—C29 1.94 (18) C30—C21—C29—O3 47.92 (19) C26—C27—N3—C28 1.1 (3) N1—C21—C29—N3 111.05 (13) C22—C27—N3—C28 −179.19 (16) C22—C21—C29—N3 −5.66 (14) C15—C14—N4—N5 0.90 (16) C30—C21—C29—N3 −135.22 (12) C15—C14—N4—C8 −179.04 (13) C15—C16—C30—C38 2.92 (16) C9—C8—N4—C14 167.31 (15) C17—C16—C30—C38 −120.84 (12) C13—C8—N4—C14 −12.7 (2) C15—C16—C30—C31 −116.44 (13) C9—C8—N4—N5 −12.6 (2) C17—C16—C30—C31 119.80 (12) C13—C8—N4—N5 167.32 (13) C15—C16—C30—C21 127.57 (12) C15—C7—N5—N4 −0.67 (15) C17—C16—C30—C21 3.80 (13) C6—C7—N5—N4 173.33 (12) N1—C21—C30—C38 140.06 (11) C14—N4—N5—C7 −0.13 (15) C22—C21—C30—C38 −89.97 (15) C8—N4—N5—C7 179.82 (12) sup-10 Acta Cryst. (2013). E69, o317 supporting information C29—C21—C30—C38 28.19 (16) C32—C37—O1—C38 −28.68 (19) N1—C21—C30—C31 −100.74 (12) C36—C37—O1—C38 152.08 (14) C22—C21—C30—C31 29.23 (16) C30—C38—O1—C37 59.83 (15) C29—C21—C30—C31 147.40 (11) Hydrogen-bond geometry (Å, º) D—H···A D—H H···A D···A D—H···A C34—H33···O3i 0.93 2.59 3.523 (3) 178 Symmetry code: (i) x, y+1, z. supporting information sup-11 Acta Cryst. (2013). E69, o317
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English
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Defining the Scope of Antimicrobial Stewardship Interventions on the Prescription Quality of Antibiotics for Surgical Intra-Abdominal Infections
Antibiotics
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8,445
Defining the Scope of Antimicrobial Stewardship Interventions on the Prescription Quality of Antibiotics for Surgical Intra-Abdominal Infections Ulrich Vogel 1,2, Armin Wiegering 3 , Christoph-Thomas Germer 3 and Johan Friso Lock 3 Güzin Surat 1,*, Ulrich Vogel 1,2, Armin Wiegering 3 , Christoph-Thomas Germer 3 and Jo 1 Department of Infection Control and Antimicrobial Stewardship, University Hospital of Würzbu 97080 Würzburg, Germany; vogel_u@ukw.de 2 Institute of Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany 3 Department of General-, Visceral-, Transplant-, Vascular- and Paediatric Surgery, University Hospital of Würzburg, 97080 Würzburg, Germany; wiegering_a@ukw.de (A.W.); germer_c@ukw.de (C.-T.G.); lock_j@ukw.de (J.F.L.) * Correspondence: surat g@ukw de 1 Department of Infection Control and Antimicrobial Stewardship, University Hospital of Würzburg 97080 Würzburg, Germany; vogel_u@ukw.de 1 Department of Infection Control and Antimicrobial Stewardship, University Hospital of Würzbur 97080 Würzburg, Germany; vogel_u@ukw.de 2 Institute of Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany 3 Department of General-, Visceral-, Transplant-, Vascular- and Paediatric Surgery, University Hospital of Würzburg, 97080 Würzburg, Germany; wiegering_a@ukw.de (A.W.); germer_c@ukw.de (C.-T.G.); lock_j@ukw.de (J.F.L.) * Correspondence: surat g@ukw.de g ( ) j * Correspondence: surat_g@ukw.de Abstract: Background: The aim of this study was to assess the impact of antimicrobial stewardship interventions on surgical antibiotic prescription behavior in the management of non-elective surgical intra-abdominal infections, focusing on postoperative antibiotic use, including the appropriateness of indications. Methods: A single-center quality improvement study with retrospective evaluation of the impact of antimicrobial stewardship measures on optimizing antibacterial use in intra-abdominal infections requiring emergency surgery was performed. The study was conducted in a tertiary hospital in Germany from January 1, 2016, to January 30, 2020, three years after putting a set of antimicrobial stewardship standards into effect. Results: 767 patients were analyzed (n = 495 in 2016 and 2017, the baseline period; n = 272 in 2018, the antimicrobial stewardship period). The total days of therapy per 100 patient days declined from 47.0 to 42.2 days (p = 0.035). The rate of patients receiving postoperative therapy decreased from 56.8% to 45.2% (p = 0.002), comparing both periods. There was a significant decline in the rate of inappropriate indications (17.4% to 8.1 %, p = 0.015) as well as a significant change from broad-spectrum to narrow-spectrum antibiotic use (28.8% to 6.5%, p ≤0.001) for postoperative therapy. The significant decline in antibiotic use did not affect either clinical outcomes or the rate of postoperative wound complications. Conclusions: Postoperative antibiotic use for intra-abdominal infections could be significantly reduced by antimicrobial stewardship interventions.   Citation: Surat, G.; Vogel, U.;Wiegering, A.; Germer, C.-T.; Lock, J.F. Defining the Scope of Antimicrobial Stewardship Interventions’ on the Prescription Quality of Antibiotics for Surgical Intra- Abdominal Infections. Antibiotics 2021, 10, 73. https://doi.org/10.3390/ antibiotics10010073 Keywords: antimicrobial stewardship; antibiotic prescription behavior; surgical intra-abdominal infections; post-operative antibiotic treatment Received: 29 December 2020 Accepted: 11 January 2021 Published: 14 January 2021 Received: 29 December 2020 Accepted: 11 January 2021 Published: 14 January 2021 Publisher’s Note: MDPI stays neu- tral with regard to jurisdictional clai- ms in published maps and institutio- nal affiliations. Defining the Scope of Antimicrobial Stewardship Interventions on the Prescription Quality of Antibiotics for Surgical Intra-Abdominal Infections The identification of inappropriate indications remains a key target for antimicrobial stewardship programs. antibiotics antibiotics antibiotics antibiotics antibiotics 1. Introduction Antimicrobial resistance (AMR) has become a global health threat and affects us all in a way no one could have imagined when the discovery of penicillin in 1928 caught public attention [1]. With the emergence of antimicrobial resistance, antimicrobial stewardship programs (ASPs) started evolving, aiming to combat this menace and promote the rational use of antibiotics. By reducing the adverse events and infections caused by multidrug-resistant bacteria (MDR), ASPs strive to optimize patient management and improve patient out- comes, globally supported by government policy interventions [2,3]. In 2011, the German parliament (Bundestag) amended the German Act on the Prevention and Control of Infec- tious Diseases (Infektionsschutzgesetz §23) [4] as a response to the medical (and social) crisis inflicted by the alarming loss of efficacy of antimicrobials induced by the inexorable spread of MDR. With no doubt, antibiotics, when appropriately prescribed, can help to save Copyright: © 2021 by the authors. Li- censee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and con- ditions of the Creative Commons At- tribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). https://www.mdpi.com/journal/antibiotics Antibiotics 2021, 10, 73. https://doi.org/10.3390/antibiotics10010073 Antibiotics 2021, 10, 73 2 of 13 people’s lives and fight infections. However, 30–50 percent of antibiotics prescribed in the United States or Germany are unnecessary or incorrect in terms of drug choice, duration or dosing and hence avoidable [5,6]. The responsibility for antibiotic (mis)use is primarily placed on the prescriber but driven and influenced by multiple factors. A substantial lack of knowledge is, by far, the most important element, but cultural, social and socio-economic reasons play their part, too, and nurture a certain prescribing manner in hospitals [7]. Intra-abdominal infections (IAIs) are a major cause of morbidity and mortality and require timely, mannered, optimal handling: adequate source control goes hand in hand with an appropriate selection of antimicrobials [8]. To advocate the more prudent use of antimicro- bial agents in the context of intra-abdominal infections, even a global alliance (AGORA) has been formed [9], and yet, antimicrobial stewardship initiatives for the treatment for IAIs remain sparse [10]. The choice of antibiotics and durations following surgical procedures in our hospital, including for emergency indications, has varied depending on the surgeons responsible for the undertaken procedures and has not always complied with existing guidelines [11,12]. The absence of documented reasons for antibiotic prescriptions are another aspect that warrant clearer evaluation and require action. 2. Methods This quality improvement study encompassed a period of 3 years (2016–2018) and was retrospectively conducted in a 1500-bed-sized tertiary hospital in Germany, with an in-hospital ASP officially launched in 2015, gradually reaching out to all departments including the department of general surgery by 2018. 1. Introduction Different antimicrobial stewardship strategies and core elements such as antibiotic ward rounds, facility-specific antibiotic-prescribing guidelines, educational programs and the surveillance of antimicro- bial use and resistance have been either introduced or intensified. We hypothesized that the continued implementation of antimicrobial stewardship standards would eventually optimize the prescription culture and decrease inappropriate antibiotic use in surgically managed intra-abdominal infections. 2.2. Patients All patients ≥18 years old undergoing emergency abdominal surgery with sus- pected IAIs between 01.01.2016 and 31.12.2018 were included with the following selection criteria: diagnosis of peritonitis (ICD-10 K65.0–K65.9), acute cholecystitis (ICD-10 K80.0– K80.01, K81.0), acute appendicitis (ICD-10 K35.2–K35.8), acute diverticulitis (ICD-10 K57.2– K57.22), intestinal perforation (K25.1–K25.2, K26.1–K26.2, K63.0–K63.2) or obstructive ileus (ICD-10 K56.5-K56.7). Patients with the following criteria were excluded from analysis: acute pancreatitis, acute mesenteric ischemia, acute leukemia, end-stage malignant disease in palliative care, an ASA score > IV, or an extra-abdominal infectious focus requiring antimicrobial therapy before and after surgery. 2.1. Study Design The effects of the implementation of a local ASP on the management of IAIs were examined by a retrospective cohort analysis. The years 2016 and 2017 are referred to as the “baseline period” (before the implementation of ASP in general surgery), and the year 2018, as the “ASP period”. The primary endpoint was defined as the total days on antibiotic therapy for intra- abdominal infections. The secondary endpoints included the appropriateness (indica- tion and documentation) of the postoperative antibiotic therapy (PAT), the empiric selection of antibiotics and the frequency of antibiotic changes. 2.4. Antimicrobial Stewardship The university hospital of Würzburg (UKW) officially launched an ASP in July 2015 complying with national and international guidelines on the implementation of ASPs in hospitals [17,18]. An antimicrobial stewardship (AMS) committee was instructed to orga- nize and coordinate the efforts needed to minimize the misuse of antibiotic prescriptions and promote evidence-based prescribing in order to reduce antimicrobial resistance and improve patients’ outcomes and safety. The first task put forward by the AMS core group was to set up regular ward rounds first in all intensive care and intermediate care units, extended to all surgical and medical wards over time, including the hospital’s biggest surgical department, where the study took place. The introduction of both the surveillance data on antimicrobial resistance and antibiotic consumption rate measured by the recom- mended daily doses per 100 patient days (RDD/100PD) for the hospital as a whole as well as for each department/unit was formally initiated. The formulary restriction of specific antibiotics (e.g., tigecycline and colistin), the creation of selective antibiotic resistogram profiles, the implementation and electronic access to antimicrobial prescribing guidelines, and mobile applications are further strategies that were gradually enforced between 2016 and 2017, still being in place. Before the implementation of an internal ASP, hospital-specific guidelines neither on IAIs nor on PAP were available, so antibiotic usage varied depending on the surgeon’s judgment and general practice of the department. Along with the antibi- otic ward rounds, the AMS core group finalized, in May 2017, the hospital’s most extensive standard treatment guidelines on PAP. In accordance with the current effective clinical practice guidelines for antimicrobial prophylaxis [19], the standard prophylactic regime changed from cefuroxime to cefazolin (depending on the procedure, it may differ). Further targets involved following antibiotic groups: the increasing resistance worldwide to car- bapenems among Pseudomonas aerugionsa and Enterobacterales is alarming [20], and given our susceptibility data showing 25% resistance of Pseudomonas aeruginosa to meropenem and the latter’s high utilization in the hospital and general surgical units, AMS strived to reduce its usage. Antibiotics belonging to the fluoroquinolones (FQs) and third-generation cephalosporins are linked to a rising prevalence of resistance amongst Enterobacterales too (e.g., ESBL) and share potent side effects such as C. difficile infections [5,21]. Our antimi- crobial resistance data reflecting > 30% resistance of E. 2.4. Antimicrobial Stewardship coli to FQs such as ciprofloxacin (CIP) made the AMS committee finally promote a drastic change in our hospital’s general antibiotic policy, also affecting the department of general surgery. 2.3. Analyzed Variables and Definitions All data were retrieved from the hospital information system and were transferred into a pseudonymous database with multiple variables containing the baseline patient charac- teristics (e.g., age, gender, indication for surgery, comorbidities and previous surgery); pre-, Antibiotics 2021, 10, 73 3 of 13 3 of 13 peri- and postoperative antibiotic therapy (e.g., the choice of agent, duration of therapy, doc- umented indication, and surgical recommendations for postoperative antibiotic therapy); surgical therapy (e.g., the duration of surgery, the severity of peritonitis, and definitive surgical source control); and postoperative 30-day outcomes (e.g., postoperative transfer, postoperative organ failure, re-intervention, postoperative complications and the length of the hospital stay). The severity of peritonitis was staged according to the Mannheim Peritonitis Index (MPI) [13]. Sepsis was defined according to the international consensus definition [14]. Surgical recommendations concerning PAT were collected from the op- eration protocol. A documented reason for the prescription of antibiotics (e.g., PAT for diffuse peritonitis) found in either the operation protocol or patients’ electronic records was counted as a “documented indication”. The assessments of the appropriateness of antibi- otic therapy were reviewed case by case by two experts, based on the in-house protocol for antimicrobial surgical prophylaxis and international guidelines on IAIs [8,11], complying with the local surveillance data on antibiotic use and resistance. Postoperative complica- tions were graded according to Clavien and Dindo [15]. Surgical site infections (SSI) were defined according to Centers for Disease Control and Prevention (CDC) criteria [16]. 2.5. Statistical Analysis All statistical analyses were performed using IBM SPSS Statistics, version 26 (Inter- national Business Machines Corporation, Armonk, NY). Descriptive data are reported Antibiotics 2021, 10, 73 4 of 13 as means with standard deviations, unless otherwise noted. Comparisons between the analyzed timeframes were performed using chi-square, Fisher’s exact or Mann–Whitney U tests, in accordance with the data scale and distribution. The level of statistical significance was 0.05 (two-sided). The UKW participates in one of the national surveillance projects on antibiotic consumption (ADKA-if-DGI), and antimicrobial use (RDD/100PD) data were provided by its twice-yearly-released surveillance report. 3. Results 3.1. Patients’ Baseline Characteristics and Indications for Emergency Surgery 3.1. Patients’ Baseline Characteristics and Indications for Emergency Surgery A total of 767 patients were analyzed (n = 495 during the baseline period; n = 272 dur- ing the ASP period). The preoperative patient characteristics are provided in Table 1 and show comparable patient characteristics except for the incidence of immunosuppressive drugs, which was significantly higher in the ASP period. The indications for emergency surgery and the surgical details including postoperative transfers are provided in Table 2. Several differences between the two periods were observed: Firstly, while the rate of acute cholecystitis decreased from 30.5% to 18.0%, the rate of intestinal obstructions in- creased from 6.1% to 20.2%. All the other sources of IAIs remained unaltered. Secondly, the incidence of peritonitis increased from 33.9% to 44.9% with higher MPIs. Table 1. Preoperative patient characteristics. Patients, No. (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Sex ratio (M:F) 411:356 268:227 143:129 0.68 Age, mean (range), y 53.3 (18–96) 52.6 (18–96) 54.5 (18–89) 0.21 Body weight, mean (SD), kg 80.4 (20.8) 79.9 (19.8) 81.4 (22.4) 0.70 BMI, mean (SD) 27.0 (6.3) 26.8 (5.8) 27.5 (7.1) 0.79 Chronic kidney disease 75 (9.8) 54 (10.9) 21 (7.7) 0.16 Liver cirrhosis 11 (1.4) 6 (1.2) 5 (1.8) 0.49 Current immunosuppressive drugs 50 (6.5) 24 (4.8) 26 (9.6) 0.011 ASA classification I 107 (14.0) 65 (13.1) 42 (15.4) 0.22 II 355 (46.3) 234 (47.3) 121 (44.5) III 220 (28.7) 140 (28.3) 80 (29.4) IV 78 (10.2) 54 (10.9) 24 (8.8) CCI 0 273 (35.6) 185 (37.4) 88 (32.4) 0.28 1–2 162 (21.1) 93 (18.8) 69 (25.4) 3–4 170 (22.2) 120 (24.2) 50 (18.4) >4 162 (21.1) 97 (19.6) 65 (23.9) Community-acquired IAI 602 (78.5) 379 (76.6) 223 (82.0) 0.081 Hospital-acquired IAI 165 (21.5) 116 (23.4) 49 (18.0) Preoperative a LOS, mean (SD), d 1.8 (4.3) 1.9 (4.6) 1.5 (3.7) 0.13 Surgery 118 (15.4) 78 (15.8) 40 (14.7) 0.70 Table 1. Preoperative patient characteristics. Antibiotics 2021, 10, 73 5 of 13 Table 1. Cont. Patients, No. 3.1. Patients’ Baseline Characteristics and Indications for Emergency Surgery (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Antibiotic therapy 134 (17.5) 85 (17.2) 49 (18.0) 0.77 Duration ABT, mean (SD), d 6.7 (5.8) 6.6 (5.6) 7.0 (6.3) 0.56 MDR 51 (6.6) 25 (5.1) 26 (9.6) 0.017 a within 30 days prior to index surgery; Abbreviations: ASP, antimicrobial stewardship program; y, years; d, days; ASA, American Society of Anesthesiologists; BMI, body mass index; CCI, Charlson comorbidity index; IAI, intra- abdominal infection; LOS, length of hospital stay; ABT, antibiotic therapy; MDR, multidrug-resistant bacteria. Table 1. Cont. a within 30 days prior to index surgery; Abbreviations: ASP, antimicrobial stewardship program; y, years; d, days; ASA, American Society of Anesthesiologists; BMI, body mass index; CCI, Charlson comorbidity index; IAI, intra- abdominal infection; LOS, length of hospital stay; ABT, antibiotic therapy; MDR, multidrug-resistant bacteria. Table 2. Intra-abdominal infections and surgical details. Patients, No. (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Time from indication to surgery, mean (median, SD), h 6.6 (4.0, 6.4) 6.6 (4.4, 6.5) 6.5 (4.0, 6.2) 0.97 Indication for surgery Appendicitis 293 (38.2) 190 (38.4) 103 (37.9) <0.001 Cholecystitis 200 (26.1) 151 (30.5) 49 (18.0) Diverticulitis 26 (3.4) 15 (3.0) 11 (4.0) Primary perforation a 86 (11.2) 55 (11.1) 31 (11.4) Postoperative leakage 70 (9.1) 49 (9.9) 21 (7.7) Intestinal obstruction 85 (11.1) 30 (6.1) 55 (20.2) Abscess 7 (0.9) 5 (1.0) 2 (0.7) Duration of surgery, mean (SD), min 91 (54) 91.9 (55.0) 90.4 (52.3) 0.61 Peritonitis 290 (37.8) 168 (33.9) 122 (44.9) 0.003 MPI b 18.3 (10.4) 17.3 (8.7) 19.7 (8.8) 0.030 Sepsis 112 (14.6) 77 (15.6) 35 (12.9) 0.31 Definitive source control 713 (93.0) 461 (93.1) 252 (92.6) 0.80 Postoperative transfer General ward 398 (51.9) 256 (51.7) 142 (52.2) 0.44 IMC 88 (11.5) 52 (10.5) 36 (13.2) ICU 281 (36.6) 187 (37.8) 94 (34.6) a hollow viscous perforation or injury except appendicitis or diverticulitis; b of patients with peritonitis; Abbrevi- ations: ASP, antimicrobial stewardship program; MPI, Mannheim peritonitis index; ABT, antibiotic therapy; IMC, intermediate care unit; ICU, intensive care unit. a hollow viscous perforation or injury except appendicitis or diverticulitis; b of patients with peritonitis; Abbrevi- ations: ASP, antimicrobial stewardship program; MPI, Mannheim peritonitis index; ABT, antibiotic therapy; IMC, intermediate care unit; ICU, intensive care unit. 3.2. Impact on Prescription Behavior 3.2. Impact on Prescription Behavior An overall reduction in the total days on antibiotic therapy (ABT) from a mean of 6.1 days to 4.8 days (p = 0.02) was noted in the ASP period, decreasing the days of therapy per 100 patient days (DOT/100PD) from 47.0 to 42.2 (p = 0.035). Details on the perioperative prescription of antibiotics and AMS assessments are provided in Table 3. The distribution of the antibiotic agents during pre-, peri- and postoperative ABT is shown in Figure 1. The significant decrease in the total antibiotic use (RDD/100PD) in the general surgery department is displayed in Figures 1 and 2. Antibiotics 2021, 10, 73 6 of 13 Table 3. Antibiotic therapy of intra-abdominal infections. Table 3. Antibiotic therapy of intra-abdominal infections. Patients, No. a according to the operation protocol to continue ABT after surgery; b documented indication for PAT within pa- tient records; c of those patients without PAT; d including perioperative prophylaxis; d, days; Abbreviations: ASP, antimicrobial stewardship program; ABT, antibiotic therapy; AMS, antimicrobial stewardship; EAT, empiric antibi- otic therapy; PAT, postoperative antibiotic therapy; SAM, ampicillin–sulbactam; CFZ, cefazolin; CXM, cefuroxime; CRO, ceftriaxone; TZP, piperacillin–tazobactam; IPM, imipenem; MEM, meropenem; CIP, ciprofloxacin; MXF, moxifloxacin; MTZ, metronidazole. 3.2. Impact on Prescription Behavior (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Total days on ABT, mean (median, SD), d 5.7 (3, 6.9) 6.1 (3, 7.0) 4.8 (1, 6.8) 0.02 Switches during ABT None 427 (55.7) 257 (51.9) 170 (62.5) 0.017 1 224 (29.2) 151 (30.5) 73 (26.8) >1 116 (15.2) 87 (17.5) 29 (10.6) Time from indication to ABT, mean (median, SD), h 3.6 (2.0, 4.8) 3.6 (3, 4.5) 3.7 (2, 5.4) 0.12 Surgeons’ recommendations a Missing 430 (56.1) 277 (56.0) 153 (56.3) <0.001 PAT 312 (40.7) 212 (42.8) 100 (36.8) No PAT 25 (3.3) 6 (1.2) 19 (7.0) Postoperative antibiotic therapy 404 (52.7) 281 (56.8) 123 (45.2) 0.002 Documented indication b 93 (12.1) 61 (12.3) 32 (11.8) 0.81 Duration, mean (SD), d 7.7 (5.6) 8.1 (5.7) 7.2 (5.4) 0.08 EAT CFZ 51 (12.6) 12 (4.3) 39 (31.7) <0.001 CXM 91 (22.5) 84 (29.9) 7 (5.7) CRO 60 (14.9) 52 (18.5) 8 (6.5) TZP 108 (26.7) 68 (24.2) 40 (32.5) IPM/MEM 66 (16.3) 46 (16.4) 20 (16.3) CIP/MXF 14 (3.5) 11 (3.9) 3 (2.4) Other 8 (1.9) 6 (2.1) 2 (1.6) Additional MTZ 224 (55.4) 164 (58.4) 60 (48.8) 0.01 AMS assessment of PAT No indication 59 (14.6) 49 (17.4) 10 (8.1) 0.015 Missing PAT c 24 (6.6) 12 (5.6) 12 (8.1) 0.36 Too long 184 (45.5) 135 (48.0) 49 (39.8) 0.038 Too short 2 (0.5) 0 2 (1.6) Too broad 89 (22.0) 81 (28.8) 8 (6.5) <0.001 Too narrow 75 (18.6) 48 (17.1) 27 (22.0) Mismatch with MTZ d 28 (4.5) 15 (3.7) 13 (6.0) 0.18 Perioperative use of CRO 98 (12.8) 80 (16.2) 18 (6.6) <0.001 Perioperative use of CIP/MXF 61 (8.0) 42 (8.5) 19 (7.0) 0.46 a according to the operation protocol to continue ABT after surgery; b documented indication for PAT within pa- tient records; c of those patients without PAT; d including perioperative prophylaxis; d, days; Abbreviations: ASP, antimicrobial stewardship program; ABT, antibiotic therapy; AMS, antimicrobial stewardship; EAT, empiric antibi- otic therapy; PAT, postoperative antibiotic therapy; SAM, ampicillin–sulbactam; CFZ, cefazolin; CXM, cefuroxime; CRO f TZP ll b IPM MEM CIP fl MXF 7 of 13 7 Antibiotics 2021, 10, 73 iotics 2021, 10, x Antibiotics 2021, 10, 73 7 of 1 , , (A) (B) Figure 1. Comparison of pre-, peri- and postoperative antibiotic therapy (A): Baseline period, 2016–2017; (B): ASP period 2018. 3.2. Impact on Prescription Behavior Abbreviations: Pre, preoperative antibiotic therapy; PAP, perioperative antibiotic prophylaxis; PAT, postoperativ antibiotic therapy; CFZ, cefazolin; CXM, cefuroxime; CRO, ceftriaxone; TZP, piperacillin–tazobactam; IPM, imipenem MEM, meropenem; CIP, ciprofloxacin; MXF, moxifloxacin. Figure 1. Comparison of pre-, peri- and postoperative antibiotic therapy (A): Baseline period, 2016–2017; (B): ASP period, 2018. Abbreviations: Pre, preoperative antibiotic therapy; PAP, perioperative antibiotic prophylaxis; PAT, postoperative antibiotic therapy; CFZ, cefazolin; CXM, cefuroxime; CRO, ceftriaxone; TZP, piperacillin–tazobactam; IPM, imipenem; MEM, meropenem; CIP, ciprofloxacin; MXF, moxifloxacin. (A) (B) Figure 1 Comparison of pre peri and postoperative antibiotic therapy (A): Baseline period 2016 2017; (B): ASP period (B) ure 1. Comparison of pre-, peri- and postoperative antibiotic therapy (A): Baseline period, 2016–2017; (B): ASP peri 8. Abbreviations: Pre, preoperative antibiotic therapy; PAP, perioperative antibiotic prophylaxis; PAT, postopera ibiotic therapy; CFZ, cefazolin; CXM, cefuroxime; CRO, ceftriaxone; TZP, piperacillin–tazobactam; IPM, imipen M, meropenem; CIP, ciprofloxacin; MXF, moxifloxacin. Figure 1. Comparison of pre-, peri- and postoperative antibiotic therapy (A): Baseline period, 2016–2017; (B): ASP period, 2018. Abbreviations: Pre, preoperative antibiotic therapy; PAP, perioperative antibiotic prophylaxis; PAT, postoperative antibiotic therapy; CFZ, cefazolin; CXM, cefuroxime; CRO, ceftriaxone; TZP, piperacillin–tazobactam; IPM, imipenem; MEM, meropenem; CIP, ciprofloxacin; MXF, moxifloxacin. Antibiotics 2021, 10, 73 Antibiotics 2021, 10, x 8 of 13 8 of 13 (A) (B) Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgical ICU/IMC; (B) General surgical wards. Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general sur- gery); carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF 3.3. Postoperative Antibiotic Therapy The rate of patients receiving PAT decreased from 56.8% to 45.2% (p = 0.002) in the ASP period. In addition, the postoperative empiric antibiotic therapy (EAT) significantly changed during the study, with fewer FQs and third-generation cephalosporins, and more fi t ti h l i (T bl 3) Th t f PAT i ifi tl d d i 0 50 100 150 200 2016 2017 2018 RDD/100 Surgical ICU/IMC 1st-/2nd-generation cephalosporins 3rd-/4th-generation cephalosporins borad-spectrum penicillins carbapenems fluoroquinolones 0 50 100 150 200 2016 2017 2018 RDD/100 General surgical wards 1st-/2nd-generation cephalosporins 3rd-/4th-generation cephalosporins broad-spectrum penicillins carbapenems fluoroquinolones Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgical ICU/IMC; (B) General surgical wards. 3.2. Impact on Prescription Behavior Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general surgery) carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF. 3.3. Postoperative Antibiotic Therapy The rate of patients receiving PAT decreased from 56.8% to 45.2% (p = 0.002) in the ASP period. In addition, the postoperative empiric antibiotic therapy (EAT) significantly changed during the study, with fewer FQs and third-generation cephalosporins, and more first generation cephalosporins (Table 3) The rate of PAT significantly decreased in patients 0 50 100 150 200 2016 2017 2018 RDD/100 Surgical ICU/IMC 1st-/2nd-generation cephalosporins 3rd-/4th-generation cephalosporins borad-spectrum penicillins carbapenems fluoroquinolones (A) (B) Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgical ICU/IMC; (B) General surgical wards. Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general sur- gery); carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF 0 50 100 150 200 2016 2017 2018 RDD/100 General surgical wards 1st-/2nd-generation cephalosporins 3rd-/4th-generation cephalosporins broad-spectrum penicillins carbapenems fluoroquinolones Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgica ICU/IMC; (B) General surgical wards. Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general surgery) carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF. (A) 0 50 100 150 200 2016 2017 2018 RDD/100 General surgical wards (A) (B) 1st-/2nd-generation cephalosporins 3rd-/4th-generation cephalosporins broad-spectrum penicillins carbapenems fluoroquinolones (B) Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgical ICU/IMC; (B) General surgical wards. Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general sur- gery); carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF Figure 2. Total antibiotic use in general surgery in RDD/100PD, 2016–2018; (A) General surgical ICU/IMC; (B) General surgical wards. 3.2. Impact on Prescription Behavior Abbreviations: RDD/100, recommended daily doses per 100 patient days; broad-spectrum penicillins = TZP; 3rd-/4th-generation cephalosporins = CRO + CAZ/FEP (ceftazidime = CAZ; cefepime = FEP is hardly used in our hospital or in general surgery); carbapenems = MEM/IPM; fluoroquinolones = CIP/LVX/MXF. 3.3. Postoperative Antibiotic Therapy 3.3. Postoperative Antibiotic Therapy The rate of patients receiving PAT decreased from 56.8% to 45.2% (p = 0.002) in the ASP period. In addition, the postoperative empiric antibiotic therapy (EAT) significantly changed during the study, with fewer FQs and third-generation cephalosporins, and more first-generation cephalosporins (Table 3). The rate of PAT significantly decreased in pa- tients with definitive source control (Table 4). Surgeons’ reported recommendations in the operation protocol resulted in no decrease for antibiotics for PAT. There was no cut in The rate of patients receiving PAT decreased from 56.8% to 45.2% (p = 0.002) in the ASP period. In addition, the postoperative empiric antibiotic therapy (EAT) significantly changed during the study, with fewer FQs and third-generation cephalosporins, and more first-generation cephalosporins (Table 3). The rate of PAT significantly decreased in patients with definitive source control (Table 4). Surgeons’ reported recommendations in the operation protocol resulted in no decrease for antibiotics for PAT. There was no cut in antibiotics with correct indications for PAT either. A trend of change in the duration of PAT Antibiotics 2021, 10, 73 9 of 13 from 8.1 to 7.2 days (p = 0.08) was observed. During the subgroup analysis of indications for surgery, only PAT in cholecystitis was significantly shortened (6.3 ± 3.9 vs. 4.3 ± 2.5; p = 0.014). Interestingly, the number of switches during ABT significantly decreased in the ASP period (Table 3). Table 4. Determining variables in postoperative antibiotic therapy. Postoperative Antibiotic Therapy, No. (%) p Value Characteristic Total (n = 404) Baseline (n = 281) ASP (n = 123) Community-acquired IAI 262 (43.5) 177 (46.7) 85 (38.1) 0.040 Hospital-acquired IAI 142 (86.1) 104 (89.7) 38 (77.6) 0.040 Indication for surgery Appendicitis 102 (34.8) 68 (35.8) 34 (33.0) 0.63 Cholecystitis 102 (51.0) 82 (54.3) 20 (40.8) 0.070 Diverticulitis 25 (96.2) 14 (93.3) 11 (100) 0.38 Primary perforation a 84 (97.7) 54 (98.2) 30 (96.8) 0.68 Postoperative leakage 66 (94.3) 47 (95.9) 19 (90.5) 0.37 Intestinal obstruction 18 (21.2) 11 (36.7) 7 (12.7) 0.010 Abscess 7 (100) 5 (100) 2 (100) Definitive source control 353 (49.5) 247 (53.6) 106 (42.1) 0.020 Peritonitis 252 (86.9) 158 (94.0) 94 (77.0) <0.001 Sepsis 109 (97.3) 76 (98.7) 33 (94.3) 0.18 Surgeons’ recommendations for PAT 299 (95.8) 204 (96.2) 95 (95.0) 0.61 a hollow viscous perforation or injury except appendicitis or diverticulitis; Abbreviations: PAT, postoperative an- tibiotic therapy. Table 4. Determining variables in postoperative antibiotic therapy. 3.3. Postoperative Antibiotic Therapy 3.3. Postoperative Antibiotic Therapy The individual assessments of PAT revealed significantly less inappropriate (no indica- tion) postoperative antibiotic therapy, shortened treatment durations (not significant) and an influence on the choice of antibiotics, with the use of more narrow-spectrum antibiotics. 3.4. Postoperative Outcomes and Complications 3.4. Postoperative Outcomes and Complications Details of the postoperative outcomes and complications are provided in Table 5. No significant differences occurred during the study for any outcome variable. No negative impacts of first- or second-generation cephalosporins in comparison to TZP or IPM/MEM for PAT were observed (results not shown). Even in patients with risk factors such as peritonitis, sepsis or ICU transfer, no negative effects or subsequent changes in the rate of postoperative antibiotics were recorded. In addition, no difference in patient outcomes with adequate surgical source control and treatment with postsurgical CFZ versus CXM was observed. Table 5. Postoperative outcomes and complications. Patients, No. (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Postoperative organ support Vasopressor therapy 195 (25.4) 127 (25.7) 68 (25.0) 0.84 Ventilation 214 (27.9) 135 (27.3) 79 (29.0) 0.60 Dialysis 21 (2.7) 12 (2.4) 9 (3.3) 0.47 Table 5. Postoperative outcomes and complications. Table 5. Postoperative outcomes and complications. 10 of 13 Antibiotics 2021, 10, 73 Table 5. Cont. Patients, No. (%) p Value Characteristic Total (n = 767) Baseline (n = 495) ASP (n = 272) Re-intervention 169 (22.0) 118 (23.8) 51 (18.8) 0.10 Surgery 135 (17.6) 94 (19.0) 41 (15.1) 0.17 Postoperative complications a None 343 (44.7) 211 (42.6) 132 (48.5) 0.14 Minor (Grade I–IIIa) 251 (32.7) 174 (35.2) 77 (28.3) Major (Grade IIIb–V) 173 (22.6) 110 (22.2) 63 (23.3) Mortality (Grade V) 30 (3.9) 18 (3.6) 12 (4.4) 0.60 Surgical site infection 94 (12.3) 62 (12.5) 32 (11.8) 0.76 New MDR 27 (3.5) 13 (2.6) 14 (5.1) 0.07 LOS, mean (SD), d 10.5 (9.0) 10.5 (9.0) 10.4 (9.1) 0.62 No. of days in ICU or IMC, mean (SD), d 4.1 (7.8) 4.1 (7.8) 4.0 (7.8) 0.61 a according to the Clavien–Dindo classification; Abbreviations: ASP, antimicrobial stewardship program imple- mented during 2018; MDR, multidrug-resistant bacteria; LOS, length of hospital stay; d, days; IMC, intermediate care unit; ICU, intensive care unit. Table 5. Cont. a according to the Clavien–Dindo classification; Abbreviations: ASP, antimicrobial stewardship program imple- mented during 2018; MDR, multidrug-resistant bacteria; LOS, length of hospital stay; d, days; IMC, intermediate care unit; ICU, intensive care unit. 4. Discussion To address this matter of the extended continuation of postoperative antibiotics, our AMS team developed hospital-specific guidelines on medical and surgical IAIs, a multidisciplinary effort with the joint participation of the departments of general surgery, hepatology and gastroenterol- ogy. The guidelines’ impact on, for example, the duration of treatment and the efficacy of restricted-duration treatment for postoperative wound complications will be discussed in one of our next papers, including the incompletely resolved issue of the documentation culture of the practitioners. Efficacious postoperative prolongation with narrow-spectrum antibiotics makes the principle of de-escalation unnecessary and demands a comparison to the culture and sensitivity results for those who postoperatively received cefazolin. Post-surgery changes to the broad-spectrum penicillin TZP, the de-escalation rates and the efficacy will also be debated then, along with the change in antimicrobial susceptibil- ity patterns with improved antimicrobial use. There is a lot of debate already regarding the best strategy for implementing or improving antimicrobial stewardship in surgical units, and the data are often inconclusive and contradictory [23,30]. Sartelli and colleagues showed that the implementation of educational programs in a general and emergency surgery unit had a significant impact on the antibacterial consumption rate. The total monthly antimicrobial use decreased by 18.8% (the endpoint was DDD/1000PD) with- out affecting patient outcomes [31]; on the contrary, Knox and Edye were less effective with their educational ASP in changing prescription behavior when targeting surgical prophylaxis [32]. The pros and cons of formulary restriction concepts in comparison to prospective audit and feedback strategies (so-called persuasive initiatives) were the sub- ject of a Cochrane meta-analysis and revealed no advantage for one or the other at 12 or 24 months [33]. Our study is a statement on successfully implemented multifaceted strategies, using all the tools a hospital’s infrastructure may provide, working in an inter- and multidisciplinary manner by collaborating with all departments and encouraging prescribers to participate in and be part of antimicrobial stewardship rather than being bystanders. We are united in one mission: to stop the spread of antimicrobial resistance and to preserve antimicrobials for the prophylaxis and treatment of infections; we know for a fact that antimicrobial stewardship works [34,35] and that antimicrobial resistance is linked to imprudent use [36]. The study has some limitations: it was single centered and the retrospective analysis incorporated a heterogeneous patient sample with uncomplicated and complicated IAIs, either community or hospital acquired. 4. Discussion This quality improvement study analyzed the impact of antimicrobial stewardship measures on the prescribing culture for antibiotics for surgical intra-abdominal infections and took a closer look at the quantity and quality of postoperatively prescribed antibiotics. Antimicrobial therapy for uncomplicated surgical IAIs with no signs of perforation or established infection is seen as prophylactic and not empiric; in consequence, the duration is restricted to a maximum of 24 h. Complicated IAIs with localized or diffuse peritonitis prompt empiric antibiotic therapy and are principally driven by the bacterial flora of the gastrointestinal tract, but without adequate source control, the most potent antibiotics will be administered to no avail [22]. Popovski et al. showed that a multimodal approach of initiating antimicrobial stewardship tools (the availability of a treatment protocol and educational programs) for the anti-infective management of IAIs may influence prescrib- ing habits and significantly decrease the days of therapy for targeted antibiotics [23]. Dubrovskaya and colleagues also developed treatment guidelines for the empiric treatment of complicated IAIs, aiming to decrease the use of ciprofloxacin and ampicillin–sulbactam (endpoint DDD/1000PD) based on the issue of resistance amongst Enterobacterales to the named antibiotics. The data, when compared with the pre-implementation period, showed a significant reduction in targeted antibiotic use, with a sustained improvement in prescribing quality [24]. Our data show similarity in one aspect: we also significantly reduced the total days of ABT (47 to 42.2 DOT/100PD in the ASP period), including a decrease in the post-surgical antibiotics we focused on (e.g., CRO, CIP and MEM/IPM). However, the relevant finding of our study is that the decrease in postsurgical antibiotics was not foiled by a rise in other broad-spectrum antibiotics but was mostly due to a signif- icant reduction in assessed inappropriate indications. It is also worth mentioning again that before and during the intervention period, no local standard for the antimicrobial management of IAIs was available. The other issue that attracted our attention concerned missing recommendations or written documentations of indications for the prescription of antibiotics in either the operation protocol or patients’ electronic records. Unfortunately, the results displayed no significant difference when comparing the pre-intervention and ASP periods. The same is true regarding the continuation of post-surgical antibiotics, although there is a movement towards reduced durations. 4. Discussion Sawyer and colleagues (STOP- IT trial) demonstrated that in patients with achieved source control in complicated IAIs, Antibiotics 2021, 10, 73 11 of 13 11 of 13 the outcomes with a fixed median duration of 4 days (intervention group) were similar to those (control group) treated until vital signs and gastrointestinal continuity had returned (mean of 8 days) [25]. The high rates of postoperative complications in both groups reason- ably raised doubts regarding the rationale for longer durations of antibacterial treatment. More and more data indicate that shorter courses of PAT (< 3 days) are as efficacious as prolonged treatment regimes when it comes to infectious complications in, for example, complex appendicitis [26], yet no randomized trials on efficacious short courses for com- plex appendicitis are available to date. Uncomplicated cholecystitis with an indication for surgery warrants no antibiotics beyond the operating room, unless there are criteria such as perforation, gangrene or empyema defining complicated cholecystitis; uncomplicated diverticulitis is usually managed medically, and surgical diverticulitis (e.g., perforated diverticulitis) is proposed to be treated postoperatively for 4 days, providing that source control has been adequate [27]. In our study, there was a trend towards a shortened dura- tion of postoperative EAT, but the difference was not significant expect for the treatment duration in cholecystitis, in compliance with current guidelines [28,29]. To address this matter of the extended continuation of postoperative antibiotics, our AMS team developed hospital-specific guidelines on medical and surgical IAIs, a multidisciplinary effort with the joint participation of the departments of general surgery, hepatology and gastroenterol- ogy. The guidelines’ impact on, for example, the duration of treatment and the efficacy of restricted-duration treatment for postoperative wound complications will be discussed in one of our next papers, including the incompletely resolved issue of the documentation culture of the practitioners. Efficacious postoperative prolongation with narrow-spectrum antibiotics makes the principle of de-escalation unnecessary and demands a comparison to the culture and sensitivity results for those who postoperatively received cefazolin. Post-surgery changes to the broad-spectrum penicillin TZP, the de-escalation rates and the efficacy will also be debated then, along with the change in antimicrobial susceptibil- ity patterns with improved antimicrobial use. There is a lot of debate already regarding the best strategy for implementing or improving antimicrobial stewardship in surgical units, and the data are often inconclusive and contradictory [23,30]. 4. Discussion Sartelli and colleagues showed that the implementation of educational programs in a general and emergency surgery unit had a significant impact on the antibacterial consumption rate. The total monthly antimicrobial use decreased by 18.8% (the endpoint was DDD/1000PD) with- out affecting patient outcomes [31]; on the contrary, Knox and Edye were less effective with their educational ASP in changing prescription behavior when targeting surgical prophylaxis [32]. The pros and cons of formulary restriction concepts in comparison to prospective audit and feedback strategies (so-called persuasive initiatives) were the sub- ject of a Cochrane meta-analysis and revealed no advantage for one or the other at 12 or 24 months [33]. Our study is a statement on successfully implemented multifaceted strategies, using all the tools a hospital’s infrastructure may provide, working in an inter- and multidisciplinary manner by collaborating with all departments and encouraging prescribers to participate in and be part of antimicrobial stewardship rather than being bystanders. We are united in one mission: to stop the spread of antimicrobial resistance and to preserve antimicrobials for the prophylaxis and treatment of infections; we know for a fact that antimicrobial stewardship works [34,35] and that antimicrobial resistance is linked to imprudent use [36]. The study has some limitations: it was single centered and the retrospective analysis ably raised doubts regarding the rationale for longer durations of antibacterial treatment. More and more data indicate that shorter courses of PAT (< 3 days) are as efficacious as prolonged treatment regimes when it comes to infectious complications in, for example, complex appendicitis [26], yet no randomized trials on efficacious short courses for com- plex appendicitis are available to date. Uncomplicated cholecystitis with an indication for surgery warrants no antibiotics beyond the operating room, unless there are criteria such as perforation, gangrene or empyema defining complicated cholecystitis; uncomplicated diverticulitis is usually managed medically, and surgical diverticulitis (e.g., perforated diverticulitis) is proposed to be treated postoperatively for 4 days, providing that source control has been adequate [27]. In our study, there was a trend towards a shortened dura- tion of postoperative EAT, but the difference was not significant expect for the treatment duration in cholecystitis, in compliance with current guidelines [28,29]. 4. Discussion This study does not provide recommendations for IAIs but demonstrates the general potential of ASPs for a rational prescription of an- timicrobials in IAIs overall. Although an improvement of patients’ outcomes could not be demonstrated, the findings provide assurance that less antibiotic consumption is not associated with an impairment of patients’ outcomes either. This quality improvement study highlights, altogether, the power of ASPs for optimizing antimicrobial use. The clin- ical efficacy in the postoperative usage of narrow-spectrum antibiotics such as cefazolin Antibiotics 2021, 10, 73 12 of 13 12 of 13 underlines the paramount effect of surgical source control and warrants further studies clarifying the usefulness of the extended continuation of antibiotics in surgical IAIs for reducing postoperative infectious complications. Author Contributions: All authors significantly contributed to the design of the study, and the acquisition and interpretation of the data. G.S. and J.F.L. analyzed the data and wrote the manuscript. U.V., C.-T.G. and A.W. contributed to the design of the study and revised the manuscript. All authors have read and agreed to the published version of the manuscript. Funding: There was no funding for this study. Funding: There was no funding for this study. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. 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 European General Data Protection Regulation (GDPR). Acknowledgments: We would like to thank Pascal Meyer-Sauter, Johannes Braun-Feldweg and Jan Rüsch for their assistance in data acquisition. The antibiotic consumption data were extracted with the support of our pharmacist Claudia Burger. Acknowledgments: We would like to thank Pascal Meyer-Sauter, Johannes Braun-Feldweg and Jan Rüsch for their assistance in data acquisition. The antibiotic consumption data were extracted with the support of our pharmacist Claudia Burger. 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Diagnosis and Management of Complicated Intra-abdominal Infection in Adults and Children: Guidelines by the Surgical Infection Society and the Infectious Diseases Society of America. Clin. Infect. Dis. 2010, 50, 133–164. [CrossRef] 13. Linder, M.M.; Wacha, H.; Feldmann, U.; Wesch, G.; Streifensand, R.A.; Gundlach, E. The Mannheim peritonitis index. An instru- ment for the intraoperative prognosis of peritonitis. Der Chir. 1987, 58, 84–92. 13. Linder, M.M.; Wacha, H.; Feldmann, U.; Wesch, G.; Streifensand, R.A.; Gundlach, E. The Mannheim peritonitis index. An instru- ment for the intraoperative prognosis of peritonitis. Der Chir. 1987, 58, 84–92. 14. Singer, M.; Deutschman, C.S.; Seymour, C.W.; Shankar-Hari, M.; Annane, D.; Bauer, M.; Bellomo, R.; Bernard, G.R.; Chiche, J.-D.; Coopersmith, C.M.; et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). JAMA 2016, 315, 801–810. [CrossRef] 13 of 13 13 of 13 Antibiotics 2021, 10, 73 15. 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https://openalex.org/W2026592742
https://www.scielo.br/j/estpsi/a/YhfMj9CLJcmFZPg7qL9Cnky/?lang=pt&format=pdf
Portuguese
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Fatores influentes no desenvolvimento do potencial criativo
Estudos de Psicologia
2,010
cc-by
6,923
Resumo Estudo teórico que aborda alguns importantes fatores influentes no desenvolvimento do potencial criativo do ser humano (família, escola, ambiente de trabalho, contexto sociocultural e saúde do indivíduo), segundo as teorias sistêmicas da criatividade. As experiências familiares são fundamentais para a formação da pessoa, a constituição de valores, crenças, sentido crítico e criatividade. A escola é onde se passa grande parte da vida e, portanto, ideal para o desenvolvimento do potencial criativo, por meio de professores criativos que, valendo-se da criatividade, podem tornar suas aulas prazerosas e estimuladoras. As organiza- ções, por sua vez, requerem indivíduos criativos, até por questão de sobrevivência no mercado. A criatividade também é influen- ciada pela cultura, dependendo da situação, das pessoas e de seus elementos constituintes. A saúde é vista como um processo de funcionamento integral de todo o ser, que aumenta e otimiza seus recursos, entre eles, a criatividade. Unitermos: Aptidão. Criatividade. Desenvolvimento psicossocial. Fatores influentes no desenvolvimento do potencial criativo Factors that influence the development of creative potential Zélia Maria Freire de OLIVEIRA1 Zélia Maria Freire de OLIVEIRA1 11111 Universidade Católica de Brasília, Programa de Pós-Graduação em Educação. Campus II Universitário Darcy Ribeiro, 70790-160, Brasília, DF, Brasil. E-mail: <zeliafreire@gmail.com>. ▼ ▼ ▼ ▼ ▼ Abstract The article is a theoretical study that aims to provide an overview of the main influential factors in the development of creative potential in human beings (family, school, work environment, the socio-cultural context and health, according to systemic theories concerning creativity. Family experiences are essential for the formation of an individual, his values, beliefs, critical sense and creativity. People spend much of their lives in school, making it the perfect place for the development of creative potential through creative teachers who, when working with creativity, can make their lessons pleasant and stimulating. Organizations, in turn, require creative individuals, even as a matter of survival in the market. Creativity is also influenced by culture, depending on the situation, the people and its constituents. Health is seen as a process of the whole operation of the entire being, that enhances and optimizes his resources, including creativity. Uniterms: Ability. Creativity. Psychosocial development. na busca de soluções. O mercado de trabalho busca pessoas criativas que saibam inovar, agir de forma rápida, criativa, competente, indo além da competição. Como acentua De Bono (1994), não basta competir, é preciso O mundo atual, com muito desenvolvimento tecnológico, científico, industrial e em tantas outras áreas, apresenta problemas ambientais, de saúde, de desorganização social e outros, o que requer criatividade ▼ ▼ ▼ ▼ ▼ Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março 2010 salientam que desenvolver o potencial criativo constitui um desafio porque o homem precisa se despir de cren- ças, ideias velhas e, muitas vezes, até de valores, para dar lugar ao novo; além disso, é também uma conquista, porque é a maneira de o homem, ao intuir, sentir, criar e fazer, encontrar sua essência maior, de se realizar e de exprimir o ser divino que habita sua alma. Para Michalko (2002), desenvolver o potencial criativo é ver o que ninguém mais vê, valendo-se de estratégias de saber ver e fazer com que seu pensamento se torne visível; é pensar naquilo que ninguém mais está pensando, o que envolve fluidez de ideias, fazer novas combinações, contemplar o outro lado da “moeda”, vasculhar outros mundos, descobrir novas formas de busca e, enfim, despertar o espírito de colaboração. haver o que o autor denomina “sur/petição”, ou seja, correr além de, apresentar um diferencial. Essa ideia também é compartilhada por Kim e Mauborgne (2001), que acentuam que as empresas, em vez de olharem dentro dos convencionais limites que definem a sua competência, precisam olhar através deles para vislum- brar territórios ainda não ocupados, que representam um campo de inovação. Paralelo a esse contexto mundial, as teorias recentes sobre criatividade - Teoria do Investimento em Criatividade, de Sternberg e Lubart (1996), Modelo Com- ponencial da Criatividade, de Amabile (1996) e Pers- pectiva de Sistemas, de Csikzentmihalyi (1996) - segundo Alencar e Fleith (2003b), concebem a criatividade como um fenômeno sociocultural, apontando uma rede complexa de interações das variáveis do indivíduo com as da sociedade para a expressão criativa e a possi- bilidade de desenvolver o potencial criativo inerente a todas as pessoas, embora varie em tipo e grau, inde- pendentemente da idade, sexo ou condição social. Sendo importante desenvolver a potencialidade criativa do homem, a fim de que possa ser o continuador do mundo e expressar o seu próprio desenvolvimento (Martínez, 1997), é necessário atentar para os diversos fatores que influenciam no desenvolvimento ou na ini- bição da criatividade, que, segundo Runco (2007), são de diferentes espécies, incluindo-se entre eles: família, escola, ambiente de trabalho, contexto sociocultural e saúde, que foram objetos deste estudo. ▼ ▼ ▼ ▼ ▼ Pela teoria do Investimento em Criatividade, a criatividade provém de seis fatores distintos que se inter- -relacionam e não podem ser vistos isoladamente: inteligência, estilos intelectuais, conhecimento, perso- nalidade, motivação e contexto ambiental. O Modelo Componencial da Criatividade explica de que forma os fatores cognitivos, motivacionais, sociais e de persona- lidade influenciam o processo criativo. A Perspectiva de Sistemas focaliza os sistemas sociais e considera a criatividade um fenômeno que se constrói entre o criador e a sua audiência, e que se vale de três fatores: o indivíduo, portador de uma herança genética e de suas próprias experiências; o domínio, que é um sistema simbólico com um conjunto de regras para repre- sentação do pensar e do agir e que, em síntese, é a cultura; o campo, parte do sistema social que tem o poder de determinar a estrutura do domínio, cuja maior função é preservá-lo como tal. Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Fator família Outra característica é ser intergeracional, sendo especialmente verdade que os valores familiares são passados de uma geração para outra; como exem- plo, cita Johann Sebastian Bach, cuja família toda possuía talento musical. Alencar e Fleith (2003a) salientam a importância de se estimular a imaginação da criança, sobretudo entre dois e seis anos, quando o jogo imaginativo ocorre com grande frequência; essa imaginação vai declinando à medida que se desenvolve a razão e o raciocínio. As autoras apontam como atitudes dos pais favorecedoras ao desenvolvimento criativo o relacionamento pais- -criança não possessivo, o estímulo à independência e à autoconfiança, a estimulação dos interesses infantis e a promoção de condições de exploração dos seus inte- resses e de seu mundo interior. Como fatores inibidores citam o autoritarismo e a crítica constante. Outro estudo, apontado por Lubart (2007), foi realizado por Sullway em 1999, cujo resultado sugere que os filhos primogênitos seriam menos abertos às experiências novas, mais responsáveis, organizados e eficientes do que os demais. Essas características se refletiam no plano da orientação profissional desses indivíduos, levando-os mais a profissões ligadas às ciên- cias físicas e matemáticas, enquanto as ciências sociais e as carreiras políticas eram mais frequentes no domínio do irmão mais novo. Atitudes estimuladoras da criatividade por parte dos pais, segundo Amabile (1989), são: dar liberdade e independência com regras e limites justos; respeitar a individualidade de cada um e ensinar a expressar as emoções, porém sabendo ter controle emocional; estimular o desenvolvimento de valores; demonstrar que aprender não é somente ter notas altas; apreciar a criatividade e incentivá-la; possuir senso de humor; tecer críticas construtivas e não destrutivas - enfim, fazer do lar um lugar para a criatividade morar. As experiências familiares são preponderantes para a formação da pessoa e a constituição de seus valores, crenças, sentido crítico - enfim, de sua criativi- dade. A criatividade na infância não é equivalente à criatividade da fase adulta, mas é difícil vislumbrar a possibilidade de um adulto criativo sem que tenha tido experiência criativa na infância (Feldman, Csikszentmihalyi & Gardner, 1994). As entrevistas realizadas por Alencar (2008) com três pioneiros brasileiros da Psicologia Escolar demonstraram bem a influência da família no desenvol- vimento da criatividade dos entrevistados, influência esta incentivadora da curiosidade e da leitura, e ainda apontaram a questão da união e estrutura da família formadora de bons hábitos. Fator família A família é o primeiro modelo para a criança: educadora, incentivadora, apoiadora e nutridora do seu desenvolvimento. Nos primeiros anos de vida, os atri- butos de personalidade dos pais, sua forma de agir e criar os filhos, o ambiente do lar e a forma de relaciona- mento são elementos de influência no desenvolvimento do potencial criativo. Se a família provê à criança expe- riências favorecedoras ao seu desenvolvimento criativo, estimuladoras de sua curiosidade natural e fortale- cedoras de sua autoestima, certamente a criatividade aflorará com maior facilidade. Segundo Martínez (1995, p. 156) “existe um critério bastante generalizado de que a infância é o repositário das maiores potencialidades criativas do indivíduo, as quais, na maioria dos casos, longe de se desenvolver, são inibidas no decorrer da vida”. Para Runco (2007), toda pessoa tem potencial para ser criativa, mas nem todas realizam esse potencial, por não terem oportunidades de desenvolvê-lo. A criatividade precisa ser exercitada com persistência, existindo para isso técnicas e estratégias de pensamento que auxiliam no desenvolvimento do potencial criativo (Alencar 2000a; Michalko, 2002; Virgolim, Fleith & Neves- -Pereira, 2006). Brandão, Alessandrini e Lima (1998) Segundo Runco (2007), a influência da família é bidirecional: os pais influenciam as crianças, por exem- plo, estimulando-as a visitarem museus, contemplarem Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março 2010 às suas frustrações. É o que indica Ochse (1990): uma porcentagem importante de indivíduos com alto grau de criatividade vem de lares com dificuldades ou des- feitos. Nesse caso, a criança vê nos aspectos limitadores do ambiente uma fonte inspiradora de sua criatividade. A poetisa Cecília Meireles perdeu seus pais muito cedo e, sem ter outros irmãos, foi morar com a avó. Assim, afirmou que sua infância de menina sozinha havia lhe dado duas coisas que pareciam negativas, porém se tornaram positivas em sua vida: o silêncio e a solidão. Sem a companhia de outras crianças, ela mergulhou no mundo mágico das letras e da imaginação (Meireles, 1994). obras de arte; mas também as crianças podem influen- ciar os pais, quando demonstram interesse por algo e os pais respondem a isso. O autor pontua que a influência familiar é longitudinal e, por isso, muitas vezes difícil de ser pesquisada. Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março 2010 Fator escola como as indicadas por Torrance (1987), Alencar (2000b), Buzan (2001), Michalko (2002), Alencar e Fleith (2003a), De La Torre (2003), e Virgolim et al. (2006). Muitas pesquisas sinalizam os bons efeitos de programas de treinamento em criatividade, entre elas a de Dias, Enumo e Azevedo Junior (2004), que investigaram os efeitos de um pro- grama de criatividade sobre o desempenho acadêmico e cognitivo de 17 alunos com dificuldade de apren- dizagem, das 2ª e 3ª séries do ensino fundamental de Vitória-ES, comparando-os a um grupo de controle. Os resultados indicaram uma melhora significativa no desempenho escolar do grupo que participou do treinamento. Os mesmos resultados positivos foram encontrados por Alencar (1975), com 791 alunos de 4ª e 5ª séries. Os alunos treinados obtiveram escores mais altos em fluência, flexibilidade e originalidade do que os não treinados. Também Fleith e Alencar (1992) imple- mentaram um programa de treinamento em criativi- dade com 36 alunos de 2º grau e novamente foram encontrados maiores escores com o grupo treinado do que com o grupo de controle. Apesar da necessidade de pessoas criativas no mundo atual, Wechsler (2001) afirma que a criatividade ainda é um fenômeno pouco implementado nas escolas. Embora possa ser aplicada a qualquer disciplina, no cotidiano da sala de aula o professor não tem, de modo geral, estimulado a criatividade dos alunos, seja por deficiências em sua formação, desconhecimento de técnicas, procedimentos e metodologias incentivadoras da criatividade, seja pela extensão do currículo a cumprir. Existem ingredientes necessários para uma pro- dução criativa, que podem prover o aluno de oportu- nidades que o levem às ações ideais de aprendizagem (Renzulli, 1992). Para o autor, é fundamental a integração conjunta das estruturas primordiais do contexto educa- cional para propiciar a expansão da criatividade na es- cola: a) o professor, que deve ter domínio de sua disci- plina e gostar do que faz; b) o aluno, cujas habilidades, estilos e interesses devem ser reconhecidos; c) o currí- culo, que deve ter, além da estrutura, conteúdo e meto- dologia, o apelo ao imaginário. Fator família A experiência de Domino, em 1979, mostrou que um grupo de crianças, em que os pais permitiam uma maior independência aos filhos, era mais flexível e bem mais criativo do que o grupo de crianças escolhidas ao acaso (Alencar & Fleith, 2003a). Também Esquivel e Hodes (2003) examinaram a influência da família no desen- volvimento da criatividade, constatando que os pais mais estimuladores da criatividade aceitavam a criança como indivíduo, davam-lhe autonomia e oportunidades criativas, enquanto formavam seus hábitos e estimu- lavam traços da personalidade. É indiscutível a influência que a família exerce no desenvolvimento do potencial criativo, bastante assinalada pelos teóricos e suas pesquisas. Pode incen- tivar a criatividade ao lidar com suas crianças, ao lhes fomentar o exercício da imaginação, da leitura, da curiosidade, ao lhes proporcionar meios de lidar com ambos os tipos de pensamento, divergente e conver- gente, ao ouvir suas histórias, prestar atenção aos seus desenhos e proporcionar um ambiente aberto ao criativo. Embora ambientes familiares repressores, com regras rígidas de conduta e sem diálogo, sejam inibidores do potencial criativo, é interessante salientar que tam- bém lares desestruturados podem levar algumas crian- ças a serem criativas como uma forma de compensação 2010 Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Fator escola Apesar da importância da criatividade no con- texto educacional, Alencar e Fleith (2003a) afirmam que aí persistem elementos que dificultam e, muitas vezes, inibem o desenvolvimento e a expressão da capacidade de criar, como a ênfase na reprodução do conhecimento e na memorização de ensinamentos, a indicação de apenas uma resposta correta para um problema e a pouca ênfase à imaginação e à fantasia. As mesmas pesquisadoras, em 2008, investigaram 398 professores de 1ª a 4ª série do ensino fundamental de escolas públi- cas e particulares, localizadas no Plano Piloto de Brasília e em outras regiões administrativas do Distrito Federal, quanto à sua percepção sobre barreiras que dificultavam e que propiciassem condições favoráveis ao desenvolvi- mento da capacidade criativa de seus alunos. As barreiras mais indicadas foram um elevado número de alunos em sala de aula e alunos com dificuldades de aprendizagem. São características do professor criativo: ser aberto a novas experiências e mudanças, ser ousado e curioso, ter confiança em si próprio, trabalhar com idealismo e paixão, proporcionar clima criativo nas aulas, permitir ao aluno pensar, desenvolver ideias e pontos de vista e fazer escolhas, valorizar o trabalho criativo, não rechaçar os erros, mas torná-los pontos do processo de aprendizagem, considerar os interesses e habilidades dos alunos (Alencar, 2002, 2004; Alencar & Fleith, 2003a, 2003b; Antunes, 2005; Fleith, 2001; Wechsler, 2001, 2002). A essa lista, Freire e Shor (1996) acrescentam que o professor precisa ser um profissional com domí- nio de várias capacidades e habilidades especializadas, entre elas: a) ser dialógico, pois o diálogo é em si criativo e recriativo; b) ter pensamento crítico e desenvolver tal pensamento em seus alunos; c) trabalhar o currículo de forma flexível e contextualizada; d) ser um artista, um político, um ser criativo e dinâmico, um líder, sem auto- ritarismo ou dominação. Na trajetória de vida dos entrevistados por Alen- car (2008) também se evidenciou o papel influente da escola, com professores incentivadores, que ensinavam com prazer e contagiavam seus alunos com essa paixão pelo ensinar e pelo aprender. Fator escola “Desde cedo, assumi meu Grande parte do comportamento criativo é aprendida e pode ser estimulada, afirma Fleith (2007), e por isso o professor precisa conhecer e utilizar técnicas que estimulem o desenvolvimento da criatividade, 86 86 86 86 86 2010 interesse pela educação por acreditar no valor do conhecimento e do processo criativo do ensino e da aprendizagem como alavanca para o desenvolvimento da sociedade e da cultura” (Alencar, 2008, p.271). Também Robert J. Sternberg, ao ser entrevistado por Henshon (2008), evidenciou influências da escola em sua formação: na escola elementar, o fato de não ter se saído bem em um teste de inteligência levou-o às pesquisas que orientaram sua vida, principalmente sobre a criati- vidade. Ele realçou o papel do professor ao estimulá-lo a não crer em tudo que lhe diziam, a ser questionador e curioso e partir em busca de desafios. Sem menosprezar os componentes tecno- lógicos inerentes à inovação, Ponti e Ferráz (2006) afir- mam que inovar depende do espírito imaginativo de indivíduos e equipes, da atitude criativa renovada e constante das pessoas e do incentivo dado pelas orga- nizações em estabelecer, conscientemente, um clima criativo que possibilite a inovação. As organizações precisam ver a inovação como um processo estratégico. Também assinalam que, ao mesmo tempo em que o fluxo tecnológico permite resolver grande parte dos problemas existentes e futuros da humanidade e que se consolida um pensamento científico de gestão em- presarial, a criatividade e a pró-atividade de sua direção revelam-se como chaves para transformar os fluxos de conhecimentos em soluções válidas para o mercado. Detectar, portanto, que perfis de gerentes são mais pró-ativos e incentivadores da inovação, os mais entu- siastas e criativos, é um fator fundamental para efetivar a inovação organizacional. As organizações que têm capacidade inovadora devem gerir os seguintes subpro- cessos: a gerência de novos conceitos, o desenvolvi- mento de novos produtos e de novos processos, a gestão do conhecimento e da tecnologia (Ponti & Ferraz, 2006). Os mesmos autores reafirmam a importância da criatividade em todas as organizações, como uma fer- ramenta de sobrevivência na contemporaneidade, pois para se construir o futuro é imprescindível ser criativo no presente e ser capaz de ver aquilo que ninguém mais vê, ser um visionário e inovador. As pesquisas de Carvalho e Alencar (2004), Oli- veira, E. (2007) e Oliveira Z. Fator escola (2007) entre outras, aponta- ram que no âmbito escolar, embora haja reconheci- mento da importância da criatividade e de se estimular o potencial criativo dos alunos, os professores e gestores pouco conhecem sobre o tema e suas técnicas, agindo mais intuitivamente. O mundo atual exige uma nova imagem do professor e de sua atividade, pontua Vallejo (2003), sendo necessários uma escola aberta e um novo profissional que deem uma resposta criativa e responsável aos problemas da comunidade onde esta escola está inse- rida. Antunes (2005) enfatiza que a proposta de se incen- tivar a criatividade na escola não é para fazer do aluno um gênio, mas sim buscar desenvolver o potencial criati- vo de cada um, não para torná-lo o melhor, mas sim para torná-lo melhor. Assim, é preciso que a escola vislumbre a criati- vidade como um meio de voltar a encantar os alunos, com aulas prazerosas, estimulando e desenvolvendo o potencial criativo que existe dentro de cada aluno. É preciso banir da escola as barreiras à expressão criativa, tornando-a formadora de cidadãos criativos para este mundo complexo em mudanças. Na mesma linha de pensamento, Cornella e Flo- res (2007) acentuam que não há inovação sem pessoas criativas e, mais, que independentemente do setor, do tipo de organização ou de produto, o fator definitivo para que a inovação tenha lugar é a energia da pessoa criativa. É preciso, então, que a organização aproveite essa energia, proporcionando-lhe meios para criar, “atrever-se mais”, encontrar na profissão “um elemento de ruptura”, dar um passo adiante e utilizar o que puder do passado, sem deixar que esse passado escravize suas ideias. Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Fator contexto sociocultural A criatividade, conforme Cropley (2006), não só é determinada por critérios sociais, mas também os determina. O produto é a face pública da criatividade e precisa ser examinado pela sociedade e receber ou não o aval dela. Ainda Cropley (2005) enfatiza que a sociedade não é simplesmente um receptor passivo dos produtos das pessoas criativas, mas ela própria determina que espécie de novidade deve ser produzida. Entretanto, também nas organizações existem barreiras à criatividade: estruturais, sociais e políticas, processuais, de recursos e individuais, segundo Alencar e Fleith (2003a). Amabile (1999, p.116) acentua que é frequente ver a criatividade ser mais destruída do que estimulada: “Sufocar a criatividade é fácil. Difícil é esti- mulá-la”. Segundo pesquisa de Bruno-Faria e Alencar (1996) com 25 funcionários de diferentes organizações, foram apontados como elementos estimuladores ou inibidores à criatividade: o ambiente físico, o sistema de comunicação empresarial, a existência de desafios, a estrutura organizacional, o estilo de trabalho e de parti- cipação, os recursos tecnológicos e materiais, os salários e benefícios, o suporte da chefia, do grupo e da organi- zação e o treinamento. A cultura é um conjunto constituído por pa- drões de comportamento, crenças, conhecimentos, costumes, que são transmitidos de geração a geração e que distinguem um grupo social, bem como estruturam os indivíduos a interagirem com seu ambiente psíquico e social (Houaiss, 2001; Lubart, 2007). A Perspectiva de Sistemas de Csikszentmihalyi (1996) apresenta o domínio como um de seus componentes, consistindo de um conjunto de regras e procedimentos simbólicos estabe- lecidos culturalmente, ou seja, conhecimento acumu- lado, estruturado, transmitido e compartilhado em uma sociedade ou por várias sociedades; os domínios po- dem ser modificados mediante contribuições criativas (Alencar & Fleith, 2003a). Um produto novo, criativo, diferente, original, pode ou não ser aceito socialmente, dependendo da cultura. Um exemplo típico disso foram as pinturas de Van Gogh, cuja genialidade só foi reconhe- cida após sua morte. Existem também diferenças entre as culturas. Segundo Niu e Sternberg (2002), existe uma diferença entre a cultura ocidental e a oriental no modo de encarar o que é criatividade e na definição de sua origem. No ocidente, há duas origens para a criatividade: uma baseia-se na criação bíblica por Deus e a outra na inspiração grega das musas. Na China, provém da ideia de produção e renovação infinita da natureza, as muta- ções do Tao, Tai-Chi ou Ying/Yang. Fator ambiente de trabalho As organizações têm se interessado pela criati- vidade mais do que qualquer outro setor da sociedade, segundo Alencar e Fleith (2003a), uma vez que necessi- tam diversificar produtos, antecipar demandas, recrutar e reter bons empregados e melhorar a qualidade de produtos e serviços, até como questão de sobrevivência no mercado. O ambiente de trabalho influencia a criati- vidade, podendo desenvolvê-la ou inibi-la. Atualmente, é muito importante o trabalho em equipes e, consequentemente, a criatividade grupal. Masi (2002) realça que a criatividade pode brotar não como fruto de um só indivíduo, mas de grupos e de coletivi- dades. A criatividade grupal decorre da combinação das personalidades que compõem o grupo e daquilo que as motiva. 2010 Uma organização criativa precisa ter capacidade de adaptação, autonomia, flexibilidade, respeitar a dignidade e o valor das pessoas, intensificar a atividade de treinamento e aperfeiçoamento de seu pessoal, realizar uma administração orientada para o futuro, saber lidar com a diversidade, incorporar criativamente novos procedimentos, políticas e experiências e valorizar as ideias inovadoras (Alencar, 1997). São desafios às organizações: a) proceder às mudanças que se fazem necessárias em culturas organizacionais há muito sedi- mentadas, marcadas pela resistência às novas ideias e refratárias às exigências do mundo moderno; b) cons- cientizar os indivíduos de sua capacidade pessoal para criar, proporcionando-lhes treinamentos estimuladores da criatividade; c) promover mudanças em comporta- mentos que afetam de forma adversa as relações inter- pessoais e o clima no ambiente de trabalho; d) construir um ambiente que valorize e cultive a criatividade. A criatividade no contexto do trabalho é uma necessidade organizacional de sobrevivência no merca- do e de adaptabilidade ao mundo em mudança cons- tante. Por isso, é imprescindível um clima favorável à criatividade, um ambiente que estimule os empregados a serem criativos, inovadores, participativos e parceiros na busca das metas organizacionais. Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Fator contexto sociocultural Não basta que a pessoa passe por um treina- mento ou receba instrução para que desenvolva e expresse o seu potencial criativo, é também necessário construir um ambiente que valorize e cultive a criativi- dade. Criatividade não é algo que acontece por acaso; ela pode ser deliberadamente desenvolvida, gerenciada, monitorada com vistas a alcançar as metas individuais e da organização. A criatividade hoje é tida como a no- va moeda de mercado, como nova força motriz e, decor- rente disso, cresce o prestígio dos profissionais compro- metidos com a inovação, o design, a imaginação e as ideias, uma classe que corresponde a 30% da força de trabalho nos Estados Unidos e 10,9% no Brasil (Rodri- gues, 2007). Também no tocante às diferenças de enfoques, os orientais incluem em suas concepções de criati- 88 88 88 88 88 Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março 2010 tomas, mas sua definição leva a um conjunto de características relacionadas às condições biológica, subjetiva e sócio-histórica do homem. Martínez (2007) afirma que esse novo enfoque de saúde possibilita relacioná-la à criatividade. O vínculo entre criatividade e saúde é complexo e não linearmente causal. É possível vê-lo em duas dimensões: a primeira delas liga-se à emoção e afirma mesmo que “a criatividade é, antes de tudo, um importante espaço de produção de emoções”; a segunda refere-se às configurações subjetivas asso- ciadas aos processos de criatividade e de saúde. A autora aponta como consequência ser possível analisar o processo de desenvolvimento da criatividade como fonte de promoção da saúde (Martínez, 2007, p.60). Desenvolver a criatividade inclui reconhecer e definir espaços próprios e saudáveis do sujeito, “na medida em que se associam as características subjetivas relaciona- das com a saúde e à produção de estados emocionais que favorecem o bem-estar do sujeito e se opõem aos processos de doença” (Martínez, 2007, p. 61). vidade os valores sociais e morais, o coletivismo e maior valor à conexão novo e velho. Ainda, executam ativi- dades criativas diferentemente dos ocidentais, e as razões para isso podem estar ligadas aos valores sociais, edu- cação e grau de modernização. Já os ocidentais tendem a focar características individuais, sucessos pessoais, gosto estético e humor. Outras diferenças entre as culturas quanto à promoção ou inibição da atividade criativa foram anali- sadas por Lubart (2007). Fator contexto sociocultural Apesar das associações de criatividade à saúde, há muitos estudos sobre criadores eminentes que eram portadores de doenças mentais ou desajustes psicoló- gicos, como o escritor francês Balzac e o cientista John Forbes Nash. Cropley (2005) pontua que a conexão entre criatividade e loucura é uma das velhas abordagens na psicologia moderna e já foi alvo de investigações empí- ricas há mais de cem anos atrás. Lubart (2007) aponta Conforme Runco (2007), a relação entre saúde e criatividade tem sido debatida por anos, mas frequen- temente o debate tem vislumbrado apenas um lado, o que analisa a criatividade e as psicopatologias e loucura, enquanto a relação entre criatividade e saúde pro- priamente dita é tida como surpreendentemente com- plicada. Apesar das associações de criatividade à saúde, há muitos estudos sobre criadores eminentes que eram portadores de doenças mentais ou desajustes psicoló- gicos, como o escritor francês Balzac e o cientista John Forbes Nash. Cropley (2005) pontua que a conexão entre criatividade e loucura é uma das velhas abordagens na psicologia moderna e já foi alvo de investigações empí- ricas há mais de cem anos atrás. Lubart (2007) aponta Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Fator contexto sociocultural A existência de inventores, por exemplo, em uma determinada geração e sociedade, prediz o nível de criatividade das gerações subsequentes. Além disso, o autor afirma que a proximidade de vários centros de trocas e atividades culturais e industriais pode ser um incentivador de uma cultura mais criativa. Ainda para Lubart (2007), uma cultura pode: a) incentivar ou inibir a criatividade, dependendo da situação, das pes- soas e de seus elementos constituintes; b) favorecer maior ou menor quantidade de atividades criativas; c) levar homens e/ou mulheres às artes; d) indicar formas que vão tomar a expressão criativa em cada área; e) modular a atividade criativa; f) permitir o afastamento das normas tradicionais pela expressão criativa; g) fazer com que a expressão criativa demonstre algumas ca- racterísticas daquela cultura. Muitas correntes psicológicas defendem que o impulso criativo leva o homem para a ação criativa em face de conflitos e tensões, e ainda que a criatividade é um fator para a promoção da saúde mental do indivíduo (Virgolim, 2007). A autora cita Maslow que, estudando pessoas saudáveis psicologicamente, demonstrou que o homem vale-se da motivação para crescer, desen- volver-se e realizar o seu self. Também aponta May, para quem a criatividade é o encontro do ser humano inten- samente consciente com o mundo, e o processo criativo é a expressão da saúde emocional da pessoa em realizar algo novo. Os progressos recentes criaram riquezas e outros meios culturais. As modernas tecnologias provocaram mudanças quanto à forma de abordar uma tarefa criati- va, e a informática possibilita novas visões criativas e novas formas de expressão (Lubart, 2007). Pode-se afirmar, com Lubart (1999), que a análise da criatividade em diversas culturas mostra que a criatividade é depen- dente do contexto. A cultura influencia a definição e o processo de criatividade, possuindo um conjunto de características que podem facilitá-la ou inibi-la. 89 89 89 89 89 FATORES INFLUENTES NO PONTENCIAL CRIATIVO Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março 2010 Conforme Runco (2007), a relação entre saúde e criatividade tem sido debatida por anos, mas frequen- temente o debate tem vislumbrado apenas um lado, o que analisa a criatividade e as psicopatologias e loucura, enquanto a relação entre criatividade e saúde pro- priamente dita é tida como surpreendentemente com- plicada. Fator saúde Osho (1999) enfatiza que a criatividade é a essên- cia da verdadeira saúde e que todas as pessoas saudá- veis são criativas. A saúde é vista como um processo de funcionamento integral de todo o ser, que aumenta e otimiza os recursos do organismo para diminuir sua vulnerabilidade aos diferentes agentes e processos causadores da doença (González Rey, 1993). Saúde, por- tanto, não é sinônimo de ausência de doença ou sin- 2010 Daí ser preponderante haver mais esclareci- mentos sobre criatividade em todos os contextos, para que, conscientes, as pessoas possam desejar o desen- volvimento de seu potencial criativo e se desvencilhar dos mitos da criatividade. Nas instituições de ensino, é preciso que os professores sejam conscientizados da relevância de se estimular a criatividade nos alunos. Também as organizações precisam adotar visão criativa, estimulando-a em seus recursos humanos, até por ques- tão de sobrevivência nesse mercado cada vez mais competitivo. estudos que relacionaram a criatividade à perturbação mental e levanta a hipótese de que certos fatores que favorecem a criatividade seriam igualmente os fatores vulneráveis aos transtornos mentais, especialmente às psicoses maníaco-depressivas e à esquizofrenia. Entre- tanto, ele mesmo afirma que a equação entre inteli- gência criativa e pensamento psicótico é controversa. A criatividade acontece quando há fatores am- bientais estabilizantes e de contensão; porém, se os fatores ambientais são estressantes e causam desequi- líbrio, a produção é incompreensível e acontecem os transtornos mentais (Lubart, 2007). Corrobora esta ideia a afirmação de Rothenberg (1990) de que, embora haja profissionais interessados em encontrar valores artís- ticos em insanos, isso não justifica fazer-se uma ligação entre capacidade criadora e doenças mentais. Não são todas as pessoas que possuem a capa- cidade de fazer algo grandioso, notável, como os gran- des gênios e ganhadores do prêmio Nobel, mas todas possuem um potencial criativo dentro de si, podendo desenvolvê-lo e usar essa capacidade criadora em sua própria vida, no seu trabalho, no seu cotidiano. É fato que doenças e emoções, principalmente as negativas, fazem com que a realidade seja modificada pela alteração dos filtros pessoais sensoriais e percepti- vos e têm um efeito sobre a criatividade, podendo afetá- -la positiva ou negativamente, alterando o processo e a produção criativa. Exemplificando, após a morte da filha Maria Julieta, o poeta Carlos Drummond de Andrade perdeu a razão de viver, a vontade de escrever e de pro- duzir (Andrade, 2002). Considerações Finais Concluindo, fica o convite para que todas as pes- soas busquem desenvolver o seu potencial criativo e conheçam técnicas que lhes possibilitem alcançar esse desenvolvimento, pois a criatividade é acessível a todos e são muitos os desafios e problemas do mundo con- temporâneo que carecem de respostas criativas. A criatividade leva a um processo de mudança e desenvolvimento pessoal e social, e deveria fazer parte da vida de cada um, bem como ser sempre incentivada em todos os ambientes onde a pessoa vive. A pessoa que quer se tornar criativa deve buscar novos caminhos, ser inovadora, ousada, curiosa, apaixonada pelo que faz e correr atrás de sonhos. Nessa caminhada são muitos os fatores influentes, sendo a família, a escola, o ambiente de trabalho, o contexto sociocultural e a saúde alguns deles, todos com importância no desenvolvimento do potencial criativo. Como enfocam as teorias sistêmicas, há outros fatores influentes que não foram tratados neste artigo, como a herança genética, as motivações intrín- secas e extrínsecas ao indivíduo, sua personalidade; entretanto, procurou-se enfocar apenas alguns fatores importantes no desenvolvimento do potencial criativo do indivíduo. Fator saúde Cabe realçar que a saúde, sob o sentido de funcionamento total e integral do ser huma- no, é facilitadora da expressão criativa. Criatividade ainda é um tema que necessita mais pesquisas e, inclusive, o estudo sobre os fatores influen- tes no desenvolvimento do potencial criativo, que são muitos. Mesmo assim, já é possível perceber que é pre- ciso investir na criatividade das pessoas, divulgar mais o assunto, para que se conscientizem de sua impor- tância e possam buscar meios para seu desenvolvi- mento, de modo que os ambientes frequentados pela maioria das pessoas possam contribuir para que sejam mais criativas. Estudos de Psicologia I Campinas I 27(1) I 83-92 I janeiro - março Referências Caracas: Fondo Editorial de la Faculdad de Humanidades de la Universidad Central de Venezuela. Antunes, C. (2005). A criatividade em sala de aula. Petrópolis: Vozes. Henshon, S. (2008). Adventurous navigator of the dimensions of high abilitlity: an interview with Robert J. Sternberg. Roeper Review, 30 (2), 75-80. Boden, M. A. (1999). Dimensões da criatividade. Porto Alegre: Artmed. Brandão, C. R., Alessandrini, C. D., & Lima, E. P. (1998). Criatividade e novas metodologias (Série temas transversais, 4). Peirópolis: Fundação Peirópolis. Houaiss, A. (2001). Dicionário Houaiss da língua portuguesa. Rio de Janeiro: Objetiva. Kim W. C., & Mauborgne, R. (2001). Creating new market space. In Harvard business review on innovation (pp.1-30). Boston: Harvard Business School Publishing Corporation. Bruno-Faria, M. F., & Alencar, E. M. L. S. (1996). Estímulos e barreiras à criatividade no ambiente de trabalho. Revista de Administração da USP, 31 (2), 50-61. Lubart, T. (1999). Creativity across cultures. In R. J. Sternberg (Org.), Handbook of creativity (pp.339-350). New York: Cambridge University Press. Buzan, T. (2001). O poder da inteligência criativa. São Paulo: Cultrix. Carvalho, O., & Alencar, E. M. L. S. (2004). Elementos favo- recedores e inibidores da criatividade na prática docente, segundo professores de geografia. Psico, 2 (35), 213-221. Lubart, T. (2007). Psicologia da criatividade. Porto Alegre: Artmed. Martínez, A. M. (1995). Como desarrollar la creatividad em la escuela. In A. M. Martínez (Orgs.), Pensar y crear: estrategias, programas y métodos (pp.156-208). Havana: Editorial Academia. Cornella, A., & Flores, A. (2007). La alquimia de la innovación. Barcelona: Deusto. Cropley, A. J. (2005). Creativity, in education and learning: a guide for teachers and educators. London: Routledge Falmer. ORES INF Martínez, A. M. (1997). A criatividade, personalidade e educação. São Paulo: Papirus. Cropley, A. J. (2006). Dimensions of creativity. Roeper Review, 28 (3), 125-130. LUENTES NO P Martínez, A. M. (2007). Criatividade e saúde nos indivíduos e nas organizações. In A. Virgolim (Org.), Talento criativo: expressão em múltiplos contextos (pp.53-64). Brasília: EdUnB. Csikszentmihalyi, M. (1996). Creativity. New York: Harper Collins. De Bono, E. (1994). Criatividade levada a sério. São Paulo: Livraria Pioneira. Martins, E. (2002). Ciência hoje das crianças 2002. Recuperado em 31 maio, 2004, disponível em http://www.2.vol. com.br/cienciahoje/che/drumond2.htm De La Torre, S. (2003). Dialogando com a criatividade. São Paulo: Madras. Masi, D. (2002). Criatividade e grupos criativos. Rio de Janeiro: Sextante. Dias, T. L., Enumo, S. R. F., & Azevedo Junior, R. R. (2004). Referências Alencar, E. L. S. (1975). Efeitos de um programa de criativi- dade em alunos de 4ª e 5ª séries. Arquivos Brasileiros de Psicologia, 27, 3-15. Alencar, E. M. L. S. (1997). A gerência da criatividade. São Paulo: Makron Books do Brasil. Alencar, E. M. L. S. (2000a). O perfil do professor facilitador e do professor inibidor da criatividade segundo estudantes de pós-graduação. Boletim da Academia Paulista de Psicologia, 19 (1), 84-94. Alencar, E. M. L. S. (2000b). O processo da criatividade. São Paulo: Makron Books do Brasil. 90 90 90 90 90 2010 psychology of creativity (pp.135-165). Cresskill, N.J.: Haptom Press. Alencar, E. M. L. S. (2002). O contexto educacional e sua influência na criatividade. Linhas Críticas, 8 (15), 165-178. Alencar E. M. l. S. (2004). Como desenvolver o potencial criador. Petrópolis: Vozes. Feldman, D. H., Csikszentmihalyi, M., & Gardner, H. (Orgs.). (1994). Changing the world: a framework for the study of creativity (pp. 69-84). Westport, CT: Praeger. Alencar E. M. l. S. (2008). A trajetória de vida de três pioneiros brasileiros da psicologia escolar. Psicologia Escolar Educacional, 12 (1), 265-278. Fleith, D. S. (2001). Criatividade: novos conceitos e idéias, aplicabilidade à educação. Revista Cadernos de Educação Especial, 17, 55-61. Alencar, E. M. L. S., & Fleith, D. S. (2003a). Criatividade: múltiplas perspectivas (3a. ed.) Brasília: EdUnB. Fleith, D. S. (2007). A promoção da criatividade no contexto escolar. In A. Virgolim (Org.), Talento criativo: expressão em múltiplos contextos (pp.145-157). Brasília: EdUnB. Alencar, E. M. L. S., & Fleith, D. S. (2003b). Contribuições teóricas recentes ao estudo da criatividade. Psicologia: Teoria e Pesquisa, 19 (1), 1-8. Fleith, D. S., & Alencar, E. M. L. S. (1992). 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A educação criativa: possibilidade para descobertas. In S. Castanho, S. & M. E. Castanho (Orgs.), Temas e textos em metodologia do ensino superior (pp.165-170). Campinas: Papirus. Renzulli, J. S. (1992). A general theory for the development of creative productivity in young people. In F. Mönks & W. Peters (Orgs.), Talent for the future (pp.51-72). Assen/ Maastricht, The Netherland: VanGorcum. Wechsler, S. M. (2002). Criatividade: descobrindo e encorajando. Campinas: Livro Pleno. Rodrigues, C. (2007, junho 1). Referências Criatividade é a nova moeda. Jornal Valor Econômico, Caderno especial de fim de semana, 348, 4-7 Recebido em: 4/6/2008 Versão final reapresentada em: 18/6/2009 Aprovado em: 3/9/2009 Rothenberg, A. (1990). Creativity and madness: new findings and old. Baltimore, MD: John Hopkins University Press.
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Applying equity-centered principles in an interprofessional global health course: a mixed methods study
BMC medical education
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Stallwood et al. BMC Medical Education (2020) 20:224 https://doi.org/10.1186/s12909-020-02141-1 Stallwood et al. BMC Medical Education (2020) 20:224 https://doi.org/10.1186/s12909-020-02141-1 Open Access * Correspondence: annalee.yassi@ubc.ca 2School of Population and Public Health, University of British Columbia, 2206 E Mall, Vancouver, BC V6T 1Z3, Canada Full list of author information is available at the end of the article Applying equity-centered principles in an interprofessional global health course: a mixed methods study Lisa Stallwood1, Prince A. Adu2,3, Kate Tairyan4, Barbara Astle5 and Annalee Yassi2* © The Author(s). 2020 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/. 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 in a credit line to the data. Abstract 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 Commo licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obta permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4 The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to t data made available in this article, unless otherwise stated in a credit line to the data. * Correspondence: annalee.yassi@ubc.ca 2School of Population and Public Health, University of British Columbia, 2206 E Mall, Vancouver, BC V6T 1Z3, Canada Full list of author information is available at the end of the article Abstract Background: Medical students, practitioners and other health professionals are commonly unprepared to address the many complex issues that emerge while conducting research in the Global South. As a response to identified deficiencies in global health education, a hybrid online/face-to-face multi-institutional credit course was developed based on the equity-centered principles advanced by the Canadian Coalition for Global Health Research (CCGHR), namely Authentic partnering, Inclusion, Shared benefits, Commitment to the future, Responsiveness to causes of inequities, and Humility. This study aimed to analyze the extent to which the course was effective in fortifying attitudes consistent with the CCGHR principles; identify successes and challenges; and assess how a course such as this can fill an identified gap. Methods: This interprofessional course was offered to 25 graduate and postgraduate students in various health professions and public health. Faculty were drawn from medicine, public health, nursing and social sciences from four universities in Western Canada. A pre-post retrospective survey, key informant interviews and participant observation were used to gather data for this study. Results: Findings showed that student attitudes regarding global health research and practice significantly evolved towards views consistent with the principles articulated. The multiple instructors and hybrid course format created both opportunities and challenges; the interprofessional nature of the cohort was considered a strong asset, as was the fact that many students came from the Global South. Some students suggested that the course could be further strengthened by concretely partnering with institutions in the Global South rather than offered solely to learners registered in universities in the Global North. Conclusions: While weaknesses were identified, results support the conclusion that a course focused on the CCGH R principles could be useful in preparing the next generation of global health researchers and practitioners to mitigate historical limitations in this field. Longitudinal follow-up is warranted to provide more definitive conclusions. Keywords: Global health education, Curriculum development/evaluation, Values/attitudes, Professional development, Interprofessional education © The Author(s). 2020 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. Background The course was free to all gradu- ate students registered at any university that was part of the Western Deans’ agreement which provided a tuition fee waiver for visiting students from partner institutions. The course partners have discussed the possibility of hosting the course every two years and alternating the hosting of the course between partner universities to as- sist with managing and sharing the workload. At this juncture, one of the partner institutions has hosted the course twice, as it ran consecutively and was more feas- ible to do so. Numerous universities have taken up the challenge to teach global health skills to the next generation of re- searchers [7]. Some universities have begun to define competencies in global health education, often, however, without considering the needs and priorities of LMICs [8]. In response to such concerns, the Canadian Coali- tion for Global Health Research (CCGHR), a non-profit organization composed of practitioners, researchers and global health students, developed a set of research prin- ciples through a multiphase research process with exten- sive consultation in Canada and with global partners [9]. The principles, serving as an ethical paradigm, consist of six interrelated principles for equity centered research and practice: Authentic partnering, Inclusion, Shared benefits, Commitment to the future, Responsiveness to causes of inequities, and Humility [10]. While major funding agencies, including the Canadian Institutes for Health Research (CIHR) are supporting collaborations between Canadian researchers and researchers from LMICs, CIHR has acknowledged the importance for considering the CCGHR principles for equitable and ethical global health research partnerships [11]. g p p In 2017, the British Columbia (BC) Chapter of the CCGHR hosted the inaugural BC Coalition Institute (BCCI-1) in Kelowna, BC to explore the application of these principles. Emerging from the positive feedback from this event, the institute organizers decided that it would be useful to design a course that embraced the principles of promoting health equity and equitable part- nership development [1] that graduate students across Western Canada would be able to undertake as part of their course requirements. In contrast with current glo- bal health courses that focus on content learning, such as rigorous research methods and global health factual knowledge, the course aimed to be transformative - unpacking student values, beliefs and assumptions that may be remnants of colonialism, and instead promote values to align with the CCGHR principles. Background This novel multi-institutional hybrid global health course was offered as a ‘for-credit’ elective course, mainly delivered online in the Summer 2019 session (May–June), through five synchronous online sessions, and included one three-day face-to-face weekend resi- dency. Each week of the course was designated to focus on one of the following topics through readings, assign- ments and discussions: introduction to the CCGHR prin- ciples; health equity; wicked problems; sustainable and equitable partnerships; ethical issues in global health; and the application of the CCGHR principles in the process of proposal development. Students worked in teams to develop and present a proposal of a global health project that illustrated the use and application of the principles at the end of the course. g Greater awareness of present global health inequities has attracted increasing numbers of students and re- searchers from multiple disciplines to participate in global health initiatives [1]. However, complex eth- ical issues emerge when health researchers from high-income countries (HICs) engage in projects in low and middle-income countries (LMICs) [2, 3]. Without the appropriate training and experience for undertaking global health research, students may un- intentionally harm or exploit already overburdened communities or individuals in low resource settings [4, 5]. Moreover, although global health may be seen in a positive light in the post-colonial world, it can sustain colonialist attitudes and behaviour through domination and unethical studies [6]. p p This graduate course was initially co-developed and co-lead by three professors (co-authors BA, KT and AY) from medical or nursing backgrounds and from three different universities in Western Canada; a PhD student (co-author PA) served as the teaching assistant. Global health practitioners from institutions in Western Canada and who teach Medicine, Nursing, Health Policy, and Population Health, attended the weekend residency and directly interacted with the students to share practical insights from their experiences in global health. This collaborative partnership embraced the diverse strengths of each team member and helped build capacity across the universities involved. The weekend residency pro- vided an opportunity for face-to-face discussion about the topics taught in the course to that point, and to introduce and apply additional techniques such as logic framework analyses. The course was hosted in one of the partner institutions, using a pre-existing graduate- level credit course number which already had been ap- proved as a hybrid (combined in-class and online) course in global health. © The Author(s). 2020 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/. 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 in a credit line to the data. Page 2 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Page 2 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Surveys y The online surveys were distributed at the beginning and end of the course with the aim of assessing changes in attitudes in global health research. The post-course survey was the same as the pre-course survey, with the addition of retrospective pre-post questionnaire items, asking students to rate their level of agreement with each statement as it was at the time of answering (post-participation in the course) and reflecting back as to their attitudes before the course, as has been done in other such studies [12]. The rationale for this technique is that respondents may have subjectively rated themselves a certain way prior to the course but after the completion of the course, they may reflect differently on what their pre- vious attitudes towards global health research truly were. All 25 students completed the pre-course sur- vey, and 24 students completed the post-course sur- vey. Qualtrics (Qualtrics, Provo, UT) was used to collect and analyze the data. In addition to multiple- choice questions to characterize attitudes about vari- ous practices in global health, students were asked to record the extent to which they agreed with a set of statements grounded in the CCGHR principles on a 5-point Likert scale; 1-strongly disagree, 2-disagree, 3- not sure, 4-agree, 5-strongly agree. The average Likert score for each question was recorded. A paired t-test was used to determine significant differences between the average responses in the pre-course ratings, retro- spective pre-course ratings and post course ratings (n = 19). The full statements are shown below, and abbreviated statements are presented in Fig. 1. Background This study was conducted, first, to examine how the course influenced student values and attitudes in global health work; secondly, to identify the successes and challenges experienced by students and course in- structors; and third, to explore the extent to which a course such as this could help fill a gap in current medical education with respect to the teaching of glo- bal health. Page 3 of 9 Page 3 of 9 Page 3 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Stallwood et al. BMC Medical Education (2020) 20:224 Statement 4 Statement 4 When planning a research project, it is important to con- sider how benefits could be distributed amongst all part- ners involved in the research process, including partners who have not yet been involved. Statement 2 Statement 2 Global health research might best benefit all stakeholders if community partners, including those who are historic- ally marginalized, are included in the research process from the very beginning. Statement 1 Statement 1 In projects funded in the Global North, global health re- search/action is most efficient when researchers from the Global North take the lead in coordinating and designing the research or intervention, as they are usually the ones who write the proposals and are best trained to do this. There were 25 students enrolled in this course – the cap set for this initial launch. The students were at dif- ferent stages in their educational careers, from a variety of educational disciplines and, although all were current students in universities in Western Canada, they came from various parts of the world, many from the Global South. Nineteen students were registered at the host university, with one or two from each of four other uni- versities. Many students from the class had already established careers - including one as an engineer, one as a university instructor, four nurses, a veterinarian, five qualified physicians and three medical residents. The remainder of the class identified themselves simply as full-time students. Three data collection methods were used for this study: an online survey on attitudes with a pre-course questionnaire as well as a retrospect- ive pre-post questionnaire; individual interviews of students and faculty of the course; and participant observation. Interviews All students, co-instructors and guest faculty involved in the course were invited to a one-on-one semi-structured interview, conducted by lead author LS, who was not af- filiated with the universities involved and not part of the teaching team. Nine students volunteered to participate as did all three lead course instructors, the PhD teaching assistant, and a senior faculty member and global health leader who participated as a facilitator in the face-to-face portion of the course. All interviews were audio- recorded, transcribed verbatim and analyzed using the- matic analysis. NVivo 12 (QSR International Pty Ltd) was used to manage the data and categorize the text re- lated to the priori and emergent themes. Statement 3 Local stakeholders do not need to be involved in all parts of the research process such as developing research ques- tions, determining data collections sites, and writing the final scientific paper, as they are often too busy. Results all statements, except statement 1, demonstrating that students, in retrospect, characterized their previous atti- tudes, values and motivations related to global health re- search differently than they had done before they had taken the course. Participant observation LS acted as a “participant observer” throughout the course itself, interacting with students and faculty as well as observing class discussions and instructor meetings. After the completion of the course, she consolidated all collected information to contextualize the data gathered through surveys and interviews. Observations offered by the co-authors were also incorporated, but, because of their positionality, care was taken to ensure that these observations did not influence the data reported herein. Page 4 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Fig. 1 Comparing consistency of student responses with CCGHR principles pre-program, retrospectively pre-program, and post program. A paired t-test was used to determine significant differences between the average responses in the pre-course ratings, retrospective pre-course ratings and post course ratings (n = 19). Differences that are significant at the 95% level are indicated with an asterisk (*). See text under methods section for full statements Fig. 1 Comparing consistency of student responses with CCGHR principles pre-program, retrospectively pre-program, and post program. A paired t-test was used to determine significant differences between the average responses in the pre-course ratings, retrospective pre-course ratings and post course ratings (n = 19). Differences that are significant at the 95% level are indicated with an asterisk (*). See text under methods section for full statements How the course influenced student attitudes towards global health research students really absorbed so much of the topics that we wanted them to think about and read and discuss among themselves (Faculty 3).” “I think all partners benefit, and if research partners are not benefiting equally, then the research process should be revised to ensure properly shared benefits.” After learning about the CCGHR principles, students commonly referred to them as a framework to guide fu- ture participation in global health research: Students also demonstrated a greater understanding of the concept of humility and the ability to reduce subjectivity in qualitative research by creating dialogue between themselves and community participants on how they are positioned in their own research. The following quotes demonstrate stu- dent beliefs that acknowledge the importance of constant re- flection after the completion of the course: “I think that the guidelines [principles] are a great lens to look at all research … []...not just research, but any partnership or recognizing any sort of rela- tionship where there may be inequity and power … [] … not only global health relationships, but other areas of research, especially in Canada like Indigen- ous populations, or working with marginalized popu- lations (student 6).” “Dialogue between the researcher and their col- leagues, supervisors, and community members is es- sential in ensuring that the researcher’s assumptions and beliefs don’t affect the research project.” During the interviews, many students demonstrated an ability to critique research projects and research articles now that they are aware of the principles. Student 2 stated: “Researchers in a position of power must always en- gage in self-reflection of where they stand in relation to the communities that they are engaging in.” “I’m actually very, very grateful because I can call on those principles to question and critically evalu- ate any proposed research project intervention.” A quarter of the class initially thought that global health research would be unlikely to provide harm to targeted communities. One student noted, “although sus- tainability may be an issue, the work involved may be providing some kind of service to the communities for the duration of the project.” Students would commonly reflect on their past experi- ences in global contexts and express how they wished they had taken this course and had their current know- ledge before pursuing these initiatives in the past. How the course influenced student attitudes towards global health research Throughout the course, excitement and desire from stu- dents to continually discuss aspects of ethical global health research was observed through online discussion posts and during the face-to-face event. The results of the pre-course, retrospective pre-course and post-course ratings revealed that students had gained a greater appreciation of the principles of equitable global health research after the completion of the course. As demon- strated in the figure below (See Fig. 1), there was a sig- nificant difference between the average Likert scores in retrospective pre-course ratings and post-course ratings for all statements. The average scores in the surveys shifted in a direction that demonstrated an evolution of student attitudes towards global health work that more closely aligned with the CCGHR research principles. There was a significant difference between the pre- course ratings and retrospective pre-course ratings from When students were asked how researchers in the Global North can promote the participation of people who are historically marginalized in their research in the Global South, after the course, there was an 18.5% in- crease in the number of students who chose to collabor- ate with their colleagues in the Global South to identify all relevant stakeholders. Students had an increased awareness of the importance of the principle of inclu- sion, as illustrated by comments in the post-course sur- vey noting that “Colleagues in the global south would be familiar with the struggles of marginalized groups.” Prior to taking the course, when students were asked to select all partners who benefit from global health re- search, ~ 80% of the class chose research participants and communities involved in research; whereas, after the Page 5 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Stallwood et al. BMC Medical Education (2020) 20:224 Stallwood et al. BMC Medical Education (2020) 20:224 faculty and students and complete high-quality final pro- jects. A faculty member stated: completion of the course, 95.8% of the class chose re- search participants and 100% of the class chose com- munities involved in research. Students evolved a greater appreciation to provide benefits to all individ- uals involved in the research process. One student wrote: “It’s quite impressive to see in such a short period of time … [] ... How the course influenced student attitudes towards global health research Student 1 reflected on her previous work with a humani- tarian medical non-governmental organization: After the completion of the course, no students held the belief that service to LMICs is always positive and al- most 70% of the class demonstrated awareness of the unforeseen harm that can indeed result from HIC activ- ities in the Global South, regardless of good intentions. The following quotes from after the completion of the course exemplified this view: “Were we actually widening inequalities with the pro- grams we’re implementing or were we really thinking about sustainability? … []... If I were to go back and work with the organization, I’d want to be more in- volved in how these decisions are being made.” “Without the application of all principles, harm may be done unintentionally at the direct community or broader levels.” Successes and challenges experienced by students and course instructors A student noted: “The diversity of students, I think it’s another hall- mark of this course … []...we had this really mature and diverse group of students who were keen, who were enthusiastic about the course … [] … this was a dream group of students that I would imagine this course being taken by (Faculty 3).” “The diversity of students, I think it’s another hall- mark of this course … []...we had this really mature and diverse group of students who were keen, who were enthusiastic about the course … [] … this was a dream group of students that I would imagine this course being taken by (Faculty 3).” “I think having the three instructors was amazing … []... it is better than having just the one professor, be- cause I got to see so many examples and experiences, and that really spoke to like Global Health, having those different experiences and how every relation- ship is different (Student 6).” Some challenges were faced due to the hybrid and multi-institutional nature of this course which precluded a lot of interaction for preparation within the instructor team. A faculty member explained that the course had to be developed and taught by … A faculty member demonstrated similar thoughts: “Very busy people with their travel schedules, with their own teaching commitments and pro- jects going on … []...I know how much effort it took to do that … relying on online communica- tion presented some challenges, especially at the beginning, but then all our team members were able to adopt … []...to that way of working to- gether (Faculty 3).” “All the principles … []... are just the pivotal things to whether a Global Health project will be successful or not and have any impact that’s useful to the people for whom it supposedly created to serve. And it’s lifelong learning. All of us have to learn that it’s not something that you can read in a book. Successes and challenges experienced by students and course instructors And so, the more you can interact with people about their experiences … []...I think, the better (Faculty 1).” Two course leaders described the challenging nature to coordinate three instructors of a course, particu- larly as the instructors apparently did not know the content of each other’s presentations until they were given, had never discussed their views on various is- sues in global health and had not determined how adjustments would be made if, for unforeseen reasons, sessions went overtime. In terms of lessons learned, Faculty 1 said: There was a strong desire expressed from three stu- dents to have research partners from the Global South involved directly in the delivery of the course. Student 9 emphasized this view by stating: “I just wish some other perspectives were presented, especially perspectives from the Global South. We are in a class, a global health class, and everybody who is teaching us about global health are [based] local [ly].” “I think the first thing that I learned is the need to spend more time talking with colleagues about their visions and to not just assume that we’re all on the same wavelength and that we all have the same un- derstanding of how things are going to flow.” Through observation, it was apparent that the course included many global perspectives from both instructors and students with vast experience and expertise on vari- ous topics of global health. Many of the discussions, class comments and presentations were initiated by stu- dents from the Global South or students who have worked in the Global South or with marginalized popu- lations. The instructor team was composed of three women, two of whom are racialized and not “main- stream white”, and the teaching assistant was African - born and raised in Ghana. Nonetheless, another weak- ness of the course identified by some students was the Successes and challenges experienced by students and course instructors The greatest perceived success was partnering across dif- ferent universities to develop and deliver this unique course based on the CCGHR principles. This was a com- mon view amongst all faculty members, and was illus- trated by the following quote from faculty 1: “I think that even with good intentions, there may be a lot of unanticipated harm to the communities, and all researchers should be aware of this so that we know that it’s not enough to have good intentions.” “The first success is that we now have a credit course that’s based on the application of the principles of CCGHR. That in itself I think is a big success. I think Students absorbed concepts and elements from class discussions in a short duration of time and used these skills and evolved attitudes to prompt discussions with Page 6 of 9 Page 6 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 the fact that we’re running it as a multi-institutional course itself is a success as well. So, both the fact -- the content innovation and the institutional innovation is a success, of course.” lack of Indigenous perspective, recognized as increas- ingly important in developing an anti-colonial attitude in global health work. Despite the lack of Indigenous stu- dents or faculty, all faculty members mentioned the quality and diversity of the students in the class as an important positive feature of the course. A faculty mem- ber stated: The majority of participants, including students and instructors, agreed that having three professors, one teaching assistant and other global health experts to fa- cilitate the course was a positive feature. Students men- tioned that this teaching style provided them with multiple perspectives, experiences and feedback relative to the global health principles. Discussion Student interest in global health has grown over the last two decades, yet, despite the acknowledgement of the importance of ethical conduct [3, 13] respectful partner- ships [9, 14], and the increasing appreciation that atti- tudes of health professionals undertaking research in LMICs is a better predictor of success than the profes- sional’s knowledge or skill set [15], few courses are avail- able that focus on principles for promoting equity in global health research. As such, courses such as this one merit attention to reorient global health education to focus not only on knowledge and technical skills but also on attitudes of aspiring global health professionals. Nonetheless careful scrutiny is needed as to how such courses are offered. “Of course, I teach or incorporate the principles as part of the course that I’m teaching, absolutely, and I’m sure other Global Health instructors do … []... But, this course is of course different because the en- tire course was supposed to be built around the prin- ciples … [] … So, I think the course is unique from that perspective … []... they were the central piece of this course” (Faculty 3). The following quote from student 6 expressed this view: “I’d say that usually it’s [global health courses] 80% content and 20% application whereas this course was very group focused and a lot more on applica- tion. It had a lot less reading and a lot more doing which was a different way of doing the course, and a different way of learning.” This course was developed to address a perceived gap in global health education by providing postgraduate medical students and other health professionals with an ethical framework to undertake equitable global health research. Students and instructors recounted this course as unique due to its focus on attitudes, values and prac- tices of research rather than content learning, which is seen as a limitation of current global health education [8]. Through observation, surveys and interviews, it was evident that students formed stronger attitudes neces- sary to conduct ethical and equity-centered research. Not only did students acquire knowledge about ethical principles to which they previously may not have been introduced, but students were able to reflect on their evolved values and attitudes from the course and discuss how these novel attitudes will be pivotal in the future while undertaking global health research. How the course could fill a gap in current global health education The instructors of this course had taught other global health graduate courses and many of the students had taken other global health courses as well. All mentioned that previous courses they taught or took focused more on content and informational learning. Page 7 of 9 Page 7 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Stallwood et al. BMC Medical Education (2020) 20:224 “I think that we spend a lot of time in schools teaching knowledge, but not as much on trans- formative learning, attitudes and real-world prob- lem solving. And I think especially in Global Health or for that matter working with indigenous communities, the principles are so important … []...Other courses I’ve taught have been much more focused on the content (Faculty 1).” more than talk. … [] … But unfortunately, many of us learn it through harsh lessons with broken part- nerships and grants not continuing. That could be the reason why you are not having the type of trust and synergy with the communities that you are try- ing to work with. Yeah, so it’s very important for me that students understand those concepts [CCGHR principles] or at least think about them before en- gaging in global health work (Faculty 3).” This point was emphasized when another instructor described a graduate global health course that she taught, Discussion To our know- ledge, this is the only multi-institutional and interdiscip- linary course that has been developed and implemented in Canada at a graduate level and focused specifically on student attitudes and practices rather than content learning. Our findings in this regard thus dovetail with those of Peluso and colleagues that global health educa- tion should focus on the attitudes and practices of stu- dents who will deal with marginalized populations in their fieldwork [16]. When the student was asked whether any previous global health course that she has taken focused on atti- tudes for global health research, the response was: “No, no, no. They never brought in that. The first time I went for the BCCI event was when they brought in the aspect of value. Nobody ever talks about values, values of inclusion and … [] ...humility (student 6).” “No, no, no. They never brought in that. The first time I went for the BCCI event was when they brought in the aspect of value. Nobody ever talks about values, values of inclusion and … [] ...humility (student 6).” Student 5 commented that this course could be rec- ommended because it “brings out the fundamental ques- tions that some people actually take for granted or may under-look.” In a description of the course’s value, an instructor said: “For us mentors to work with our students early on to understand that … []...yes, we have this privilege of having resources and coming from a place where knowledge is more accessible … []...we have to con- sider the concept of humility and shut up and listen When comparing the pre-course ratings to the retro- spective pre-course ratings, it became evident that stu- dents changed their understandings regarding appropriate Stallwood et al. BMC Medical Education (2020) 20:224 Stallwood et al. BMC Medical Education (2020) 20:224 Page 8 of 9 Page 8 of 9 lead multiple global health initiatives, they were all cur- rently living in the Global North. Other universities have made better use of online learning modalities to create direct partnering between North and South and some- times across institutions in multiple countries. For ex- ample, McMaster University’s Master of Science in Global Health program is delivered through a model in which universities from several continents offer joint learning. Discussion Such programs underline the perspective that global health is not about the Global North working with the Global South to address problems in the Global South, but rather facilitates a larger global perspective on our interconnected world and its unequal implica- tions for health equity. Perhaps future offerings of this course can expand in this regard. attitudes for global health research from prior to taking the course; therefore, had we only compared the original pre-course ratings to post-course ratings, the data would not have exhibited the true extent to which students learned from the course. The retrospective pre-course score, based on a greater understanding of the issues in- volved, therefore seemed to be more accurate in assessing attitudes of the students before the course and revealed that students acquired new insight that enabled them to see limitations in their previous views and attitudes to- wards global health research that they had not seen at the start of the class. Our approach thus echoed the findings of others [17] on the value of a retrospective pre-post analysis. y Inter-institutional, interdisciplinary approaches and in- terprofessional collaboration have been identified as use- ful in delivering global health courses [16, 18], and interdisciplinary teaching has produced the type of changes in student knowledge, attitudes, beliefs and skills that align well with the purpose of this course [19]. However, some students and instructors alike commen- ted on challenges attributable to having three professors leading the course, whose views were not perfectly aligned. Some participants in this course found the lack of clarity in leadership during the three-day workshop to be detrimental, while others liked the informality, the absence of the traditional hierarchy between instructors and students, and the multiplicity of views and ap- proaches. Peluso and colleagues [16] noted that differ- ences amongst faculty sometimes raise tensions and emphasized the importance of clarifying roles and re- sponsibilities of each faculty member involved. The di- versity of the cohort of students in this course was another important feature. Students from many profes- sions, places of origin and varying stages in their educa- tional and professional careers mimicked the type of collaboration that often exists in the interdisciplinary field of global health. Conclusion Global health education has been slow to provide re- searchers and practitioners with the necessary attitudes to address common issues that arise while undertaking global health work. This study showed a clear evolution of students’ views regarding global health research and practice, with evidence indicating that students acquired an increased understanding and appreciation of the CCGHR principles. With proper preparation and strat- egies to address challenges related to the multi- instructor, multi-dimensionality of the course, and en- suring a stronger Indigenous presence, concerns could be mitigated to ensure continued success. While longitu- dinal follow-up would be useful to ascertain the extent of application of the CCGHR principles in field settings, and direct involvement of institutions from the Global South could be advantageous, we argue that a course fo- cusing on changing attitudes, and contributing to build- ing a community-of-practice, is worth considering to promote the qualities widely believed to be of value in promoting global health. A limitation identified in the course was the recogni- tion of the lack of integration of Indigenous knowledge and concrete participation from First Nations communi- ties. Instructors committed to ensuring that future itera- tions of the course would have a better representation of Indigenous perspectives, with at least one session de- voted specifically to coloniality both in the Global North and Global South, and at minimum of one Indigenous guest speaker. Another limitation noted was that al- though the students and instructors had diverse personal and professional backgrounds and were involved in or HICs: High-income countries; LMICs: Low and middle-income countries; CCGHR: Canadian Coalition for Global Health Research; CIHR: Canadian Discussion Adams and colleagues [1] acknowledged the challenge of working in interdisciplinary teams with varying perspectives that do not always align, but the au- thors noted the importance for evolving global health pro- fessionals to adopt skills and experience that will allow them to effectively work in these environments. Importantly, this course not only emerged from the BC Coalition for Global Health, that runs a summer in- stitute every second year, but students in the course are supported to participate in the summer institute, pre- senting the projects they developed in class. This helps solidify the involvement of trainees in a community-of- practice of global health practitioners and researchers, which itself may serve to encourage application of the principles, further preparing the next generation of glo- bal health researchers. Naidoo and Vernillo illuminated the value of a community of practice, a group of individ- uals with a common interest and desire to contribute to improving health ethics and strengthen the broader community through interdisciplinary collaboration [20]. Abbreviations HICs: High-income countries; LMICs: Low and middle-income countries; CCGHR: Canadian Coalition for Global Health Research; CIHR: Canadian Page 9 of 9 Page 9 of 9 Page 9 of 9 Stallwood et al. BMC Medical Education (2020) 20:224 Institute for Health Research; BC: British Columbia; BCCI-1: BC Coalition Institute 8. Eichbaum Q. The problem with competencies in Global Health education. Acad Med. 2015;90(4):414–7. 9. Plamondon KM, Bisung E. The CCGHR principles for Global Health research: centering equity in research, knowledge translation, and practice. Soc Sci Med. 2019;239:112530. Acknowledgments The authors wish to thank all the students who participated in this research and Karen Lockhart for her helpful feedback on early drafts of this manuscript. 10. Canadian Coalition for Global Health Research (CCGHR). Principles for global health research. 2017. Available from: http://www.ccghr.ca/resources/ principles-global-health-research/. 11. Global health research training module. 2020. Available from: https://cihr- irsc.gc.ca/lms/e/globalhealth/. Accessed 28 July 2019. Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. 18. Liu Y, Zhang Y, Liu Z, Wang J. Gaps in studies of global health education: an empirical literature review. Glob Health Action. 2015;8:25709. 19. Cooper H, Carlisle C, Gibbs T, Watkins C. Developing an evidence base for interdisciplinary learning: a systematic review. J Adv Nurs. 2001;35(2):228–37. Funding This work was supported by the Canadian Institutes of Health Research (CIHR) grant ROH-115212: “Promoting Health Equity by Addressing the Needs of Health Workers: A Collaborative, International Research Program”. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 16. Peluso MJ, Hafler JP, Sipsma H, Cherlin E. Global health education programming as a model for inter-institutional collaboration in interprofessional health education. J Interprof Care. 2014;28(4):371–3. 17. Bhanji F, Gottesman R, de Grave W, Steinert Y, Winer LR. The retrospective pre-post: a practical method to evaluate learning from an educational program. Acad Emerg Med Off J Soc Acad Emerg Med. 2012;19(2):189–94. Authors’ information Not applicable. 15. Ventres WB, Wilson CL. Beyond ethical and curricular guidelines in global health: attitudinal development on international service-learning trips. BMC Med Educ. 2015;15:68. Publisher’s Note Consent for publication Not applicable. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Competing interests The authors declare that they have no competing interests. Received: 28 April 2020 Accepted: 6 July 2020 Received: 28 April 2020 Accepted: 6 July 2020 Received: 28 April 2020 Accepted: 6 July 2020 Ethics approval and consent to participate 20. Naidoo S, Vernillo AT. Adapting a Community of Practice Model to design an innovative ethics curriculum in healthcare. Med Princ Pract. 2014; 23(Suppl 1):60–8. Ethics approval was obtained from the University of British Columbia Behavioural Ethics Review Board (certificate # H19–01487). Written informed consent was given by all participants in the study. Behavioural Ethics Review Board (certificate # H19–01487). Written informed consent was given by all participants in the study. Authors’ contributions LS designed the study, collected, analyzed, interpreted the data and drafted the manuscript; PA, KT, BA, and AY all provided substantial contributions to the conception of the work, and participated in the drafting and revising of the manuscript. All authors read and approved the final manuscript. 12. Rockwell SK, Kohn H. Post-Then-Pre Evaluation. J Ext. 1989;27(2). Available from: https://www.joe.org/joe/1989summer/a5.php. Accessed 28 July 2019. 13. Godard B, Haddad S, Huish R, Weinstock D. Introduction to ethics and Global Health. BMC Med Ethics. 2018;19(1):51. 14. Boum Y, Burns BF, Siedner M, Mburu Y, Bukusi E, Haberer JE. Advancing equitable global health research partnerships in Africa. BMJ Glob Health. 2018;3(4):e000868. Author details 1 Author details 1Faculty of Health Science, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. 2School of Population and Public Health, University of British Columbia, 2206 E Mall, Vancouver, BC V6T 1Z3, Canada. 3British Columbia Centre for Disease Control, 655 W 12th Ave, Vancouver, BC V5Z 4R4, Canada. 4Faculty of Health Sciences, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada. 5School of Nursing, Trinity Western University, 7600 Glover Rd, Langley, BC V2Y 1Y1, Canada. References 1. Adams LV, Wagner CM, Nutt CT, Binagwaho A. The future of global health education: training for equity in global health. BMC Med Educ. 2016;16(1): 296. 1. Adams LV, Wagner CM, Nutt CT, Binagwaho A. The future of global health education: training for equity in global health. BMC Med Educ. 2016;16(1): 296. 2. Murphy J, Hatfield J, Afsana K, Neufeld V. Making a commitment to ethics in global health research partnerships: a practical tool to support ethical practice. J Bioethical Inq. 2015;1:137–46. 3. Yassi A, Breilh J, Dharamsi S, Lockhart K, Spiegel JM. The ethics of ethics reviews in Global Health research: case studies applying a new paradigm. J Acad Ethics. 2013;11(2):83–101. 4. Addiss DG, Amon JJ. Apology and unintended harm in Global Health. Health Hum Rights. 2019;1:19–32. 5. Pinto AD, Upshur REG. Global health ethics for students. Dev World Bioeth. 2009;9(1):1–10. 6. Kim JU, Oleribe O, Njie R, Taylor-Robinson SD. A time for new north-south relationships in global health. Int J Gen Med. 2017;10:401–8. 7. Crump JA, Sugarman J. Training (WEIGHT) the WG on EG for GH. Ethics and best practice guidelines for training experiences in Global Health. Am J Trop Med Hyg. 2010;83(6):1178–82.
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Qeios · Definition, February 8, 2020 Open Peer Review on Qeios Nasal Cavity and Paranasal Sinuses Cancer pN2 TNM Finding v8 National Cancer Institute Qeios ID: B1U4FU · https://doi.org/10.32388/B1U4FU Source National Cancer Institute. Nasal Cavity and Paranasal Sinuses Cancer pN2 TNM Finding v8. NCI Thesaurus. Code C133062. Nasal cavity and paranasal sinuses cancer with metastasis in a single ipsilateral lymph node, 3 cm or smaller in greatest dimension and ENE(+); or metastasis in a single ipsilateral lymph node larger than 3 cm but not larger than 6 cm in greatest dimension and ENE(-); or metastases in multiple ipsilateral lymph nodes , none larger than 6 cm in greatest dimension and ENE(-); or metastases in bilateral or contralateral lymph nodes, none larger than 6 cm in greatest dimension and ENE(-). (from AJCC 8th Ed.) Qeios ID: B1U4FU · https://doi.org/10.32388/B1U4FU 1/1
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Boletín de Estudios Económicos Bulletin of Economic Studies Haciendo realidad la revolución ASG Making the ESG revolution a reality Vol. LXXVII / Diciembre 2022 Núm. 233 DOI: https://doi.org/10.18543/bee772332022 PRÓLOGO / FOREWORD Valores ASG y su efecto en las organizaciones ESG values and their effect on organisations Laura Baselga-Pascual, Guillermo Badía doi: https://doi.org/10.18543/bee.2642 Publicado en línea: marzo de 2023 Acceso Abierto, Copias Impresas y Derechos de Autoría El Boletín de Estudios Económicos es una revista de acceso abierto, lo que significa que todo el contenido está disponible gratuitamente para los usuarios y sus instituciones. Los usuarios pueden leer, descargar, copiar, distribuir, imprimir, buscar o enlazar los textos completos de los artículos, o utilizarlos para cualquier otro fin lícito, sin pedir permiso previo a la Editorial o al autor; siempre que se cite adecuadamente el trabajo original y se indique claramente cualquier modificación del mismo. 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Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 https://bee.revistas.deusto.es DEUSTO BUSINESS ALUMNI BOLETIN DE ESTUDIOS ECONOMICOS Vol. LXXVII - N.º 233 - Diciembre 2022 doi: https://doi.org/10.18543/bee772332022 Valores ASG y su efecto en las organizaciones Laura Baselga-Pascual Guillermo Badía Deusto Business School Editores Invitados del número especial “Los Valores ASG: ¿cómo hacerlos realidad en las organizaciones?” doi: https://doi.org/10.18543/bee.2642 Publicado en línea: marzo de 2023 La iniciativa de este Número Especial del Boletín de Estudios surge con la pretensión de establecer un foro donde ahondar y extender el conocimiento en las múltiples temáticas de investigación relacionadas con los criterios ambiental, social y de buen gobierno (ASG), y su efecto en las organizaciones. En este número se abordan problemáticas desde distintas perspectivas con el objetivo de generar un conocimiento holístico. Algunas de las cuestiones que surgen en este campo y que todavía están por superar son, por ejemplo: • Buen gobierno corporativo: ¿Cómo podemos medirlo? ¿Qué tipos de indicadores existen? ¿Cómo se construyen? ¿Son los indicadores disponibles buenas aproximaciones del buen gobierno? ¿Qué relaciones existen entre el buen gobierno y el desempeño de la organización? • Compromiso social y medioambiental de las organizaciones: ¿En qué medida pueden las organizaciones contribuir a un mundo descarbonizado? ¿Pueden tener un impacto positivo sobre el calentamiento global? ¿Qué productos financieros se consideran sostenibles? ¿Son los productos financieros sostenibles más rentables? ¿Proporcionan una mayor diversificación al inversor? ¿Reducen el riesgo? • Impacto social de la empresa: ¿Qué políticas favorecen el desarrollo del capital humano en las organizaciones? ¿Están las buenas práctiBoletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 https://bee.revistas.deusto.es 14 LAURA BASELGA-PASCUAL Y GUILLERMO BADÍA cas respecto a políticas sociales vinculadas al desempeño y/o valoración de las empresas? • Inversión socialmente responsable (ISR): ¿Cuál es el objetivo de las ISR? ¿Es posible la descarbonización del planeta y el crecimiento económico? ¿Puede contribuir la ISR a una mayor estabilidad financiera? ¿Cómo se trasladan las políticas y valores ASG a las entidades financieras? ¿Es la inversión de impacto una opción verdaderamente sostenible? • Nuevas regulaciones vinculadas a las finanzas sostenibles: Informes no financieros, obligaciones sobre divulgación, nueva taxonomía de la UE, normativa vinculada a la economía circular. Estas cuestiones son de gran relevancia dada la evolución de los valores ASG en las organizaciones que ha tenido lugar en los últimos años. Inicialmente se consideraba algo accesorio, ornamental; posteriormente un elemento diferenciador; y, hoy en día, son condición necesaria, aunque no suficiente, para competir en un mercado global comprometido. La responsabilidad social y medioambiental derivada del compromiso con los factores ASG en las organizaciones se encuentra ligada a una mejor gobernanza y mayores estándares éticos. De la búsqueda del beneficio para el accionista, se ha evolucionado a satisfacer las necesidades de otros grupos de interés, lo que, en última instancia, parece estar relacionado con el valor de la organización y puede conducir a un círculo virtuoso. Sin embargo, a pesar de las iniciativas relacionadas con la sostenibilidad en los últimos años, la ciencia sigue señalando que el estado del entorno continúa deteriorándose. Por ejemplo, el estudio de 2021 de EUROSIF (Foro Europeo sobre Inversión Sostenible)1 señala que el cambio climático se está acelerando impulsado por un aumento continuo de la temperatura global, la pérdida de biodiversidad se está produciendo a un ritmo sin precedentes, y las disparidades socioeconómicas han aumentado. Este panorama alienta un proceso de reflexión y discusión acerca de nuevas herramientas y mecanismos alternativos que permitan diseñar y construir una economía realmente sostenible, tanto medioambiental como socialmente. Durante las últimas décadas, los participantes en los mercados financieros han ido acogiendo progresivamente aspectos relacionados con la 1 https://www.spainsif.es/wp-content/uploads/2021/10/Presentacion-estudio-anual-.pdf Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 doi: https://doi.org/10.18543/bee.2642 • https://bee.revistas.deusto.es VALORES ASG Y SU EFECTO EN LAS ORGANIZACIONES 15 sostenibilidad al incluir en sus procesos de inversión y financiación criterios no financieros, como los ASG. A principios de 2020, según el Global Sustainable Investment Review (GSIR), la inversión sostenible mundial alcanzó los 35,3 billones de dólares en cinco grandes mercados (Australasia, Canadá, Europa, Estados Unidos y Japón), lo que supuso un aumento del 15% en los últimos dos años (2018-2020). El mercado español en particular también siguió manteniendo la senda de crecimiento de años anteriores. Los activos ASG nacionales aumentaron en un 10% con respecto a 2019 (Estudio Spainsif, 2021). Desde la perspectiva de la inversión, según la Comisión Europea, la incorporación de los factores ASG en las decisiones conduce a inversiones a más largo plazo en actividades y proyectos económicos sostenibles. Las consideraciones medioambientales podrían incluir la mitigación del cambio climático y la adaptación al mismo, así como las relativas al medio ambiente en general como, por ejemplo, la preservación de la biodiversidad, la prevención de la contaminación y la economía circular. Las consideraciones sociales se refieren a cuestiones de desigualdad, inclusión, relaciones laborales, inversión en capital humano y comunidades, así como a cuestiones de derechos humanos. La gobernanza de las instituciones públicas y privadas —incluidas las estructuras de gestión, las relaciones con los empleados y la remuneración de los ejecutivos— desempeña un papel fundamental para garantizar la inclusión de las consideraciones sociales y medioambientales en el proceso de toma de decisiones. Por su parte, desde la perspectiva de la financiación, las finanzas sostenibles se entienden como aquella financiación que favorece el crecimiento económico, pero reduciendo al mismo tiempo las presiones sobre el medio ambiente y teniendo en cuenta los aspectos sociales y de gobernanza. La academia en general, y la investigación en particular, desempeñan un papel destacado en la configuración y desarrollo de sistemas innovadores alternativos a través de publicaciones científicas y de transferencia que permitan la posterior divulgación de los resultados. En este número se presentan varios artículos de investigación y transferencia que favorecen dicho desarrollo. Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 doi: https://doi.org/10.18543/bee.2642 • https://bee.revistas.deusto.es ESG values and their effect on organisations Laura Baselga-Pascual Guillermo Badía Deusto Business School Guest Editors of the special issue entitled ‘ESG values: how to make them a reality in organisations’ The motivation for this Special Issue of the Bulletin of Economic Studies was triggered by the goal to provide a forum to further and disseminate the knowledge about the multiple research topics related to environmental, social and good governance (ESG) criteria, and their effect on organisations. This issue addresses several themes from different perspectives with the aim of generating holistic knowledge. Some of the issues that arise in this field and have yet to be overcome include: • Good corporate governance: How can it be measured? What types of indicators exist? How are they constructed? Are the available indicators good proxies for good governance? What is the relationship between good governance and organisational performance? • The social and environmental commitment of organisations: To what extent can organisations contribute to a decarbonised world? Can they have a positive impact on global warming? What financial products can be considered to be sustainable? Are sustainable financial products more profitable? Do they provide greater investor diversification? Do they reduce risk? • Companies’ social impact: What policies support the development of human capital in organisations? Are good practices regarding social policies linked to companies’ performance and/or value? • Socially Responsible Investment (SRI): What is the purpose of SRI? Is it possible to have both a decarbonised planet and economic growth? Can SRI contribute to greater financial stability? How are ESG Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 https://bee.revistas.deusto.es 18 LAURA BASELGA-PASCUAL AND GUILLERMO BADÍA policies and values brought into financial institutions? Is impact investing a truly sustainable option? • New regulations linked to sustainable finance: non-financial reporting, disclosure obligations, new EU taxonomy, regulations linked to the circular economy. These issues are highly important given the development of ESG values that has taken place in organisations in recent years. They were initially seen as a superfluous, merely decorative feature; later they were perceived as a differentiating element; and today they are a necessary— albeit insufficient—condition for competing in an engaged global market. Social and environmental responsibility derived from a commitment to ESG factors in organisations is linked to better governance and higher ethical standards. There has been a shift from merely maximising shareholders’ profits to meeting the needs of other stakeholders, which ultimately seems to be connected with organisational value and can lead to a virtuous circle. However, despite the sustainability-related initiatives in recent years, scientific research still shows that the state of the environment continues to deteriorate. For example, the 2021 Eurosif (European Sustainable Investment Forum)1 Report noted that climate change is accelerating driven by a continued rise in global temperature, biodiversity loss is occurring at an unprecedented rate, and socio-economic disparities have increased. This scenario urges a process of reflection and discussion about new tools and alternative mechanisms to design and build a truly sustainable economy, both environmentally and socially. In recent decades, financial market participants have progressively embraced sustainability by including non-financial criteria such as ESG values in their investment and financing processes. At the start of 2020, according to the Global Sustainable Investment Review (GSIR), global sustainable investment reached US$35.3 trillion across five major markets (Australasia, Canada, Europe, the United States and Japan), a 15% increase over the previous two years (2018-2020). In particular, the Spanish market also followed the path of sustained growth as in previous years. Domestic ESG assets increased by 10% compared to 2019 (Spainsif study, 2021). From an investment perspective, according to the Euro- 1 https://www.spainsif.es/wp-content/uploads/2021/10/Presentacion-estudio-anual-.pdf Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 doi: https://doi.org/10.18543/bee.2642 • https://bee.revistas.deusto.es ESG VALUES AND THEIR EFFECT ON ORGANISATIONS 19 pean Commission, incorporating ESG factors into investment decisions leads to longer-term investments in sustainable economic activities and projects. Environmental considerations could include climate change mitigation and adaptation, as well as broader environmental considerations such as the preservation of biodiversity, pollution prevention and the circular economy. Social considerations relate to issues of inequality, inclusion, labour relations, investment in human capital and communities, as well as human rights issues. The governance of public and private institutions— including management structures, employee relations and executive compensation—plays a key role in ensuring that social and environmental considerations are included in the decision-making process. From a financing perspective, sustainable finance is understood to be financing that supports economic growth while reducing pressures on the environment and taking into account social and governance aspects. Academia in general, and research in particular, plays a leading role in shaping and developing alternative innovative systems through research and knowledge transfer publications for the subsequent dissemination of results. This issue contains a number of research and knowledge transfer articles that support this development. Boletín de Estudios Económicos ISSN (Papel): 0006-6249 • ISSN (Electrónico): 2951-6722 • Vol LXXVII - N.º 233 - Diciembre 2022, págs. 13-19 doi: https://doi.org/10.18543/bee.2642 • https://bee.revistas.deusto.es
https://openalex.org/W4280608141
https://sapientia.ualg.pt/bitstream/10400.1/18472/1/fgene-13-866758.pdf
English
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2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation
Frontiers in genetics
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cc-by
13,750
ORIGINAL RESEARCH published: 16 May 2022 doi: 10.3389/fgene.2022.866758 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation Miriam Ruocco 1*, Marlene Jahnke 2*, João Silva 3, Gabriele Procaccini 1 and Emanuela Dattolo 1 1Stazione Zoologica Anton Dohrn, Naples, Italy, 2Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden, 3Centre of Marine Sciences, University of Algarve, Faro, Portugal Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein- coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients. Edited by: Serena Aceto, University of Naples Federico II, Italy Reviewed by: Lauric Reynes, UMI3614 Biologie évolutive et écologie des algues (EBEA), France Aline Finger, Royal Botanic Garden Edinburgh, United Kingdom Edited by: Serena Aceto, University of Naples Federico II, Italy Edited by: Serena Aceto, University of Naples Federico II, Italy Reviewed by: Lauric Reynes, UMI3614 Biologie évolutive et écologie des algues (EBEA), France Aline Finger, Royal Botanic Garden Edinburgh, *Correspondence: Miriam Ruocco miriam.ruocco@szn.it Marlene Jahnke marlene.jahnke@gu.se Specialty section: This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics Received: 31 January 2022 Accepted: 19 April 2022 Published: 16 May 2022 Keywords: seagrass, SNPs, 2b-RAD, outlier loci, latitude, flowering INTRODUCTION taxonomical diversity, they successfully colonized most coastal shores worldwide (Spalding, 2003; Larkum et al., 2006), providing fundamental ecosystem services (Ruiz- Frau et al., 2017) and contributing to climate change mitigation (Marbà et al., 2015; Stankovic et al., 2021). The current distribution of seagrass species along geographical and depth gradients is influenced by their tolerance window for environmental drivers, such as light, temperature and salinity (Short et al., 2007). Environmental heterogeneity in space and time can impose a strong selective pressure driving adaptive divergence of populations (Linhart and Grant, 1996; Bergland et al., 2016; Urban et al., 2020). Quantifying the extent of this differentiation and identifying loci underlying such divergence is a major aim of evolutionary and ecological genetics (Feder and Mitchell-Olds, 2003; Savolainen et al., 2013) and seascape genomics (Selkoe et al., 2016). Environmental gradients, where environmental factors change along a geographic scale, offer a great opportunity for understanding patterns and processes responsible for phenotypic changes of populations (Endler, 2020). There are examples from a variety of species, where phenotypes tend to change in predictable ways across large-scale gradients such as latitude, altitude, or water depth (Endler, 2020). These geographical patterns can reflect genetic variation or phenotypic plasticity and eventually represent adaptive variation in response to selection gradients (Conover et al., 2009; Sanford and Kelly, 2011; Schneider and Meyer, 2017). To date, population genetic studies in seagrasses have mostly relied on a limited number of nuclear DNA markers (e.g., simple sequence repeats, SSRs). Such studies have aided in resolving main geographic differentiation and structure of seagrass populations (e.g., Alberto et al., 2006; Arnaud-Haond et al., 2007; Alberto et al., 2008; Serra et al., 2010; Hernawan et al., 2017; Bijak et al., 2018; Jackson et al., 2021). Indices of genetic diversity based on SSRs have also been correlated with local environmental disturbances (Jahnke et al., 2015b), fundamental plant traits such as flowering synchronization (Jahnke et al., 2015a) and ecosystem functioning and resilience (Reusch et al., 2005; Hughes and Stachowicz, 2011). In a few studies, molecular polymorphisms have been functionally characterized through genome scan approaches and related to contrasting habitat types, depth and latitudinal gradients (Oetjen and Reusch, 2007; Oetjen et al., 2010; Jahnke et al., 2019). INTRODUCTION Yet, gene expression studies employing common-garden or reciprocal transplantation approaches have collectively suggested local adaptation of seagrass populations to thermal or light gradients (Franssen et al., 2011; Winters et al., 2011; Franssen et al., 2014; Jueterbock et al., 2016; Dattolo et al., 2017), even if the heritability of the observed phenotypic differences remain elusive. Variation in specific environmental variables (e.g., temperature or photoperiod) across geographical clines is directly related to aspects of phenotypic and genetic divergence among populations in land plants (Linhart and Grant, 1996; Hut and Beersma, 2011; Hut et al., 2013). For instance, climate is one of the most important drivers of adaptive phenotypic traits in forest trees (Richardson et al., 2009; Eckert et al., 2010). Fitness-related traits such as survival, growth and biomass partitioning have been shown to vary along temperature gradients associated with altitudinal and latitudinal clines or according to different precipitation and aridity regimes (Aitken and Hannerz, 2001; St Clair et al., 2005). Similarly, other traits associated with major life history events, e.g., seed dormancy and flowering time, were found to follow a clear latitudinal pattern in Arabidopsis thaliana accessions collected throughout the European range of the species (Debieu et al., 2013). In particular, timing of flowering across accessions was linked to molecular polymorphisms in key regulatory genes that control this trait, such as FRIGIDA and FLOWERING LOCUS C (Le Corre et al., 2002; Stinchcombe et al., 2004; Shindo et al., 2005). Cymodocea nodosa (Ucria) Ascherson is a marine dioecious angiosperm present throughout the Mediterranean Sea and the adjoining Atlantic coasts and the dominant species structuring subtidal seagrass ecosystems along North West Africa and South West Europe (Green and Short, 2003; Alberto et al., 2008). Recent species distribution models predict the most relevant environmental variables defining its distribution to be sea surface temperature (SST) and salinity (Chefaoui et al., 2016). Large inter-regional and local-scale variations in abundance and structure (i.e., morphology and biomass allocation), as well as the extant of sexual reproduction (as seed production) in C. nodosa have been described and correlated with different environmental conditions [i.e., seasonal patterns of Photosynthetically Active Radiation (PAR) and SST], and evolutionary contexts (i.e., genetic diversity) (Máñez-Crespo et al., 2020). Populations inhabiting distinct biogeographical regions have also been shown to possess a differential resilience, performance and recovery capacity under local perturbations (e.g., shading) (Tuya et al., 2019; Tuya et al., 2021). Citation: Ruocco M, Jahnke M, Silva J, Procaccini G and Dattolo E (2022) 2b- RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front. Genet. 13:866758. doi: 10.3389/fgene.2022.866758 May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 1 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. Frontiers in Genetics | www.frontiersin.org INTRODUCTION The higher sensitivity of certain meadows to disturbance, as those at the peripheral distribution of the species in the Canary Islands, has been attributed to their genetic isolation and low genetic diversity (Tuya et al., 2019; Tuya et al., 2021). An important geographic heterogeneity was also observed in C. nodosa plants In marine plants, these studies are still hampered due to the absence of genomic resources for most species (with few exceptions e.g., Zostera marina) and the general unfeasibility to perform molecular genetic studies across multiple generations. The reproduction of seagrasses under controlled conditions is indeed still challenging, and life cycles are often too long, which prevent identifying heritable variations (Hu et al., 2020; Pazzaglia et al., 2021). Seagrasses are the only group of flowering plants that has returned to the sea, (re)adapting their physiology and morphology to a completely submerged lifestyle (Wissler et al., 2011; Golicz et al., 2015; Lee et al., 2016; Olsen et al., 2016; Lee et al., 2018). Despite their low May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 2 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. FIGURE 1 | Sampling scheme and environmental characteristics of the selected sites. (A) Sampling locations of C. nodosa: GC—Las Palmas de Gran Canaria (Lat: 27°N, Canary Islands); FA—Faro (Lat: 36°N, Portugal); EB—Ebro Delta (Lat: 40°N, Spain). (B) Annual patterns of photoperiod for the different sampling sites. Daylight hours were derived from annual data and averaged for every 15 days (https://www.timeanddate.com). (C) Long term monthly means of Sea Surface Temperature (SST) registered on the Atlantic and Mediterranean waters from NOAA derived from data for years 1971–2000 (https://psl.noaa.gov/data/gridded/data.noaa.ersst.v4. html). FIGURE 1 | Sampling scheme and environmental characteristics of the selected sites. (A) Sampling locations of C. nodosa: GC—Las Palmas de Gran Canaria (Lat: 27°N, Canary Islands); FA—Faro (Lat: 36°N, Portugal); EB—Ebro Delta (Lat: 40°N, Spain). (B) Annual patterns of photoperiod for the different sampling sites. Daylight hours were derived from annual data and averaged for every 15 days (https://www.timeanddate.com). (C) Long term monthly means of Sea Surface Temperature (SST) registered on the Atlantic and Mediterranean waters from NOAA derived from data for years 1971–2000 (https://psl.noaa.gov/data/gridded/data.noaa.ersst.v4. html). from contrasting thermal environments (warm-adapted vs. cold- adapted plants) in response to heatwaves, in terms of diversion of carbon reserves and biomass allocation (Marín-Guirao et al., 2018). Frontiers in Genetics | www.frontiersin.org Study Sites and Sample Collection y p Individual shoots of Cymodocea nodosa were collected at three locations across the Atlantic-Mediterranean boundary from shallow-water meadows (1–4 m depth), thus encompassing most of the latitudinal distribution range of the species (Alberto et al., 2006; Cunha and Araújo, 2009). Collection sites were selected based on their geographic position along a latitudinal gradient and for sampling feasibility. Two sampling stations were located in the north-eastern Atlantic Ocean, i.e., Las Palmas de Gran Canaria (El pajar) (GC)—Canary Islands, Spain (27°45′14″N, 15°40′18″W) and in the Ria Formosa lagoon (Ilha da Culatra) (FA)—Faro, Portugal (36°59′23″N, 7°50′01″W), while the latter was located in the western Mediterranean Sea, i.e., Ebro Delta (EB)—Spain (40°34′48″N, 0°35′45″E) (Figure 1A). The Canary Islands represent the western distributional limit of the species, and are close to its southern distributional limit in Banc d’Arguin in Mauritania (Green and Short, 2003). The Ebro population represents the northernmost sampling site in our study, although the species extends up to the north Adriatic Sea (Venice lagoon, 45.60°N) (Rismondo et al., 2003; Sfriso and Facca, 2007). Bioinformatic analyses were performed using the computer cluster of the Bioinforma Service of Stazione Zoologica Anton Dohrn (SZN), Naples (Italy). As no genome sequence is currently available for C. nodosa, the analysis followed a modified de novo pipeline available at https://github.com/z0on/2bRAD_denovo. Reads were first ‘demultiplexed’ based on barcodes and then adaptors were removed, then a quality filtering was performed using the Fastx-toolkit (Gordon and Hannon, 2010). Only reads containing 100% bases with a PHRED quality score of at least 20 were retained for downstream analysis. After trimming and quality filtering, we obtained a total of 82,883,209 reads. Individually trimmed fastq files were then merged to collect tags found in at least two individuals with a minimum depth of five for genotyping. Reads that had more than seven observations without reverse-complement were removed. Subsequently, tags were clustered with CD-hit (Li and Godzik, 2006) allowing for up to three mismatches, followed by the creation of a “reads-derived reference genome” based on 30 fake chromosomes, on which individual trimmed fastq files were mapped back using Bowtie 2 aligner (Langmead et al., 2009). In Gran Canaria, daylight hours oscillate between 10 h d−1–14 h d−1 throughout the year (Figure 1B). In the other two sites, there are greater fluctuations of daylight during seasons: the minimum is ca. INTRODUCTION However, molecular studies addressing how environmental gradients could affect local adaptation of natural populations through adaptive genetic variation at specific loci are currently missing in this species. in marine engineering species (e.g., kelp, Guzinski et al., 2020; Fucales, Reynes et al., 2021a or Mediterranean corals, Pratlong et al., 2021) shedding first light on the detection of candidate SNPs for local adaptation of populations. In the present study, we used 2b-RAD genotyping (Wang et al., 2012) to characterize population differentiation and levels of genetic diversity among three populations of C. nodosa distributed along the Atlantic-Mediterranean transition region (i.e., Gran Canaria and Faro in the Atlantic and Ebro Delta in the Mediterranean; Figure 1A). Our main aim was to search for outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. The underlying hypothesis was that such genetic polymorphisms could be associated to local adaptation of populations to varying photoperiod-temperature regimes across latitudes. We also used SNP markers for assessing the clonality level of populations and compared these data, together with genetic diversity and differentiation, with estimates based on 7 SSR markers previously developed for the species. Restriction-site-associated DNA sequencing (RAD-Seq) techniques represent a family of cost-effective techniques compared to e.g., whole-genome sequencing that can be employed in non-model species without a reference genome and guarantee high-resolution population genomics data for demographic analyses (Andrews et al., 2016; Shafer et al., 2017). In addition, these approaches offer better opportunities in respect to those based on other markers (e.g., SSRs) to identify loci with a putative signal of selection from the background of neutral variation, and to test their functional importance by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in natural populations (Storz, 2005; Biswas and Akey, 2006). RAD-seq approaches have been applied May 2022 | Volume 13 | Article 866758 3 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. Study Sites and Sample Collection 9 h d−1 in winter, while the maximum is 15 h d−1 during the summer solstice (Figure 1B). In Gran Canaria, the average seawater temperature (SST) during the year is about 19°C (Figure 1C). Faro, the coldest of our sites, displays an average SST during the year of around 16.5°C while Ebro Delta in the Mediterranean, despite its northern latitude, has an average seawater temperature of 18°C (Figure 1C). Twenty C. nodosa shoots were collected by snorkeling at each site at a reciprocal distance of around 3–5 m to minimize the risk of sampling within the same clonal patch (Arnaud-Haond et al., 2007; Serra et al., 2010; Jahnke et al., 2017; Jahnke et al., 2019). This number of samples can be considered representative of the meadows and it is comparable to what generally used in 2b-RAD studies (e.g., De Wit et al., 2020; Jahnke et al., 2022). Subsequently, leaf material (about 5–7 cm) was carefully cleaned from epiphytes and dried in silica gel prior to DNA isolation. SNP-calling was performed using The Genome Analysis Toolkit (GATK) version 3.8 (McKenna et al., 2010). A first round of putative variants was generated using GATK’s UnifiedGenotyper, followed by base quality score recalibration (BQSR/BaseRecalibrator and PrintReads) based on a high confidence (>75th quality percentile) SNPs dataset. The realigned and recalibrated reads were then used to perform a second round of UnifiedGenotyper. We used the variant quality score recalibration (VQSR) step to generate an adaptive error model using the SNPs that were consistently genotyped across the technical replicates. A further filtration step was performed with vcftools (Danecek et al., 2011) to remove poorly-genotyped samples and to select only biallelic loci genotyped in at least 90% of individuals, and with a maximum heterozygosity of 50%. Harsh genotyping rate cut-off is recommended for best quality and to avoid RAD loci affected by null alleles because of mutations in the restriction site. 2b-RAD Genotyping Genomic DNA was extracted using the NucleoSpin® 96 Plant II kit (Macherey-Nagel) following the manufacturer’s instructions. DNA quality and quantity were checked through 1% agarose gel electrophoresis, and the QubitTM dsDNA BR assay kit (Thermo Fisher Scientific). 2b-RAD libraries were prepared following a modification of the protocol described by Wang et al., 2012 and available at https://github.com/z0on/2bRAD_denovo. Briefly, genomic DNA (~100 ng) was digested using the type 2b restriction enzyme BcgI to produce uniform fragments of 36- bp, to which adaptors were ligated on the cohesive ends. The fragments were then amplified with barcoded adaptors and purification of the target bands was carried out by 2% agarose MATERIALS AND METHODS gel-electrophoresis. Subsequently, gel fragments were cleaned using a MinElute Gel Extraction Cleaning Kit (Qiagen) and pooled equimolarly into a single pool. Four individuals from each locality were used as technical replicates (i.e., replicated library preparation and sequencing). These technical replicates were used in the analysis step to assess the overall accuracy of genotyping, set quality filtering criteria, and quantify error rates between samples. In total, 70 C. nodosa samples (20 individuals +4 technical replicates for EB and FA; 18 individuals +4 technical replicates for GC) were successfully sequenced on two lanes of an Illumina NovaSeq platform, generating 50-bp paired-end reads, at the Science for Life Laboratory (SciLifeLab) Genomics, SNP&SEQ Technology Platform in Uppsala University, Sweden. Only reads 1 (“forward reads”) were used for this analysis. Frontiers in Genetics | www.frontiersin.org Outlier Loci Identification and Functional Annotation To identify putative loci under selection, we used two statistical tools employing two different approaches based on FST and PCA, respectively, i.e., BayeScan v. 2.1 (Foll and Gaggiotti, 2008) and pcadapt v. 4 (Luu et al., 2017; Privé et al., 2020). BayeScan estimates FST for each SNP locus to perform a genomic scan for outlier FST values through a Bayesian method. It was used with prior odds set to 100, using thresholds of q = 0.3 and posterior probability P > 0.7 (Foll and Gaggiotti, 2008). The pcadapt method tests how much each variant is associated with population structure, assuming that outlier variants are indicative of local adaptation. Based on the scree plot (Jackson, 1993), we set 2 as the best number of principal components, and used the Manhattan plot and Histogram of p-values to graphically examine the presence of outliers. Significant outliers were then determined using the Bonferroni correction method for multiple comparisons with the R function p. adjust and α = 0.001. The outputs from the two methods were compared for overlap and shared loci were considered as the “best outliers”. Allele frequency of shared outlier loci was determined with GENEPOP 4.7.5 (Rousset, 2008). Outlier identification was repeated after removal of clone samples from the dataset (i.e., keeping only distinct MLLs for each population). To determine if shared and non-shared outlier loci could be included in a potential coding sequence, chromosome regions of a length of 80 bp, corresponding to two adjacent 2b-RAD tags around each SNP of interest, were mapped against three available C. nodosa transcriptomes [Ruocco et al., 2017, Cymodocea nodosa Cn_1 Transcriptome (Project ID: 1264710) by Joint Genome Institute (JGI) and Dattolo et al. (unpublished)] by using the blastn algorithm (Altschul et al., 1997). Unambiguous positive-matches were determined if a percentage of identity ≥90% was found in stretches of sequences of at least 25 bp around the SNP position. This criterion for mapping was used to filter out possible errors that could result from non-specific similarities among homologous sites. Subsequently, the SNPs-carrying contigs were functionally annotated using the online Mercator- MapMan4 annotation tool (Schwacke et al., 2019). Genetic diversity and differentiation, as well as clonal diversity results were compared with those obtained for the same populations using 7 highly polymorphic SSR markers (microsatellites) developed for C. Population Genomic Analyses To choose the best estimate of number of clusters (K), we used the ADMIXTURE’s cross-validation procedure with default settings. The hypothetical number of K was set from 1 to 15. PCA and ADMIXTURE analyses were re- calculated after removal of outlier loci confirmed by both employed approaches in the dataset (see 2.4), in order to determine whether outliers had disproportionate or distortive effects on the genetic structure analysis. As the analysis with all loci and only neutral loci showed similar patterns (data not shown), we kept all loci in the analyses. Significance levels of genic differentiation for each population pair (exact G test) across all loci was calculated with GENEPOP 4.7.5 (Rousset, 2008) with default Markov chain parameters (Dememorisation = 10000, Batches = 100, Iterations per batch = 5000). Pair-wise Weir and Cockerham mean and weighted FST estimates between C. nodosa populations were calculated with vcftools (Danecek et al., 2011). Observed heterozygosity (Ho) as well as FIS across all loci for each population were calculated using the R package diveRsity 1.9.90 (Keenan et al., 2013). The number of distinct Multi Locus Lineages (MLLs) for each population was calculated using the R package poppr (Kamvar et al., 2014; Kamvar et al., 2015). The genetic distance limit for setting delimitation of clones (Hamming distance >0.073) was determined based on the maximum genetic distance detected between technical replicates (i.e., “confirmed clones”). The genetic distance tree of individual samples obtained with poppr is depicted in Supplementary Figure S1. After clone delimitation, FST, FIS, and heterozygosity (Ho) were recalculated keeping only distinct MLLs per population. and N is the number of samples (Dorken and Eckert, 2001). Observed heterozygosity and inbreeding coefficient, as well as pairwise FST between populations were obtained with GenAlEx 6.503 (Peakall and Smouse, 2012). Outlier Loci Identification and Functional Annotation nodosa (Ruggiero et al., 2004; Supplementary Table S1) and used in previous population genetics studies (Ruggiero et al., 2005a and b; Tuya et al., 2019). Only a subset of samples could be genotyped with both techniques (12 individuals for GC; 18 for FA and 12 for EB). Multiplex PCR amplifications were conducted in 25 μL reaction volumes containing 12.5 μL QIAGEN Multiplex PCR Master Mix (QIAGEN), and 0.5 μL DNA (6–10 ng). Thermal cycling consisted of 95°C for 15′, 35 cycles of 94°C for 60″, 58°C for 90″, and 72°C for 90″, followed by 72°C for 30’. PCR products were analyzed on an Automated Capillary Electrophoresis Sequencer 3730 DNA Analyzer (Applied Biosystems). Linkage disequilibrium (LD) and deviations from Hardy-Weinberg equilibrium (HWE) at each locus and across all loci in each population were tested with Genepop 4.7.5 (Rousset, 2008), using 1000 dememorisations, 100 batches and 1000 iterations per batch. LD was not detected among loci, indicating they behaved independently. The number of MLGs was identified using the GIMLET software (Valière, 2002). Clonal diversity was calculated as the R ratio: R = G-1/N-1, where G is the number of genotypes Population Genomic Analyses Our final dataset was thinned in order to keep one SNP per RAD fragment with maximal allele frequency (script thinner. pl with criterion = maxAF; https://github.com/z0on/2bRAD_denovo). May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 4 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. Technical replicates were discarded from further analyses after examination for concordance in genotype estimates. Individual genetic variation was explored by a Principal Component Analysis (PCA) using the R package adegenet v. 2.1.3 (Jombart, 2008) and by using ADMIXTURE 1.3.0 (Alexander and Lange, 2011). To choose the best estimate of number of clusters (K), we used the ADMIXTURE’s cross-validation procedure with default settings. The hypothetical number of K was set from 1 to 15. PCA and ADMIXTURE analyses were re- calculated after removal of outlier loci confirmed by both employed approaches in the dataset (see 2.4), in order to determine whether outliers had disproportionate or distortive effects on the genetic structure analysis. As the analysis with all loci and only neutral loci showed similar patterns (data not shown), we kept all loci in the analyses. Significance levels of genic differentiation for each population pair (exact G test) across all loci was calculated with GENEPOP 4.7.5 (Rousset, 2008) with default Markov chain parameters (Dememorisation = 10000, Batches = 100, Iterations per batch = 5000). Pair-wise Weir and Cockerham mean and weighted FST estimates between C. nodosa populations were calculated with vcftools (Danecek et al., 2011). Observed heterozygosity (Ho) as well as FIS across all loci for each population were calculated using the R package diveRsity 1.9.90 (Keenan et al., 2013). The number of distinct Multi Locus Lineages (MLLs) for each population was calculated using the R package poppr (Kamvar et al., 2014; Kamvar et al., 2015). The genetic distance limit for setting delimitation of clones (Hamming distance >0.073) was determined based on the maximum genetic distance detected between technical replicates (i.e., “confirmed clones”). The genetic distance tree of individual samples obtained with poppr is depicted in Supplementary Figure S1. After clone delimitation, FST, FIS, and heterozygosity (Ho) were recalculated keeping only distinct MLLs per population. Technical replicates were discarded from further analyses after examination for concordance in genotype estimates. Individual genetic variation was explored by a Principal Component Analysis (PCA) using the R package adegenet v. 2.1.3 (Jombart, 2008) and by using ADMIXTURE 1.3.0 (Alexander and Lange, 2011). RESULTS Accuracy of 2b-RAD Genotyping The 2b-RAD sequencing generated an average of 1,184,045.85 reads ± SD 425,645.65 reads per sample (Supplementary Table S2). Using a set of 2,100 SNPs that were reproducible across technical replicates as a training set for the VQSR, we estimated the (true) transition/transversion ratio as Ti/Tv = 1.61. When applying this recalibration we chose a tranche with 99% truth May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 5 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. sensitivity as the cut off to call all SNPs from the overall dataset obtained a genotype dataset of 7 562 SNPs for 63 individuals FIGURE 2 | Distribution of transitions and transversions in the SNPs dataset. Percentages (%) of transitions and transversions of the whole set of 7,562 SNPs identified for 63 individuals is depicted using an alluvial diagram. FIGURE 3 | Population structure analysis and clonal diversity. (A) Principal Component Analysis (PCA) displaying the three C. nodosa populations collected along a latitudinal gradient of distribution (i.e., Gran Canaria, Faro and Ebro). (B) Admixture plot of the C. nodosa populations at K = 4. (C) Number of distinct Multi Locus Lineages (MLLs) identified at each sampling site. (D) Weir and Cockerham FST weighted estimate between populations. FIGURE 2 | Distribution of transitions and transversions in the SNPs dataset. Percentages (%) of transitions and transversions of the whole set of 7,562 SNPs identified for 63 individuals is depicted using an alluvial diagram. FIGURE 2 | Distribution of transitions and transversions in the SNPs dataset. Percentages (%) of transitions and transversions of the whole set of 7,562 SNPs FIGURE 2 | Distribution of transitions and transversions in the SNPs dataset. Percentages (%) of transitions and transversions of the whole set of 7,562 SNPs identified for 63 individuals is depicted using an alluvial diagram. FIGURE 3 | Population structure analysis and clonal diversity. (A) Principal Component Analysis (PCA) displaying the three C. nodosa populations collected along a latitudinal gradient of distribution (i.e., Gran Canaria, Faro and Ebro). (B) Admixture plot of the C. nodosa populations at K = 4. (C) Number of distinct Multi Locus Lineages (MLLs) identified at each sampling site. (D) Weir and Cockerham FST weighted estimate between populations. FIGURE 3 | Population structure analysis and clonal diversity. (A) Principal Component Analysis (PCA) displaying the three C. Population Differentiation, Genetic and Genotypic Diversity BayeScan identified 9 FST outlier SNPs across all samples at q<0.3 and P >0.7 (Supplementary Figure S2A; Supplementary Table S10), while pcadapt identified 188 outliers based on PCA with a Bonferroni corrected p-value ≤0.001 (Supplementary Figure S2B,C; Supplementary Table S10). All 9 outliers identified by BayeScan were included among those identified by pcadapt (9 shared outliers; Supplementary Figure S2D). Interestingly, the frequency of the alternative allele for the 9-shared outliers was maximum in individuals from the Ebro population (Supplementary Table S11). The functional annotation of the 9-shared outlier SNPs is provided in Table 2, while full annotation of all outliers identified with one or both methods is provided in Supplementary Table S12. Principal Component Analysis (PC1 = 35.2% and PC2 = 25.6% total variance; Figure 3A) showed a strong genetic differentiation among the three sampling sites along the latitudinal gradient and this was further confirmed by results from ADMIXTURE analysis (Figure 3B). In this analysis, K = 4 was identified as the “optimal K” with the lowest cross-validation error of 0.239 (Supplementary Table S6). The three sampled populations had different levels of clonality. The C. nodosa population from Ebro Delta exhibited the highest genotypic richness (i.e., 11 distinct MLLs over 15 individuals, R = 0.71), in respect to Faro and Gran Canaria populations [i.e., only 2 (R = 0.05) and 4 (R = 0.23) distinct MLLs, respectively] (Figure 3C ,Table 1). In particular, in the C. nodosa population from Ria Formosa lagoon (Faro), one MLL largely dominated over the other (Figure 3C). To support clonal determination with SNP markers, we compared these data with those obtained for a subset of samples of the same populations using previously developed polymorphic SSR markers (Supplementary Table S7). Based on microsatellites, the C. nodosa population from Ebro Delta exhibited the highest genotypic richness with 11 MLGs over 12 samples (R = 0.91), while in Gran Canaria 6 distinct MLGs were identified (R = 0.45). In Faro, a single MLG was identified with microsatellite markers (Supplementary Table S8). Five of the 9 shared outlier SNPs could be associated to specific contigs using available C. nodosa transcriptomes (Table 2). Two of these SNPs-carrying contigs (chr1_555347 and chr1_645789) encoded for proteins with a function in transcription regulation (“Regulation of transcription, DNA-templated”). RESULTS For each population, the following information are shown: acronym, geographic coordinates (latitude and longitude), number of sequenced individuals N and number of additional technical replicates in parenthesis, number of individuals retained after filtering procedures and removal of technical replicates, total number of distinct Multi Locus Lineages (MLLs), R value (G-1/N-1), observed heterozygosity (Ho) and inbreeding coefficient (FIS). TABLE 1 | Information on sampling sites, sample details and genetic indices obtained with 2b-RAD genotyping. For each population, the following information are shown: acronym, geographic coordinates (latitude and longitude), number of sequenced individuals N and number of additional technical replicates in parenthesis, number of individuals retained after filtering procedures and removal of technical replicates, total number of distinct Multi Locus Lineages (MLLs), R value (G-1/N-1), observed heterozygosity (Ho) and inbreeding coefficient (FIS). Sampling site Acronym Coordinates Total N N after filtering MLLs R Ho FIS Las Palmas de Gran Canaria—Canary Islands GC 27°45′14″N, 15°40′18″W 18 (4) 14 4 0.23 0.13 −0.20 Ria Formosa lagoon—Faro, Portugal FA 36°59′23″N, 7°50′01″W 20 (4) 20 2 0.05 0.24 −0.52 Ebro Delta, Spain EB 40°34′48″N, 0°35′45″E 20 (4) 15 11 0.71 0.21 −0.13 Total — — 58 (12) 49 17 — — — intermediate in Ebro and lowest in Gran Canaria (Table 1). Values of genetic differentiation (exact G test), FST, FIS, and observed heterozygosity (Ho) indicated above have been obtained following clones’ removal from the dataset. Genetic diversity and differentiation analyses repeated using SSR markers (Supplementary Table S8) gave comparable results across populations. changes (Figure 2). The most frequent changes were G ↔T (1857) and A ↔G (1686) (Figure 2; Supplementary Table S4). Genotyping correspondences among technical replicated individuals was 89 ± 6% (Supplementary Table S5). For population differentiation analysis, our final dataset was further thinned to remove technical replicates, two samples that were clear outliers in an exploratory PCA and to only keep one SNP per RAD fragment with maximum allele frequency, resulting in 4,941 loci for 49 individuals. Frontiers in Genetics | www.frontiersin.org RESULTS nodosa populations collected along a latitudinal gradient of distribution (i.e., Gran Canaria, Faro and Ebro). (B) Admixture plot of the C. nodosa populations at K = 4. (C) Number of distinct Multi Locus Lineages (MLLs) identified at each sampling site. (D) Weir and Cockerham FST weighted estimate between populations. obtained a genotype dataset of 7,562 SNPs for 63 individuals (Supplementary Table S3). Overall, transversions were more frequent than transitions and composed 56% of the identified obtained a genotype dataset of 7,562 SNPs for 63 individuals (Supplementary Table S3). Overall, transversions were more frequent than transitions and composed 56% of the identified sensitivity as the cut-off to call all SNPs from the overall dataset. After filtering out seven poorly genotyped samples as well as highly heterozygous sites (possible lumped paralogous), we May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 6 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. TABLE 1 | Information on sampling sites, sample details and genetic indices obtained with 2b-RAD genotyping. For each population, the following information are shown: acronym, geographic coordinates (latitude and longitude), number of sequenced individuals N and number of additional technical replicates in parenthesis, number of individuals retained after filtering procedures and removal of technical replicates, total number of distinct Multi Locus Lineages (MLLs), R value (G-1/N-1), observed heterozygosity (Ho) and inbreeding coefficient (FIS). Sampling site Acronym Coordinates Total N N after filtering MLLs R Ho FIS Las Palmas de Gran Canaria—Canary Islands GC 27°45′14″N, 15°40′18″W 18 (4) 14 4 0.23 0.13 −0.20 Ria Formosa lagoon—Faro, Portugal FA 36°59′23″N, 7°50′01″W 20 (4) 20 2 0.05 0.24 −0.52 Ebro Delta, Spain EB 40°34′48″N, 0°35′45″E 20 (4) 15 11 0.71 0.21 −0.13 Total — — 58 (12) 49 17 — — — TABLE 1 | Information on sampling sites, sample details and genetic indices obtained with 2b-RAD genotyping. For each population, the following information are shown: acronym, geographic coordinates (latitude and longitude), number of sequenced individuals N and number of additional technical replicates in parenthesis, number of individuals retained after filtering procedures and removal of technical replicates, total number of distinct Multi Locus Lineages (MLLs), R value (G-1/N-1), observed heterozygosity (Ho) and inbreeding coefficient (FIS). Sampling site Acronym Coordinates Total N N after filtering MLLs R Ho FIS TABLE 1 | Information on sampling sites, sample details and genetic indices obtained with 2b-RAD genotyping. Population Differentiation, Genetic and Genotypic Diversity Full annotation of all outlier SNPs obtained with one or both methods can be retrieved from Supplementary Table S12. SNP ID E- value Identity (%) Query match Best hit C. nodosa Best hit A. thaliana Description TAIR GO biological process TAIR MapMan BIN Mutation chr1_673698a — — — No hits found — — — — — chr1_421195a 3E- 10 36/ 37 (97) (11:47) TRINITY_DN164033_c0_g1_i1 AT3G13682 Lysine-specific histone demethylase 1 homolog 2. Involved in H3K4 methylation of target genes including the flowering loci FLC and FWA Histone H3-K4 methylation 26.7 NS: Glu/Gly chr1_555347a 3E- 10 36/ 37 (97) (31:67) TRINITY_DN7669_c0_g1_i6 AT5G64060 NAC domain containing protein 103 Regulation of transcription, DNA- templated 27.3.27 NS: Ala/Thr chr1_549579a — — — No hits found — — — — — chr2_19511a 8E- 11 34/ 34 (100) (7:40) TRINITY_DN5447_c0_g1_i3 — — Not assigned, unknown — — chr1_379730a — — — No hits found — — - — — chr2_1253a 0.005 27/ 29 (93) (20:48) TRINITY_DN226_c2_g1_i1 — — Not assigned, unknown 35.2 — chr1_645789a 1E-9 35/ 36 (97) (21:56) TRINITY_DN7020_c1_g2_i3 AT5G04840 bZIP protein Positive regulation of transcription, DNA-templated, regulation of transcription, DNA- templated 27.3.35 NS: Ala/Val chr1_656786 — — — No hits found — — — — — aOutlier SNPs, retained after clone removal by at least one method. bContig names assigned based on the Cymodocea nodosa transcriptome by JGI. aOutlier SNPs, retained after clone removal by at least one method. bContig names assigned based on the Cymodocea nodosa transcriptome by JGI. associated to genes involved in functions relevant to environmental adaptation. Notably, one SNP-carrying contig encoded for a protein with a key role in chromatin remodelling via histone methylation, and specifically linked to the regulation of photoperiodism and flowering time in land plants (He, 2009; Zhou et al., 2018; Martignago et al., 2019). This supports our initial hypothesis that specific genetic polymorphisms linked to important traits (e.g., flowering) could be present in C. nodosa inhabiting different latitudes possibly underlying local adaptation of populations to different photoperiod-temperature cues or other environmental parameters. those, 27% SNPs-carrying contigs were associated to signalling (14%) and RNA metabolism (13%), while 54% of SNPs were not assigned (Figure 4). Within the “RNA” BIN (n. 27), 7 contigs encoded for transcription factors of various families (e.g., GARP, NAC, WRKY, bZIP) (Supplementary Table S12). In the “signalling” BIN (n. Population Differentiation, Genetic and Genotypic Diversity 30), 9 contigs were associated to receptor kinases (e.g., DUF 26), which play a critical role in plant response to stimuli and defence (Dievart et al., 2020), while 2 were wall associated kinases, which are involved in sensory and signal transduction pathways between the inner and outer surroundings of cell walls (Kohorn, 2001; Supplementary Table S12). p Our population genomic data, based on both SSRs and SNPs markers, showed a clear genetic differentiation among the three populations analysed. Besides being genetically differentiated, they also exhibited variable levels of genetic and genotypic diversity. Previous studies on the genetic structure of C. nodosa along its distributional range based on SSRs, revealed a strong genetic discontinuity between Atlantic and Mediterranean regions and a certain divergence between western and eastern Mediterranean (Alberto et al., 2008). Yet, a great heterogeneity was found across populations in terms of clonal and genetic diversity (Ruggiero, 2004; Alberto et al., 2006; Alberto et al., 2008; Máñez-Crespo et al., 2020). A trend for decreasing allelic richness from the eastern Mediterranean towards the Atlantic was also advocated to explain the low ability of Atlantic populations to Population Differentiation, Genetic and Genotypic Diversity One SNP (chr1_421195) was specifically associated to a gene involved in chromatin remodelling (“Histone H3-K4 methylation”) and photoperiodism/regulation of flowering time, namely Lysine- specific histone demethylase 1 homolog 2 (Martignago et al., 2019; Table 2). All three annotated SNPs involved non- synonymous aminoacid substitutions (Table 2). The other two SNPs associated with specific contigs had unknown functions (Table 2). When the analysis of the outlier SNPs was repeated keeping only distinct MLLs for each population, 8 over the 9 shared-outliers were significantly retained by at least one method (pcadapt at P ≤0.01) (Table 2). BayeScan identified the same loci as “top outliers” but with a lower (ns) posterior probability P >0.3. Genetic differentiation (based on allele frequencies across all loci) was significant for each population pair comparison (see exact G test in Supplementary Table S9). Global weighted pairwise FST values ranged from 0.31 to 0.43, with Faro and Gran Canaria exhibiting the highest differentiation (Figure 3D). Overall, inbreeding coefficient values (FIS) were negative for all populations, with the lowest value observed in Faro (Table 1). Mean observed heterozygosity (Ho) was highest in Faro, Overall, 83 from the total of 188 outlier SNPs identified via Bayescan and/or pcadapt could be included in 14 different MapMan BINs (Figure 4; Supplementary Table S12). Among May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 7 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. TABLE 2 | Functional annotations of the 9 significant outlier SNPs shared between BayeScan and pcadapt. SNPs ID; E-value; identity with %; bp of the query match; contig name (representing the best hit of the blast analysis against available transcriptomesb); name, description and related GO of the best hit of Arabidopsis thaliana according to TAIR (https://www.arabidopsis.org/index.jsp); bin codes of MapMan classification; and mutation type of the SNP (NS, nonsynonymous; SYN, synonymous), are outlined. Full annotation of all outlier SNPs obtained with one or both methods can be retrieved from Supplementary Table S12. TABLE 2 | Functional annotations of the 9 significant outlier SNPs shared between BayeScan and pcadapt. SNPs ID; E-value; identity with %; bp of the query match; contig name (representing the best hit of the blast analysis against available transcriptomesb); name, description and related GO of the best hit of Arabidopsis thaliana according to TAIR (https://www.arabidopsis.org/index.jsp); bin codes of MapMan classification; and mutation type of the SNP (NS, nonsynonymous; SYN, synonymous), are outlined. DISCUSSION Populations distributed over broad latitudinal gradients often show patterns of clinal variation in phenotype and/or genotype (Hut and Beersma, 2011; De Frenne et al., 2013; Bergland et al., 2016; Machado et al., 2016). Through a genome-wide SNPs analysis based on 2b-RAD genotyping, we here demonstrated the presence of differentiated polymorphisms in three populations of the seagrass C. nodosa along a latitudinal gradient encompassing the Atlantic-Mediterranean transition region. Confirmed by two differentiation-based outlier tests, we identified 9 outlier SNPs, three of which could be reliably May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 8 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. FIGURE 4 | Functional annotation of 83 outlier loci displaying a positive match with transcribed regions. Functional annotation of SNPs with a positive blast hit against C. nodosa transcriptomes is depicted using a sunburst diagram. Each sequence has been assigned to a MapMan BIN category and sub-category based on its biological role or enzymatic activity. The definition of the BINs is included in the figure legend. A detailed description of BIN sub-categories can be retrieved from Supplementary Table S12. reduced representation libraries with moderate sequencing depth are also characterized by a substantial degree of missing data, error in SNP calling due to sequencing errors, lack of read depth or other sources of spurious allele calls (Mastretta-Yanes et al., 2015), which makes the designations of clones challenging (Kamvar et al., 2015). The challenge lies in particular in deciding on a threshold between designating a clone vs. a unique genotype. Several possible thresholds have been discussed (Kamvar et al., 2015), and we decided to use the difference between technical replicates as threshold for setting the limit we believe to be sequencing errors. While details differ slightly between SSRs and SNPs, general patterns are similar, and are also confirmed by other genetic parameters, particularly the inbreeding index FIS that is influenced by clonality. All three populations exhibited strongly negative FIS values based on the SNP genotyping, but the most clonal population (Faro) exhibited the lowest FIS (-0.51). Negative FIS has been shown to be strongly linked to the degree of clonality in facultative sexually reproducing species driven by genetic drift, both in theoretical (Prugnolle and De Meeûs, 2008) and population genetic assessments (Arnaud-Haond et al., 2020; Reynes et al., 2021b). DISCUSSION Moreover, FIS has been shown to be not as sampling-sensitive as genotypic richness (R) and has been suggested as the measure of choice for assessing the importance of clonal reproduction in seagrasses (Arnaud- Haond et al., 2020). FIGURE 4 | Functional annotation of 83 outlier loci displaying a positive match with transcribed regions. Functional annotation of SNPs with a positive blast hit against C. nodosa transcriptomes is depicted using a sunburst diagram. Each sequence has been assigned to a MapMan BIN category and sub-category based on its biological role or enzymatic activity. The definition of the BINs is included in the figure legend. A detailed description of BIN sub-categories can be retrieved from Supplementary Table S12. While SNPs may have their challenges in clone detection, one of the main advantages of reduced representation sequencing is the possibility to identify locus-specific polymorphisms potentially responsible for local adaptation of populations to specific environmental conditions (Zimmerman et al., 2020). Here, we identified nine SNPs potentially involved in environmental adaptation of C. nodosa populations along its latitudinal distribution (Table 2). These nine outlier loci could either be under selection themselves, or they could be linked to loci involved in local adaptation. The high levels of linkage disequilibrium generated by the lack of recombination in clonal populations could conserve such linkage between neutral and selected sites to a higher degree than in sexually reproducing species. However, the consequences of clonal reproduction on genomic architecture and the effects on the theory of local adaptation are so far little investigated. The three loci with a functional annotation encoded for proteins with a role in regulation of transcription. In all three loci, the mutation at the protein level was non-synonymous, hence providing a change in the aminoacid sequence. Interestingly, when considering the functional annotation of the whole outliers’ dataset (Supplementary Table S12), the biological processes “signalling” and “regulation of transcription” constituted a large part of those associated with our sequences. In total, nine transcription factors (TF) of different families (e.g., NAC domain-containing TFs, WRKY, bZIP, and JUMONJI), were found across the outlier-dataset. Similarly, a number of cysteine-rich receptor-like protein kinases, cell wall-associated ser/thr kinases, and inositol 1,3,4-trisphosphate 5/6-kinase family proteins, were resist disturbances (Tuya et al., 2021). Our results are in line with these findings, as the Gran Canaria population (GC), exhibited the lowest genetic diversity (as observed heterozygosity, Ho) both with SSRs and SNPs markers. Frontiers in Genetics | www.frontiersin.org DISCUSSION Genotypic richness (R) has been found to be highly variable across C. nodosa populations, even at small geographical scales (Alberto et al., 2006, 2008; Tuya et al., 2019). For instance, in the Canary Islands, the average R value previously calculated with available microsatellite markers was around 0.6, while it could vary from 0.3 to 0.9 for different meadows (Alberto et al., 2006; Máñez-Crespo et al., 2020). Genotypic richness obtained here for the Gran Canaria population with 7 SSR markers was within this range (0.4), while genotypic richness assessed with the SNP-dataset was lower (0.2). The C. nodosa population of the Ria Formosa lagoon (FA) has been historically considered monoclonal. Alberto et al., 2008 using SSR markers found only 5 genets over 220 ramets. Here using SSRs, we identified one single MLG over 18 samples analyzed, while using SNPs, 2 distinct MLLs could be detected. In general, we found a non-perfect match in the clonal discrimination power of SSRs and SNPs. SNPs have generally slower average mutation rates than SSRs; hence, each SNP is typically less informative (Allendorf, 2017). However, this is normally compensated by the much higher number of SNP markers, such that RAD-Seq can perform as well as, or better than SSRs in detecting population structure/ divergence (Lemopoulos et al., 2019; Camacho-Sanchez et al., 2020; Sunde et al., 2020). However, SNP-datasets based on May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 9 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. identified. This highlights the fundamental role signal integration and gene-regulatory networks could play for enabling adaptation to environmental conditions, as they allow to coordinate extracellular signals and intracellular regulatory machinery (Lopez-Maury et al., 2008). LOCUS family influence flowering time in responses to the ambient growth temperature (Posé et al., 2013; Capovilla et al., 2015). We cannot exclude that this polymorphism could also be linked to differences in other environmental settings across sites or to a differential regulation of specific biological processes among the analysed populations. Notably, one of the 9-shared outlier SNPs was specifically associated with photoperiodism and regulation of flowering time (chr1_421195), which is in an ecologically important life history trait. The timing of floral transition is critical to reproductive success in plants and varies across latitudes in response to changes in photoperiod and temperature patterns (Bäurle and Dean, 2006; Wilczek et al., 2010; Brambilla and Fornara, 2013). DISCUSSION In Arabidopsis, this trait is genetically controlled by a network of flowering genes, whose expression is regulated by various chromatin modifications, among which is a central regulator of flowering, FLOWERING LOCUS C (FLC) (He, 2009; Wilczek et al., 2010). FLC inhibits floral transition largely by reducing the expression of flowering-time integrators, such as SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) (He et al., 2003; He, 2009). The regulation of FLC expression is associated with various “active” chromatin modifications including histone H3 lysine-4 (H3K4) methylation and various “repressive” histone modifications, as H3K4 demethylation and H3 lysine-27 (H3K27) methylation (He, 2009). Chr1_421195 was included in a contig encoding for Lysine- specific histone demethylase 1 homolog 2 (LDL2). In Arabidopsis, this gene is involved in H3K4 (de)methylation of target genes including FLC. FLC is down-regulated by LDL2 and ldl2 mutants display increased H3K4me3 levels at FLC compared to wild type (Martignago et al., 2019). LDL2 is additionally involved in the control of H3K4 methylation state of FWA, a homeodomain- containing transcription factor which interferes with floral transition (Jiang et al., 2007) and controls primary seed dormancy related-genes (Zhao et al., 2015). A similar function in regulating the histone methylation pattern of flowering genes has been also suggested for LDL homologs in other plant species (Gu et al., 2016). The mutation we identified for this locus in C. nodosa populations was non-synonymous, leading to a substitution of a Glutamic acid (Glu) in Glycine (Gly). We cannot establish the real effect of this substitution at the protein level, but as it will modify the charge of the peptide, it could potentially result in a loss of interactions with other molecules or could induce differences in the regulation of other genes related to the flowering pattern (Caicedo et al., 2004). It is worth noticing that the frequency of the alternative alleles of the locus chr1_421195 was maximum in individuals from the Ebro population (Supplementary Table S11), whereas the reference allele was present in Faro and Gran Canaria. Although we expected this locus to diverge in populations exposed to large differences in photoperiod, this was not the case as e.g. Faro and Ebro had the strongest similarity in daylight and seasonality variations among sampling sites. DISCUSSION However, studies in terrestrial plants have demonstrated that even small differences in the duration of the light period might have large effects on flowering time (Roden et al., 2002). In addition, the strong level of the differentiation at this locus across populations could also be related to differences in the temperature regimes rather than photoperiodic cues. In Arabidopsis, vernalization-induced flowering is mediated by epigenetic regulations of FLC (Sharma et al., 2020); while other studies indicated several genes belonging to the FLOWERING Across the whole dataset of outlier SNPs (Supplementary Table S12), other loci with a functional annotation, were involved in the regulation of flowering time and circadian rhythms. Chr1_659852 was associated to a contig encoding for PWWP domain protein 3, which is specifically involved in the regulation of FLC and flowering time. PWWP domain proteins (PDPs) function together with other components (e.g., FLOWERING LOCUS VE and MULTICOPY SUPPRESSOR OF IRA 5) to regulate the function of the PRC2 histone methyltransferase complex, thereby facilitating the maintenance of H3K27me3 on FLC (Zhou et al., 2018). In addition, other two SNPs-carrying contigs (chr1_546361 and chr1_474761) encoded for transcription factors involved in flowering regulation and response to temperature stimulus. The first encoded for the protein JMJD5/JMJ30, which contains a jumonji-C (jmjC) domain, the second for EARLY FLOWERING MYB PROTEIN (EFM). In Arabidopsis, JMJD5 has a histone demethylase activity (H3- K36 specific) and interacts with EFM to repress the floral pathway integrator FT, thus negatively regulating flowering (Yan et al., 2014). In addition, EFM participate in the flowering thermosensory pathway of Arabidopsis (Gan et al., 2014). Taken together, our results highlight that polymorphisms at flowering-related loci and transcription factors could make an important contribution to genetic adaptation of C. nodosa across latitude, although this should be further confirmed by larger-scale studies and ad hoc common-garden or reciprocal transplantation experiments (Reusch et al., 2014; Pazzaglia et al., 2021). Flowering- regulating loci, integrating annual responses to light and temperature patterns through complex gene-regulatory networks, determine the timing of reproduction, which is crucial for fitness and survival of populations (Austen et al., 2017), besides the plasticity of single long- lasting genotypes (Pazzaglia et al., 2021). This could also contribute to differences in flowering phenology observed in this species along the depth gradient (Buia and Mazzella, 1991) or across regions (Máñez- Crespo et al., 2020). REFERENCES Arnaud-Haond, S., Stoeckel, S., and Bailleul, D. (2020). New Insights into the Population Genetics of Partially Clonal Organisms: when Seagrass Data Meet Theoretical Expectations. Mol. Ecol. 29, 3248–3260. doi:10.1111/mec.15532 Aitken, S. N., and Hannerz, M. 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All authors contributed in drafting the work, revised it critically, and gave final approval for publication. ACKNOWLEDGMENTS The raw Illumina sequences used in the study are available in the Sequence Read Archive (SRA) repository under NCBI Bioproject PRJNA814006. Vcf files are available as Supplementary Material (Data Sheet 2). We deeply thank all the staff of Tjärnö Marine Laboratory (Strömstad, Sweden) for the hospitality, and for logistical and technical supports. Sequencing was performed at Science for Life Laboratory (SciLifeLab) - Genomics, SNP&SEQ Technology Platform in Uppsala University, Sweden. Part of sequence data used for outlier SNPs functional annotation were produced by the US Department of Energy Joint Genome Institute https://www. jgi.doe.gov/in collaboration with the user community. We also thank Fernando Tuya for the collection of C. nodosa samples in Las Palmas de Gran Canaria. We are grateful to the SZN- Bioinforma service and in particular to Marco Miralto for the support with computer cluster usage and software installation. We deeply thank Arturo Santaniello for his invaluable help with the 2b-RAD bioinformatic analyses. DISCUSSION Yet, epigenetic modifications, such as histone modifications, seem to play an important role in the regulation of flowering-related gene networks, and potentially other phenology- related pathways, in C. nodosa. In support of this, a recent work has demonstrated different levels of global genomic cytosine methylation (5-mC) in C. nodosa populations from contrasting thermal environments, as well as a low level of gene body methylation (predicted by high CpGO/E ratio) in transcripts with a differential expression depending on plants’ origin (Entrambasaguas et al., 2021). While we acknowledge that our study including only three C. nodosa populations with a high level of clonality in at least two of them, has limitations, it sheds first light on genetic polymorphisms and related biological processes that could contribute to environmental adaptation of C. nodosa and potentially other seagrass species across their biogeographic May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 10 2b-RAD Genotyping in Cymodocea nodosa Ruocco et al. Plus project. The work has been partially supported by the project Marine Hazard, PON03PE_00203_1, Italian Ministry of Education, University and Research (MIUR). Sequencing was financially supported by Centre for Marine Evolutionary Biology (http://www.cemeb.science.gu.se). MJ was supported by the Swedish Research Council Formas (Grant No. 2020-0008). This study received Portuguese national funds from FCT - Foundation for Science and Technology through projects UIDB/04326/2020, UIDP/04326/2020 and LA/P/0101/2020. range of distribution. In addition, we are aware that, although genome scan methods have been often applied in partially clonal organisms, there is a general lack of predictive works about the power of such methods in case of very strong clonality rate, as in our case. Future seascape genomic studies based on upgraded whole-genome information and employing a larger number of populations (or species) along latitudinal clines would allow a higher power for detecting signature of selection associated to local environmental settings in seagrasses. FUNDING The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fgene.2022.866758/ full#supplementary-material The research leading to these results received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 730984, ASSEMBLE REFERENCES Control of Flowering by Ambient Temperature. J. Exp. Bot. 66 (1), 59–69. doi:10.1093/jxb/eru416 Gordon, A., and Hannon, G. (2010). Fastx-toolkit. FASTQ/A Short-Reads Preprocessing Tools. Available at: http://hannonlab. cshl. edu/fastx_toolkit Chefaoui, R. M., Assis, J., Duarte, C. M., and Serrão, E. A. (2016). Large-Scale Prediction of Seagrass Distribution Integrating Landscape Metrics and Environmental Factors: The Case of Cymodocea Nodosa (Mediterranean- Atlantic). Estuaries Coasts 39, 123–137. doi:10.1007/s12237-015-9966-y Green, E. P., and Short, F. T. (2003). World Atlas of Seagrasses. University of California Press. 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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. Copyright © 2022 Ruocco, Jahnke, Silva, Procaccini and Dattolo. 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. GERMINATION 1 and ABA Signaling-Related Genes. Front. Plant Sci. 6, 159. doi:10.3389/fpls.2015.00159 Zhou, J.-X., Liu, Z.-W., Li, Y.-Q., Li, L., Wang, B., Chen, S., et al. (2018). Arabidopsis PWWP Domain Proteins Mediate H3K27 Trimethylation on FLC and Regulate Flowering Time. J. Integr. Plant Biol. 60, 362–368. doi:10.1111/jipb.12630 Zimmerman, S. J., Aldridge, C. L., and Oyler-Mccance, S. J. (2020). An Empirical Comparison of Population Genetic Analyses Using Microsatellite and SNP Data for a Species of Conservation Concern. BMC genomics 21, 382. doi:10. 1186/s12864-020-06783-9 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. Frontiers in Genetics | www.frontiersin.org May 2022 | Volume 13 | Article 866758 REFERENCES 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. May 2022 | Volume 13 | Article 866758 Frontiers in Genetics | www.frontiersin.org 15
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Keywords: structural health monitoring, steel truss bridges, strain, temperature In this study, short-term monitoring was carried out for an existing long-span bridge, which has been managed by a local government, with the aim of evaluating its present performance toward planning future maintenance strategies. The bridge studied is a cantilever steel truss bridge, which was completed and opened to traffic in 1937. Consequently, the performance of Gerber hinges was evaluated, then information on repair was obtained. Performance Evaluation of Hinges in Long-Span Cantilever Steel Truss Bridges by Structural Health Monitoring Takeshi Miyashita,* Eiji Iwasaki, and Masatsugu Nagai Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan (Received June 20, 2016; accepted December 1, 2016) (Received June 20, 2016; accepted December 1, 2016) 179 179 Sensors and Materials, Vol. 29, No. 2 (2017) 179–186 MYU Tokyo S & M 1310 1. Introduction Owing to the aging of bridges in Japan, effective and efficient maintenance has been demanded.(1) Until now, visual inspection is the most effective maintenance method. However, work optimization for this type of inspection is difficult, and quantitative information about stress properties, which is necessary for effective maintenance, cannot be obtained. On the other hand, aiming at efficient maintenance, it is considered that the use of ICRT (ICT: Information and Communication Technology + IRT: Information and Robot Technology) technologies will continue to increase in the near future.(2) One example related with the initiative for the use of ICRT technologies is bridge monitoring, which involves a large number of sensors installed along the bridge in order to monitor its condition and diagnose its soundness.(3) One of the problems that have arisen is that there are only a few applications of both types of inspection in long-span bridges administrated by local governments. Of course, cost represents a major issue for its application, but this is not the only obstacle. There is also the technical difficulty of arranging sensors throughout the entire bridge, constructing a measurement system, and analyzing a large amount of data. Notwithstanding these difficulties, since July of 2014, bridge inspection every 5 years has become mandatory in Japan. Henceforth, it is expected that the demands for methods of evaluating current conditions and methods of bridge monitoring will continue to increase. In this research, aiming at the establishment of a strategy for the future maintenance of long- span bridges administrated by local governments, a short-term monitoring is carried out. More than one hundred sensors are installed along the bridge in order to evaluate its current performance. Herein, strain responses, which are affected by temperature, are focused on in order to evaluate the performance of hinges. *Corresponding author: e-mail: mtakeshi@vos.nagaokaut.ac.jp http://dx.doi.org/10.18494/SAM.2017.1419 ISSN 0914-4935 © MYU K.K. 180 Sensors and Materials, Vol. 29, No. 2 (2017) 2. Bridge of Study The bridge of study is Chosei Bridge, an 850.8-m-long bridge built over Shinano River, located in Niigata Prefecture. It is a 13-span (67.50 + 11@65.00 + 67.50 m) cantilever (Gerber) steel truss bridge completed and opened to traffic in 1937 (Fig. 1). The road width corresponding to this bridge is 7.50 m. The pedestrian bridge adjacent to Chosei Bridge was constructed in 1972. From 1995 to 1996, movable supports and a bridge fail-safe system corresponding to a Gerber hinge section were replaced and installed, respectively. In 2003, construction works to implement nondrain expansion devices in all Gerber hinges were carried out. Figure 2 shows the current condition of the Gerber hinges. In 2006, during the repainting of the 2nd span, considerable corrosion in the lower chords of the main structure was found, and it was determined that it was necessary to repair those damaged sections. On the basis of the corrosion condition examination performed that year, a repair design was drawn up. Then, from 2007 to 2011, the lower chords were repaired (patching of steel plates and member replacements). However, no loading test was performed after the repair, so the stress state and other current properties of the bridge were not determined. 3.1 Outline The measured items are the strain of each span, acceleration, vertical deflection, and temperature in the span center vicinity as a representative point. Additionally, since the adjacent pedestrian bridge shares the same pier with Chosei Bridge, for reference, acceleration measurements of 3 spans corresponding to the pedestrian bridge were carried out. In total, 130 points were measured. The measurement location is shown in Fig. 3. To classify vehicle type, a previously installed web camera, originally used for monitoring snow conditions, was used. However, in this paper, strain responses, which are affected by temperature, are focused on among the sensors. Suspended span Fail-safe system Bearing Fig. 2. (Color online) Current condition of Gerber hinges. Suspended span Fail-safe system Bearing Fig. 1. (Color online) Bridge of study (Chosei Bridge). Fig. 2. (Color online) Current condition of Gerber hinges. Fig. 1. (Color online) Bridge of study (Chosei Bridge). Fig. 2. (Color online) Current condition of Gerber hinges. Fig. 1. (Color online) Bridge of study (Chosei Bridge). Sensors and Materials, Vol. 29, No. 2 (2017) 181 8th span Suspended 9th span Anchored 10th span Suspended 11th span Anchored 12th span Suspended 13th span Anchored To station Strain on upper chord Strain on diagonal Displacement & acceleration 1st span Anchored 2nd span Suspended 3rd span Anchored 4th span Suspended 5th span Anchored 6th span Suspended 7th span Anchored To town Temperature Fig. 3. (Color online) Measurement location. To town 1st span Anchored 2nd span Suspended 3rd span Anchored 4th span Suspended 5th span Anchored 6th span Suspended 7th span Anchored To town 3rd span Anchored 2nd span Suspended 4th span Suspended 5th span Anchored 6th span Suspended 1st span Anchored 7th span Anchored 8th span Suspended 9th span Anchored 10th span Suspended 11th span Anchored 12th span Suspended 13th span Anchored To station Strain on upper chord Strain on diagonal Displacement & acceleration Temperature Fig. 3. (Color online) Measurement location. To station 12th span Suspended 10th span Suspended 9th span Anchored 8th span Suspended Temperature Fig. 3. (Color online) Measurement location. Free-flow traffic monitoring was carried out, starting at 2:00 of June 13 and ending at 14:00 of June 17, 2013, with a total of 108 h (388800 s) of monitoring. The sampling frequency was 200 Hz. After completing the measurements, all the measurement systems were removed. For the monitoring period, a file text of approximately 18.8 GB was obtained. 3.1 Outline In this research, attention was focused on strain data that helps to determine stress properties. Since the bridge of study is quite long (850.8 m), it was difficult to gather together all the sensors’ wirings in the same place. It was also difficult to close the road to traffic for long periods of time, so the bridge was divided into 3 blocks, and a measurement system was constructed for each block (Tokyo Sokki Kenkyujyo TMR-211 and 221). All sensors were connected by wires, and the order of measurements, such as starting and ending, were transmitted to each block via wireless signal. 3.3 Temperature measurement and web camera The vicinity of the 7th span’s center was selected as the representative point to measure the temperature. The temperature measurement was carried out using the thermocouple T-GF-0.65 (Tokyo Sokki Kenkyujyo), which uses the Seebeck effect. It was installed above the pedestrian bridge, in a position not reached by the sun. In order to classify vehicle type, a previously installed web camera (Panasonic BB-HCM381), originally used to monitor snow conditions, was used. It was installed above the upper lateral bracing located in the vicinity of P1 in the 2nd span. 4.1 Temperature measurement Temperature variation corresponding to the vicinity of the 7th span’s center, measured with the installed thermocouple, is shown in Fig. 5. During the measurement period, the maximum temperature was 34.9 °C, and the minimum temperature was 21.9 °C. The temperature when the initial measurement was carried out, on May 22, 2013, was 21 °C. 3.2 Strain measurement To measure the strain, self-temperature compensation-type uniaxial strain gauges for general use (Tokyo Sokki Kenkyujyo) were employed. Strain was measured in the upper chord located in the vicinity of each span’s center on the downstream side. Additionally, in the cantilever span, measurement points were provided at the 2 diagonal bracing members that connect from the Gerber hinge to the span center. In order to consider the effect of axial force and bending moments, 4 strain gauges were attached at each cross section of each element. To calculate the section force from the measured strain, members’ coordinate systems shown in Fig. 4, Young’s modulus E of steel (= 200 GPa), cross-sectional area A, cross-sectional coefficients Wyi and Wzi (i = 1, 2, 3, 4), axial force Nx, bending moments around y- and z-axes My and Mz, measured strain εi, and the following formula were used. Nx, My, and Mz are obtained by the least squares method. 182 Sensors and Materials, Vol. 29, No. 2 (2017) x y z o My Mz Nx 1 2 3 4 Fig. 4. (Color online) Coordinate system of members. x y z o My Mz Nx 1 2 3 4 34.9 ℃ 21.9 ℃ Time (s) 0 10 20 30 40 2:00 0:00 0:00 0:00 0:00 14:00 Temperature (℃) 13 June 14 June 15 June 16 June 17 June Fig. 5. (Color online) Temperature during monitoring period. Fig. 4. (Color online) Coordinate system of members. Fig. 5. (Color online) Temperature during monitoring period. 1 E 1/A 1/ Wz1 1/ Wy1 1/A 1/ Wz2 1/ Wy2 1/A 1/ Wz3 1/ Wy3 1/A 1/ Wz4 1/ Wy4 Nx Mz My = ε1 ε2 ε3 ε4 (1) 3.3 Temperature measurement and web camera 1 E 1/A 1/ Wz1 1/ Wy1 1/A 1/ Wz2 1/ Wy2 1/A 1/ Wz3 1/ Wy3 1/A 1/ Wz4 1/ Wy4 Nx Mz My = ε1 ε2 ε3 ε4 (1) 3.3 Temperature measurement and web camera 1 E 1/A 1/ Wz1 1/ Wy1 1/A 1/ Wz2 1/ Wy2 1/A 1/ Wz3 1/ Wy3 1/A 1/ Wz4 1/ Wy4 Nx Mz My = ε1 ε2 ε3 ε4 (1) (1) 4.2 Strain measurement 6. (Color online) Upper chord’s normal stress for each span. (a) 1st, (b) 2nd, (c) 3rd, (d) 4th, (e) 5th, (f) 6th, (g) 7th, (h) 8th, (i) 9th, (j) 10th, (k) 11th, (l) 12th, and (m) 13th spans. 4.2 Strain measurement Figure 6 shows the upper chord’s normal stress for each span. The black solid line represents the normal stress, which is the sum of the static stress component caused by temperature variation, and the dynamic stress component caused by the live load. To separate the two components, a moving average is carried out. Here, 20000 data items for each time are considered. From this moving average, the static stress component is determined and represented by the blue solid line. Then, the blue solid line’s value is subtracted from the black solid line’s value in order to obtain the dynamic stress component. 183 Sensors and Materials, Vol. 29, No. 4.2 Strain measurement 2 (2017) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (a) (b) (c) (d) (e) (f) (g) (h) (i) (j) (k) (l) (m) Fig. 4.2 Strain measurement Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) (a) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (b) (b) (a) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (d) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (c) (c) (d) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (f) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (e) (f) (e) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (h) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (g) (h) (g) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (j) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (i) (j) (i) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (k) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (l) (l) (k) Static Static+Dynamic -50 -40 -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) -30 -20 -10 0 10 20 30 2:00 0:00 0:00 0:00 0:00 14:00 13 June 14 June 15 June 16 June 17 June Time (s) ss ert S ( m m / N 2) Dynamic (m) (m) Fig. 4.2 Strain measurement 6. (Color online) Upper chord’s normal stress for each span. (a) 1st, (b) 2nd, (c) 3rd, (d) 4th, (e) 5th, (f) 6th, (g) 7th, (h) 8th, (i) 9th, (j) 10th, (k) 11th, (l) 12th, and (m) 13th spans. 184 Sensors and Materials, Vol. 29, No. 2 (2017) Table 1 shows each component of the minimum normal stress for each span during the monitoring period. As shown in Table 1, the 6th span is the span that presented the minimum normal stress, which is −44.6 MPa. An analysis of the data corresponding to this stress and vehicle identification using the web camera are shown in Fig. 7. From Fig. 7(c), it is determined that the dynamic stress component when the normal stress reached its minimum is −11.6 MPa. As shown in Table 1, the dynamic stress component on the 4th span is −19.7 MPa. An analysis of the data corresponding to this stress and vehicle identification using the web camera are shown in Fig. 8. Then, from Table 1, it is found that the dynamic stress component on the 6th span is −33.7 MPa. Now, using the temperature variation during the period of monitoring (34.9 − 21.9 = 13.0 °C), the steel coefficient of linear expansion (12 × 10−6/deg), and Young’s coefficient of steel (200 GPa), the temperature stress is calculated. Its value is −31.2 MPa. Because this stress is of the same magnitude as that of the static stress component presented in the 6th span, it is inferred that the Gerber hinge movable part is not working, and that it is fixed. Considering this, the relationship between temperature and the static stress component is shown in Fig. 9. In 5th, 6th, and 8th spans, the coefficient of determination R2 of 0.9 is exceeded. Among these 3 spans, the 6th and 8th spans are cantilever spans, and a high correlation between temperature and the static stress component corresponding to the upper chord of both spans is found. Therefore, it is considered that the Gerber hinges of these spans should be repaired preferentially. Table 1 Minimum normal stress during the monitoring period. 4.2 Strain measurement Span 1 2 3 4 5 6 7 8 9 10 11 12 13 Static + dynamic −15.8 −21.9 −20.5 −24.8 −28.8 −44.6 −34.1 −24.4 −28.5 −21.9 −19.6 −24.6 −20.4 Static −5.4 −9.8 −8.2 −7.4 −19.5 −33.7 −25.5 −16.3 −15.4 −10.1 −11.8 −13.0 −13.2 Dynamic −13.3 −16.9 −16.5 −19.7 −17.3 −18.0 −17.7 −13.8 −18.8 −17.1 −16.0 −16.7 −16.3 Unit: N/mm2 Fig. 7. (Color online) Minimum normal stress during monitoring period (upper chord in 6th span). (a) Whole figure. (b) Static component in square. (c) Dynamic component in square. (d) Identified vehicle. Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 0.5 1 1.5 2 2.5 3 3.5 x 10 5 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) 2:00 0:00 0:00 0:00 0:00 13 June 14 June 15 June 16 June 17 June 14:00 0 500 1000 1500 2000 2500 3000 3500 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 1000 2000 3000 Static + Dynamic Static -44.6MPa Stress (N/mm2) -10 -5 0 5 10 Time (s) 0 1000 2000 3000 0 500 1000 1500 2000 2500 3000 3500 -10 -5 0 5 10 Time (s) Stress (N/mm2) Dynamic -11.6MPa (a) (b) (c) (d) Table 1 Minimum normal stress during the monitoring period. Span 1 2 3 4 5 6 7 8 9 10 11 12 13 Static + dynamic −15.8 −21.9 −20.5 −24.8 −28.8 −44.6 −34.1 −24.4 −28.5 −21.9 −19.6 −24.6 −20.4 Static −5.4 −9.8 −8.2 −7.4 −19.5 −33.7 −25.5 −16.3 −15.4 −10.1 −11.8 −13.0 −13.2 Dynamic −13.3 −16.9 −16.5 −19.7 −17.3 −18.0 −17.7 −13.8 −18.8 −17.1 −16.0 −16.7 −16.3 Unit: N/mm2 Table 1 Stress (N/mm2) -10 -5 0 5 10 Time (s) 0 1000 2000 3000 0 500 1000 1500 2000 2500 3000 3500 -10 -5 0 5 10 Time (s) Stress (N/mm2) Dynamic -11.6MPa (c) Fig. 7. (Color online) Minimum normal stress during monitoring period (upper chord in 6th span). (a) Whole figure. (b) Static component in square. (c) Dynamic component in square. (d) Identified vehicle. Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 0.5 1 1.5 2 2.5 3 3.5 x 10 5 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) 2:00 0:00 0:00 0:00 0:00 13 June 14 June 15 June 16 June 17 June 14:00 0 500 1000 1500 2000 2500 3000 3500 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 1000 2000 3000 Static + Dynamic Static -44.6MPa Stress (N/mm2) -10 -5 0 5 10 Time (s) 0 1000 2000 3000 0 500 1000 1500 2000 2500 3000 3500 -10 -5 0 5 10 Time (s) Stress (N/mm2) Dynamic -11.6MPa (a) (b) (c) (d) 0 500 1000 1500 2000 2500 3000 3500 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 1000 2000 3000 Static + Dynamic Static -44.6MPa (b) Stress (N/mm2) -40 -30 -20 -10 0 10 20 30 40 Time (s) 0 0.5 1 1.5 2 2.5 3 3.5 x 10 5 -40 -30 -20 -10 0 10 20 30 40 Time (s) Stress (N/mm2) 2:00 0:00 0:00 0:00 0:00 13 June 14 June 15 June 16 June 17 June 14:00 (a) (b) (a) (c) (d) (d) Fig. 7. (Color online) Minimum normal stress during monitoring period (upper chord in 6th span). (a) Whole figure. (b) Static component in square. (c) Dynamic component in square. (d) Identified vehicle. 185 Sensors and Materials, Vol. 29, No. 2 (2017) Fig. 8. (Color online) Minimum dynamic normal stress during monitoring period (upper chord in 4th span). (a) Whole figure. (b) Static component in square. (c) Dynamic component in square. (d) Identified vehicle. Table 1 Stress (N/mm2) -40 -30 -20 -10 0 10 20 Time (s) 0 0.5 1 1.5 2 2.5 3 3.5 x 10 5 -50 -40 -30 -20 -10 0 10 20 30 Time (s) Stress (N/mm2) 2:00 0:00 0:00 0:00 0:00 13 June 14 June 15 June 16 June 17 June 14:00 0 500 1000 1500 2000 2500 3000 3500 -20 -10 0 10 20 Time (s) Stress (N/mm2) Static + Dynamic Static -24.8MPa 20 10 0 -10 -20 0 1000 2000 3000 Time (s) Stress (N/mm2) 0 500 1000 1500 2000 2500 3000 3500 -20 -15 -10 -5 0 5 10 15 20 Time (s) Stress (N/mm2) Dynamic -19.7MPa 20 10 0 -10 -20 Stress (N/mm2) 0 1000 2000 3000 Time (s) (a) (b) (c) (d) Stress (N/mm2) -40 -30 -20 -10 0 10 20 Time (s) 0 0.5 1 1.5 2 2.5 3 3.5 x 10 5 -50 -40 -30 -20 -10 0 10 20 30 Time (s) Stress (N/mm2) 2:00 0:00 0:00 0:00 0:00 13 June 14 June 15 June 16 June 17 June 14:00 (a) 0 500 1000 1500 2000 2500 3000 3500 -20 -10 0 10 20 Time (s) Stress (N/mm2) Static + Dynamic Static -24.8MPa 20 10 0 -10 -20 0 1000 2000 3000 Time (s) Stress (N/mm2) (b) 0 500 1000 1500 2000 2500 3000 3500 -20 -15 -10 -5 0 5 10 15 20 Time (s) Stress (N/mm2) Dynamic -19.7MPa 20 10 0 -10 -20 Stress (N/mm2) 0 1000 2000 3000 Time (s) (c) (a) (c) (d) (d) Fig. 8. (Color online) Minimum dynamic normal stress during monitoring period (upper chord in 4th span). (a) Whole figure. (b) Static component in square. (c) Dynamic component in square. (d) Identified vehicle. Table 1 m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.409 Temperature (℃) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.463 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.338 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.240 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.961 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.945 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.721 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.949 Temperature (℃) 15 20 25 30 35 Temperature (Celsius) R2 = 0.771 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.278 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.512 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.536 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.838 (a) (b) (c) (d) (e) (f) (g) (h) (i) (j) (k) (l) (m) Fig. 9. (Color online) Relationship between temperature and the static stress component. Table 1 (a) 1st, (b) 2nd, (c) 3rd, (d) 4th, (e) 5th, (f) 6th, (g) 7th, (h) 8th, (i) 9th, (j) 10th, (k) 11th, (l) 12th, and (m) 13th spans. Table 1 Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.463 (b) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.338 (c) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.240 (d) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.409 Temperature (℃) (a) (d) (b) (a) (c) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.949 (h) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.721 (g) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.961 (e) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.945 (f) (f) (h) (e) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.536 (l) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.278 (j) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.512 (k) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.838 (m) Temperature (℃) m m / N ( ss ert S 2) -40 -30 -20 -10 0 10 20 30 10 15 20 25 30 35 Temperature (Celsius) R2 = 0.771 (i) (l) (k) (j) (i) Fig. References 1 M. Nagai and T. Miyashita: Recent Topics on Steel Bridge Engineering in Japan—Design and Maintenance, Proc. 10th Korea-China-Japan Symp. Steel Structures (CD-ROM). p y p ( ) 2 Cross-Ministerial Strategic Innovation Promotion Program: Homepage of Cross-Ministerial Strategic Innovation Promotion Program, http://www.jst.go.jp/sip/k07.html (accessed June 2016). 3 C. Boller, F. K. Chang, and Y. Fujino: Encyclopedia of Structural Health Monitoring (Wiley, New Jersey, 2009). Table 1 9. (Color online) Relationship between temperature and the static stress component. (a) 1st, (b) 2nd, (c) 3r (d) 4th, (e) 5th, (f) 6th, (g) 7th, (h) 8th, (i) 9th, (j) 10th, (k) 11th, (l) 12th, and (m) 13th spans. 186 Sensors and Materials, Vol. 29, No. 2 (2017) 5. Conclusions In this research, aiming at the establishment of strategies for the future maintenance of long-span bridges administrated by local governments, a short-term monitoring was carried out. Here, more than one hundred sensors were installed along a bridge in order to evaluate its current performance. Herein, strain responses, which are affected by temperature, are focused on. Results after 4.5 d of monitoring showed that, in the case of the upper chord’s normal stress, the static stress component fluctuation is larger than the dynamic stress component fluctuation. The minimum static stress component was found to be of the same magnitude as that of the temperature stress. Therefore, it was inferred that the Gerber hinge movable part was not working, and that it was fixed. Additionally, on the basis of the relationship between each span temperature and the static stress component, a high correlation between temperature and the static stress component corresponding to the upper chord of the 6th and 8th spans was found. It is considered that the Gerber hinges of these spans should be repaired preferentially. About the Authors Takeshi Miyashita received his B.S., M.S., and Ph.D. degrees from the University of Tokyo, Japan, in 2001, 2002, and 2005, respectively. From 2006 to 2008, he was an assistant professor at Nagaoka University of Technology, Japan. From 2008 to 2012, he was an especially appointed lecturer at Nagaoka University of Technology. Since 2012, he has been an associate professor at Nagaoka University of Technology. His research interests are in bridge engineering, structural health monitoring, and CFRP repair. Takeshi Miyashita received his B.S., M.S., and Ph.D. degrees from the University of Tokyo, Japan, in 2001, 2002, and 2005, respectively. From 2006 to 2008, he was an assistant professor at Nagaoka University of Technology, Japan. From 2008 to 2012, he was an especially appointed lecturer at Nagaoka University of Technology. Since 2012, he has been an associate professor at Nagaoka University of Technology. His research interests are in bridge engineering, structural health monitoring, and CFRP repair. Eiji Iwasaki received his B.S., M.S., and Ph.D. degrees from Nagaoka University of Technology, Japan, in 1985, 1987, and 1990, respectively. From 1990 to 1998, he was an assistant professor at Nagaoka University of Technology, Japan. From 1998 to 2000, he was an associate professor at National Institute of Technology, Tokuyama College, Japan. From 2000 to 2012, he was an associate professor at Nagaoka University of Technology. Since 2012, he has been a professor at Nagaoka University of Technology. His research interests are in structural analysis and weathering steel bridges. Eiji Iwasaki received his B.S., M.S., and Ph.D. degrees from Nagaoka University of Technology, Japan, in 1985, 1987, and 1990, respectively. From 1990 to 1998, he was an assistant professor at Nagaoka University of Technology, Japan. From 1998 to 2000, he was an associate professor at National Institute of Technology, Tokuyama College, Japan. From 2000 to 2012, he was an associate professor at Nagaoka University of Technology. Since 2012, he has been a professor at Nagaoka University of Technology. His research interests are in structural analysis and weathering steel bridges. Masatsugu Nagai received his B.S., M.S., and Ph.D. degrees from Osaka University, Japan, in 1971, 1973, and 1982, respectively. From 1973 to 1988, he belonged to the bridge design department of Kawasaki Heavy Industries, Ltd. From 1988 to 1996, he was an associate professor at Nagaoka University of Technology. From 1996 to 2013, he was a professor at Nagaoka University of Technology. About the Authors Since 2013, he has been a professor emeritus at Nagaoka University of Technology. His main field is cable-supported bridges and hybrid structures. Masatsugu Nagai received his B.S., M.S., and Ph.D. degrees from Osaka University, Japan, in 1971, 1973, and 1982, respectively. From 1973 to 1988, he belonged to the bridge design department of Kawasaki Heavy Industries, Ltd. From 1988 to 1996, he was an associate professor at Nagaoka University of Technology. From 1996 to 2013, he was a professor at Nagaoka University of Technology. Since 2013, he has been a professor emeritus at Nagaoka University of Technology. His main field is cable-supported bridges and hybrid structures.
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Federated learning for multi-center imaging diagnostics: a simulation study in cardiovascular disease
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Federated learning for multi‑center imaging diagnostics: a simulation study in cardiovascular disease OPEN Akis Linardos1*, Kaisar Kushibar1, Sean Walsh2, Polyxeni Gkontra1 & Karim Lekadir1 Deep learning models can enable accurate and efficient disease diagnosis, but have thus far been hampered by the data scarcity present in the medical world. Automated diagnosis studies have been constrained by underpowered single-center datasets, and although some results have shown promise, their generalizability to other institutions remains questionable as the data heterogeneity between institutions is not taken into account. By allowing models to be trained in a distributed manner that preserves patients’ privacy, federated learning promises to alleviate these issues, by enabling diligent multi-center studies. We present the first simulated federated learning study on the modality of cardiovascular magnetic resonance and use four centers derived from subsets of the M&M and ACDC datasets, focusing on the diagnosis of hypertrophic cardiomyopathy. We adapt a 3D-CNN network pretrained on action recognition and explore two different ways of incorporating shape prior information to the model, and four different data augmentation set-ups, systematically analyzing their impact on the different collaborative learning choices. We show that despite the small size of data (180 subjects derived from four centers), the privacy preserving federated learning achieves promising results that are competitive with traditional centralized learning. We further find that federatively trained models exhibit increased robustness and are more sensitive to domain shift effects. Diagnostic tools based on artificial intelligence models have shown promising results in a variety of single-center studies across multiple medical imaging ­domains1, but their generalizability to unseen distributions remains understudied, and their application in clinical practice is still far from realized. As data remains segregated in different institutions, such studies have mostly focused on limited single-center datasets for their training and evaluation. Aside from the obvious issue of having a small sample size, evaluation in such a set-up is question- able, as no assumptions can be made on how this performance translates to unseen centers. For ML methods to generalize to unseen datasets, it is often assumed that newly seen data is independent and identically distributed (IID) to the one seen during training—i.e. each data point comes from the same probability distribution and is mutually independent to all others. www.nature.com/scientificreports www.nature.com/scientificreports 1Department of Mathematics and Computer Science, University of Barcelona, 08007 Barcelona, Spain. 2Radiomics, 4000 Liège, Belgium. *email: linardos.akis@ub.edu Federated learning for multi‑center imaging diagnostics: a simulation study in cardiovascular disease OPEN F h l d h i d i h h i h b li i d i h di For these reasons, related research in domains other than segmentation has been more limited, with studies tangential to diagnosis popping up only as early as 2020 in breast density ­classification13, and lung tumor survival ­prediction14. With the emergence of the COVID-19 pandemic, the urgent need for diagnostic tools circumvented common obstacles and allowed researchers to collaborate in federated learning diagnosis for the first ­time15,16. Very recently, an open-source framework that integrates FL along with the functionality of end-to-end encryp- tion to protect against inversion attacks was developed, trained and tested on paediatric X-ray ­classification17.h i In this work, we focus on the diagnosis of cardiovascular disease (CVD) based on Cardiac MRI. The impor- tance of furthering our understanding on the structure and function of the heart is highlighted by the prevalence of CVD in the population, which accounts for one third of annual ­deaths18,19. Cardiac MRI has been the go-to modality for this task, allowing the assessment and delineation of the three heart segments—i.e. the myocardium, and the left and right ventricle blood pools—to identify the presence of anomalies such as myocardic infarctions or cardiomyopathies. Based on this modality, and by leveraging hand crafted features, Machine Learning (ML) diagnostic tools have been developed with some success in single-center ­datasets20,21. g p g To enable AI studies in CMR diagnosis, there have been public challenges for cardiac MRI segmentation and diagnosis such as “Automatic Cardiac Diagnosis Challenge” dataset (ACDC) and the “Multi-Centre, Multi- Vendor and Multi-Disease Cardiac Segmentation Challenge” dataset (M&M). Despite it’s name, M&M now also includes diagnostic labels. We will be using subsets from these datasets in our study and provide more details on the data acquisition and annotation in “Dataset” section. q In terms of the Cardiac MRI modality, there has been a lot of literature on deep learning-based ­segmentation22–30 with diagnosis typically being a follow-up step, leveraging the segmentation masks and utiliz- ing models such as random ­forests31,32, support vector ­machines33 or a simple diagnostic ­rule34. These diagnosis models focus on two timepoints of the cardiac MRI per-patient: the phase of End-Diastole (ED) (maximum heart relaxation) and the phase of End-Systole (ES) (maximum heart contraction). Current such studies have emphasized on the aforementioned ACDC ­dataset35, a single center dataset hosting 100 subjects and five labels (20 subjects each). Federated learning for multi‑center imaging diagnostics: a simulation study in cardiovascular disease OPEN a less explored topic, and segmentation steps are often a prerequisite for diagnosis models to be accurate. The data scarcity problem is even more prominent in this case, as the ground truth information for the presence of disease is of a much more sensitive nature, and clinical registries are lacking. Label imbalance and demographic variabilities become more relevant as well, as different institutions usually contain different types of diseases, while in segmentation the expected ground truth is the same in all cases—i.e. a mask of the segmented parts. From a data science standpoint, segmentation allows for more flexible methods of data augmentation (even GAN-based generation), whereas, in diagnosis tasks, augmentation should be done with extreme care to avoid shifting the true value of corresponding labels. This often requires human-expert validation depending on the augmentation method, lest it risks adding noise. Segmentation also has the advantage of freely using 2D slices and patch-based approaches, which allows one to extract many training samples from a single scan, while in diagnosis, a single 3D volume (or sometimes series of longitudinal data) is used as a single training data point. h l d h d h h h b l d h d a less explored topic, and segmentation steps are often a prerequisite for diagnosis models to be accurate. The data scarcity problem is even more prominent in this case, as the ground truth information for the presence of disease is of a much more sensitive nature, and clinical registries are lacking. Label imbalance and demographic variabilities become more relevant as well, as different institutions usually contain different types of diseases, while in segmentation the expected ground truth is the same in all cases—i.e. a mask of the segmented parts. From a data science standpoint, segmentation allows for more flexible methods of data augmentation (even GAN-based generation), whereas, in diagnosis tasks, augmentation should be done with extreme care to avoid shifting the true value of corresponding labels. This often requires human-expert validation depending on the augmentation method, lest it risks adding noise. Segmentation also has the advantage of freely using 2D slices and patch-based approaches, which allows one to extract many training samples from a single scan, while in diagnosis, a single 3D volume (or sometimes series of longitudinal data) is used as a single training data point. Federated learning for multi‑center imaging diagnostics: a simulation study in cardiovascular disease OPEN For this reason, the data heterogeneity present in multi-center medical data poses a significant problem, as in all cases such data is non-IID—a direct result of the usage of different acquisi- tion protocols, different scanners and varying demographics.f pf y g g p To overcome the core obstacle of data scarcity and to better understand the effects of data heterogeneity that is present in between different centers, institutions need to come together in collaboration. This has thus far been difficult, as institutions are inclined to keep a tight grip on their medical data due to privacy regulations (e.g. GDPR in the European Union and HIPAA in the United States). While an obvious approach for collaborators would be to share their data on a central server (CDS, Fig. 1A), this endangers patients’ privacy by increasing the chance of data leakage. Distributed learning allows for AI models to be trained across multiple edge devices or centers, without data ever leaving its original ­place2,3. In 2017, Google proposed Federated ­learning4 (FL, Fig. 1B) a framework that allows deep learning models to be distributed and trained on local data, aggregating only their parameters in a central server. The central server only ever sees a complex representation of the initial data, as learned by the local models, and those representations are combined by an algorithm called FederatedAveraging before being redistributed for subsequent training. g q g Privacy preserving federated learning systems for medical image analysis have been mainly explored in the context of segmentation for ­brain5–8, ­prostate9 and COVID-19 affected ­regions10–12. Segmentation is still an open problem and faces multiple challenges, especially at the data collection stage as expert manual annotation is time- consuming and exhibits inter- and intra-operator variability in the segmentation masks. However, diagnosis is Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ 3D CNN Central Server Models trained locally in each center Central Server 3D CNN Data collected in a single server A) Collaborave Data Sharing (CDS) B) Federated Learning (FL) Figure 1. A diagram of the two collaborative learning frameworks. For FL only models are transferred, while in the CDS case, the data itself is transferred to the central server and all training happens there. Figure 1. A diagram of the two collaborative learning frameworks. For FL only models are transferred, while in the CDS case, the data itself is transferred to the central server and all training happens there. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Center Vendor Spatial resolution (mm) Slice thickness ­(mm2) NOR HCM Total Vall d’Hebron Philips 1.1516–1.2362 10.0 21 25 46 Sagrada Familia Siemens 0.9765–1.6200 8.0–10.0 33 37 70 SantPau Canon 0.7955–1.8228 10.0 14 10 24 ACDC Siemens 1.3400–1.6800 5.0-10.0 20 20 40 Total 88 92 180 Table 1. Dataset description, including meta-data and the class distribution of Normal (NOR) and h h i di h (HCM) f h l d b f h M&M d ACDC d d Table 1. Dataset description, including meta-data and the class distribution of Normal (NOR) and Table 1. Dataset description, including meta-data and the class distribution of Normal (NOR) and hyperthropic cardiomyopathy (HCM) for the selected subset from the M&M and ACDC datasets used in this study. hyperthropic cardiomyopathy (HCM) for the selected subset from the M&M and ACDC datasets used in th study. thus causing local models to overfit on different tasks. For this reason, we focus only on diagnosing hypertrophic cardiomyopathy (HCM)—i.e. a binary classification between normal (NOR) subjects and subjects suffering from HCM. HCM is the most common heritable cardiomyopathy, occurring in approximately as 0.29%—i.e. 1:344—of the adult ­population38,39. Contrary to previous work on cardiac MRI diagnosis, our main goal here is to test the feasibility of cardiac MRI diagnosis in between multiple centers and highlight the importance of evaluating both IID and non-IID performance (i.e. testing models on partitions of the centers seen during the training and also on unseen centers) in a principled manner.i thus causing local models to overfit on different tasks. For this reason, we focus only on diagnosing hypertrophic cardiomyopathy (HCM)—i.e. a binary classification between normal (NOR) subjects and subjects suffering from HCM. HCM is the most common heritable cardiomyopathy, occurring in approximately as 0.29%—i.e. 1:344—of the adult ­population38,39. Contrary to previous work on cardiac MRI diagnosis, our main goal here is to test the feasibility of cardiac MRI diagnosis in between multiple centers and highlight the importance of evaluating both IID and non-IID performance (i.e. testing models on partitions of the centers seen during the training and also on unseen centers) in a principled manner.i p p Previous work in federated learning diagnosis on COVID-1915,16 and paediatric X-ray ­classification17 has focused on the development of state of the art federated learning frameworks—the latter one open-sourcing their pipeline which also integrates an encryption mechanism. www.nature.com/scientificreports/ In this study, we focus on the effects multi-center data has on this frameworks, conducting a systematic comparative analysis between the CDS and FL paradigms, test- ing a variety of data curation and augmentation techniques. By evaluating in two distinct cross-validation set-ups and repeating the experiments multiple times, we gain a robust estimate of both IID and non-IID performance, showcasing the gap between the two. Our model follows the notoriously hard to train 3D-CNN ­architecture40, leveraging transfer learning by using an instance of the network that has been pretrained on action recognition. Concretely, our contributions can be summarized as follows: • We present, to the best of our knowledge, the first federated learning study on CMR diagnosis and demon- strate that FL performance is comparable to CDS, while preserving patient privacy.f We present, to the best of our knowledge, the first federated learning study on CMR diagnosis and demon- strate that FL performance is comparable to CDS, while preserving patient privacy.f • We propose a technique of inducing different priors to the model by leveraging the ground truth masks, illustrating an effective way to constrain the solution space and improve performance for deep learning-based multi-center CMR diagnosis in both collaborative learning set-ups.if • We propose a technique of inducing different priors to the model by leveraging the ground truth masks, illustrating an effective way to constrain the solution space and improve performance for deep learning-based multi-center CMR diagnosis in both collaborative learning set-ups.if • We apply a diverse set of data augmentations to artificially increase the data size and study their effect in a principled way on the collaborative learning frameworks, repeating the experiments with different CNN weight initializations to gain an estimate of model ­robustness41. We also test a variation of the FL algorithm in this context, which assigns an equal vote to all centers in the training data and show that it is beneficial in some cases. www.nature.com/scientificreports/ • Finally, by using two distinct repeated cross validation set-ups—one that uses a part of all centers as test set per fold and another that uses a whole center as test set per fold—we get an estimate of both on-site and out- of-site performance, showing that the two differ substantially and highlighting their importance for future diagnosis studies.i • Finally, by using two distinct repeated cross validation set-ups—one that uses a part of all centers as test set per fold and another that uses a whole center as test set per fold—we get an estimate of both on-site and out- of-site performance, showing that the two differ substantially and highlighting their importance for future diagnosis studies.i g To boost future research in the field, we make our code available for the research community. g • To boost future research in the field, we make our code available for the research community. Federated learning for multi‑center imaging diagnostics: a simulation study in cardiovascular disease OPEN Khened et al.31 reported promising results on multi-label diagnosis but evaluated on a limited hold-out test set of 10 samples. On the same task, Cetin et al.33 used an SVM on top of radiomic features derived from manual segmentations, while Wolterink et al.32 evaluated a random forest classifier instead, both using a cross validation scheme. Liu et al.34 used an automated deep-learning based segmentation scheme, following up with a diagnostic rule. Despite the impressive classification performance reported in these studies, these models are both trained and evaluated solely on a single-center dataset (ACDC), and thus, no assumptions can be made regarding their generalization to unseen centers and larger datasets. To deploy such models in the real world, one has to assume that new subjects being tested are IID to those seen during training and evaluation. In the domain of medical imaging, where data is highly heterogeneous between centers, this assumption is far from ­true36. Furthermore, as these studies focus on a single center, no privacy preservation measures are studied, which are otherwise necessary for deployment of such models. y y Despite the widespread interest in automated CMR diagnosis methods, multi-centric and distributed learning studies in the field are currently lacking. In this paper, we conduct our study with four centers, three of which were derived from the M&M ­dataset37, and the fourth being a subset of ­ACDC35. We test the CDS and FL col- laborative learning frameworks. As FL trains local models in each center, multi-label classification is a very chal- lenging problem in the case of the M&M dataset where many labels have little to no overlap between the centers, Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 Table 1.   Dataset description, including meta-data and the class distribution of Normal (NOR) and hyperthropic cardiomyopathy (HCM) for the selected subset from the M&M and ACDC datasets used in this study. Methods An example of the induced priors used in this study: (A) a baseline that is the 1-channel cardiac MRI, (B) the baseline multiplied by the segmentation mask, (C) the baseline split into three channels, one for each part of the heart (right ventricle blood pool, left ventricle blood pool, and myocardium). A) Baseline MRI Figure 2. An example of the induced priors used in this study: (A) a baseline that is the 1-channel cardiac MRI, (B) the baseline multiplied by the segmentation mask, (C) the baseline split into three channels, one for each part of the heart (right ventricle blood pool, left ventricle blood pool, and myocardium). exceeds 15 mm, given that this observation was otherwise unexplained by abnormal loading conditions hypertension, valvular, congenital disease) or infiltrative cardiomyopathies. ness exceeds 15 mm, given that this observation was otherwise unexplained by abnormal loading conditions (e.g., hypertension, valvular, congenital disease) or infiltrative cardiomyopathies. Segmentation rules. ACDC’s contours were manually drawn by experts on 3D volumes of the LV and RV cavi- ties and the myocardium at the timepoints of interest–i.e. ED and ES. Annotation adhered to the following rules: LV and RV are completely covered. The papillary muscle is included into the cavity, and the contours follow the limit defined by the aortic valve. The RV cavity and the root of the pulmonary artery are clearly separated. RV is defined as the region on the right of heart with a significant contraction between ventricular diastole and systole. The data-providers also supply clear illustrations of the annotation rules in their ­work35. M&M ­segmentation37 was built on top of ACDC’s Standard Operating Procedure (SOP). The contours were corrected based on the consensus of two in-house annotators according to the following rules: a. LV and RV cavities must be completely covered, with papillary muscles included. b. No interpolation of the LV myocardium must be performed at the base. c. RV must have a larger surface in end-diastole compared to end-systole and avoid the pulmonary artery. Data preprocessing. As a first step, we apply N4 bias field correction to remove non-uniformity of low fre- quencies inherent to ­MRI42. Then we resample the volumes to a common spacing of 1 ×1× 1 ­mm3 on the entirety of the data used. Methods The original spacing of the images vary, but all centers trim their original spacing, with the only exception of SantPau that in many cases interpolates its spatial resolution to reach a 1 ×1× 1 ­mm3 spacing. We crop the volumes using a 150×150× 10 voxel window, centered on the center of the bounding box of non-zero values on their corresponding segmentation masks. Induced priors. Leveraging the segmentation masks that are provided by clinicians as part of the M&M and ACDC datasets, we consider the following set-ups for our dataset: (1) a baseline that is the 1-channel MRI; (2) the MRI image multiplied by the segmentation mask (thus inducing a shape prior); and (3) the MRI image split into three channels, corresponding to left ventricle blood pool, right ventricle blood pool, and myocardium, inducing a strong prior of the heart structure (see Fig. 2). Notably, the initial layer of ResNet3D, was pretrained on action recognition RGB images and thus expects a 3-channel input. For this reason, the baseline and masked MRIs are copied three times before being fed to the model. Reinitializing the initial layer to a 1-channel input results in substantially worse performance, which, for brevity, we don’t report in this paper. Two timepoints are extracted from the 3D volumes corresponding to the ED and ES phases. The two timepoints are fed as separate samples to the network so as to leverage more data; however, the two timepoints are always in the same set (train, validation, test). Data harmonization. A main obstacle when learning from multi-center MRI data is the inter-site variability, which is present even when the same acquisition protocol is ­used43,44. To adapt the image intensities on the same scale, we apply Nyúl histogram ­matching45 followed by a rescaling to [0, 1]. Concretely, we match the histogram of each image to the average histogram of all images from the training centers. As averaging is an aggregate query to the local data, it does not require access to individual subject data and thus preserves privacy. The final average histogram Haverage used for the histogram matching process is calculated as: Haverage = K  k=1 Nk N Nk  n=1 Hk n, where K is the total number of centers, Nk the number of samples for center k, and N the total sample size of all centers. Methods Dataset. We base our experiments on a unique dataset derived from a combination of M&M (a multi-cen- tric dataset gathered in a coordinated effort under the EuCanShare ­project37) and ACDC (a single center dataset presented as a challenge in ­201835). Both datasets are composed of T1-weighted Cardiac Cine MRI sequences. M&M consists of 6 centers and 4 labels corresponding to dilated cardiomyopathy (DCM), hypertrophic cardio- myopathy (HCM), abnormal right ventricle (RV) and subjects without cardiac disease (NOR)37.i Because of severe label imbalance between centers, training a federated model on multi-label classification becomes a complex problem as local models overfit to a subset of the labels or even a single label (for example one center only has DCM cases). In our experiments, we consider the task of binary classification (HCM vs. NOR), using a subset of M&M in which the chosen labels are most balanced. Thus, we use 3 centers from the M&M dataset, namely Sagrada Familia, Vall d’Hebron and SantPau and complement them with a subset of the ACDC dataset as a 4th center. The final form of the dataset we used is outlined in Table 1. hi For the M&M challenge, all patients signed the informed consent, the study protocol was approved by the Ethical Committee for Clinical Research for each institution involved, and it follows the ethical guidelines of the Declaration of Helsinki. The authors of the ACDC challenge have also received approval by their ethical committees to make it publicly available. As these are both public datasets, no direct approval from the ethical committee was necessary on our side. Diagnosis rules. On the ACDC dataset, an HCM label was allocated if the patient’s left ventricular cardiac mass exceeds 110 g/m2 For the M&M centers, the diagnosis of HCM was allocated when left ventricular wall thick- Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ A) Baseline MRI B) Masked MRI C) MRI per-structure split into 3 channels Figure 2. An example of the induced priors used in this study: (A) a baseline that is the 1-channel cardiac MRI, (B) the baseline multiplied by the segmentation mask, (C) the baseline split into three channels, one for each part of the heart (right ventricle blood pool, left ventricle blood pool, and myocardium). www.nature.com/scientificreports/ Baseline MRI B) Masked MRI C) MRI per-structure split into 3 channels Figure 2. Methods • Shape and Intensity Augmentations: includes all aforementioned augmentations, plus random MRI spike artifacts, random MRI bias field artifact, noise sampled from a Gaussian with µ = 0 and σ ∼(0, 0.25) , random gamma transformations (randomly changes contrast of an image by raising its values to a random power within a specified range). During training on one of these set-ups (except the No Augmentations set-up), an augmentation is sampled from the aforementioned pools and is applied on the input data with a probability of 50%. That means that every image has a 50% chance of being augmented. These types of data augmentations are known to be effective in improving a model’s generalization as they introduce domain shift effects. However, the chosen augmentations are also reflective of clinical reality as we avoid extreme cases of elastic deformation and consider the random noise augmentation as representative of bad acquisitions, which often escape quality control. All augmentations used and studied in this work were obtained using the TorchIO ­library47 and are illustrated in Fig. 3. 3D‑CNN model. 3D-CNNs have the potential to retrace the success story of 2D-CNNs; however, their immense size is cause of two major drawbacks—i.e. a high computational cost and the curse of dimensionality which causes them to ­overfit40. In medical imaging, where data is very scarce, 3D-CNNs have been used suc- cessfully by applying transfer learning schemes, utilizing data from entirely different ­domains48. In our case, we use the 3D-CNN ResNet18 model as defined by Tran et al.49 and, instead of initializing the weights randomly, we load an instance of the model that has been pretrained on the action recognition dataset Kinetics-40050. This is beneficial because the early layers of the network tend to extract similar features (such as edges or blobs) irrespective of the domain that are beneficial to all imaging ­tasks51. To constrain the model from overfitting, we freeze the initial layers and train a newly initialized linear layer with a sigmoid activation function to the task of binary classification of HCM vs NOR. Concretely, out of the 33,166,785 parameters our network has in total, only the 512 parameters of the final linear layer are trained in this case. Methods where K is the total number of centers, Nk the number of samples for center k, and N the total sample size of all centers. h f h k d h l h l In the majority of our experiments, we crop our inputs with segmentation masks, and thus only the values within the mask are used for the histogram matching as well. As we use two distinct evaluation set-ups, in some cases not all centers are calculated in the average. This is further clarified in “Evaluation Procedure” section where these set-ups are also explained. Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ Default Random Flip Random Affine Random Spike Random Noise Random Elastic Deformation Random Bias Shape Augmentations Basic Augmentations Intensity Augmentations Random Gamma Figure 3. Illustration of augmentation techniques used in our analysis on a single CMR image slice. Shape Augmentations Intensity Augmentations Default Figure 3. Illustration of augmentation techniques used in our analysis on a single CMR image slice. Data augmentation. Due to the limited number of samples in the M&M dataset, we test several data augmentation techniques to artificially increase the size of the training set. These techniques also apply domain shift effects and make the representations learned more invariant to certain features, which can improve gen- eralization to unseen ­datasets46. To test how this dataset shift affects our framework, we compare four different augmentation set-ups and repeat the experiments both for FL and CDS. These set-ups are as follows: • No Augmentations. g • Basic Augmentations: affine transformations (rotation by varying degrees), horizontal and vertical flipping in axial view. g • Basic Augmentations: affine transformations (rotation by varying degrees), horizontal and vertical flipping in axial view. Shape Augmentations: includes the basic augmentations plus elastic deformation. • Shape Augmentations: includes the basic augmentations plus elastic deformation. • Shape and Intensity Augmentations: includes all aforementioned augmentations, plus random MRI spike artifacts, random MRI bias field artifact, noise sampled from a Gaussian with µ = 0 and σ ∼(0, 0.25) , random gamma transformations (randomly changes contrast of an image by raising its values to a random power within a specified range). Methods Thus we also tested a modified version of the FederatedAveraging algorithm where each model gets an equal weight during aggregation, which we will be refering to as FL-EV (as in Equal Voting). In this case the averaging equation becomes: Wt+1 ←−1 K K  k=1 wk t+1. Evaluation procedure. As we are dealing with data of small size, simple hold-out methods are inefficient to accurately represent the performance of our ­models52. Thus, all models are validated under a 5-fold cross valida- tion scheme that utilizes the entire dataset. Concretely, we split the dataset into five folds, so that 20% is unseen during the training procedure and is used as a test set. From the remaining 80% we use 90% for training and 10% as validation. The purpose of the validation set is simply to find the early stop point. h p p p yi y p p In the past, federated learning performance has been evaluated under a collaborative cross validation (CCV) set-up5. In this set-up, cross validation is coordinated across centers so that each center splits its data into train, validation and test sets using the same percentage allocation. As a result, the final test set of each fold is an aggregate of different centers. However, when dealing with multi-center data, one has to take into account that a model should be deployable to centers unseen during the training and an estimate of out-of-site performance is required. For this reason, we are also estimating how our model generalizes to unseen centers under a different set-up that is Leave Center Out Cross Validation (LCO-CV). In this case, the data is split into as many folds as there are centers present (in our case 4 folds) and each fold uses a different center as testing set. This cross valida- tion scheme has been used before in other distributed learning ­studies53. In both CCV and LCO-CV cases, FL and CDS are using the exact same split of the data so that all folds are comparable. A schematic of this evaluation procedure is presented in Fig. 4. For the CDS set-up, at each epoch a single model is trained and then evaluated. Methods An illustration of a single iteration for: (A) Collaborative Cross Validation (CCV), where centers coordinate their splitting across 5 folds so that each center provides 20% of its data as test set and the rest as training and validation, (B) Leave Center Out Cross Validation (LCO-CV) which runs for as many iterations as there are centers in the dataset, each time using a different center as test set, and the rest as training and validation. www.nature.com/scientificreports/ A) Collaborative Cross Validation (CCV) B) Leave Center Out Cross Validation (LCO-CV) Validation Train Vall d’Hebron Sagrada Familia SantPau ACDC Test Figure 4. An illustration of a single iteration for: (A) Collaborative Cross Validation (CCV), where centers coordinate their splitting across 5 folds so that each center provides 20% of its data as test set and the rest as training and validation, (B) Leave Center Out Cross Validation (LCO-CV) which runs for as many iterations as there are centers in the dataset, each time using a different center as test set, and the rest as training and validation. Figure 4. An illustration of a single iteration for: (A) Collaborative Cross Validation (CCV), where centers coordinate their splitting across 5 folds so that each center provides 20% of its data as test set and the rest as training and validation, (B) Leave Center Out Cross Validation (LCO-CV) which runs for as many iterations as there are centers in the dataset, each time using a different center as test set, and the rest as training and validation. Wt+1 ←− K  k=1 nk n wk t+1, where n is the total sample size and nk the sample size of center k.h where n is the total sample size and nk the sample size of center k.h p p The reason that the FederatedAveraging algorithm weights the model parameters by a factor proportionate to the sample size of the center, is so that the better informed models outweigh the ­others4. However, medical centers are liable to domain shift effects due to different scanners, acquisition protocols, and different demo- graphics from center to center. Given that data from different centers tends to be severely imbalanced (in our case Sagrada Familia has three times the size of SantPau), weighting the models by the sample is liable to add severe bias towards some cases over others. Methods In our preliminary experiments, 256, 512, 1024 and 2048 channels on the linear layer were tested and 512 was found to perform best.hf y p This, however, introduces a second problem: a strong bias on the model for a completely different domain and data modality. To find a proper trade-off between the issue of bias and overfitting, we experimented by fine tuning the pre-trained layers with varying learning rates (1e-4, 1e-5, 1e-6, 1e-7 and 0) while the newly initialized linear layer was always trained with a much higher learning rate of 0.01. Our preliminary experiments showed that for the pre-trained layers, a learning rate of 1e-5 performed best, and thus we used this configuration for all subsequent experiments. The models are trained for a maximum of 100 epochs, stopping early if validation performance stagnates for 10 epochs. In our experiments, the early stopping occurred on the 20–30th epoch. Federated learning. We first initialize a global model and then distribute it across the four centers. It is fundamental that on every step, including the initialization the model being distributed is identical, otherwise the aggregation across models will result in a non-sense representation and training will not ­progress4. The mod- els are trained for seven iterations—i.e. on seven batches of data—on each center and are aggregated after each epoch. To parse the entire data within the same number of iterations on each center, a different batch size is used. After training locally, the models are aggregated using the FederatedAveraging ­algorithm4. Concretely, each model makes an update step in its respective center k using a learning rate η and the gradients gk so that p pf After training locally, the models are aggregated using the FederatedAveraging ­algorithm4. Concretely, each model makes an update step in its respective center k using a learning rate η and the gradients gk so that wk t+1 ←−wt −ηgk, ∀k Then, these weights are aggregated to the global model in a way that is proportionate to the sample size of each center, Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ A) Collaborative Cross Validation (CCV) B) Leave Center Out Cross Validation (LCO-CV) Validation Train Vall d’Hebron Sagrada Familia SantPau ACDC Test Figure 4. Methods The two evaluation techniques imply different adaptation set-ups as for the CCV we are standardizing using an average from all of the centers, while for LCO-CV we consider one center entirely unseen. Figure 5. Histograms of different center intensities before and after histogram standardization. The two evaluation techniques imply different adaptation set-ups as for the CCV we are standardizing using an avera from all of the centers, while for LCO-CV we consider one center entirely unseen. N4 Bias Correcon Resampling to 1x1x1 mm Cropping to 150x150x10 Induce Priors Histogram Training CDS training FL training Data Augmentations Leave Center Out - Cross Validation Collaborative Cross Validation Train set Test set Train set Test set Histogram Matching Histogram Training Merge all centers into one pool for training Local model copies trained on all four centers Flow of train set Flow of test set Federated evaluation Merge test sets Flow of model Evaluation on merged test set Induce Priors CDS training FL training Data Augmentations Histogram Matching Merge the three train centers into one pool for training Local model copies trained on each of the three train centers Evaluation on unseen center Evaluation on unseen center Split into folds Figure 6. An overview of the pipeline used for the experiments in this study. Histogram Training Figure 6. An overview of the pipeline used for the experiments in this study. challenging because of this limitation, and in this example we can see this by the presence of a second peak on Vall d’Hebron’s intensity distribution.h hallenging because of this limitation, and in this example we can see this by the presence of a second peak on Vall d’Hebron’s intensity distribution.h y The overall pipeline is summarized in Fig. 6. Methods For the FL set-up, however, the evaluation process is more complex: (1) train the local copies of the model for one epoch; (2) send the local models to the server; (3) aggregate all local models to obtain an updated global model; (4) send copies of the updated global model to all centres; (5) evaluate the model on each centre locally. In this study, steps 2 and 4 are simulated within a single server; in the real world, however, these are the points where communication bottlenecks would occur due to possible bandwidth ­limitations4. The best model based on validation performance is used to predict the test set. After the entire cross validation procedure is complete, the Area Under the Receiver Operating Characteristic Curve score (AUC) is calculated based on the predictions derived from each respective test set. In the case of CCV, to ensure fairness in comparison, the same folds are used for the FL and the CDS scheme. We repeat each experiment five times—i.e. using five different network weight initalizations. The reason for this is that a DL model’s performance is liable to vary, as different initializations tend to converge to different ­optima41. By repeating each experiment five times and calculating the average AUC across repetitions, we obtain a more accurate estimate of the true performance and an estimate of the framework’s robustness. Regarding data harmonization, in the LCO-CV, the reference histogram used from matching does not include the test center, thus making the task harder when compared to CCV where all centers are used for the derived average. The histograms of each center before and after the standardization are outlined in Fig. 5. In this dia- gram, one example of an LCO-CV iteration is visualized where Vall d’Hebron is the test set. Vall d’Hebron in this case is matched to the histogram average as calculated by the train centers. Notably, the test set becomes more Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ Figure 5. Histograms of different center intensities before and after histogram standardization. The two evaluation techniques imply different adaptation set-ups as for the CCV we are standardizing using an average from all of the centers, while for LCO-CV we consider one center entirely unseen. Figure 5. Histograms of different center intensities before and after histogram standardization. Results In the initial experiments, we compare the baseline data to a curated version with induced shape priors as visu- alized in Fig. 2. The results are outlined in Table 2. For both collaborative learning frameworks, performance improves as we induce a shape prior (Masked MRI) and peaks when we use the per-structure split—a prior of the heart’s structure. FL exhibits similar performance to CDS in all cases, however the standard deviations are much lower in the case of FL. Moreover, the difference in performances of CDS and FL decreases after constraining the solution space using the shape priors.f g A systematic comparative study is conducted on the different augmentation set-ups using both the CCV and LCO-CV evaluation procedures. We find that CCV performance drops in all collaborative learning frameworks (Table 3 and Fig. 7) once augmentations are introduced.f In the case of LCO-CV, where the train and testing sets come from different distributions, CDS performance consistently improves from additional augmentations, reaching its highest when the most augmentations are applied (Fig. 7). FL also benefits from the basic augmentations of rotation and flipping, but its performance drops as shape and intensity augmentations are introduced, and CDS surpasses FL. Interestingly, models trained under an FL framework (either FL or FL-EV) exhibit incredibly consistent results across different initializations of the same set-ups, while CDS-framed models show a high amount of variance. https://doi.org/10.1038/s41598-022-07186-4 Scientific Reports | (2022) 12:3551 | www.nature.com/scientificreports/ Table 2. AUC results for different curation types for Collaborative Data Sharing (CDS) and Federated Learning (FL). The reported numbers are calculated across five repeated experiments with different seeds Curation type Baseline MRI Masked MRI MRI per-structure split CDS 0.727 ± 0.0298 0.810 ± 0.0120 0.856 ± 0.011 FL 0.747 ± 0.0005 0.826 ± 0.0005 0.861 ± 0.003 Table 2. AUC results for different curation types for Collaborative Data Sharing (CDS) and Federated Learning (FL). The reported numbers are calculated across five repeated experiments with different seeds. Table 3. Collaborative Cross Validation (CCV) performance evaluated using the AUC metric. Each number represents the average AUC, calculated across five repeated experiments with different seeds. Results Augmentations Framework Vall d’Hebron Sagrada Familia ACDC SantPau Total None CDS 0.898 ± 0.004 0.862 ± 0.008 0.797 ± 0.026 0.853 ± 0.005 0.856 ± 0.011 FL 0.942 ± 0.002 0.896 ± 0.001 0.799 ± 0.003 0.867 ± 0.005 0.861 ± 0.003 FL-EV 0.941 ± 0.002 0.874 ± 0.003 0.803 ± 0.002 0.875 ± 0.002 0.852 ± 0.002 Basic CDS 0.861 ± 0.014 0.784 ± 0.012 0.778 ± 0.041 0.845 ± 0.016 0.809 ± 0.021 FL 0.927 ± 0.002 0.872 ± 0.002 0.798 ± 0.001 0.807 ± 0.001 0.844 ± 0.002 FL-EV 0.933 ± 0.001 0.859 ± 0.001 0.774 ± 0.001 0.818 ± 0.004 0.835 ± 0.002 Shape CDS 0.897 ± 0.006 0.810 ± 0.023 0.770 ± 0.024 0.803 ± 0.017 0.827 ± 0.018 FL 0.933 ± 0.002 0.871 ± 0.004 0.826 ± 0.001 0.901 ± 0.002 0.848 ± 0.002 FL-EV 0.916 ± 0.001 0.852 ± 0.001 0.825 ± 0.001 0.883 ± 0.001 0.839±0.001 Shape and intensity CDS 0.897 ± 0.009 0.821 ± 0.008 0.859 ± 0.028 0.833 ± 0.025 0.849 ± 0.018 FL 0.905 ± 0.001 0.886 ± 0.001 0.785 ± 0.005 0.858 ± 0.003 0.839 ± 0.003 FL-EV 0.917 ± 0.001 0.870 ± 0.002 0.800 ± 0.003 0.880 ± 0.002 0.842 ± 0.002 Table 3. Collaborative Cross Validation (CCV) performance evaluated using the AUC metric. Each number represents the average AUC, calculated across five repeated experiments with different seeds. Table 4. Leave Center Out (LCO-CV) performance evaluated using the AUC metric. Each number represen the average AUC calculated across five repeated experiments with different network initializations. Results Augmentations Framework Vall d’Hebron Sagrada Familia ACDC SantPau Total None CDS 0.870 ± 0.020 0.809 ± 0.010 0.616 ± 0.064 0.784 ± 0.026 0.732 ± 0.008 FL 0.897 ± 0.002 0.815 ± 0.001 0.599 ± 0.002 0.835 ± 0.001 0.746 ±0.001 FL-EV 0.894 ± 0.001 0.816 ± 0.001 0.566 ± 0.002 0.837 ± 0.001 0.779 ± 0.004 Basic CDS 0.916 ± 0.014 0.816 ± 0.016 0.654 ± 0.068 0.776 ± 0.019 0.759 ± 0.016 FL 0.922 ± 0.002 0.855 ± 0.001 0.554 ± 0.002 0.818 ± 0.001 0.791 ± 0.001 FL-EV 0.886 ± 0.007 0.868 ± 0.001 0.532 ± 0.003 0.810 ± 0.001 0.773 ± 0.005 Shape CDS 0.900 ± 0.024 0.834 ± 0.028 0.641 ± 0.084 0.796 ± 0.013 0.764 ± 0.022 FL 0.861 ± 0.002 0.879 ± 0.001 0.668 ± 0.003 0.845 ± 0.007 0.766 ± 0.001 FL-EV 0.803 ± 0.003 0.869 ± 0.001 0.632 ± 0.008 0.821 ± 0.001 0.737 ± 0.004 Shape and intensity CDS 0.901 ± 0.031 0.829 ± 0.013 0.743 ± 0.048 0.793 ± 0.018 0.776 ± 0.008 FL 0.887 ± 0.001 0.807 ± 0.003 0.472 ± 0.003 0.840 ± 0.003 0.731 ± 0.009 FL-EV 0.892 ± 0.001 0.854 ± 0.005 0.471 ± 0.002 0.844 ± 0.001 0.768 ± 0.003 Table 4. Leave Center Out (LCO-CV) performance evaluated using the AUC metric. Each number represents the average AUC calculated across five repeated experiments with different network initializations. To analyze the different centers individually, it is more interesting to focus on the LCO-CV set-up (Table 4). In this case, the out-of-domain performance is evaluated as the testing center in each fold is entirely unseen. The most striking difference pertains to ACDC, where CDS outperforms the FL method in most cases, and by a margin of 0.3 on the AUC metric when intensity augmentations are introduced. In terms of the FL-EV scheme, Sagrada Familia—the largest of all centers in the used cohort—seems to be the only center to benefit from the scheme by a substantial margin. This occurs when the maximum amount of augmentations are introduced to the data, where FL-EV outperforms FL by a margin of 0.05 on Sagrada Familia, reflected in the total result.t l As HCM diagnosis is based mostly on the ED phase of the left ventricle, we also test the FL LCO-CV set-up using only the ED images. Discussion Automatic CMR diagnosis has thus far focused on isolated centers, with training happening locally and evalua- tion limited to IID subsets of the ­data31–34. We have presented the first federated CMR diagnosis study and show- cased two distinct evaluation set-ups to quantify both IID and non-IID performance. The gap in performance between the two evaluation frameworks was found to be critical, with LCO-CV consistently displaying worse results by a margin of approximately 0.1 on the AUC metric. This clearly suggests that for such models to be reliable and eventually adopted clinically, the LCO-CV set-up needs to be adopted in future research to account for non-IID performance. The necessity of this is exemplified by the presence of bias against ACDC on the shape and intensity set-up where FL exhibits an AUC performance of about 0.85 to 0.89 for the M&M centers but only 0.472 for ACDC (Table  4). Although lower performance is also seen in the CCV case for ACDC, the magnitude is not as critical (0.785 on AUC, Table 3). As M&M was part of a coordinated data collection within the EuCan- Share ­project37 acquisition protocols were bound to be more similar than that of ACDC which was collected in 2018 as part of a ­challenge35. We believe this to be a possible explanation for the exhibited bias against this center. p g p p g Our results reveal a couple of interesting behaviors on federated learning in this use case. Although FL has consistently been outperformed by CDS in medical imaging studies in the past, here FL outperforms CDS in the majority of our experiments. This result may come as surprising at first; however, FL has no inherent dis- advantage over a CDS set-up. In the past, it has been shown that averaging the weights of copies of the same model in different stages of the training process boosts performance by approximating a lower point in the loss ­space54,55. We believe that, although in the case of FL the averaging happens at the same stage, with copies trained on different datasets, a similar effect occurs and becomes apparent in the use case of CMR, possibly due to the low amount of data. Furthermore, averaging across models seems to result in a stabilizing effect, and a higher performance of FL across different initializations of the same model, (exhibited by our repeated experiments over the same set-ups, Fig. 7). Results AUC performance is higher when no augmentations are introduced in this case at 0.78, dropping off to 0.77 with Basic augmentations down to 0.763 when shape and intensity augmentation are introduced. The results were again incredibly consistent between different initializations.h h g yf The highest score under the LCO-CV evaluation is achieved when both ED and ES are used in an FL se and Basic augmentations are present. https://doi.org/10.1038/s41598-022-07186-4 Scientific Reports | (2022) 12:3551 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 7. CDS, FL and FL-EV are tested given four data augmentation set-ups and for each set-up the experiment is repeated with 5 different network initializations, both for the CCV and LCO-CV set-ups. AUC is evaluated across all folds and we obtain 5 AUC metrics per set-up whose error bars are displayed here. Figure 7. CDS, FL and FL-EV are tested given four data augmentation set-ups and for each set-up the experiment is repeated with 5 different network initializations, both for the CCV and LCO-CV set-ups. AUC is evaluated across all folds and we obtain 5 AUC metrics per set-up whose error bars are displayed here. Conclusions In conclusion, through extensive analysis and experiments, we demonstrated that, even with a small sample size of 180 subjects derived from four centers, federated learning for Cardiac MRI diagnosis achieves promising per- formance that is comparable to collaborative data sharing. We highlighted the importance of a principled evalu- ation that accounts for both in and out of site performance and showed how models trained under a federated learning framework exhibit increased robustness and can be more sensitive to domain shift effects. As different centers seem to benefit in different ways from the interplay of augmentations and the collaborative learning frameworks, we believe that further research is required to delineate the underlying factors. In the future, bigger datasets with a wider diversity of centers should be used to systematically analyze and further verify these effects. Furthermore, our study was constrained to binary classification, but in the future semi-supervised federated learning methods will be needed to integrate labels that don’t fully overlap between centers to enable multi-label classification. Also, as we used segmentation masks supplied by clinicians, the current pipeline still relies on expert support to provide these segmentations and could be replaced by an automated federated segmentation pipeline, appended as a first step to the current pipeline.hi i There is still a lot of fields in automated image-based diagnosis where federated learning has yet to make a presence, including prediction of prevalent diseases like retinopathy, diabetes, neurological disorders and cases of cancer in breast, liver or colon. Tangential fields like that of survival and treatment outcome prediction that are still underdeveloped due to the lack of data would also stand to benefit from the impact of federated learning and warrant similar exploration. We firmly believe that such studies will be a fundamental step to pave the way for multi-center studies going forward. www.nature.com/scientificreports/ need to tackle data scarcity, using more data both for more effective training and reliable evaluation. Our side experiment on just ED showed that our results are transferable, and FL translates well to this set-up with a decent performance when no augmentations are used.h p g This is one of the ways that we went about tackling the main limitations of this study—i.e. the small size of our data. While the impact of this limitation naturally puts in question the generalizability of our results, we con- ducted principled and diligent evaluations to minimize this negative effect. This includes our choice to emphasize on cross-validation schemes and repetitive experiments—i.e. conducting five experiments per configuration, each fully cross validated with 5 folds and different seeds. Furthermore, to ensure our evaluation was strong in spite of this limitation, we further evaluated our results from a collaborative standpoint (test sets from centers included in the training set) but also leave-center-out to account for out-of-site generalizability. While we strongly believe that these evaluation principles should be ever-present in studies where such limitations are faced, they might not be enough. The solution then lies in the obvious direction: moving from simulated experiments to real-world federated studies, leveraging a high number of hospitals and institutes to overcome data scarcity.f Such a large-scale task, however, is anything but straightforward. Hospitals usually lack specialized staff and need to be closely guided on the technical requirements. This includes hardware powerful enough for deep learning models to train and a stable internet. The clinical requirements are even more challenging, requiring multiple expert annotators and consistency across sites. On that regard, crowd-sourcing portals that enable col- laborative annotation across sites are a promising ­solution56. In addressing all of these requirements and tackling roadblocks along the way, the most important component will not so much be a matter of scientific mettle, but a skill in human communication and coordination. Our focus is aimed at realizing such studies in the future. Discussion p g Regarding the chosen augmentations, it’s important to note that as CMR diagnosis largely relies on shape, deformation augmentations should be handled with care. As illustrated in Fig. 3, our deformations are of a low scale. Although this type of augmentation still gives us a boost in performance in the CDS case it’s still less than the advantage we obtain from Basic augmentations. Furthermore, the FL set-ups both suffer from the addition of this augmentation compared to just using the Basic ones—even though they do better than no augmentation at all. In the case of using a single timepoint (ED) these domain shift effects are even greater, as FL performance drops even when Basic augmentations are introduced. This is indicative that even small deformations are causing domain shift effects that affect performance, to which federated set-ups are particularly sensitive.htf tff This increased sensitivity to domain shift effects could stem from the way the Federated Averaging algo- rithm aggregates weights per round. Federated Averaging combines weights based on the respective data-size contribution, irrespective of possible domain shift effects. Interestingly, our FL-EV variant—which combines all datasets uniformly—does not see any benefit from augmentations and behaves very differently from the vanilla FL aggregation (Tables  3, 4). This variation hints that more sophisticated variants of the averaging algorithm accounting for domain shift effects will be interesting to explore.f tf With regards to this FL-EV variant, it’s interesting to look into how the equal voting affects performance from a per-center standpoint. Sagrada Familia (Table 4) under shape and intensity augmentations benefits from the equal voting by a margin of 0.05 on the AUC metric. When Sagrada Familia is the test set, SantPau’s vote increases while Vall d’Hebron decreases (based on their sample sizes). Thus, the explanation for the observed differences could be that Sagrada Familia’s data distribution is much closer to SantPau’s than Vall d’Hebron’s and benefits from the effect on votes. We believe this warrants further exploration in the future, studying a spectrum of intermediate voting schemes that are not entirely equal nor as imbalanced as the per-center sample size. We should also acknowledge that, while clinical reality mainly uses the ED timepoint for diagnosis, we focused the main bulk of our experiments on using both the ES and ED timepoints. This decision stemmed from our Scientific Reports | (2022) 12:3551 | https://doi.org/10.1038/s41598-022-07186-4 www.nature.com/scientificreports/ Data availibility ACDC35 was part of MICCAI 2017 Challenge and maintains its own website at: https://​acdc.​creat​is.​insa-​lyon.​fr. It can be made readily available after registration and/or contact with the authors. M&Ms was part of MICCAI 2020 ­challenge37,57 and maintains its own website at https://​www.​ub.​edu/​mnms/. It can be made readily avail- able by filling the form. The diagnostic labels are also available upon explicit request to the challenge organizers. The code used for all of the described experiments is made available open-source in the following link: https://​ github.​com/​Linar​dos/​feder​ated-​HCM-​diagn​osis. 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Acknowledgementsh g This project has received funding from the European Union’s Horizon 2020 research and innovation programme nder Grant agreement No. 952103, EuCanImage. g This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant agreement No. 952103, EuCanImage. Competing interests p g Sean Walsh declares the following financial interests/personal relationships which may be considered as poten- tial competing interests: within and outside the submitted work, is the recipient of grants/sponsored research agreements in the areas of medical imaging, artificial intelligence, data science, applied to the clinical specialties of oncology and respiratory medicine. He holds a leadership position within Oncoradiomics SA, has shares in the company Oncoadiomics SA, and is co-inventor of submitted patents on behalf Oncoradiomics SA. 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The kinetics human action video dataset. arX https://doi.org/10.1038/s41598-022-07186-4 Scientific Reports | (2022) 12:3551 | © The Author(s) 2022 Additional information Correspondence and requests for materials should be addressed to A.L. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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. 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Chilblain-like lesions onset during SARS-CoV-2 infection in a COVID-19-vaccinated adolescent: case report and review of literature
˜The œItalian Journal of Pediatrics/Italian journal of pediatrics
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© The Author(s) 2022. 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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Paparella et al. Italian Journal of Pediatrics (2022) 48:93 https://doi.org/10.1186/s13052-022-01296-5 Open Access Abstract Background:  COVID toes or chilblain-like skin lesions have been widely reported during COVID-19 pandemic. Most cases were described in patients with negative microbiological tests for SARS-CoV-2, therefore the possible relation- ship with SARS-CoV-2 infection, as well as with the nowadays broadly available mRNA-based vaccination, has not been fully elucidated. Case presentation:  We here describe the case of a 14-year-old male who developed chilblain-like skin eruptions during SARS-CoV-2 infection despite two mRNA-based vaccine doses and review the clinical and epidemiological characteristics of chilblain-like lesions as a cutaneous presentation of COVID-19 in children. Conclusions:  Most children and adolescent with COVID toes have a mild or asymptomatic SARS-CoV-2 infection. Our report aims to highlight the possible onset of these skin lesions in vaccinated children, if infection has occurred, and the potential use of systemic corticosteroids as a first line treatment. Additional evidence is required to better understand SARS-CoV-2 infection and cutaneous manifestations in children and determine the relationship between chilblain-like lesions and COVID-19 vaccination. Keywords:  COVID-19, Chilblain-like lesions, Case report, SARS-CoV-2 vaccination, Children perniosis-like or chilblain-like lesions (CLLs), also called COVID toes [2], characterized by vascular lesions due to microthrombosis and endothelial inflammation [3]. Chilblain‑like lesions onset during SARS‑CoV‑2 infection in a COVID‑19‑vaccinated adolescent: case report and review of literature Roberto Paparella1*   , Luigi Tarani1, Enrico Properzi1, Francesco Costantino1, Chiara Saburri1, Roberta Lucibello1, Antonio Richetta2, Alberto Spalice1 and Lucia Leonardi1 Background Coronavirus disease 2019 (COVID-19) pandemic is caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), first isolated in  Wuhan, China, in December 2019 and subsequently rapidly spreading worldwide [1]. In addition to systemic symp- toms, several cutaneous manifestations related to COVID-19 infection have been observed, including l Despite an increased incidence of CLLs during COVID- 19 pandemic, the true relationship between SARS-CoV-2 infection and this type of skin manifestation is still uncer- tain, since the majority of cases occurred with no evi- dence of positive reverse transcriptase-polymerase chain reaction (RT-PCR) test or serum antibodies [4]. However, given that the second wave of COVID-19 pandemic has been followed by a second outbreak of CLLs, a link not only of an epidemiological but also a causal nature is very likely [5]. Moreover, an increasing number of reports of 1 Department of Maternal and Child Health and Urology, Sapienza University of Rome, Rome, Italy Full list of author information is available at the end of the article Paparella et al. Italian Journal of Pediatrics (2022) 48:93 Paparella et al. Italian Journal of Pediatrics Page 2 of 5 CLLs shortly after SARS-CoV-2 vaccination is observed [6]. Here we present the case of a 14-year-old asympto- matic COVID-19 male showing COVID toes despite two vaccine  doses, with a short review of what is currently known about CLLs as a cutaneous presentation in the context of pediatric COVID-19. CLLs shortly after SARS-CoV-2 vaccination is observed [6]. Here we present the case of a 14-year-old asympto- matic COVID-19 male showing COVID toes despite two vaccine  doses, with a short review of what is currently known about CLLs as a cutaneous presentation in the context of pediatric COVID-19. Fig. 2  Characteristic aspect of chilblain‐like lesions of left toes Fig. 2  Characteristic aspect of chilblain‐like lesions of left toes Case presentation Our patient, indeed, had confirmed COVID-19 and CLLs, as already described in literature [9].f CLLs affect dorsal aspect of the toes, lateral sides of the feet, soles and less often fingers; clinical manifesta- tions are variable, as they could present as dusky ery- thematous and edematous macules or plaques, purpuric lesions, or blisters formation, associated to pain, itching or no symptoms [10]. They share pathologic features with idiopathic and autoimmune-related chilblains: vacuolar interface dermatitis with necrotic keratinocytes, dermal edema, perivascular and perieccrine sweat gland lym- phocytic inflammation, and frequent vascular changes (endothelialitis, microthrombi, fibrin deposition, and vascular immune deposits) [10–12].h Fig. 3  Almost complete resolutions of skin lesions after two (A) and six weeks (B) Fig. 3  Almost complete resolutions of skin lesions after two (A) and six weeks (B) The exact pathogenic mechanisms of CLLs in COVID- 19 are still matter of debate. They resemble idiopathic chilblains, but are usually unrelated to classical risk fac- tors such as exposure to cold or humid weather [13]. Some authors suggest that CLLs might also represent an indirect consequence of the COVID-19 pandemic due to lifestyle changes derived from community containment and lockdown measures [14]. The decreased physical activity and being barefoot during quarantine may have played a role in the pathogenesis of these lesions [15], although this hypothesis apparently poorly befits the third COVID-19 wave. Type-I interferon (IFN-1) signaling is also involved in CLLs pathogenesis [7]. In pediatric patients, microan- giopathic modifications with skin eruption and vasculitic neuropathic pain features are secondary to the strong IFN-1 response, which causes downregulation of other cytokines, not leading to a cytokine storm [16]. These findings contribute to explain why COVID-19-induced CLLs occur during mild or asymptomatic SARS-CoV-2 infections, in contrast to the different pathogenesis of thrombotic-related acral-ischemia with hypercoagu- lopathy state and elevated D-dimer levels in severely ill COVID-19 patients [17]. Fig. 3  Almost complete resolutions of skin lesions after two (A) and six weeks (B) At the last follow-up evaluation, six weeks after our first observation, clinical remission was confirmed Fig. 3B. Case presentation A 14-year-old male patient presented to our hospital with CLLs on his left toes. His medical history was unre- markable, except for two epileptic seizures at the age of 13 with non-specific electroencephalography abnormali- ties and brain magnetic resonance imaging  showing a retrocerebellar arachnoid cyst. There was no family his- tory of cutaneous or autoimmune conditions. No recent exposure to cold temperatures, traumatic injuries or drug intake were reported. He had completed  primary COVID-19 vaccination cycle (two doses of Comirnaty mRNA-based vaccine) four months before CLLs onset Fig. 1. Fig. 2  Characteristic aspect of chilblain‐like lesions of left toes blood count, coagulation tests, liver and renal and pan- creatic function tests, blood electrolytes, and urinalysis were all within normal limits. Erythrocyte sedimentation rate, C-reactive protein, and serum C3 and C4 levels were normal. The cutaneous findings were compatible with COVID-19 CLLs, with diagnostic validation by a derma- tologist. Oral prednisone was initiated at 1 mg/kg daily, leading to a quick improvement of the symptoms and attenuation of the skin lesions. Lupus anticoagulant, anti-β2 glycoprotein I IgG and IgM and anti-cardiolipin IgG and IgM, antinuclear antibody and  extractable nuclear antigen panel were negative. The capillaroscopic examination revealed “non-specific changes”. SARS-CoV-2 nasopharyngeal swab RT-PCR test resulted positive approximately one month before our first evaluation, being performed because of a household close contact. During the first days of his asymptomatic SARS-CoV-2 infection he developed swollen, erythema- tous lesions of left toes Fig. 2 associated with nighttime localized itching and walking difficulties.h fi The patient was admitted to our pediatric outpatient service after the onset of a new, similar, painful lesion on the right fifth finger, three weeks after the onset of the initial, persisting cutaneous manifestations. At this time, SARS-CoV-2 nasopharyngeal swab tested negative. Physical examination was otherwise normal. Complete i Two weeks later, the patient showed a good clinical response; skin lesions had almost disappeared Fig. 3A and no symptoms were reported, allowing gradual sys- temic steroid withdrawal and shift to topical treatment. Fig. 1  Timeline portraying the patient’s clinical history Fig. 1  Timeline portraying the patient’s clinical history Page 3 of 5 Page 3 of 5 Paparella et al. Italian Journal of Pediatrics (2022) 48:93 Paparella et al. Italian Journal of Pediatrics typical COVID-19-related symptoms or a positive con- tact history, in particular household viral exposure [8], makes the association between skin lesions and SARS- CoV-2 infection very likely. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. 11. Kanitakis J, Lesort C, Danset M, Jullien D. Chilblain-like acral lesions during the COVID-19 pandemic (“COVID toes”): Histologic, immunofluorescence, and immunohistochemical study of 17 cases. J Am Acad Dermatol. 2020;83(3):870–5. Consent for publication protective towards these late cutaneous manifestations if infection has occurred. In addition, a few cases of CLLs onset in vaccinated patients with not confirmed COVID‐19 infection have been reported [6]. Written informed consent for publication of clinical details and/or clinical images was obtained from the patient’s parent/guardian. A copy of the con- sent form is available for review by the Editor of this journal. Availability of data and materials Data sharing not applicable to this article as no datasets were generated or analyzed during the current study. 12. El Hachem M, Diociaiuti A, Concato C, Carsetti R, Carnevale C, CiofiDe- gliAtti M, et al. A clinical, histopathological and laboratory study of 19 consecutive Italian paediatric patients with chilblain-like lesions: lights and shadows on the relationship with COVID-19 infection. J Eur Acad Dermatol Venereol. 2020;34(11):2620–9. Acknowledgements Not applicable. 9. Neri I, Conti F, Virdi A, Guglielmo A, Leonardi L, Corsini I, et al. Chilblains in a child with confirmed SARS-CoV-2 infection: a red flag for late-onset skin manifestation in previously infected individuals. J Eur Acad Dermatol Venereol. 2021;35(6):e357–9. Available from: https://​doi.​org/​10.​1111/​jdv.​ 17194. Cited 6 Mar 2022. Competing interests Th h d l h Guidelines for the specific treatment of COVID-19 induced chilblains are still lacking. The management of idiopathic chilblains focuses primarily on the avoid- ance of unprotected exposure to cold conditions, not applicable to CLLs due to the different pathogenetic mechanisms. Other mainstay pharmacologic therapies include corticosteroids and calcium channel blockers [19, 20]. Oral cinnarizine showed as well good results in patients with COVID-19-associated CLLs, probably due to its antihistaminic and calcium channel blocking properties [21]. A successful combination of nitroglyc- erin with enoxaparin has also been reported [22]. The authors declare that they have no competing interests. Discussion and conclusions During the COVID-19 pandemic, numerous pediatric patients reporting CLLs with suspected SARS-CoV-2 infection were described. It was postulated that nega- tivity of testing could be probably explained by the low viral load and infectivity at the time of the skin lesions, since CLLs are generally a late manifestation  of a mild or asymptomatic disease [7]. Moreover, during the first COVID-19 wave, most of suspected SARS-CoV-2-associ- ated CLLs were unconfirmed because of unavailability of RT-PCR testing. CLLs affect late childhood age, usually with a favorable prognosis and an indolent course, with a duration of weeks to months. Despite negativity of RT- PCR and serology testing, the presence of concomitant Another intriguing issue is the relationship between CLLs and SARS‐CoV‐2 vaccination. Our report repre- sents a peculiar case of CLLs in a vaccinated patient with ongoing SARS-CoV-2 infection. Literature reports suggest that these lesions are not idiopathic, but rather represent an immunologic response to SARS-CoV-2, showing a positive IFN-1 signature [18]. Whilst during first pandemic wave children were not yet vaccinated, due to the recent surprising observations of CLLs fol- lowing COVID-19 mRNA-based vaccination, it is tempting to speculate that vaccination might not be Paparella et al. Italian Journal of Pediatrics (2022) 48:93 Paparella et al. Italian Journal of Pediatrics (2022) 48:93 Page 4 of 5 References J Am Acad Dermatol. 2021;85(1):46–55. 6. McMahon DE, Amerson E, Rosenbach M, Lipoff JB, Moustafa D, Tyagi A, et al. Cutaneous reactions reported after Moderna and Pfizer COVID-19 vaccination: A registry-based study of 414 cases. J Am Acad Dermatol. 2021;85(1):46–55. 7. Hubiche T, Cardot-Leccia N, Le Duff F, Seitz-Polski B, Giordana P, Chiaverini C, et al. Clinical, Laboratory, and Interferon-Alpha Response Charac- teristics of Patients With Chilblain-like Lesions During the COVID-19 Pandemic. JAMA Dermatol. 2021;157(2):202. 7. Hubiche T, Cardot-Leccia N, Le Duff F, Seitz-Polski B, Giordana P, Chiaverini C, et al. Clinical, Laboratory, and Interferon-Alpha Response Charac- teristics of Patients With Chilblain-like Lesions During the COVID-19 Pandemic. JAMA Dermatol. 2021;157(2):202. Authors’ contributions RP conceptualized and drafted the work. LL conceptualized and revised the work. AR, CS and RL contributed to data acquisition. LT, EP, FC and AS revised and supervised the work. All authors read and approved the final manuscript. 10. Rongioletti F, Ferreli C, Sena P, Caputo V, Atzori L. Clinicopathologic correlations of COVID-19–related cutaneous manifestations with special emphasis on histopathologic patterns. Clin Dermatol. 2021;39(1):149–62. 10. Rongioletti F, Ferreli C, Sena P, Caputo V, Atzori L. Clinicopathologic correlations of COVID-19–related cutaneous manifestations with special emphasis on histopathologic patterns. Clin Dermatol. 2021;39(1):149–62. Abbreviations CLL Chilbl i lik CLLs: Chilblain-like lesions; COVID-19: Coronavirus disease 2019; IFN-1: Type-I interferon; RT-PCR: Reverse transcriptase-polymerase chain reaction; SARS- CoV-2: Severe acute respiratory syndrome coronavirus. 8. Poizeau F, Oger E, Barbarot S, Le Corre Y, Samimi M, Brenaut E, et al. Chilblains during lockdown are associated with household exposure to SARS-CoV-2: a multicentre case–control study. Clin Microbiol Infect. 2022;28(2):285–91. 8. Poizeau F, Oger E, Barbarot S, Le Corre Y, Samimi M, Brenaut E, et al. Chilblains during lockdown are associated with household exposure to SARS-CoV-2: a multicentre case–control study. Clin Microbiol Infect. 2022;28(2):285–91. References 1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A Novel Coro- navirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–33. In conclusion, CLLs are a peculiar dermatologi- cal finding in COVID-19 disease. Most pediatric patients with COVID toes have a mild or asymptomatic SARS-CoV-2 infection, implying that these cutane- ous manifestations are the prerogative of children with a favorable disease course. Of note our case confirms that CLLs also occur in vaccinated children and that systemic corticosteroids might be a first line treatment for this COVID-19 sequela. Since there is currently limited information on the pathogenesis and the treat- ment of CLLs, further studies are required to update the body of knowledge about the mechanisms of SARS- CoV-2 infection in children, with regard in particular to dermatological manifestations, and the relationship between CLLs and SARS‐CoV‐2 vaccination. 2. Molaee H, Emadi SN, M’Imunya JMN, Davoudi-Monfared E, Mohammed A, Razavi Z. Chilblain or perniosis-like skin lesions in children during the COVID -19 pandemic: A systematic review of articles. Dermatol Ther. 2022;35(3):e15298. Available from: https://​doi.​org/​10.​1111/​dth.​15298. Cited 5 Mar 2022 2. Molaee H, Emadi SN, M’Imunya JMN, Davoudi-Monfared E, Mohammed A, Razavi Z. Chilblain or perniosis-like skin lesions in children during the COVID -19 pandemic: A systematic review of articles. Dermatol Ther. 2022;35(3):e15298. Available from: https://​doi.​org/​10.​1111/​dth.​15298. Cited 5 Mar 2022 3. Naderi-Azad S, Vender R. Lessons From the First Wave of the Pandemic: Skin Features of COVID-19 Can Be Divided Into Inflammatory and Vascu- lar Patterns. J Cutan Med Surg. 2021;25(2):169–76. 3. Naderi-Azad S, Vender R. Lessons From the First Wave of the Pandemic: Skin Features of COVID-19 Can Be Divided Into Inflammatory and Vascu- lar Patterns. J Cutan Med Surg. 2021;25(2):169–76. 4. Le Cleach L, Dousset L, Assier H, Fourati S, Barbarot S, Boulard C, et al. Most chilblains observed during the COVID-19 outbreak occur in patients who are negative for COVID-19 on polymerase chain reaction and serol- ogy testing*. Br J Dermatol. 2020;183(5):866–74. y 5. Piccolo V, Bassi A, Russo T, Mazzatenta C, Baraldi M, Argenziano G, et al. Chilblain-like lesions and COVID-19: second wave, second outbreak. J Eur Acad Dermatol Venereol. 2021;35(5):e316–8. Available from: https://​doi.​ org/​10.​1111/​jdv.​17145. Cited 5 Mar 2022. 6. McMahon DE, Amerson E, Rosenbach M, Lipoff JB, Moustafa D, Tyagi A, et al. Cutaneous reactions reported after Moderna and Pfizer COVID-19 vaccination: A registry-based study of 414 cases. 13. Jimenez-Cebrian AM, Castro-Mendez A, García-Podadera B, Romero-Gal- isteo R, Medina-Alcántara M, Garcia-Paya I, et al. Clinical Manifestations of COVID-19 in the Feet: A Review of Reviews. J Clin Med. 2021;10(10):2201. Author details 1 1 Department of Maternal and Child Health and Urology, Sapienza University of Rome, Rome, Italy. 2 Unit of Dermatology, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy. Received: 3 May 2022 Accepted: 6 June 2022 Received: 3 May 2022 Accepted: 6 June 2022 Declarations Ethics approval and consent to participate Not applicable. 13. Jimenez-Cebrian AM, Castro-Mendez A, García-Podadera B, Romero-Gal- isteo R, Medina-Alcántara M, Garcia-Paya I, et al. Clinical Manifestations of COVID-19 in the Feet: A Review of Reviews. J Clin Med. 2021;10(10):2201. Page 5 of 5 Paparella et al. Italian Journal of Pediatrics (2022) 48:93 Paparella et al. Italian Journal of Pediatrics (2022) 48:93 14. Herman A, Peeters C, Verroken A, Tromme I, Tennstedt D, Marot L, et al. Evaluation of Chilblains as a Manifestation of the COVID-19 Pandemic. JAMA Dermatol. 2020;156(9):998. 15. Roca-Ginés J, Torres-Navarro I, Sánchez-Arráez J, Abril-Pérez C, Sabalza- Baztán O, Pardo-Granell S, et al. Assessment of Acute Acral Lesions in a Case Series of Children and Adolescents During the COVID-19 Pandemic. JAMA Dermatol. 2020;156(9):992. 16. Arkin LM, Moon JJ, Tran JM, Asgari S, O’Farrelly C, Casanova J-L, et al. From Your Nose to Your Toes: A Review of Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic-Associated Pernio. J Invest Dermatol. 2021;141(12):2791–6. 17. Papa A, Salzano AM, Di Dato MT, et al. COVID-19 Related Acro-Ischemic Neuropathic-like Painful Lesions in Pediatric Patients: A Case Series. Anesth Pain Med. 2021;11(2):e113760. 18. Lesort C, Kanitakis J, Donzier L, Jullien D. Chilblain-like lesions after BNT162b2 mRNA COVID-19 vaccine: a case report suggesting that ‘COVID toes’ are due to the immune reaction to SARS-CoV-2. J Eur Acad Dermatol Venereol. 2021;35(10):e630–2. Available from: https://​doi.​org/​10.​1111/​jdv.​ 17451. Cited 12 Mar 2022. 19. Ganor S. Corticosteroid therapy for pernio. J Am Acad Dermatol. 1983;8(1):136. 20. Rustin MH, Newton JA, Smith NP, Dowd PM. The treatment of chilblains with nifedipine: the results of a pilot study, a double-blind placebo- controlled randomized study and a long-term open trial. Br J Dermatol. 1989;120(2):267–75. 21. Mazzatenta C, Piccolo V, Argenziano G, Bassi A. Oral cinnarizine for the treatment of COVID-19-associated chilblain-like lesions: An old drug for a new disease? Dermatol Ther. 2022;35(5):e15365. Available from: https://​ doi.​org/​10.​1111/​dth.​15365. Cited 6 Mar 2022. 22. Weingarten M, Abittan B, Rivera-Oyola R, Abittan AI, Weingarten M, Lebwohl M. Treatment of COVID-19 induced chilblains with topical nitro- glycerin. Int J Dermatol. 2020;59(12):1522–4. 22. Weingarten M, Abittan B, Rivera-Oyola R, Abittan AI, Weingarten M, Lebwohl M. Treatment of COVID-19 induced chilblains with topical nitro- glycerin. Int J Dermatol. 2020;59(12):1522–4. 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O-glycosylation disorders pave the road for understanding the complex human O-glycosylation machinery
Current opinion in structural biology
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Version of the following full text: Publisher’s version Downloaded from: http://hdl.handle.net/2066/207328 Download date: 2024-10-24 Addresses 1 1 Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands In contrast to N-glycosylation defects, the identification of O-glycosylation disorders is much more challenging. In humans, O-glycans are initiated by seven different mono- saccharides that can be further extended to complex O- glycan structures. For mucin O-glycosylation (O-linked N- acetylgalactosamine, O-GalNAc), the most common form of O-glycosylation, over 20 polypeptide GalNAc trans- ferases are known with tissue and substrate-specific activi- ties [6,7]. Isofocusing of ApoC-III was developed to detect defects in mucin type O-glycosylation [8]. Although many of the Golgi homeostasis disorders showed abnormal mucin type O-glycosylation of ApoC-III, only mutations in poly- peptide GalNAc transferase 2 (GALNT2) could be detected with this test. So far, the complexity of O-glycan structures renders it impossible to design a single screening test for diagnostics of O-glycosylation disorders. 2 Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Corresponding author: Lefeber, Dirk J (Dirk.Lefeber@radboudumc.nl) O-glycans are important for protein structure, folding, stability, recognition, expression, and processing, and they are known to modulate enzyme activity [9,10,11,12–15]. Furthermore, highly negatively charged O-mucin glycans can bind water, forming protective layers and preventing bacterial adhesion [16]. The func- tion of an O-glycan can be tissue, protein, and site- specific, alongside mediating different functions through- out development [17]. That, O-glycans play not only O-glycosylation disorders pave the road for understanding the complex human O-glycosylation machinery Walinka van Tol1,2, Hans Wessels2 and Dirk J Lefeber1,2 ScienceDirect machinery Walinka van Tol1,2, Hans Wessels2 and Dirk J Lefeber1,2 Over 100 human Congenital Disorders of Glycosylation (CDG) have been described. Of these, about 30% reside in the O- glycosylation pathway. O-glycosylation disorders are characterized by a high phenotypic variability, reflecting the large diversity of O-glycan structures. In contrast to N- glycosylation disorders, a generic biochemical screening test is lacking, which limits the identification of novel O-glycosylation disorders. The emergence of next generation sequencing (NGS) and O-glycoproteomics technologies have changed this situation, resulting in significant progress to link disease phenotypes with underlying biochemical mechanisms. Here, we review the current knowledge on O-glycosylation disorders, and discuss the biochemical lessons that we can learn on 1) novel glycosyltransferases and metabolic pathways, 2) tissue- specific O-glycosylation mechanisms, 3) O-glycosylation targets and 4) structure-function relationships. Additionally, we provide an outlook on how genetic disorders, O- glycoproteomics and biochemical methods can be combined to answer fundamental questions regarding O-glycan synthesis, structure and function. synthesis of activated sugars (with the exception of CMP-N-acetylneuraminic acid) that are subsequently transported to the endoplasmic reticulum (ER) and Golgi apparatus, where glycans are assembled and modified on proteins. Glycosylation affects many aspects of protein function, including protein folding, enzyme activity and cell-to-cell and cell-to-extracellular matrix (ECM) interac- tions. Therefore, it is not surprising that glycosylation disorders present with a broad range of clinical phenotypes. synthesis of activated sugars (with the exception of CMP-N-acetylneuraminic acid) that are subsequently transported to the endoplasmic reticulum (ER) and Golgi apparatus, where glycans are assembled and modified on proteins. Glycosylation affects many aspects of protein function, including protein folding, enzyme activity and cell-to-cell and cell-to-extracellular matrix (ECM) interac- tions. Therefore, it is not surprising that glycosylation disorders present with a broad range of clinical phenotypes. Currently, over 100 different Congenital Disorders of Gly- cosylation (CDG) have been described [1,2], the majority affecting the N-glycosylation pathway. Broad availability of an adequate screening assay for abnormal N-glycosylation, isofocusing of serum transferrin (TIEF), has resulted in the identification of defects in glycosyltransferases, nucleotide sugar transporters and enzymes involved in sugar metabo- lism, which are all directly linked to glycosylation. In recent years, more complex mechanisms have been identified underlying abnormal N-glycosylation related to Golgi traf- ficking, homeostasis and vesicular transport [3,4,5]. Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com Note: To cite this publication please use the final published version (if applicable). Available online at www.sciencedirect.com Available online at www.sciencedirect.com Introduction Mice knockout systems have provided invalu- able lessons about O-glycan function, for example, the role of O-fucosylation of thrombospondin type 1 repeats (TSRs) by POFUT2 in epithelial organization and expression of signaling factors during gastrulation [20]. In humans, a more complete understanding of the human O-glycosylation machinery can be accomplished by study- ing genetic defects in O-glycosylation. Identification of an increasing number of genetic O-glycosylation disorders has been facilitated by the emergence of next generation sequencing (NGS) [2]. Furthermore, recent develop- ments in glycopeptide analysis revealed previously unidentified O-glycosylation enzymes and their targets, which can be linked to disease. 3D structural models of human glycosyltransferases are rare, especially since these types of proteins are embedded in the membrane of the ER and Golgi apparatus making crystallization extremely daunting. However, in recent years, some structures have been resolved and modeled. Taken together, new opportunities arise to link findings from genetic disease with fundamental research to increase our understanding of the mechanisms of O-glycosylation. In this review, we illustrate the importance of inherited O- glycosylation disorders to elucidate the structural aspects of the O-glycosylation machinery (Figure 1). Glycosami- noglycan biosynthesis disorders are not discussed and have been described in great detail by others [21]. For elaborate descriptions of O-glycosylation disorder pheno- types, we recommend the reviews of Wopereis et al. [22], Hennet [21] and Jaecken and Pe´anne [3]. Current Opinion in Structural Biology 2019, 56:107–118 Introduction O-glycomics, the profiling of the complete set of glycans produced by specific cell types, offers potential as a generic functional test. Methods have been developed for the comparative analysis of O-glycans from complex samples [27–30]. Unfortunately, O-glycomics has thus far not contributed to the functional confirmation of O-glycosylation disor- ders. This can be explained by the fact that O-glycosyla- tion is highly dependent on the specific attachment site, and O-glycans do not have a general consensus sequence with the exception of O-fucose glycans (C2X3-5S/TC3 and WX5CX2/3S/TCX2G; C = conserved cysteines of epider- mal growth factor (EGF)-like or TSRs, S/T = serine or threonine, X = any residue) and O-glucose glycans (C1XSXPC2). Therefore, it is essential to study O-glycan structures in their protein context. Identification of aber- rant O-glycopeptides by direct LC–MS/MS analysis of intact O-glycopeptides in patient samples or model sys- tems would be preferred, thus providing a complete overview of the affected O-glycans and O-glycosylation sites. Despite the challenges in the field of O-glycopro- teomics (reviewed in Ref. [31]), first studies have dem- onstrated the potential of LC–MS/MS for holistic O- glycopeptide profiling. In 2016, Hoffmann et al. [32] analyzed intact O-glycopeptides in human blood plasma in an untargeted fashion by analyzing HILIC enriched and fractionated glycopeptides by reversed phase LC– MS/MS using multistage collision induced dissociation (CID) and electron transfer dissociation (ETD) fragmen- tation experiments. In total, 31 O-GalNAc sites and regions from 22 proteins were identified, which included 11 novel O-glycosylation sites and regions. More recently, King et al. [33] performed high collision energy dissoci- ation (HCD) and ETD LC–MS/MS analysis of de-sialy- lated glycopeptides purified by lectin chromatography from AB RhD-positive platelets and blood plasma. Their analysis detected 1123 O-GalNAc sites from 649 glyco- proteins, which not only provided novel biological insights but above all demonstrated the feasibility of holistic O-glycoproteomics. important, but also complex roles, is illustrated by the vast amount of O-glycan enzymes that upon knockout, caused embryonic lethality or tissue-specific phenotypes in mice [18,19]. Mice knockout systems have provided invalu- able lessons about O-glycan function, for example, the role of O-fucosylation of thrombospondin type 1 repeats (TSRs) by POFUT2 in epithelial organization and expression of signaling factors during gastrulation [20]. important, but also complex roles, is illustrated by the vast amount of O-glycan enzymes that upon knockout, caused embryonic lethality or tissue-specific phenotypes in mice [18,19]. www.sciencedirect.com Introduction Glycosylation, the addition of carbohydrate chains to pro- teins, is the most common post-translational and co-trans- lational modification. It is initiated by the cytosolic Current Opinion in Structural Biology 2019, 56:107–118 108 Carbohydrates Thus, together with NGS, functional tests are highly warranted for a more rapid identification of inherited O-glycosylation disorders, and to increase our understand- ing of O-glycosylation mechanisms. O-glycomics, the profiling of the complete set of glycans produced by specific cell types, offers potential as a generic functional test. Methods have been developed for the comparative analysis of O-glycans from complex samples [27–30]. Unfortunately, O-glycomics has thus far not contributed to the functional confirmation of O-glycosylation disor- ders. This can be explained by the fact that O-glycosyla- tion is highly dependent on the specific attachment site, and O-glycans do not have a general consensus sequence with the exception of O-fucose glycans (C2X3-5S/TC3 and WX5CX2/3S/TCX2G; C = conserved cysteines of epider- mal growth factor (EGF)-like or TSRs, S/T = serine or threonine, X = any residue) and O-glucose glycans (C1XSXPC2). Therefore, it is essential to study O-glycan structures in their protein context. Identification of aber- rant O-glycopeptides by direct LC–MS/MS analysis of intact O-glycopeptides in patient samples or model sys- tems would be preferred, thus providing a complete overview of the affected O-glycans and O-glycosylation sites. Despite the challenges in the field of O-glycopro- teomics (reviewed in Ref. [31]), first studies have dem- onstrated the potential of LC–MS/MS for holistic O- glycopeptide profiling. In 2016, Hoffmann et al. [32] analyzed intact O-glycopeptides in human blood plasma in an untargeted fashion by analyzing HILIC enriched and fractionated glycopeptides by reversed phase LC– MS/MS using multistage collision induced dissociation (CID) and electron transfer dissociation (ETD) fragmen- tation experiments. In total, 31 O-GalNAc sites and regions from 22 proteins were identified, which included 11 novel O-glycosylation sites and regions. More recently, King et al. [33] performed high collision energy dissoci- ation (HCD) and ETD LC–MS/MS analysis of de-sialy- lated glycopeptides purified by lectin chromatography from AB RhD-positive platelets and blood plasma. Their analysis detected 1123 O-GalNAc sites from 649 glyco- proteins, which not only provided novel biological insights but above all demonstrated the feasibility of holistic O-glycoproteomics. Thus, together with NGS, functional tests are highly warranted for a more rapid identification of inherited O-glycosylation disorders, and to increase our understand- ing of O-glycosylation mechanisms. O-glycosylation disorders: current status and screening methods g Most of the currently known O-glycosylation disorders have been identified through genetic techniques. The clinical phenotypes are highly variable, which is linked to the large number of different O-glycan types. O-glycosyl- ation defects have now been identified for each type of O- glycan, and an overview of the known O-glycosylation disorders is provided in Figure 1 and Table 1. Thus far, assays for functional validation of mutations are largely lacking, except for the dystroglycanopathies. This is a group of disorders affecting the O-mannosyl glycan on the a-dystroglycan (aDG) protein that is essential for binding to extracellular matrix components (Table 1; O-mannose). Functional confirmation of O-mannosylation defects is possible by histochemical detection of the O-mannosyl glycan of aDG in muscle biopsies [23]. Together with NGS of patients, this has resulted in the identification of novel Golgi glycosyltransferases, while mass spectrome- try of recombinant aDG has recently resolved the com- plete O-mannose glycan structure [24,25,26]. Although functional tests still need to be developed, the O-glycosylation disorders that have been identified have aided structural biology in a number of ways. Despite the fact that O-glycan disorders are very heterogeneous, patients generally show tissue-specific phenotypes, hint- ing toward tissue-specific O-glycan targets and function. Studying O-glycosylation disorders has 1) led to the discovery of new glycosyltransferases and metabolic path- ways, 2) provided insight in tissue-specific glycosylation pathways, 3) aided in the discovery of O-glycosylation targets and 4) elucidated structure-function relations of O-glycosyltransferases and nucleotidyltransferases (Figure 1). www.sciencedirect.com Patient phenotypes aid in the identification of O- glycosylation targets The phenotype of some O-glycosylation deficiencies resembles the phenotype of genetic defects in potential target proteins. Hence, phenotypic characterizations can point to potential glycosylation targets. For instance, mutations in FGF23 cause familial tumoral calcinosis paired with increased re-adsorption of phosphate by the renal proximal tubule. Interestingly, patients carrying mutations in the polypeptide GalNAc transferase GALNT3 present with exactly the same phenotype [52– 57] (Table 1: O-GalNAc), suggesting a shared mechanism of disease. Indeed, Kato et al. [13] demonstrated that the phosphatonin FGF23 is O-glycosylated at Thr178 by GALNT3, preventing the furin protease cleavage of FGF23 and regulating phosphate re-absorption [13]. There are over 20 polypeptide GalNAc transferases. Some share substrate specificities and have overlapping expression in different tissues [6,7]. Nevertheless, O- GalNAc glycosylation of FGF23 seems a non-redundant function of GALNT3 [13]. Despite the large number of GALNTs, only GALNT3 and GALNT2 deficiency have been reported. Khetarpal et al. showed that loss of func- tion of GALNT2 lowered high-density lipoprotein O-glycosylation disorders: current status and screening methods The O-fucose glycan initiated by POFUT1 is extended with N-acetylglucosamine (GlcNAc) by LNFG [reviewed in Ref. 47]. Interestingly, LNFG patients pres- ent with a completely different phenotype of vertebral malsegmentation, spondylocostal dysostosis (SDO) [48,49]. This phenotype is also associated with defects in Notch signaling, and other types of SDO are all caused by defects in proteins involved in Notch1 signaling [50]. Another recent article reports that the POGLUT1 D233E mutation causes muscular dystrophy [51]. Investigating other POGLUT1 targets could shed light on the mecha- nisms underlying the different phenotypes. The different phenotypes for POFUT1 and POGLUT1 deficiency pro- vide opportunities to investigate tissue-specific targets and O-glycosylation mechanisms. each type of discovery in the O-glycosylation field, cov- ering the majority of the O-glycosylation disorder core types. O-glycosylation disorders: current status and screening methods Below, we will provide recent examples of Current Opinion in Structural Biology 2019, 56:107–118 Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 109 Figure 1 Genomics O- Glycomics O-Glycoproteomics Discovery of O-glycosylation: Enzymes and pathways Tissue- specific pathways Function and targets Structure function relations Understanding O-glycosylation mechanisms O-glycosylation disorder phenotypes n core M3 POMK S/T α β1,4 β1,3 3 1 β1,4 β1,4 β1,3 α1,3 LARGE CTP PP CDP- ISPD P Rbo Rbo P Rbo P Rbo P Cadherin/protocadherin- specific O-mannosylation core M1 extendable to core M2 B4GAT1 B4GALT* OGT EOGT GALNT2 GALNT1/4-20 GALNT3 TMEM5 FKRP FKTN B3GALNT2 POMGNT2 POMT2 POMT1 α β1,2 S/T S/T α EGF-like domain GlcNAcylation β S/T β β1,4 S/T S/T α Collagen Lysin (Lys) hydroxylation Collagen hydroxylysin (hLys) O-glycosylation β α1,2 hLys hLys Lys EGF-like domain glucosylation β α1,3 α1,3 S/T TSR domain fucosylation EGF-like domain fucosylation S/T α β1,3 α β1,3 β1,4 α2,3/α2,6 S/T POFUT1 POGLUT1 LH3 POMT1 POMT2 POMGNT1 LH3 LH1/2/3 POFUT2 XXYLT1 GXTLT2 GLT25D2 TMTC1/4 TMTC2/3 GLT25D1 GXTLT1 SiaT* LNFG B4GALT1 B3GLCT Current Opinion in Structural Biology terization of O-glycosylation disorders is indispensable to accomplish a better understanding of the human O-glycosylation mecha ypic heterogeneity of the O-glycosylation disorders reflects the high diversity of O-glycan structures with a high tissue-specificity. ypic characterization and modern omics techniques such as genomics, glycomics, and glycoproteomics complement each other i O-glycosylation disorder phenotypes Genomics O-Glycomics O-Glycoproteomics Discovery of O-glycosylation: Structure function relations Enzymes and pathways Tissue- specific pathways Function and targets Characterization of O-glycosylation disorders is indispensable to accomplish a better understanding of the human O-glycosylation mechanisms. Phenotypic heterogeneity of the O-glycosylation disorders reflects the high diversity of O-glycan structures with a high tissue-specificity. Phenotypic characterization and modern omics techniques such as genomics, glycomics, and glycoproteomics complement each other in the Current Opinion in Structural Biology 2019, 56:107–118 Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com 110 Carbohydrates (Table 1: O-glucose) deficiency, both resulting in Dowl- ing-Degos disease. The shared phenotype, characterized by reticular pigmentation of the skin [43,44], indicates a similar underlying pathomechanism. Indeed, both enzymes are involved in the regulation of Notch signal- ing, however, by the addition of different glycan types. POFUT1 stabilizes EGF-like repeats by the addition of O-fucose glycans, and POGLUT1 through the addition of O-glucose glycans [11]. Interestingly, POGLUT1 also shows O-xylosyltransferase activity, but the function of O- xylose on EGF-like domains remains to be investigated [45,46]. Discovery of new glycosyltransferases and metabolic pathways Firstly, genetic defects in O-glycosylation with a charac- teristic phenotype have aided the discovery of new O- glycosylation gene candidates. For example, NGS has resulted in the identification of new genes causing dys- troglycanopathy that is characterized by muscular dystro- phy and, in severely affected individuals, eye and brain abnormalities. Dystroglycanopathies are caused by defec- tive O-mannosylation of aDG, leading to aberrant cell-to- ECM connections. Genetic analysis of patients with dystroglycanopathy features has revealed mutations in ISPD (CRPPA), FKTN and TMEM5(RXYLT1) [34–37] (Table 1; O-mannose). The function of these proteins has been elucidated the last three years [24,26,38,39,40]. Identification of ISPD as a cytosolic cytidyltransferase even led to the discovery of a new mammalian nucleotide sugar: CDP-ribitol [38]. Soon after, FKTN and FKRP were identified as ribitol 5- phosphate (Rbo5P) glycosyltransferases, and Rbo5P moi- eties were detected on the functional O-mannosyl glycan of aDG [24,26,39]. TMEM5 was identified as a b1,4- xylosyltransferase, adding xylose onto the second Rbo5P of unique O-mannosyl glycans on aDG [24,40]. Subse- quently, mass spectrometry of genetically engineered aDG led to the discovery of glycerol 3-phosphate (Gro3P) on the glycan, indicating the existence of a CDP-glycerol biosynthesis pathway [25]. This was further supported by the finding that FKRP and FKTN can use CDP- glycerol as substrates for glycosylation [41]. If CDP- glycerol and Gro3P have a regulatory role in O-mannosyl glycan extension remains to be investigated [25]. An interesting observation is that these findings on aDG show high overlap with the wall teichoic acids in gram- positive bacteria, that contain repeating units of Rbo5P and Gro3P [42]. The O-mannosylation disorders are a classical example of how we learn about novel mecha- nisms and even completely new human metabolic path- ways, initiated by genetic screening of patients with distinct O-glycosylation disorder phenotypes. (Figure 1 Legend Continued) discovery of (tissue-specific) O-glycosylation transferases, pathways, targets and O-glycan function. Enzymes causing known O-glycan disorders are in black. Enzymes in grey have not been associated with an O-glycosylation disorder. *Hypothesized enzyme or multiple possible glycosyltransferases. GalNAc = N-acetylgalactosamine; GlcNAc = N-acetylglucosamine; Rbo = ribitol; P = phosphate. A legend for the glycan symbols is presented in Table 1. O-glycosylation disorders can provide insight in tissue- specific pathways Secondly, the phenotypes associated with O-glycosylation disorders can provide important insights about tissue- specific glycosylation mechanisms. This is nicely illus- trated by POFUT1 (Table 1; O-fucose) and POGLUT1 Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 111 Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 111 cholesterol (HDL-C) levels in human, mice, rats and cynomolgus monkeys. GALNT2 exhibited species-spe- cific glycosylation targets, including PLTP, a regulator of HDL metabolism in plasma [58]. PLTP activity was altered by absence of GALNT2 O-GalNAc modifications, explaining the findings in GALNT2 patients. The involve- ment of additional GALNT2 targets in the disease phe- notype remains to be investigated. unique O-GlcNAc transferase that modifies nucleocyto- plasmic proteins, a process that can be reversed by OGA (O-GlcNAcase) [63–65]. All five patient mutations that have been described so far reside in the N-terminal tetratricopeptide (TPR) repeats of OGT, which are involved in the substrate recognition and specificity of OGT [66]. OGT patient-derived cells and model cell lines with patient mutations showed normal O-GlcNAcylation [59,60,62]. This homeostasis was suggested to be main- tained by a reduced expression of OGA [59,60] or by temporal dynamics in O-GlcNAcylation kinetics [62]. In addition, OGT is involved in proteolytic maturation of HCF1 [14,67], and it has been suggested that the Likewise, mutations in OGT (O-GlcNAc-transferase) and HCF1 (host cell factor 1, a transcriptional regulator of the cell cycle) (cause similar intellectual disability (ID) phe- notypes [59,60,61,62] (Table 1: O-GlcNAc). OGT is a Table 1 Table 1 List of reported congenital O-glycosylation disorders with their associated OMIM numbers, phenotypes and method of diagnostics. Affected glycan structures on serine or threonine (S/T) residues are given for each enzyme deficiency. Enzymes in black: reported O-glycan defects. Enzymes in grey: no reported patients. *Hypothesized enzyme or multiple possible glycosyltransferases. **Putative O-glycosylation disorders. LGMD = Limb-Girdle Muscular Dystrophy; MEB = Muscle Eye Brain disease; WWS = Walker-Warburg Syn- drome; ID = Intellectual Disability. This table does not include the glycosaminoglycan biosynthesis disorders, or disorders known to affect multiple glycosylation pathways, including O-glycosylation O-GalNAc Gene Function OMIM Disease Tissue Current diagnostics GALNT2 Polypeptide GalNAc transferase 602274 Reduced high-density lipoprotein cholesterol Brain Genetics, ApoC-III IEF GALNT3 Polypeptide GalNAc transferase 601756 Familial tumoral calcinosis Subcutaneous tissues, skin, bone Genetics O-GlcNAc Gene Function OMIM Disease Tissue Current diagnostics OGT O-GlcNAc transferase proteolytic processing 300255 X-linked ID Brain, skeleton, heart, face, genitalia, eye Genetics EOGT EGF-domain-specific O-GlcNAc transferase 614789 Adams-Oliver syndrome Skin, skeleton Genetics www.sciencedirect.com Current Opinion in Structural Biology 2019, 56:107–118 List of reported congenital O-glycosylation disorders with their associated OMIM numbers, phenotypes and method of diagnostics. Affected glycan structures on serine or threonine (S/T) residues are given for each enzyme deficiency. Enzymes in black: reported O-glycan defects. Enzymes in grey: no reported patients. *Hypothesized enzyme or multiple possible glycosyltransferases. **Putative O-glycosylation disorders. LGMD = Limb-Girdle Muscular Dystrophy; MEB = Muscle Eye Brain disease; WWS = Walker-Warburg Syn- drome; ID = Intellectual Disability. This table does not include the glycosaminoglycan biosynthesis disorders, or disorders known to affect multiple glycosylation pathways, including O-glycosylation List of reported congenital O-glycosylation disorders with their associated OMIM numbers, phenotypes and method of diagnostics. Affected glycan structures on serine or threonine (S/T) residues are given for each enzyme deficiency. Enzymes in black: reported O-glycan defects. Enzymes in grey: no reported patients. *Hypothesized enzyme or multiple possible glycosyltransferases. **Putative O-glycosylation disorders. LGMD = Limb-Girdle Muscular Dystrophy; MEB = Muscle Eye Brain disease; WWS = Walker-Warburg Syn- drome; ID = Intellectual Disability. Current Opinion in Structural Biology 2019, 56:107–118 Table 1 This table does not include the glycosaminoglycan biosynthesis disorders, or disorders known to affect multiple glycosylation pathways, including O-glycosylation O-GalNAc O-GalNAc Gene Function OMIM Disease Tissue Current diagnostics GALNT2 Polypeptide GalNAc transferase 602274 Reduced high-density lipoprotein cholesterol Brain Genetics, ApoC-III IEF GALNT3 Polypeptide GalNAc transferase 601756 Familial tumoral calcinosis Subcutaneous tissues, skin, bone Genetics O-GlcNAc Gene Function OMIM Disease Tissue Current diagnostics Gene Function OMIM Disease Tissue Current diagnostics GALNT2 Polypeptide GalNAc transferase 602274 Reduced high-density lipoprotein cholesterol Brain Genetics, ApoC-III IEF GALNT3 Polypeptide GalNAc transferase 601756 Familial tumoral calcinosis Subcutaneous tissues, skin, bone Genetics O-GlcNAc Current Opinion in Structural Biology 2019, 56:107–118 112 Carbohydrates O-Galactose O-Galactose Gene Function OMIM Disease Tissue Current diagnostics PLOD1 Helical lysyl hydroxylase (LH1) 153454 Ehlers-Danlos syndrome, kyphoscoliotic type, 1 Skeleton, skin, muscle Lysyl-protocollagen hydroxylase activity in skin fibroblasts, genetics PLOD2 Telopeptide lysyl hydroxylase (LH2) 601865 Bruck-syndrome 2 Skeleton, skin Genetics PLOD3 Lysyl hydroxylase/ hydroxylysyl galactosyltransferase/ galactosylhydroxylysyl glucosyltransferase (LH3) 603066 Lysyl hydroxylase 3 deficiency Skeleton, skin, eye, cochlea or auditory nerve Glucosyltransferase activity in serum or lymphoblastoid cells, genetics O-Glucose Gene Function OMIM Disease Tissue Current diagnostics POGLUT1 O-glucosyltransferase 615618 1) Dowling-Degos disease 4 2) Muscular dystrophy 1) Skin 2) Muscle Genetics O-Fucose Gene Function OMIM Disease Tissue Current diagnostics POFUT1 O-fucosyltransferase 607491 Dowling-Degos disease 2 Skin Genetics LFNG O-fucose b-1,3- GlcNAc transferase 602576 Spondylocostal Dysostosis 3 Axial skeleton Genetics, enzyme activity assay B3GLCT (B3GALTL) O-fucose b-1,3- glucose transferase 610308 Peter’s Plus Syndrome Eye, face, skeleton, lips Genetics, ELISA of properdin serum levels O-Galactose Gene Function OMIM Disease Tissue Current diagnostics PLOD1 Helical lysyl hydroxylase (LH1) 153454 Ehlers-Danlos syndrome, kyphoscoliotic type, 1 Skeleton, skin, muscle Lysyl-protocollagen hydroxylase activity in skin fibroblasts, genetics PLOD2 Telopeptide lysyl hydroxylase (LH2) 601865 Bruck-syndrome 2 Skeleton, skin Genetics PLOD3 Lysyl hydroxylase/ hydroxylysyl galactosyltransferase/ galactosylhydroxylysyl glucosyltransferase (LH3) 603066 Lysyl hydroxylase 3 deficiency Skeleton, skin, eye, cochlea or auditory nerve Glucosyltransferase activity in serum or lymphoblastoid cells, genetics O-Glucose 1) Dowling-Degos disease 4 2) Muscular dystrophy Dowling-Degos disease 2 Spondylocostal Dysostosis 3 Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com www.sciencedirect.com Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 113 O-Mannose Gene Function OMIM Disease Tissue Current diagnostics ISPD (CRPPA) CDP-ribitol synthase 614631 WWS, MEB, LGMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy POMT1 Protein O- mannosyltransferase 607423 WWS, MEB,LGMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy, O- mannosyltransferase activity assay POMT2 Protein O- mannosyltransferase 607439 WWS, MEB, LGMD Muscle, brain, eye, heart POMK (SGK196) Protein O-mannosyl kinase 615247 WWS, MEB, LGMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy POMGNT2 (GTDC2) O-mannose b-1,4-GlcNAc transferase 614828 WWS Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy B3GALNT2 b-GlcNAc b-1,3-GalNAc transferase 610194 WWS, MEB, ID Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy FKTN b-GalNAc-3 Rbo5P transferase 607440 WWS, MEB, LGMD, FCMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy FKRP Rbo5P-1 Rbo5P transferase 606596 WWS, MEB, LGMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy TMEM5(RXYLT1) Rbo5P b-1,4-xylose transferase 605862 WWS, MEB Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy B4GAT1 xylose b-1,4-GlcA transferase 605517 WWS Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy LARGE a-xylose b-1,3-GlcA transferase b-GlcA a1,3-Xyl transferase 603590 WWS, MEB, LGMD Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy POMGNT1 O-mannose b-1,2-GlcNAc transferase 606822 WWS, MEB, LGMD, nonsyndromic retinitis pigmentosa Muscle, brain, eye, heart Genetics, IIH6/VIA4-I on muscle biopsy, O-Man b-1,2 GlcNAc- transferase activity assay TMTC3** Putative O- mannosyltransferase 617218 Cobblestone lissencephaly Periventricular nodular heterotopia Brain, minimal muscle and eye involvement Genetics TMTC2** Putative O- mannosyltransferase 615856 Sensorineural hearing loss Cochlea or auditory nerve Genetics X-linked ID in some OGT patients is linked to insufficient activated HCF1 [60]. Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com Table 1 Taken together, it is plausible that ID genes are regulated or glycosylated by OGT, and this should be addressed in further studies for a better under- standing of the disease mechanisms. TMTC2 and TMTC3 mutations have very different phe- notypes. TMTC3 mutations are associated with lissence- phaly (6 families, 9 patients) and periventricular nodular heterotopia with ID and epilepsy (three siblings) [70,71]. Both phenotypes are associated with deficient neuronal migration. TMTC2 deficiency is associated with sensori- neural hearing loss [72,73], suggesting that the TMTCs have different, tissue-specific targets. Mutations in Cad- herin-23 and Protocadherin-15 cause Usher syndrome, which is characterized by deafness and blindness, and can cause non-syndromic recessive hearing loss [74–76]. Hence, it is tempting to speculate that TMTC2 is involved in the O-mannosylation of these proteins. How- ever, direct demonstration of enzyme activity of the TMTCs is still lacking and whether the TMTC3 and TMTC2 disease phenotypes are directly related to TMTC2 and TMTC3 mutations have very different phe- notypes. TMTC3 mutations are associated with lissence- phaly (6 families, 9 patients) and periventricular nodular heterotopia with ID and epilepsy (three siblings) [70,71]. Both phenotypes are associated with deficient neuronal migration. TMTC2 deficiency is associated with sensori- neural hearing loss [72,73], suggesting that the TMTCs have different, tissue-specific targets. Mutations in Cad- herin-23 and Protocadherin-15 cause Usher syndrome, which is characterized by deafness and blindness, and can cause non-syndromic recessive hearing loss [74–76]. Hence, it is tempting to speculate that TMTC2 is involved in the O-mannosylation of these proteins. How- ever, direct demonstration of enzyme activity of the TMTCs is still lacking and whether the TMTC3 and TMTC2 disease phenotypes are directly related to For a long time, POMT1 and POMT2 were believed to be the only human O-mannosyltransferases. In 2017, glycoproteomics in HEK293 knock-out cells revealed that the O-mannosylation of cadherins and protocadherins is independent of these two enzymes [68]. Using a similar approach, four new O-mannosyltransferases were identi- fied. TMTC1-4, which specifically glycosylate cadherins and protocadherins, and thus have different targets than the POMT1/POMT2 glycosyltransferases (Table 1: O-mannose) [68,69]. Interestingly, patients with 114 Carbohydrates hypomannosylation of cadherins, protocadherins or other proteins remains to be investigated. answered about the O-glycosylation machinery. Although we know in many diseases which O-glycan core structure is affected, for most, their exact attachment site and tissue- specific protein targets remain to be elucidated. Modeling mutations to study structure-function relations of O-glycosylation proteins So far, most O-glycosylation defects that have been identi- fied affect the core sugar of O-glycans. In the last few years, NGS has been applied more frequently, and probably will lead to the identification of additional disorders that affect more distal monosaccharides on O-glycan structures. Func- tional validation of these disorders will require develop- mentsintheglycoproteomicsfield,since large scalein-depth characterization of the exact glycan structure of intact gly- copeptides is still challenging. Furthermore, it is important to develop in-silico approaches to identify differential O- glycopeptides and interpret complex glycobiology by novel bioinformatic approaches. Combined analysis of O-glyco- peptide data and patient meta data by machine learning is of particular interest to associate protein specific O-glycosyla- tion changes to the physiopathology of O-glycosylation dis- orders. Taken together, understanding the disease mecha- nisms of the O-glycosylation disorders will contribute to our understanding of O-glycosylation mechanisms, while vice versa, new mechanistic insights are highly warranted to develop new therapeutic strategies. In the last few years, crystal structures have been solved of enzymes related to O-glycosylation disorders, for example of OGT [78], POMK [79], POMGNT1 [80] and ISPD [38]. Known disease-causing mutations can be modeled in 3D structures, helping to understand the function of specific enzymatic domains and with it, underlying disease mecha- nisms. For example, the crystal structure of ISPD revealed a N-terminal cytidyltransferase domain and a C-terminal domain connected via a linker helix [38]. Surprisingly, the C-terminal domain did not share homology with any known enzyme domains. No missense mutations have been reported in the C-terminal domain, but the c.1114_1116del (p.Val372del) mutation is reported for five patients. The absence of the Val residue leads to relatively mildphenotype(LGMD)comparedtolargerdeletionslikea deletion of exon 6–8 or 9–10 (WWS). Taken together, this demonstrates that the C-terminal domain is important for ISPD function, either contributing to the stability of the enzyme, or having a enzymatic function on its own [38], a question that so far remains unanswered. For POMGNT1, one study has reported a correlation between mutations closer to the 50 end of the gene with more severe hydroceph- alus than mutations near the 30 end. However, correlations with enzymatic activity or structure have not been estab- lished yet [81]. Taken together, much work remains to elucidate the 3D structure of many O-glycosylation enzymes. However, if such models are accomplished, struc- ture-function relationships can be studied utilizing described O-glycosylation patient mutations. Table 1 In the future, the development of more advanced O-glycopeptide profiling methods is essential to facilitate these discoveries. Ideally, untargeted O-glycoproteomics LC–MS/MS tech- nology will evolve to enable robust high-throughput analy- sis for the in-depth characterization of intact O-glycopep- tides in biological samples. The screening of patient groups with similar clinical presentations or with different genetic O-glycosylation defects (e.g. in different GALNTs) with genomics and O-glycoproteomics will lead to the discovery of glycosylation genes and tissue-specific targets, respec- tively. As illustrated in this review, comparing the pheno- types of other known disorders to the phenotype of O- glycosylation disorders can hint to the respective targets. Finally, B3GLCT deficiency leads to Peter’s Plus syn- drome, a severe disorder characterized by anterior eye chamber defects (Table 1: O-fucose). B3GLCT attaches glucose via a b-1,3 linkage to O-fucose (synthesized by POFUT2) on TSRs of proteins. In search for B3GLCT targets linked to the eye defects, Dubail et al. [77] found that ADAMTS9 haploinsufficient mice showed a similar eye phenotype [77]. Glycosylation with glucose-b-1,3- fucose by POFUT2 and B3GLCT ensures proper secre- tion of ADAMTS9 during development. Taken together, the identification of new genetic O-glycosylation disor- ders can provide important insights about the targets and functions of specific O-glycans. References and recommended reading Papers of particular interest published within the period of review g Papers of particular interest, published within the period of review, have been highlighted as: g Papers of particular interest, published within the period of review, have been highlighted as:  of special interest Modeling mutations to study structure-function relations of O-glycosylation proteins Additionally, this will lead to a better understanding of disease mecha- nisms, and will hopefully be accompanied by the emergence of new treatment opportunities. Current Opinion in Structural Biology 2019, 56:107–118 Conflict of interest statement Nothing declared. Nothing declared. References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:  of special interest  of outstanding interest 1. 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This review summarizes the glycosylation genes that are not only neces- sary for mouse embryonic development, but also for pathway-specific glycosylation genes, of which deletion causes a much milder phenotype. Stanley pinpoints the lessons that we have learned from these mouse models and also discusses general strategies for generating and inter- preting the phenotype of mice in relation to human CDG. 3.  Jaeken J, Pe´ anne R: What is new in CDG? J Inherit Metab Dis 2017, 40:621-625. This review highlights recently discovered CDG. The authors also give a complete overview of all currently known CDG and their phenotypes. 4. Climer LK, Dobretsov M, Lupashin V: Defects in the COG complex and COG-related trafficking regulators affect neuronal Golgi function. Front Neurosci 2015, 9. 20. 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Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 115 Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 115 2. Ng BG, Freeze HH: Perspectives on glycosylation and its congenital disorders. Trends Genet 2018, 34:466-476. 2. Ng BG, Freeze HH: Perspectives on glycosylation and its congenital disorders. Trends Genet 2018, 34:466-476. 19.  Stanley P: What have we learned from glycosyltransferase knockouts in mice? J Mol Biol 2016, 428:3166-3182. Conclusions  of outstanding interest We illustrated that studying the complex phenotypes of O- glycosylation disorders has enabled the elucidation of O- glycosylation proteins, targets, and O-glycan structure and function. Nevertheless, many questions remain to be 1. Pe´ anne R, de Lonlay P, Foulquier F, Kornak U, Lefeber DJ, Morava E, Pe´ rez B, Seta N, Thiel C, Van Schaftingen E et al.: Congenital disorders of glycosylation (CDG): quo vadis? 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The authors applied a more holisticO-glycoproteomic approach of blood plasma proteins to analyze site-specific glycosylation with short mucin- type core-1 and core-2 O-glycans. They identified 31 O-glycosylation sites and regions belonging to 22 glycoproteins. 44. 44. Duchatelet S, Clerc H, Machet L, Gaboriaud P, Miskinyte S, Kervarrec T, Hovnanian A: A new nonsense mutation in the POGLUT1 gene in two sisters with Dowling-Degos disease. J Eur Acad Dermatol Venereol 2018, 32(12):e440-e442. 45. Takeuchi H, Ferna´ ndez-Valdivia RC, Caswell DS, Nita-Lazar A, Rana NA, Garner TP, Weldeghiorghis TK, Macnaughtan MA, Jafar- Nejad H, Haltiwanger RS: Rumi functions as both a protein O-glucosyltransferase and a protein O-xylosyltransferase. Proc Nat Acad Sci U S A 2011, 108:16600-16605.  Dziegiel MH, Woetmann A, Vakhrushev SY, Wandall HH: Characterizing the O-glycosylation landscape of human plasma, platelets, and endothelial cells. Blood Adv 2017, 1: 429-442.  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The structures of the substrate and product complexes show the mechanisms of how local conformational states are likely responsible for the ability of POGLUT1 to transfer both glucose and xylose to serine residues on EGF-domains. This study demonstrated how the structure of glycosyltransferases can shed light on the substrate specificity and glycosylation mechanisms. 34. Willer T, Lee H, Lommel M, Yoshida-Moriguchi T, de Bernabe DBV, Venzke D, Cirak S, Schachter H, Vajsar J, Voit T et al.: ISPD loss- of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome. Nat Genet 2012, 44: 575-580. 35. Roscioli T, Kamsteeg E-J, Buysse K, Maystadt I, van Reeuwijk J, van den Elzen C, van Beusekom E, Riemersma M, Pfundt R, Vissers LELM et al.: Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan. Nat Genet 2012, 44:581-585. 47. 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Interestingly, in fibroblasts of some ISPD patients, theO-glycosylation of a-dystroglycan could be restored, proposing ribitol as a potential therapy for ISPD dystroglycanopathy. 39. Gerin I, Ury B, Breloy I, Bouchet-Seraphin C, Bolsee J, Halbout M, G ff J V D M i li GG S N l ISPD d  Graff J, Vertommen D, Muccioli GG, Seta N et al.: ISPD produces CDP-ribitol used by FKTN and FKRP to transfer ribitol phosphate onto alpha-dystroglycan. Nat Commun 2016, 7. 51. Servia´ n-Morilla E, Takeuchi H, Lee TV, Clarimon J, Mavillard F, Area-Go´ mez E, Rivas E, Nieto-Gonza´ lez JL, Rivero MC, Cabrera- Serrano M et al.: A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss. EMBO Mol Med 2016, 8:1289. phosphate onto alpha dystroglycan. Nat Commun 2016, 7. This paper demonstrated for the first time the presence of CDP-ribitol in mammalian cells and tissues. Furthermore, ribitol supplementation in mice caused this metabolite to increase. 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King SL, Joshi HJ, Schjoldager KT, Halim A, Madsen TD, D i i l MH W A V kh h SY W d ll HH Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 117 Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 117 67. Capotosti F, Guernier S, Lammers F, Waridel P, Cai Y, Jin J, Conaway JW, Conaway RC, Herr W: O-GlcNAc transferase catalyzes site-specific proteolysis of HCF- 1. Cell 2011, 144:376-388. 58. Khetarpal Sumeet A, Schjoldager Katrine T, Christoffersen C, R h A Ed d A d C R tt H ik M 58. Khetarpal Sumeet A, Schjoldager Katrine T, Christoffersen C, Ragha an A Edmondson Andre C Re tter Heiko M 58.  Khetarpal Sumeet A, Schjoldager Katrine T, Christoffersen C, Raghavan A, Edmondson Andrew C, Reutter Heiko M, g , , , Ahmed B, Ouazzani R, Peloso Gina M, Vitali C et al.: Loss of function of GALNT2 lowers high-density lipoproteins in humans, nonhuman primates, and rodents. Cell Metab 2016, 24:234-245. 68. Larsen ISB, Narimatsu Y, Joshi HJ, Yang Z, Harrison OJ, Brasch J, Shapiro L, Honig B, Vakhrushev SY, Clausen H et al.: Mammalian O-mannosylation of cadherins and plexins is independent of protein O-mannosyltransferase 1 and 2. J Biol Chem 2017, 292 (27):11586-11598 http://dx.doi.org/10.1074/jbc.M117.794487. This study demonstrates the differences in glycosylation targets between species usingO-glycoproteomics. Using glycoproteomics, the authors show that GALNT2 deficiency in humans, nonhuman primates, and rodents lowers high-density lipoproteins, likely via the reduction of phos- pholipid transfer protein (PLTP) activity. The authors also demonstrate that GALNT2 has different glycosylation targets in the different species (e. g. ANGPTL3 and ApoC-III in humans). 69.  Larsen ISB, Narimatsu Y, Joshi HJ, Siukstaite L, Harrison OJ, Brasch J, Goodman KM, Hansen L, Shapiro L, Honig B et al.: Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins. Proc Nat Acad Sci U S A 2017, 114(42):11163-11168. 59.  Vaidyanathan K, Niranjan T, Selvan N, Teo CF, May M, Patel S, Weatherly B, Skinner C, Opitz J, Carey J et al.: Identification and characterization of a missense mutation in the O-linked beta- N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability. J Biol Chem 2017, 292:8948-8963. The authors apply aO-glycoproteomics approach on ‘SimpleCells’, HEK239 with knockout of COSMC and POMGNT1 that have truncated O-GalNAc and O-mannose glycans. Additional knockout of POMT1/2 or a combination of TMTC1-4 showed that the TMTCs are putative protein O- mannosyltransferases of specifically cadherins and protocadherins. This clearly shows how O-glycoproteomics can be used to study the function of putative glycosyltransferases. Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 117 Runge CL, Indap A, Zhou Y, Kent JW Jr, King E, Erbe CB, Cole R, Littrell J, Merath K, James R et al.: Association of TMTC2 with human nonsyndromic sensorineural hearing loss. JAMA Otolaryngol Head Neck Surg 2016, 142:866-872. 61. Koufaris C, Alexandrou A, Tanteles GA, Anastasiadou V, Sismani C: A novel HCFC1 variant in male siblings with intellectual disability and microcephaly in the absence of cobalamin disorder. Biomed Rep 2016, 4:215-218. 74. Bolz H, von Brederlow B, Ramirez A, Bryda EC, Kutsche K, Nothwang HG, Seeliger M, del CSCM, Vila MC, Molina OP et al.: Mutation of CDH23, encoding a new member of the cadherin gene family, causes Usher syndrome type 1D. Nat Genet 2001, 27:108-112. 62.  Selvan N, George S, Serajee FJ, Shaw M, Hobson L, Kalscheuer V, Prasad N, Levy SE, Taylor J, Aftimos S et al.: O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018, 293:10810-10824. Here, two novel mutations in OGT are identified. All known mutations of OGT were engineered into a human embryonic stem cell line using 62.  Selvan N, George S, Serajee FJ, Shaw M, Hobson L, Kalscheuer V, Prasad N Levy SE Taylor J Aftimos S et al : O GlcNAc  Prasad N, Levy SE, Taylor J, Aftimos S et al.: O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018, 293:10810-10824.  Prasad N, Levy SE, Taylor J, Aftimos S et al.: O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018, 293:10810-10824. 75. Bork JM, Peters LM, Riazuddin S, Bernstein SL, Ahmed ZM, Ness SL, Polomeno R, Ramesh A, Schloss M, Srisailpathy CR et al.: Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of the novel cadherin-like gene CDH23. Am J Hum Genet 2001, 68:26-37. g g , Here, two novel mutations in OGT are identified. All known mutations of OGT were engineered into a human embryonic stem cell line using CRISPR/Cas9. In these cells,O-GlcNAc, OGT and OGA levels were unaltered when addressed using western blot. Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 117 The underlying disease mechanisms of TMTC2 and TMTC3 deficiency should be further explored. This paper is describing a L254F mutation inO-GlcNAc transferase (OGT), leading to X-linked intellectual disability (XLID). Interestingly, in cells from these patients, a decrease in steady-state OGT protein levels was observed but steady-state global O-GlcNAc levels were not altered, and the decrease of OGT activity was compensated by decreased O- GlcNAcase (OGA) promoter activity. The mutation did not affect the capability of OGT to splice HCF1. However, the authors do demonstrate that the L254F mutation in OGT affects the expression of a subset of genes, including genes linked to intellectual disability, suggesting this as the underlying disease mechanism. 70. Farhan SMK, Nixon KCJ, Everest M, Edwards TN, Long S, Segal D, Knip MJ, Arts HH, Chakrabarti R, Wang J et al.: Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy. Hum Mol Genet 2017, 26:4278-4289. 71. 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OGT and OGA levels were slightly reduced and globalO-GlcNAc levels were unaffected, as was also independently demonstrated by Vaidyabathan et al. [59] in cells from another patient. Recombinant OGT with the p. Arg84Pro mutation had reduced glycosylation activity and showed reduced proteolytic processing of the HCF1 protein. The reduced pro- cessing of HCF1 is suggested to be part of the underlying disease mechanism. 72. Guillen-Ahlers H, Erbe CB, Chevalier FD, Montoya MJ, Zimmerman KD, Langefeld CD, Olivier M, Runge CL: TMTC2 variant associated with sensorineural hearing loss and auditory neuropathy spectrum disorder in a family dyad. Mol Genet Genomic Med 2018, 6(4):653-659. 73. 78. Lazarus MB, Nam Y, Jiang J, Sliz P, Walker S: Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature 2011, 469:564-567. 116 Carbohydrates Basmanav FB, Oprisoreanu AM, Pasternack SM, Thiele H, Fritz G, Wenzel J, Grosser L, Wehner M, Wolf S, Fagerberg C et al.: 43. Basmanav FB, Oprisoreanu AM, Pasternack SM, Thiele H, Fritz G, Wenzel J, Grosser L, Wehner M, Wolf S, Fagerberg C et al.: Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com www.sciencedirect.com et al.: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha- dystroglycan. Proc Natl Acad Sci U S A 2016, 113:9280-9285. 81. Taniguchi K, Kobayashi K, Saito K, Yamanouchi H, Ohnuma A, Hayashi YK, Manya H, Jin DK, Lee M, Parano E et al.: Worldwide distribution and broader clinical spectrum of muscle–eye– brain disease. Hum Mol Genet 2003, 12:527-534. 79. Nagae M, Mishra SK, Neyazaki M, Oi R, Ikeda A, Matsugaki N, Akashi S, Manya H, Mizuno M, Yagi H et al.: 3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy. Genes Cells 2017, 22:348-359. 80. Kuwabara N, Manya H, Yamada T, Tateno H, Kanagawa M, Kobayashi K, Akasaka-Manya K, Hirose Y, Mizuno M, Ikeguchi M Current Opinion in Structural Biology 2019, 56:107–118 Mechanistic insights from human O-glycosylation disorders van Tol, Wessels and Lefeber 117 Analyses of the differential transcriptomes of the OGT variant–expressing stem cells showed that genes involved in cell fate determination and liver X receptor/retinoid X receptor signaling were deregulated, potentially contributing to the clin- ical phenotypes of OGT patients. 76. Ahmed ZM, Riazuddin S, Ahmad J, Bernstein SL, Guo Y, Sabar MF, Sieving P, Riazuddin S, Griffith AJ, Friedman TB et al.: PCDH15 is expressed in the neurosensory epithelium of the eye and ear and mutant alleles are responsible for both USH1F and DFNB23. Hum Mol Genet 2003, 12:3215-3223. 63. Jackson SP, Tjian R: O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation. Cell 1988, 55:125-133. 77.  Dubail J, Vasudevan D, Wang LW, Earp SE, Jenkins MW, Haltiwanger RS, Apte SS: Impaired ADAMTS9 secretion: a potential mechanism for eye defects in Peters Plus Syndrome. Sci Rep 2016, 6:33974. 64. Hanover JA, Cohen CK, Willingham MC, Park MK: O-linked N- acetylglucosamine is attached to proteins of the nuclear pore. Evidence for cytoplasmic and nucleoplasmic glycoproteins. J Biol Chem 1987, 262:9887-9894. The authors aim to investigate the underlying disease mechanism of Peters Plus Syndrome caused by mutations in B3GLCT. Their mouse model with Adamts9 haploinsufficiency demonstrated congenital corneal opacity and Peters anomaly. Mass spectrometry of recombinant ADAMTS9 expressed in HEK293F cells demonstrated that TSRs of ADAMTS9 carry the glucoseb1-3fucose disaccharide. Secretion of ADAMTS9 was reduced upon B3GLCT knockdown, proposing this as the underlying disease mechanism of Peters anomaly. 65. Wells L, Gao Y, Mahoney JA, Vosseller K, Chen C, Rosen A, Hart GW: Dynamic O-glycosylation of nuclear and cytosolic proteins: further characterization of the nucleocytoplasmic b-N-acetylglucosaminidase, O-GlcNAcase. J Biol Chem 2002, 277:1755-1761. 66. Jinek M, Rehwinkel J, Lazarus BD, Izaurralde E, Hanover JA, Conti E: The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha. Nat Struct Mol Biol 2004, 11:1001-1007. 78. Lazarus MB, Nam Y, Jiang J, Sliz P, Walker S: Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature 2011, 469:564-567. Current Opinion in Structural Biology 2019, 56:107–118 www.sciencedirect.com et al.: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha- dystroglycan. Proc Natl Acad Sci U S A 2016, 113:9280-9285. 81. Taniguchi K, Kobayashi K, Saito K, Yamanouchi H, Ohnuma A, Hayashi YK, Manya H, Jin DK, Lee M, Parano E et al.: Worldwide distribution and broader clinical spectrum of muscle–eye– brain disease. Hum Mol Genet 2003, 12:527-534. 118 Carbohydrates 118 Carbohydrates www.sciencedirect.com
https://openalex.org/W2102832476
http://www.ajnr.org/content/ajnr/34/9/1853.full.pdf
English
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Is Severe Pain Immediately after Spinal Augmentation a Predictor of Long-Term Outcomes?
American journal of neuroradiology
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ABSTRACT BACKGROUND AND PURPOSE: Severe, immediate postprocedural pain and the need for analgesics after vertebroplasty can be a discouraging experience for patients and caregivers. The goal of this study was to investigate whether the presence of severe pain immediately after vertebroplasty predicts short- and long-term pain relief. MATERIALS AND METHODS: A chart review was performed to categorize patients regarding pain severity and analgesic usage immedi- ately after vertebroplasty ( 4 h). “Severe” pain was defined as at least 8 of 10 with the 10-point VAS. Outcomes were pain severity and pain medication score and usage at 1 month and 1 year after vertebroplasty. Outcomes and clinical characteristics were compared between groups by using the Wilcoxon signed-rank test and the Fisher exact test. RESULTS: Of the 429 vertebroplasty procedures identified, 69 (16%) were associated with severe pain, and 133 (31%) were associated with analgesic administration immediately after the procedure. The group experiencing severe pain had higher preprocedure median VAS rest pain scores (5 [IQR, 2–7]) and activity pain scores (10 [IQR, 8–10]) compared with patients who did not experience severe pain (3 [IQR, 1–6]; P  .0208, and 8 [IQR, 7–10]; P  .0263, respectively). At 1 month postprocedure, VAS rest and activity pain scores were similar between the severe pain group and the nonsevere pain group (P  .16 and P  .25, respectively) and between the group receiving pain medication and the group not receiving pain medication (P  .25 and P  .67, respectively). This similarity continued for 1 year after the procedure. Analgesic usage was similar among all groups at 1 year postprocedure. CONCLUSIONS: Patients with severe pain immediately after vertebroplasty have similar long-term outcomes compared with patients without severe pain. Severe, immediate postprocedural pain; pain before hospital discharge; and the need for analgesics after vertebroplasty can be a discouraging experience for patients and caregivers. Despite the literature establishing vertebroplasty as a technique for manage- ment of painful compression fractures, the short- and long-term outcomes in patients with severe, immediate postprocedural pain, to our knowledge, have not been investigated previously. The goal of our current study is to investigate whether the pres- ence of severe pain immediately after spinal augmentation proce- dures or the need for immediate postprocedure analgesics pre- dicts short- and long-term pain relief. Received September 24, 2012; accepted after revision December 5. From the Departments of Radiology (Y.W.C., J.S.M., A.E.R., J.J.O., D.F.K.), and Neuro- surgery (D.F.K.), Mayo Clinic, Rochester, Minnesota. Please address correspondence to Jennifer S. McDonald, PhD, Department of Radiology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905; e-mail: mcdonald.jennifer@mayo.edu http://dx.doi.org/10.3174/ajnr.A3505 Outcomes? Augmentation a Predictor of Long-Term Is Severe Pain Immediately after Spinal Kallmes Y.W. Cho, J.S. McDonald, A.E. Rad, J.J. Ocel and D.F. http://www.ajnr.org/content/34/9/1853 https://doi.org/10.3174/ajnr.A3505 doi: 2013, 34 (9) 1853-1856 AJNR Am J Neuroradiol http://www.ajnr.org/content/34/9/1853 https://doi.org/10.3174/ajnr.A3505 doi: 2013, 34 (9) 1853-1856 AJNR Am J Neuroradiol of October 23, 2024. This information is current as ORIGINAL RESEARCH SPINE Is Severe Pain Immediately after Spinal Augmentation a Predictor of Long-Term Outcomes? Y.W. Cho, J.S. McDonald, A.E. Rad, J.J. Ocel, and D.F. Kallmes ABSTRACT In addition, our study will attempt to determine whether characteristics of the patient or the procedure can predict which patients will experience severe pain immediately after the procedure. S pinal augmentation procedures, including vertebroplasty and kyphoplasty, have been used widely for palliation of pain- related osteoporotic and pathologic compression fractures of the spine. The literature abounds with both prospective and retro- spective studies attempting to characterize many different aspects of the spinal augmentation procedures such as procedure efficacy, characteristics of fractures in success of augmentation, sequelae of spinal augmentation procedures, and a variety of other topics.1-4 However, there is a paucity of research investigating clinical signs or symptoms directly related to the procedure as predictors of outcome after spinal augmentation. S p k AJNR Am J Neuroradiol 34:1853–56 Sep 2013 www.ajnr.org 1853 Statistical Analysis our institution was the source of data for this study. Patients in this data base have previously been included in other published studies that have not specifically examined patients with immedi- ate postprocedure severe pain.1,4-14 Patients who underwent a vertebroplasty procedure at our institution from 2005–2011 were included in the study. Patients were excluded if they did not have immediate postprocedure pain data within 3 hours after the vertebroplasty or at either 1 month or 1 year postprocedure. We performed statistical analyses by using JMP (version 9; SAS Institute, Cary, North Carolina). Continuous variables were pre- sented as median and IQR, and categoric variables were presented as percentages. Preprocedural, procedural, and postprocedural characteristics and outcomes were compared between groups by using the Wilcoxon signed-rank test and the Fisher exact test. Statistical significance was defined as P  .05. postprocedure. Retrospective medical chart review was performed to confirm data base records and retrieve additional clinical information. Data recorded included preprocedure descriptors (demograph- ics; pain severity; prescribed analgesics; number, level, and acuity of each fracture; number of chronic fractures that were not treated because they were not amenable to vertebroplasty; and benign or malignant nature of the fracture), procedural descriptors (unilat- eral vs bilateral transpedicular approach, number of augmenta- tions performed, distribution of cement, and complications), and postprocedural descriptors (pain severity and medications ad- ministered within 3 hours after the procedure and at 1-month and 1-year follow-ups). Pain severity was measured at both rest and activity by using the 10-point VAS.15 Medication scores were re- corded as follows: 0  no medications, 1  over-the-counter analgesics, 2 non-narcotic prescription medication as needed, 3  oral narcotic analgesic as needed, 4  scheduled oral narcotic or analgesic patches, and 5  intravenous narcotics. MATERIALS AND METHODS Study Population and Data Retrieval Institutional review board approval was obtained before this ret- rospective study. A vertebroplasty patient data base maintained at AJNR Am J Neuroradiol 34:1853–56 Sep 2013 www.ajnr.org 1853 Table 1: Vertebroplasty patient and procedure characteristics Table 1: Vertebroplasty patient and procedure characteristics Type of Pain Pain Medication All Severe Nonsevere P Value Given Not Given P Value No. patients 429 69 360 133 296 Patient characteristics Age (median, IQR) 75 (65–82) 75 (65–82) 75 (65–83) .99 75 (65–83) 75 (65–82) .66 Female (%) 257 (40) 41 (59) 216 (60) .99 88 (66) 169 (57) .09 No. with chronic, untreated fractures (%) 142 (33) 27 (39) 115 (32) .27 59 (44) 83 (28) .0012 No. with fractures because of malignancy (%) 74 (18) 15 (24) 59 (17) .21 25 (20) 49 (18) .49 Median VAS rest pain score (IQR) 4 (1–6) 5 (2–7) 3 (1–6) .0208 3 (1–6) 4 (1–6) .54 Median VAS activity pain score (IQR) 9 (7–10) 10 (8–10) 8 (7–10) .0263 10 (8–10) 9 (7–10) .0022 Median pain duration (months, IQR) 2 (1–4) 2 (1–3) 2 (1–4) .76 1 (1–3) 2 (1–4) .0317 No. receiving pain medication (%) 401 (99) 60 (98) 341 (99) .56 126 (99) 275 (99) .99 Median pain medication score (IQR) 3 (3–3) 3 (3–3) 3 (3–3) .85 3 (3–3) 3 (3–3) .0058 Vertebroplasty procedure characteristics Median cement volume (mL) (IQR) 3.5 (2.0–5.0) 3.5 (2.0–5.0) 3.2 (2.0–4.6) .88 3.7 (2.0–5.0) 3.0 (2.0–4.5) .15 Unilateral needle placement (%) 306 (77) 46 (74) 260 (78) .51 89 (75) 217 (78) .51 Median no. levels treated (IQR) 1 (1–2) 1 (1–2) 1 (1–2) .84 1 (1–2) 1 (1–2) .28 3 levels treated (%) 48 (11) 11 (16) 37 (10) .21 22 (17) 26 (9) .0205 Complications (%) 95 (23) 17 (25) 78 (22) .75 30 (23) 65 (22) .99 Cement embolus (%) 19 (4) 4 (6) 15 (4) .53 7 (5) 12 (4) .62 Extravertebral leakage (%) 75 (17) 12 (18) 63 (18) .87 22 (17) 53 (18) .89 RESULTS All vertebroplasty procedures performed from 2005–2011 by 8 independent operators were identified. Of 877 total procedures performed during this timeframe, 448 (51%) procedures were excluded because they lacked 3-hour postprocedure pain data or lacked either 1-month or 1-year follow-up information on pain and medication, leaving 429 included procedures. Of these 429 procedures, 69 (16%) were associated with severe pain in the 3 hours after the vertebroplasty procedure. A total of 133 (31%) of 429 procedures were associated with administration of some pain medications in the 3 hours after the vertebroplasty procedure. Overall characteristics were very similar between the severe pain/pain medication groups and their respective control groups (Table 1). The severe pain group had significantly higher prepro- cedure median VAS rest pain scores (5 [IQR, 2–7]) compared with the nonsevere pain group (3 [IQR, 1–6]) (P  .0208). Me- dian VAS activity pain scores were also significantly higher in the severe pain group (10 [IQR, 8–10]) compared with the nonsevere pain group (8 [IQR 7–10]) (P  .0263). The patient group that received pain medication immediately after the procedure also had higher median VAS activity pain scores (10 [IQR, 8–10]) compared with the group that did not receive pain medication (9 [(IQR, 7–10]) (P  .0022). There was a higher percentage of pa- tients in the pain medication group with chronic fractures who were not treated because they were not amenable to vertebro- plasty compared with the control group (59 [44%] of 133 vs 83 [28%] of 296; P  .0013). Patients in the pain medication group Patients were categorized by pain and analgesic requirements within 3 hours of vertebroplasty. Patients were divided into 2 groups: those with immediate postprocedure pain scores 8 (“se- vere pain group”) and those whose pain scores were  8 (“non- severe pain group”) in the 3 hours after the vertebroplasty proce- dure. “Immediate postprocedure pain” was defined as that recorded before discharge from the hospital on the day of the procedure, typically 2–4 hours after vertebroplasty. Patients were also divided into whether they received pain medication in the 3 hours immediately after the procedure. 1854 Cho Sep 2013 www.ajnr.org 1854 Table 2: Postvertebroplasty pain and medication usage at 1-month and 1-year follow-ups Type of Pain Pain Medication All Severe Nonsevere P Value Given Not Given P Value One-month follow-up No. DISCUSSION also had a shorter median duration of pain before the procedure compared with the control group (1 month [IQR 1–3] vs 2 months [IQR 1–4]; P  .0378). There was no difference in the percentage of patients who had 3 or more levels treated between the severe pain group and the nonsevere pain group (P  .21). However, there was a higher percentage of these patients in the pain medication group compared with the control group (22 [17%] of 133 vs 26 [9%] of 296; P  .0205). All other clinical and procedural characteristics were similar between the severe pain group and the nonsevere pain group and between the pain med- ication group and the no-pain-medication group. This study demonstrated that severe, postprocedure pain after spine augmentation did not predict greater pain severity at either 1 or 12 months after the procedure compared with patients not experiencing severe, postprocedure pain. This equivalence in pain outcomes was present, though the patients with severe, immedi- ate postprocedure pain presented with greater baseline pain com- pared with the control group. We did observe that patients with severe pain were more likely to have a worsened medication score, indicating a need for stronger analgesics, at 1 month and 1 year postprocedure compared with patients who did not have severe pain. This finding may explain why patients with severe pain re- ported similar levels of pain at 1 month and 1 year postprocedure compared with patients without severe pain; however, we could not confirm if or how frequently patients were taking these anal- gesics. Taken together, these findings are highly relevant to spinal augmentation practitioners, as they can reassure patients that se- vere, postprocedure pain does not mean that their medium-term and long-term pain outcomes will be suboptimal. Rates of loss to follow-up were similar between the severe pain group and the nonsevere pain group and between the pain med- ication group and the no-pain-medication group at 1 month and 1 year after the procedure (Table 2). At 1 month postprocedure, VAS rest and activity pain scores were similar between the severe pain group and the nonsevere pain group (P  .16 and P  .25, respectively) and between the pain medication group and the no- pain-medication group (P  .25 and P  .67, respectively). RESULTS patients (% lost to follow-up) 399 (7) 68 (1) 331 (8) 123 (8) 276 (7) No. patients with pain scores 369 61 308 113 256 Median VAS rest pain score (IQR) 0 (0–3) 2 (0–3) 0 (0–3) .16 0 (0–2) 0 (0–3) .25 Median VAS activity pain score (IQR) 4 (0–6) 3 (0–5) 4 (0–6) .25 3 (0–6) 4 (0–6) .67 No. patients with pain medication scores 383 60 323 119 264 Median pain medication score (IQR) 3 (0–4) 3 (0–4) 3 (1–4) .17 3 (1–4) 3 (0–4) .33 Change in pain medication score from prevertebroplasty Unchanged (%) 99 (26) 12 (20) 87 (27) .34 31 (26) 68 (26) .99 Improved (%) 167 (43) 21 (35) 146 (45) .16 52 (43) 115 (44) .99 Worsened (%) 117 (31) 27 (45) 90 (28) .0097 36 (31) 81 (31) .99 One-year follow-up No. patients (% lost to follow-up) 307 (28) 46 (33) 261 (28) 100 (25) 207 (30) No. patients with pain scores 288 44 244 93 195 Median VAS rest pain score (IQR) 0 (0–2) 0 (0–3) 0 (0–2) .0247 0 (0–3) 0 (0–2) .43 Median VAS activity pain score (IQR) 3 (0–6) 4 (0–6) 3 (0–6) .17 3 (0–6) 3 (0–6) .78 No. patients with pain medication scores 176 29 147 59 117 Median pain medication score (IQR) 3 (1–4) 3 (1–4) 3 (1–4) .30 3 (1–4) 3 (1–4) .65 Change in pain medication score from prevertebroplasty Unchanged (%) 63 (36) 9 (31) 54 (37) .67 25 (42) 38 (32) .24 Improved (%) 63 (36) 9 (31) 54 (37) .67 23 (39) 40 (34) .62 Worsened (%) 50 (28) 11 (38) 39 (27) .26 11 (19) 39 (33) .0514 Table 2: Postvertebroplasty pain and medication usage at 1-month and 1-year follow-ups Type of Pain Table 2: Postvertebroplasty pain and medication usage at 1-month and 1-year follow-ups Pain Medication AJNR Am J Neuroradiol 34:1853–56 Sep 2013 www.ajnr.org 18 REFERENCES 1. Layton KF, Thielen KR, Koch CA, et al. Vertebroplasty, first 1000 levels of a single center: evaluation of the outcomes and complica- tions. AJNR Am J Neuroradiol 2007;28:683–89 1. Layton KF, Thielen KR, Koch CA, et al. Vertebroplasty, first 1000 levels of a single center: evaluation of the outcomes and complica- tions. AJNR Am J Neuroradiol 2007;28:683–89 Previous studies have evaluated the predictive value of early pain severity after spine augmentations. In a study of 181 verte- broplasty procedures, Hodler et al16 described that immediate postprocedural pain relief was the best predictor of midterm out- come of vertebroplasty. Weill et al17 showed that pain reduction achieved initially remained stable in 73% of their patients after 6 months. Heini et al18 also found stable results after 1 year. Our current study expands on this prior literature by offering larger patient cohorts and detailed analysis of potential factors that might influence long-term outcomes. 2. Masala S, Mastrangeli R, Petrella MC, et al. Percutaneous vertebro- plasty in 1,253 levels: results and long-term effectiveness in a single centre. Eur Radiol 2009;19:165–71 3. McKiernan F, Faciszewski T, Jensen R. Quality of life following ver- tebroplasty. J Bone Joint Surg Am 2004;86-A:2600–06 3. McKiernan F, Faciszewski T, Jensen R. Quality of life following ver- tebroplasty. J Bone Joint Surg Am 2004;86-A:2600–06 4. Rad AE, Kallmes DF. Pain relief following vertebroplasty in patients with and without localizing tenderness on palpation. AJNR Am J Neuroradiol 2008;29:1622–26 5. Rad AE, Kallmes DF. Correlation between preoperative pain dura- tion and percutaneous vertebroplasty outcome. AJNR Am J Neuro- radiol 2011;32:1842–45 g g Our study had several limitations. First, a large number of patients were excluded from the study on the basis of incomplete records at 3 hours postprocedure or at 1 month or 1 year postpro- cedure. It is unclear how this may have affected the findings of the study. REFERENCES Second, although pain is the most common complaint and can be debilitating, the use of the subjective pain scoring (0–10) was likely a suboptimal evaluation tool of the effectiveness of ver- tebroplasty.19-22 In some cases in our study, pain at the puncture site continued for a few days after the procedure; therefore, VAS scores may have improved further if they had been evaluated later.20 Better functional assessment of patient response to verte- broplasty is likely necessary, as subjective assessment of pain scales is subject to substantial interobserver and intraobserver variabil- ity. Third, as with most studies on vertebroplasty, there was a potential for bias when patients are evaluated at follow-up. It is possible that the nurse or physician administering the follow-up questions could have influenced the responses of the patients. Furthermore, it is possible that responses to the follow-up ques- tions were occasionally provided by family members or health care providers who interacted with the patients on a daily basis, particularly with cases in which the patient was unable to give responses because of disability or dementia.1 Fourth, although we could identify new prescriptions for analgesics after the proce- dure, we could not confirm if and how frequently patients were actually taking this medication. Finally, new fractures during the follow-up interval may have confounded pain outcomes. A num- ber of patients who had immediate postprocedure relief had re- current pain symptoms at the short- or long-term follow-up sec- ondary to factors such as new metastatic lesions or development of new compression fractures. 6. Rad AE, Gray LA, Sinaki M, et al. Role of physical activity in new onset fractures after percutaneous vertebroplasty. Acta Radiol 2011;52:1020–23 7. Miller FG, Kallmes DF, Buchbinder R. Vertebroplasty and the pla- cebo response. Radiology 2011;259:621–25 p gy 8. McDonald RJ, Gray LA, Cloft HJ, et al. The effect of operator vari- ability and experience in vertebroplasty outcomes. Radiology 2009;253:478–85 9. McDonald RJ, Achenbach SJ, Atkinson EJ, et al. Mortality in the vertebroplasty population. AJNR Am J Neuroradiol 2011;32:1818–23 10. Leake CB, Brinjikji W, Cloft HJ, et al. Trends of inpatient spine augmentation: 2001–08. AJNR Am J Neuroradiol 2011;32:1464–68 11. Knavel EM, Rad AE, Thielen KR, et al. Clinical outcomes with hemi- vertebral filling during percutaneous vertebroplasty. AJNR Am J Neuroradiol 2009;30:496–99 12. Khosla A, Diehn FE, Rad AE, et al. Disclosures: Jennifer McDonald—UNRELATED: Grants/Grants Pending: GE Health- care. David Kallmes—UNRELATED: Consultancy: ev3,* Codman,* Medtronic;* Grants/Grants Pending: MicroVention,* Micrus,* ev3,* Benvenue,* Sequent;* Roy- alties: UVA Patent Foundation; Payment for Development of Educational Presen- tations: ev3,* CareFusion;* Travel/Accommodations/Meeting Expenses Unrelated to Activities Listed: MicroVention.* (*Money paid to institution.) REFERENCES Neither subendplate cement deposition nor cement leakage into the disk space during verte- broplasty significantly affects patient outcomes. Radiology 2012;264:180–86 13. Harvey RE, Kallmes DF. Discharge disposition following vertebro- plasty. AJNR Am J Neuroradiol 2011;32:1614–16 14. Ehteshami Rad A, Luetmer MT, Murad MH, et al. The association between the duration of preoperative pain and pain improvement in vertebral augmentation: a meta-analysis. AJNR Am J Neuroradiol 2012;33:376–81 15. Dworkin RH, Turk DC, Farrar JT, et al. Core outcome measures for chronic pain clinical trials: IMMPACT recommendations. Pain 2005;113:9–19 16. Hodler J, Peck D, Gilula LA. Midterm outcome after vertebroplasty: predictive value of technical and patient-related factors. Radiology 2003;227:662–68 17. Weill A, Chiras J, Simon JM, et al. Spinal metastases: indications for and results of percutaneous injection of acrylic surgical cement. Radiology 1996;199:241–47 gy 18. Heini PF, Walchli B, Berlemann U. Percutaneous transpedicular vertebroplasty with PMMA: operative technique and early results. A prospective study for the treatment of osteoporotic compression fractures. Eur Spine J 2000;9:445–50 DISCUSSION How- ever, a significantly higher percentage of patients had worsened medication scores (ie, from a score of 1 for over-the-counter nar- cotics to a score of 3 for prescription narcotics) in the severe pain group at 1 month compared with the nonsevere pain group (27 [45%] of 60 vs 90 [28%] of 323; P  .0097). At 1 year postproce- dure, VAS rest and activity pain scores were similar between the severe pain group and the nonsevere pain group and between the pain medication group and the no-pain-medication group. Med- ication scores at 1 year were statistically similar between all groups, though the severe pain group still demonstrated a higher percentage of patients with worsened medication scores com- pared with the nonsevere pain group (11 [38%] of 29 vs 39 [27%] of 147; P  .26). In addition to providing prognostic clarity, our study can also be used to identify which factors, if any, will predict the occur- rence of severe, immediate postprocedure pain. The only factor noted to correlate with such pain was the severity of baseline pain, but that parameter alone likely will not provide substantial guid- ance. Among the numerous factors that logically might predict immediate pain severity—including numbers of treated levels, unipedicular or bipedicular approaches, cement leakage, or chronic fractures that were untreated because they were not ame- nable to vertebroplasty—none correlated with severe, immediate pain. Patients who had 3 or more levels treated were more likely to receive pain medication immediately after the procedure com- pared with patients who had fewer levels treated; however, the 1855 incidence of reported severe pain was similar between these 2 groups. CONCLUSIONS p 19. McGraw JK, Cardella J, Barr JD, et al. Society of Interventional Ra- diology quality improvement guidelines for percutaneous verte- broplasty. J Vasc Interv Radiol 2003;14:S311–15 Patients with severe pain after vertebroplasty have similar long-term outcomes and improvements compared with pa- tients with no severe pain. Patient and procedural characteris- tics did not predispose patients to having immediate severe pain after vertebroplasty. 20. Kobayashi K, Shimoyama K, Nakamura K, et al. Percutaneous verte- broplasty immediately relieves pain of osteoporotic vertebral com- pression fractures and prevents prolonged immobilization of pa- tients. Eur Radiol 2005;15:360–67 21. Grados F, Depriester C, Cayrolle G, et al. Long-term observations of vertebral osteoporotic fractures treated by percutaneous vertebro- plasty. Rheumatology (Oxford) 2000;39:1410–14 22. Alvarez L, Perez-Higueras A, Quinones D, et al. Vertebroplasty in the treatment of vertebral tumors: postprocedural outcome and qual- ity of life. Eur Spine J 2003;12:356–60 Cho Sep 2013 www.ajnr.org 1856
https://openalex.org/W2242714981
http://pdf.blucher.com.br/chemicalengineeringproceedings/cobeqic2015/248-33007-251713.pdf
English
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FATTY ACIDS PROFILE OF CHIA OIL-LOADED LIPID MICROPARTICLES
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2,015
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3,995
1 Universidade Tecnológica Federal do Paraná, Departamento de Alimentos 2 Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Tecnologia de Alimentos *odinei@utfpr.edu.br 1 Universidade Tecnológica Federal do Paraná, Departamento de Alimentos 2 Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Tecnologia de Alimentos *odinei@utfpr.edu.br ABSTRACT – Encapsulation of poly unsaturated fatty acid (PUFA) is known to be an alternative to increase its stability during processing and storage. Chia (Salvia hispanica L.) oil has raised interest as a reliable source of both omega-3 and omega-6 but its encapsulation must be better evaluated. In this work, chia oil was extracted and encapsulated in stearic acid microparticles by the hot homogenization technique. UV-Vis spectroscopy coupled with Multivariate Curve Resolution with Alternating Least-Squares methodology demonstrated that no oil degradation or tocopherol loss was expected to occur during the encapsulation procedure. After lyophilization, the fat acids profile of the oil loaded microparticles was determined by gas chromatography and compared to that of the in natura oil. Both omega-3 and omega-6 were effectively encapsulated keeping the same omega-3:omega-6 ratio presented in the in natura oil. FATTY ACIDS PROFILE OF CHIA OIL-LOADED LIPID MICROPARTICLES M. F. SOUZA1, J. L. SANCHEZ2, P. VALDERRAMA2, E. BONA2, A. A. C. TANAMATI1, F. V. LEIMANN2, O. H. GONÇALVES2* M. F. SOUZA1, J. L. SANCHEZ2, P. VALDERRAMA2, E. BONA2, A. A. C. TANAMATI1, F. V. LEIMANN2, O. H. GONÇALVES2* 1 Universidade Tecnológica Federal do Paraná, Departamento de Alimentos 2 Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Tecnologia de Alimentos *odinei@utfpr.edu.br 1. INTRODUCTION The choice of consuming functional foods has directed the market to offer of products containing omega-3, antioxidants and other components with high nutritional value. Chia oil have high nutritional value since most of its constituents are triglycerides with PUFA acids presented in larger proportions and omega-3 content are between 60 and 68% (Capitani et al. 2012). However, polyunsaturated fatty acids are susceptible to oxidation (Ixtaina et al. 2011), which can lead to the reduction of nutritional value and sensory quality. Encapsulation is a promising alternative to protect PUFAs against oxidation (Salminen et al. 2013; Muchow et al. 2009). Lipid hot homogenization has been used to encapsulate PUFAs due to the high compatibility between them and the encapsulating solid matrix. However, relatively high temperatures are required and so thermal degradation of the encapsulated compound should be evaluated, which unfortunately is not reported in most of the available works in literature. The objective of this work was to encapsulate chia oil in lipid microparticles and investigate the thermal stability of chia oil in the temperature used for its encapsulation. Concentration of its main fatty acids (omega-3 and omega-6) inside the particles was determined in order to verify if both are encapsulated in the same proportions on solid matrix. 2. EXPERIMENTAL SECTION 2.1. Materials Chia seeds were acquired from the local market. Stearic acid (Sigma-Aldrich, 99.5%) and Tween 80 (Dinâmica, 97%) were used as encapsulant and surfactant, respectively. Distilled water was used as continuous phase. Methanol (Isofar, 99.8%), chloroform (Vetec, 99.5%), ammonium chloride (Vetec, 99.5%), KBr (Sigma-Aldrich, spectrophotometric standard) and sulphuric acid (Vetec, 95%) were used as received. 2.2. Chia oil extraction and quantification of degradation products by MCR-ALS The total moisture of the chia seeds was determined and then adjusted to 80% by adding distilled water. Then, the extraction was performed according to the methodology described by Bligh and Dyer (1959). Chia oil was stored at -10°C protected from light. The quantification of oil degradation products was carried out to determine if chia oil was prone to degrade in the temperature used in the encapsulation procedure (75°C). A sample of in natura chia oil were heated and aliquots were collected at 30, 40, 50, 60, 70 e 75ºC. The sample was then kept at 75ºC and aliquots were also collected after regular time intervals for 120 minutes. UV-Visible spectra (Ocean Optics, Red Tide USB650, 1 nm resolution) were obtained and the formation of degradation products was evaluated by Multivariate Curve Resolution Alternating Least-Squares method (MCR-ALS) as described by Gonçalves et al. 2014. The spectrum bands recovered by MCR-ALS were attributed to their respective compounds according to Valderrama et al. (2011). 2.3. Microparticles production and characterization Chia oil-loaded microparticles were obtained by the hot homogenization technique (Gonzalez-Mira et al. 2010). The aqueous phase was prepared dissolving Tween 80 (0,300g) in distilled water (25g) and heating to 75°C under gentle stirring. Separately, stearic acid (0,625g) was melted at 75°C in a borosilicate double walled vessel. Chia oil was then added to the molten lipid and mixed for 1 minute. Then, the aqueous phase was added to the vessel and stirred for 3 minutes resulting in an oil-in-water macroemulsion. Sonication (Fisher- Scientific – Ultrasonic Dismembrator 120 W, 1/8” tip) was carried out for 3 minutes in a pulse regime (30 seconds on and 10 seconds off). The sonicated mixture was cooled in ice bath resulting in the formation of solid lipid particles dispersed in water. They were freeze dried before analysis. The same procedure was also carried out without the addition of chia oil to obtain blank microparticles. Fourier Transform Infrared Spectroscopy (FTIR, Shimadzu IR Affinity-1) of the lyophilized particles or in natura oil was used to qualitatively evaluate the oil loaded microparticles. Particles morphology were observed using optical microscopy (BIOVAL, L2000A) coupled to a digital camera (DCM130E). To determine the encapsulation efficiency (Equation 1), an aliquot of the microparticles dispersion was filtered (Amicon, 100 kDa) at 14,500 rpm for 15 minutes. The fatty acids concentration in the liquid ([FA]non- encapsulated) was determined by GC as described previously. The microparticles were freeze- dried and the total amount of fatty acids (encapsulated and non-encapsulated, [FA] total) was also determined. 𝐸𝐸(%) = 100[𝐹𝐴]𝑡𝑜𝑡𝑎𝑙‒ [𝐹𝐴]𝑛𝑜𝑛‒ 𝑒𝑛𝑐𝑎𝑝𝑠𝑢𝑎𝑙𝑡𝑒𝑑 [𝐴𝐺]𝑡𝑜𝑡𝑎𝑙 (1) 2.4. Transesterification and Gas Chromatography (CG) 3.1. Quantification of degradation 20 30 40 50 60 70 80 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0, relative concentration (-) temperature (°C) 0 20 40 60 80 100 120 0,0 0,1 0,2 0,3 0,4 0,5 0,6 , relative concentration (-) heating time at 75°C (min) ( ) 0 20 40 60 80 100 120 0,0 0,1 0,2 0,3 0,4 0,5 0,6 relative concentration (-) heating time at 75°C (min) It is worth noting that thermal degradation is a concern because the hot homogenization technique requires relatively high temperature and chia oil is rich in unsaturated fatty acids. Recuperated spectra showed the presence of tocopherol as expected (Ixtaina et al. 2011) and that its concentration started to decreased only when the sample was heated to 75°C for 2 hours. The formation of degradation compounds such as conjugated dienes and trienes and hydrolysis products was also detected only after heating to 75°C for 2 hours. Gonçalves et al. (2014) demonstrated that the formation of degradation products, the disappearance of the tocopherol and the temperature in which degradation begins are highly dependent on the oil composition and origin. In the encapsulation procedure proposed in this work, chia oil remained at 75°C for approximately 7 minutes. These results strongly indicate that on appreciable thermal degradation of the chia oil is expected to takes place during its microencapsulation and that the proposed procedure can be safely used to encapsulate chia oil without losing its nutritional properties. 2.4. Transesterification and Gas Chromatography (CG) Fatty acids quantification was performed by CG using methyl tricosanoate (23:0) as internal standard according to Hartman and Lago methodology (Hartman and Lago 1973; Milinsk et al. 2008). Fatty acid methyl esters (FAMEs) were separated and identified by comparing with chromatograph standards (Sigma-Aldrich, F.A.M.E. Mix C14-C22). The equipment used was as follows: gas chromatograph (Shimadzu, GC-2010 Plus AF) equipped with capillary injector Split/Splitless, flame ionization detector (FID), flow and pressure automatic controllers and a 100% dimethylpolysiloxane capillary column (Rtx-1, 30m x 0,25mm x 0,25µm). More details of the experimental conditions can be found elsewhere (Milinsk et al. 2008). The transesterefications were performed in triplicate. 3.1. Quantification of degradation Figures 1 presents the data of thermal degradation of the in natura chia oil (before encapsulation) at different temperatures. Figures 1 presents the data of thermal degradation of the in natura chia oil (before encapsulation) at different temperatures. Figure 1- Relative concentration profile of tocopherol (- - - -) and dienes/trienes conjugated/hydrolysis products (——) of in natura chia oil (before encapsulation): (a) at different temperatures and (b) over time at 75°C. 20 30 40 50 60 70 80 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 relative concentration (-) temperature (°C) C D 0 20 40 60 80 100 120 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 relative concentration (-) heating time at 75°C (min) C D It is worth noting that thermal degradation is a concern because the hot homogenization technique requires relatively high temperature and chia oil is rich in unsaturated fatty acids. Recuperated spectra showed the presence of tocopherol as expected (Ixtaina et al. 2011) and that its concentration started to decreased only when the sample was heated to 75°C for 2 hours. The formation of degradation compounds such as conjugated dienes and trienes and hydrolysis products was also detected only after heating to 75°C for 2 hours. Gonçalves et al. (2014) demonstrated that the formation of degradation products, the disappearance of the tocopherol and the temperature in which degradation begins are highly dependent on the oil composition and origin. In the encapsulation procedure proposed in this work, chia oil remained at 75°C for approximately 7 minutes. These results strongly indicate that on appreciable thermal degradation of the chia oil is expected to takes place during its microencapsulation and that the proposed procedure can be safely used to encapsulate chia oil without losing its nutritional properties. Figure 1- Relative concentration profile of tocopherol (- - - -) and dienes/trienes conjugated/hydrolysis products (——) of in natura chia oil (before encapsulation): (a) at different temperatures and (b) over time at 75°C. 0,7 C D 0,7 C D different temperatures and (b) over time at 75°C. 20 30 40 50 60 70 80 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 relative concentration (-) temperature (°C) D 0 20 40 60 80 100 120 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 relative concentration (-) heating time at 75°C (min) D different temperatures and (b) over time at 75 C. 3.2. Chia Oil Encapsulation The chromatograms of the chia oil before encapsulation (in natura) are presented in Figure 2. Figure 3 presents the fatty acids profile of the lyophilized oil-loaded microparticles and Figure 4 presents the fatty acids profile of the non-encapsulated oil. Both are compared to the in natura chia oil. Figure 2 – Chromatogram of in natura chia oil (before encapsulation). 5 10 15 20 25 0,0 0,5 1,0 1,5 2,0 C23:0 C20:0 C18:3 n-3 C18:2 n-6 C18:1 n-9 C18:0 C16:0 uV (x10 5) tempo de retençao (min) C14:0 C22:0 Figure 3 – Chromatograms of in natura chia oil (red) and oil-loaded microparticles (free + encapsulated oil) (black). Figure 4 – Chromatograms of the non-encapsulated (free) chia oil (red) and particles containing chia oil encapsulated (black). 5,0 7,5 10,0 12,5 15,0 17,5 0 1 2 3 4 5 6 C18:1 t9 uV (x10 4) tempo de retençao (min) oleo de chia in natura particulas contendo oleo de chia C16:0 C14:0 C18:0 C18:1 n-9 C18:2 n-6 C18:3 n-3 C20:0 5,0 7,5 10,0 12,5 15,0 17,5 0,0 0,1 0,2 0,3 uV (x10 5) tempo de retençao (min) particulas contendo oleo de chia fraçao de oleo nao encapsulado C18:0 C14:0 C16:0 C18:3 n-3 C18:2 n-6 C18:1 n-9 Oil extraction from the chia seeds resulted in a yield of 19.8 wt%. Bligh-Dyer is a suitable technique to extract unsaturated fatty acids because no heat is required and a wild range of lipids can be extracted. It is possible to observe in Figure 1 the peaks correspondent to linoleic acid (omega-6) and alpha-linolenic (omega-3) at retention times of approximately 12 and 14 minutes, respectively. As expected, chia oil is a valuable source of omega-3 and 6. The total omega-3 and omega-6 concentration found were (565.52 ± 24.4) and (181.94 ± 5.75) g/100 g FA, which is in accordance with the literature (Capitani et al. 2012). It is possible to observe (Figure 3) that omega-3 and 6 were presented in the microparticles, however both peaks are less pronounced due to the presence of the encapsulant (stearic acid). The chromatogram of the oil-loaded microparticles (Figure 4) presented a well pronounced peak related to stearic acid (C18:0) as well as other small peaks corresponding to impurities. 3.2. Chia Oil Encapsulation High encapsulation efficiencies were found for omega-3 and 6 meaning that the hot h i i h i i i di d l h d Figure 2 – Chromatogram of in natura chia oil (before encapsulation). 5 10 15 20 25 0,0 0,5 1,0 1,5 2,0 C23:0 C20:0 C18:3 n-3 C18:2 n-6 C18:1 n-9 C18:0 C16:0 uV (x10 5) tempo de retençao (min) C14:0 C22:0 Figure 2 – Chromatogram of in natura chia oil (before encapsulation). 2 0 tempo de retençao (min) Figure 4 – Chromatograms of the non-encapsulated (free) chia oil (red) and particles containing chia oil encapsulated (black). 0 3 Figure 4 – Chromatograms of the non-encapsulated (free) chia oil (red) and particles containing chia oil encapsulated (black). Figure 3 – Chromatograms of in natura chia oil (red) and oil-loaded microparticles (free + encapsulated oil) Figure 3 – Chromatograms of in natura chia oil (red) an oil-loaded microparticles (free + encapsulated oil) (black). 5,0 7,5 10,0 12,5 15,0 17,5 0 1 2 3 4 5 6 C18:1 t9 uV (x10 4) tempo de retençao (min) oleo de chia in nat particulas contendo oleo de chia C16:0 C14:0 C18:0 C18:1 n-9 C18:2 n-6 C18:3 n-3 C20:0 encapsulated (black). 5,0 7,5 10,0 12,5 15,0 17,5 0,0 0,1 0,2 0,3 uV (x10 5) tempo de retençao (min) particulas contendo oleo de chia fraçao de oleo nao encapsulado C18:0 C14:0 C16:0 C18:3 n-3 C18:2 n-6 C18:1 n-9 oleo de chia in natura particulas contendo oleo de chia tempo de retençao (min) Oil extraction from the chia seeds resulted in a yield of 19.8 wt%. Bligh-Dyer is a suitable technique to extract unsaturated fatty acids because no heat is required and a wild range of lipids can be extracted. It is possible to observe in Figure 1 the peaks correspondent to linoleic acid (omega-6) and alpha-linolenic (omega-3) at retention times of approximately 12 and 14 minutes, respectively. As expected, chia oil is a valuable source of omega-3 and 6. The total omega-3 and omega-6 concentration found were (565.52 ± 24.4) and (181.94 ± 5.75) g/100 g FA, which is in accordance with the literature (Capitani et al. 2012). It is possible to observe (Figure 3) that omega-3 and 6 were presented in the microparticles, however both peaks are less pronounced due to the presence of the encapsulant (stearic acid). 3.3. Microparticles Characterization Figure 5 and 6 present optical microscopy images of the blank microparticles (no chia oil added) and chia oil-loaded microparticles, respectively. Figure 7 presents the infrared spectra of in natura chia oil, blank microparticles and chia oil-loaded microparticles (spectra were normalized in order to enable the comparison). Figure 5 –Optical microscopy image of the blank microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. Figure 7 – FTIR spectra of in natura chia, blank microparticles and chia oil-loaded microparticles. Microparticles presented diameters of about 5 to 10 micrometers, which was expected due to the low sonication time and potency applied. In the case of blank microparticles, spike- like morphology was formed which is characteristic of the stearic acid α-phase. Microparticles containing chia oil presented spherical morphology indicating that the solid lipid matrix was plasticized by the chia oil and that β-phase was formed. The comparison between both morphologies suggested that chia oil was effectively encapsulated, thus corroborating the Gas Chromatography analyses. The FTIR spectra of in natura chia oil presented the =C-H stretching band at 3010 cm-1. This band is of interest because it is not presented by the encapsulant. The same band is presented by the oil-loaded microparticles but with lower intensity suggesting that the oil located inside the stearic acid particles. This blinding effect is known to occur in other encapsulated systems (CIT). Figure 5 –Optical microscopy image of the blank microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. Figure 7 – FTIR spectra of in natura chia, blank microparticles and chia oil-loaded microparticles. Figure 5 –Optical microscopy image of the blank microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. F c Figure 7 – FTIR spectra of in natura chia, blank microparticles and chia oil-loaded microparticles. Figure 5 –Optical microscopy image of the blank microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. Figure 6 –Optical microscopy image of oil-loaded microparticles. microparticles. Microparticles presented diameters of about 5 to 10 micrometers, which was expected due to the low sonication time and potency applied. In the case of blank microparticles, spike- like morphology was formed which is characteristic of the stearic acid α-phase. Microparticles containing chia oil presented spherical morphology indicating that the solid lipid matrix was plasticized by the chia oil and that β-phase was formed. 3.2. Chia Oil Encapsulation However, several authors do not present encapsulation efficiency in their works, probably assuming maximum values (Salminen et al. 2013; Muchow et al. 2009), which could lead to erroneous conclusions. Encapsulation of omega-3 and 6 rich oils by spray drying are 70-80% (Rodea-González et al. 2012). nanostructure lipid carriers finding an efficiency of 88.5%. However, several authors do not present encapsulation efficiency in their works, probably assuming maximum values (Salminen et al. 2013; Muchow et al. 2009), which could lead to erroneous conclusions. Encapsulation of omega-3 and 6 rich oils by spray drying are 70-80% (Rodea-González et al. 2012). 3.3. Microparticles Characterization The comparison between both morphologies suggested that chia oil was effectively encapsulated, thus corroborating the Gas Chromatography analyses. The FTIR spectra of in natura chia oil presented the =C-H stretching band at 3010 cm-1. This band is of interest because it is not presented by the encapsulant. The same band is presented by the oil-loaded microparticles but with lower intensity suggesting that the oil located inside the stearic acid particles. This blinding effect is known to occur in other encapsulated systems (CIT). 3.2. Chia Oil Encapsulation The chromatogram of the oil-loaded microparticles (Figure 4) presented a well pronounced peak related to stearic acid (C18:0) as well as other small peaks corresponding to impurities. High encapsulation efficiencies were found for omega-3 and 6 meaning that the hot homogenization technique is indicated to encapsulate these compounds. Oil extraction from the chia seeds resulted in a yield of 19.8 wt%. Bligh-Dyer is a suitable technique to extract unsaturated fatty acids because no heat is required and a wild range of lipids can be extracted. It is possible to observe in Figure 1 the peaks correspondent to linoleic acid (omega-6) and alpha-linolenic (omega-3) at retention times of approximately 12 and 14 minutes, respectively. As expected, chia oil is a valuable source of omega-3 and 6. The total omega-3 and omega-6 concentration found were (565.52 ± 24.4) and (181.94 ± 5.75) g/100 g FA, which is in accordance with the literature (Capitani et al. 2012). It is possible to observe (Figure 3) that omega-3 and 6 were presented in the microparticles, however both peaks are less pronounced due to the presence of the encapsulant (stearic acid). The chromatogram of the oil-loaded microparticles (Figure 4) presented a well pronounced peak related to stearic acid (C18:0) as well as other small peaks corresponding to impurities. High encapsulation efficiencies were found for omega-3 and 6 meaning that the hot homogenization technique is indicated to encapsulate these compounds. Encapsulation efficiency of omega-3 and omega-6 were (95.4 ± 0.6) and (92.3 ± 1.9)% respectively. No significant difference was detected between the encapsulation efficiency of omega-3 and omega-6 (p < 0.05), therefore the omega-3:omega-6 ratio found for in natura oil (3.11 ± 0.05) was maintained after encapsulation (3.14 ± 0.14) at a significance level of 95%.Encapsulation of liquid lipids in solid lipid matrices is expected to be greater than the obtained by other methods due the inherent compatibility between encapsulant and the encapsulated compound. Lacatusu et al. (2013) obtained encapsulated fish oil in nanostructure lipid carriers finding an efficiency of 88.5%. However, several authors do not present encapsulation efficiency in their works, probably assuming maximum values (Salminen et al. 2013; Muchow et al. 2009), which could lead to erroneous conclusions. Encapsulation of omega-3 and 6 rich oils by spray drying are 70-80% (Rodea-González et al. 2012). nanostructure lipid carriers finding an efficiency of 88.5%. 5. REFERENCES BLIGH, E. G.; DYER, W. J. A Rapid Method of Total Lipid Extraction and Purification. Canadian Journal of Biochemistry and Physiology 37 (8): 911–17, 1959. CAPITANI, M. I.; SPOTORNO, V.; NOLASCO, S. M.; TOMÁS, M. C. Physicochemical and functional 124 characterization of by-products from chia (Salvia hispanica L.) seeds of Argentina. LWT - Food Sci. Technol. v. 45, n. 1, p. 94–102, 2012. GONÇALVES, R. P; MARÇO, P. H.; VALDERRAMA, P. Thermal Edible Oil Evaluation by UV-Vis Spectroscopy and Chemometrics. Food Chemistry 163 (November): 83–86, 2014. GONZALEZ-MIRA, E.; EGEA, M. A.; GARCIA, M. L.; SOUTO, E. B “Design and Ocular Tolerance of Flurbiprofen Loaded Ultrasound-Engineered NLC.” Colloids and Surfaces. B, Biointerfaces 81 (2). Elsevier B.V.: 412–21, 2010. HARTMAN, L.; LAGO, R. C. A. Rapid preparation of fatty acid methyl from lipids. Lab. Pract. V. 22, p. 474-131 476, 1973. IXTAINA, V. Y.; MARTÍNEZ, M.. L.; SPOTORNO, V.; MATEO, C. M.; MAESTRI, DAMIÁN, M.; DIEHL, B. W. K.; NOLASCO, S. M.; TOMÁS, M. C. Characterization of chia seed oils obtained by pressing and solvent 134 extraction. J. Food Compos. Anal. v. 24, n. 2, p. 166-174, Mar. 2011. LACATUSU, I.; MITREA, E.; BADEA, N.; STAN, R.; OPREA, O.; MEGHEA, A. Lipid Nanoparticles Based on Omega-3 Fatty Acids as Effective Carriers for Lutein Delivery. Preparation and in Vitro Characterization Studies. Journal of Functional Foods 5 (3). Elsevier Ltd: 1260–69, 2013. MILINSK, M. C.; MATSUSHITA, M.; VISENTAINER, J. V.; OLIVEIRA, C. C.; SOUZA, N. E. de . Comparative Analysis of Eight Esterification Methods in the Quantitative Determination of Vegetable Oil Fatty Acid Methyl Esters (FAME). Journal of the Brazilian Chemical Society 19 (8): 1475–83, 2008. MUCHOW, M.; SCHMITZ, E. I.; DESPATOVA, N.; MAINCENT, P.; MÜLLER, R. H. Omega-3 Fatty Acids-Loaded Lipid Nanoparticles for Patient-Convenient Oral Bioavailability Enhancement. Pharmazie 64: 499–504, 2009. RODEA-GONZÁLEZ, D. A.; CRUZ-OLIVARES, J.; ROMÁN-GUERRERO, A.; RODRÍGUEZ-HUEZO, M. E.; VERNON-CARTER, E. J.; PÉREZ-ALONSO, C. Spray- Dried Encapsulation of Chia Essential Oil (Salvia Hispanica L.) in Whey Protein Concentrate-Polysaccharide Matrices.” Journal of Food Engineering 111 (1): 102–9, 2012. SALMINEN, H.; HELGASON, T.; KRISTINSON, B.; KRISTBERGSSON, K.; WEISS, J. Formation of Solid Shell Nanoparticles with Liquid Ω-3 Fatty Acid Core. Food Chemistry 141 (3). Elsevier Ltd: 2934–43, 2013. VALDERRAMA, P.; MARÇO, P.H.; LOCQUET, N.; AMMARI, F.; RUTLEDGE, D. N. 4. CONCLUSIONS Chia oil was extracted using the Bligh & Dyer method (no heating required) with the following properties: 19.8 wt% yield, total omega-3 concentration of 565.52 ± 24.4 g/100 gFA and omega 3:omega 6 ratio of (3.11 ± 0.05). Multivariate Curve Resolution demonstrated that the chia oil did not presented degradation of tocopherol at the temperature and time used in the microcapsules production (75°C for 7 minutes). The oil was encapsulatd in stearic acid forming spheric microparticles (5-10 micrometers). Gas Chromatography demonstrated that the oil was effectively encapsulated in the microparticles and this result was also corroborated by the particles morphology and FTIR analysis. Encapsulation efficiency was high for both ômega-3 and ômega-6 keeping the ômega 3:ômega 6 relation presented by the in natura oil. 5. REFERENCES A Procedure to Facilitate the Choice of the Number of Factors in Multi-Way Data Analysis Applied to the Natural Samples: Application to Monitoring the Thermal Degradation of Oils Using Front-Face Fluorescence Spectroscopy. Chemometrics and Intelligent Laboratory Systems 106 (2). Elsevier B.V.: 166–72, 2011.
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Research impact – what is it, after all? Editorial impact series part 1
RAUSP Management Journal
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Introduction 283 Nothing in science has any value to society if it is not communicated, and scientists are beginning to learn their social obligations. Anne Roe (American psychologist 1904 – 1991), The Making of a Scientist (1953), p. 17. The impact of research on society or societal impact, has been widely discussed at an international level, not only because of its undeniable importance to justify the resources invested in research but also because of its inclusion in the assessments of research institutions to obtain financing. For a long time, the research impact assessment had taken into account only the scientific impact, that is, in essence, the relevance of the published research to other subsequent research. The relevance of the research, in this case, is measured mainly through citations obtained in other academic publications, especially scientific journals, which gave rise to the impact indicators of journals that we currently use (e.g. JCR, SJR, Index H, etc.). ( g J , J , , ) Despite not being new, this discussion on the impact of science on society has gained more momentum in the past two decades due to some reasons: ( g J , J , , ) Despite not being new, this discussion on the impact of science on society has gained more momentum in the past two decades due to some reasons:  a demand for transparency of investments in research financed with public resources, mainly in terms of the generated outcomes;  a more significant concern with the use of scientific evidence to support decision- making (in both public and business sectors; and  the need to demonstrate how research is contributing to the society’s grand challenges – in other words, its relevance and impact on society – and not just for science itself (Brook, 2018; Alla, Hall, Whiteford, Head, & Meurk, 2017). Regarding specifically in the management field, the debate about “research rigour vs relevance” to organisational practice also has a long history (Vermeulen, 2005). With the development of management as a science, it is conveyed that there has been a separation and a distance between administrative science and professional practice in the area, creating a gap between what is produced in academia and what is done in organisations. © Luisa Veras de Sandes-Guimarães and Flavio Hourneaux Junior. Published in RAUSP Management Journal. Published by Emerald Publishing Limited. This article is published under the Creative Commons Attribution (CC BY 4.0) license. Anyone may reproduce, distribute, translate and create derivative works of this article (for both commercial and non-commercial purposes), subject to full attribution to the original publication and authors. The full terms of this license may be seen at http://creativecommons.org/licences/by/4.0/legalcode Editorial Editorial Editorial Editorial Research impact – what is it, after all? Editorial impact series part 1 Table 1. Different definitions for research impact Introduction As a result, it is stated that much of the research carried out at universities has little use or relevance for business and practitioners’ needs (Banks et al., 2016; Hughes, Webber, & O’Regan, 2019). In this sense, we would like to contribute to a more informed and critical discussion on this topic. In this editorial, we aim to present the (several) definitions of impact. In other forthcoming issues of RAUSP Management Journal, we will deepen this theme by addressing the forms of impact assessment, the criticisms on the research impact, improvements and contributions in the academic context. RAUSP Management Journal Vol. 55 No. 3, 2020 pp. 283-287 Emerald Publishing Limited 2531-0488 DOI 10.1108/RAUSP-07-2020-202 RAUSP Management Journal Vol. 55 No. 3, 2020 pp. 283-287 Emerald Publishing Limited 2531-0488 DOI 10.1108/RAUSP-07-2020-202 What is research impact? The literature presents several different definitions for the impact of research on society. This variety reflects the different ways of thinking about the nature of research and its either potential or actual contribution. This type of impact is perceived differently by institutions, funding agencies, countries, within different research contexts and cultures. Consequently, this conceptual diversity generates different approaches to demonstrate and assess this type of impact (Pedersen, Grønvad, & Hvidtfeldt, 2020). Table 1 presents some of these definitions. 284 We can notice that in all these definitions the impact is treated as some kind of contribution, influence, value, change, effect or benefit that scientific research brings to society in its most diverse spheres (economic, social, health, public policies, etc.), directly or indirectly. yp f p Besides these different views and definitions of research impact, a common distinction found in the literature is between instrumental or conceptual impact. The instrumental type refers to the direct impact of research on actions, problem-solving and decision-making by policymakers and practitioners. It is the influence of some specific research in making a decision or in defining the solution to a particular problem. The conceptual impact occurs when research influences the knowledge, understanding and attitudes of policymakers and practitioners, changing the ways of thinking on a specific question or choice or playing an awareness role (Nutley, Walter, & Davies, 2007). ( y, , , ) Additionally, there have been several studies addressing different perspectives on who or what can be the object of the eventual impact of research. Some of these perspectives are: Table 1. Introduction Different definitions for research impact Definition Author(s) Demonstrable contribution that excellent research makes to society and the economy, of benefit to individuals, organisations and nations Edwards and Meagher (2020) Effects and outcomes of being involved in conducting research, and the value and benefit associated with using knowledge produced by researchers Peter, Kothari, and Masood (2017) Direct or indirect contribution of research processes or outputs that have informed (or resulted in) the development of new policy/practices or revisions of existing policy/ practices, at various levels of governance Alla et al. (2017) Changes in awareness, knowledge and understanding, ideas, attitudes and perceptions and policy and practice as a result of research Morton (2015) Contribution of research to knowledge production, capacity- building, informing policy or product development, health and health sector benefits and broader social and economic benefits Donovan (2011) Effect on, change or benefit to the economy, society, culture, public policy or services, health, the environment or quality of life, beyond academia Research Excellence Framework (REF) (2020) Effect or benefit perceived by society, derived from products developed in the scope of postgraduate activities Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (2019)  Economic impact: most studies on the impact of science on society focus on economic impacts, for which several measurement econometric models have been created since the 1950s (Bornmann, 2013; Godin & Doré, 2005). The economic impact is associated with the benefit that the research brings to the economic capital of a nation, region or even an organisation (Bornmann, 2013). It is usually associated to efficiency or productivity gains, generation of competitive advantage or jobs created, seeking to associate the investments in research with the generated returns (return on investment - ROI) (Gunn & Mintrom, 2017; Russell Group Universities, 2012; Bessette, 2003). Activities associated with this type of impact include the generation of intellectual property (patents deposited and granted) and its commercialisation (e.g. funds received through licensing), new business generated at universities (spin-offs), etc (Perkman et al., 2015; Kalika, Shenton, & Dubois, 2016; Bornmann, 2013; Yeo, 2018). Definition  Economic impact: most studies on the impact of science on society focus on economic impacts, for which several measurement econometric models have been created since the 1950s (Bornmann, 2013; Godin & Doré, 2005). The economic impact is associated with the benefit that the research brings to the economic capital of a nation, region or even an organisation (Bornmann, 2013). It is usually associated to efficiency or productivity gains, generation of competitive advantage or jobs created, seeking to associate the investments in research with the generated returns (return on investment - ROI) (Gunn & Mintrom, 2017; Russell Group Universities, 2012; Bessette, 2003). Activities associated with this type of impact include the generation of intellectual property (patents deposited and granted) and its commercialisation (e.g. funds received through licensing), new business generated at universities (spin-offs), etc (Perkman et al., 2015; Kalika, Shenton, & Dubois, 2016; Bornmann, 2013; Yeo, 2018). Editorial 285  Social impact: refers to the contribution of research and the generated knowledge to changes in behaviours, customs, habits and practices (among other aspects) that generates well-being and quality of life for individuals and groups (Godin & Doré, 2005). Some researchers, due to the confusion between societal impact and social impact, seek to associate social impact with the set of other impacts listed below (Bornmann, 2013). In this sense, societal impact would then be the umbrella term for impact of research on society, and social impact a more specific term representing the impact of research on the various social aspects of life.  Impact on public policies: it is related to how scientific knowledge informs and influences the process that involves public policies and responsible managers. It includes changes in interests, attitudes and knowledge concerning an issue of public interest that involves science and technology, contribution to public debate and policy negotiation, as well as the influence of research in decision-making and in public actions that generate changes in a specific policy, legislation or project in the policy community (Godin & Doré, 2005; Escribano-Ferrer, Webster, & Gyapong, 2017).  Organisational impact: it is the impact of research on the activities of organisations, contributing to their management, including planning, work organisation technologies, general management activities (marketing, accounting, purchasing, etc.) and human resources (Godin & Doré, 2005). This type of impact includes, for example, contributions to improving the organisational performance due to changes in practices and processes, the understanding the importance of diversity (gender, ethnicity, etc.) leading to changes in the organisation’s internal policies, etc.  Cultural impact: these are benefits to cultural capital in all its forms. When research contributes by enriching and stimulating the creativity, imagination and cultural production of individuals and groups, in addition to collaborating in the understanding and preservation of the national cultural heritage (Brook, 2018; Bornmann, 2013; Russell Group Universities, 2012). Examples include collaboration with museum professionals resulting in improvements for the preservation of cultural heritage; new ways of thinking that influence creative practice; involvement with marginalised audiences leading to an increase in cultural participation (Research Excellence Framework [REF], 2019). Editorial  Educational impact: it is related to contributions of research to the functioning of education systems at its various levels, including curricula, pedagogical tools, instruments, processes and technologies that contribute both to the improvement of  Educational impact: it is related to contributions of research to the functioning of education systems at its various levels, including curricula, pedagogical tools, instruments, processes and technologies that contribute both to the improvement of RAUSP 55,3 teaching and the learning of new knowledge (Godin & Doré, 2005; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior [CAPES], 2019). Examples include influence on the design and ways of delivering subjects to educational institutions; changes in the curriculum proposed by research; contribution to the development of innovative pedagogical proposals (Research Excellence Framework [REF], 2019). In addition to these types of impacts above, we can also find some additional categories in the literature, such as environmental, health, technological, legal and capacity-building impacts. As the reader can notice, many or maybe all of the impact types listed here can be achieved or addressed somehow in management research. We will go back to this subject in some of the next editorials. 286 Luisa Veras de Sandes-Guimarães and Flavio Hourneaux Junior Faculdade de Economia, Administração e Contabilidade, Universidade de São Paulo, São Paulo, Brazil References Alla, K., Hall, W. D., Whiteford, H. A., Head, B. W., & Meurk, C. S. (2017). How do we define the policy impact of public health research? a systematic review. Health Research Policy and Systems, 15(1), 8410.1186/s12961-017-0247-z. https://doi.org/10.1186/s12961-017-0247-z. Banks, G. C., Pollack, J. M., Bochantin, J. E., Kirkman, B. L., Whelpley, C. E., & Boyle, E. H. (2016). Management’s science-practice gap: a grand challenge for all stakeholders. Academy of Management Journal, 59(6), 2205–2231. https://doi.org/10.5465/ amj.2015.0728. Bessette, R. W. (2003). Measuring the economic impact of university-based research. The Journal of Technology Transfer, 28(3/4), 355–361. https://doi.org/10.1023/A:1024917601088. Bornmann, L. (2013). What is societal impact of research and how can it be assessed? a literature survey. Journal of the American Society for Information Science and Technology, 64(2), 217–233. https://doi.org/10.1002/asi.22803. Brook, L. (2018). Evidencing impact from art research: analysis of impact case studies from the REF 2014. The Journal of Arts Management, Law, and Society, 48(1), 57–69. https://doi.org/10.1080/ 10632921.2017.1386148. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). (2019). GT impacto e relevância econômica e social: Relatorio Final de Atividades, Brasília, DF: CAPES. Donovan, C. (2011). State of the art in assessing research impact: introduction to a special issue. Research Evaluation, 20(3), 175–179. https://doi.org/10.3152/095820211X13118583635918. Edwards, D. M., & Meagher, L. R. (2020). A framework to evaluate the impacts of research on policy and practice: a forestry pilot study. Forest Policy and Economics, 114, 101975, doi: https://doi. org/10.1016/j.forpol.2019.101975. Escribano-Ferrer, B., Webster, J., & Gyapong, M. (2017). Assessing the impact of health research on health policies: a study of the dodowa health research Centre, Ghana. BMC Health Services Research, 17(1), 435. https://doi.org/10.1186/s12913-017-2383-0. Godin, B., & Doré, C. (2005). Measuring the impacts of science: beyond the economic dimension., Paper presented at the HIST Lecture, Helsinki Institute for Science and Technology Studies, Helsinki, available at: www.csiic.ca/PDF/Godin_Dore_Impacts.pdf Gunn, A., & Mintrom, M. (2017). Evaluating the non-academic impact of academic research: design considerations. Journal of Higher Education Policy and Management, 39(1), 20–30. https://doi. org/10.1080/1360080X.2016.1254429. Hughes, T., Webber, D., & O’Regan, N. (2019). Achieving wider impact in business and management: analysing the case studies from REF 2014. Studies in Higher Education, 44(4), 628–642. https:// doi.org/10.1080/03075079.2017.1393059. Editorial Kalika, M., Shenton, G., & Dubois, P. (2016). What happens if a business school disappears? the intellectual foundations of BSIS. Journal of Management Development, 35(7), 878–888. https:// doi.org/10.1108/JMD-10-2014-0120. Morton, S. (2015). Progressing research impact assessment: a ’contributions’ approach. Research Evaluation, 24(4), 405–419. https://doi.org/10.1093/reseval/rvv016. 287 Nutley, S. References M., Walter, I., & Davies, H. T. O. (2007). Using Evidence: How Research Can Inform Public Services, Bristol, UK: Policy Press. Pedersen, D. B., Grønvad, J. F., & Hvidtfeldt, R. (2020). Methods for mapping the impact of social sciences and humanities — a literature review. Research Evaluation, 29(1), 4–21. https://doi.org/ 10.1093/reseval/rvz033. Perkman, M., Fini, R., Ross, J.-M., Salter, A., Silvestri, C., & Tartari, V. (2015). Accounting for universities’ impact: using augmented data to measure academic engagement and commercialisation by academic scientists. Research Evaluation, 24(4), 380–391. https://doi.org/ 10.1093/reseval/rvv020. Peter, N., Kothari, A., & Masood, S. (2017). Identifying and understanding research impact: a review for occupational scientists. Journal of Occupational Science, 24(3). https://doi.org/10.1080/ 14427591.2016.1277547. Research Excellence Framework (REF). (2019). REF 2021: Panel criteria and working methods. Retrieved from www.ref.ac.uk/publications/panel-criteria-and-working-methods-201902/ Research Excellence Framework (REF). (2020). REF impact. Retrieved from https://re.ukri.org/ research/ref-impact/ Russell Group Universities. (2012). The Social Impact of Research Conducted in Russell Group Universities, London: Russell Group Universities. Vermeulen, F. (2005). On rigor and relevance: fostering dialectic progress in management research. Academy of Management Journal, 48(6). https://doi.org/10.5465/amj.2005.19573102. Yeo, B. (2018). Societal impact of university innovation. Management Research Review, 41(11), 1309– 1335. https://doi.org/10.1108/MRR-12-2017-0430.
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Genetic deficiency of NOD2 confers resistance to invasive aspergillosis
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1 Cytokines & Inflammation, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris, France. 2 Department of Experimental Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. 3 Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany. 4 Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. 5 ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Campus de Gualtar, 4710-057 Braga, Portugal. 6 Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. 7 Département Infection et Epidémiologie, Unité Histopathologie Humaine et Modèles Animaux, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris, France. 8 Department of Gastroenterology and Hepatology, Radboud University Medical Center, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. 9 Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal. 10 Serviço de Hematologia e Transplantação de Medula, Hospital de Santa Maria, 1649-035 Lisboa, Portugal. 11 Serviço de Transplantação de Medula Óssea (STMO), Instituto Português de Oncologia do Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal. 12 Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. 13 Department of Microbiology and Immunology, KU Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. 14 Department of Laboratory Medicine and National Reference Center for Medical Mycology, University Hospitals Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. 15 Department of Hematology, University Hospitals Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. These authors jointly supervised this work: Oumaima Ibrahim-Granet, Frank L. van de Veerdonk. Correspondence and requests for materials should be addressed to Frank L. van de Veerdonk. (email: Frank.vandeveerdonk@Radboudumc.nl) Genetic deficiency of NOD2 confers resistance to invasive aspergillosis Mark S. Gresnigt 1,2,3, Cristina Cunha4,5, Martin Jaeger2, Samuel M. Gonçalves4,5, R.K.Subbarao Malireddi 6, Anne Ammerdorffer 2, Rosalie Lubbers2, Marije Oosting2, Orhan Rasid 1, Grégory Jouvion7, Catherine Fitting1, Dirk J. de Jong8, João F. Lacerda9,10, António Campos Jr.11, Willem J.G. Melchers 12, Katrien Lagrou 13,14, Johan Maertens13,15, Thirumala-Devi Kanneganti6, Agostinho Carvalho 4,5, Oumaima Ibrahim-Granet1 & Frank L. van de Veerdonk2 Invasive aspergillosis (IA) is a severe infection that can occur in severely immunocompro- mised patients. Efficient immune recognition of Aspergillus is crucial to protect against infection, and previous studies suggested a role for NOD2 in this process. However, thorough investigation of the impact of NOD2 on susceptibility to aspergillosis is lacking. Common genetic variations in NOD2 has been associated with Crohn’s disease and here we investi- gated the influence of these genetic variations on the anti-Aspergillus host response. A NOD2 polymorphism reduced the risk of IA after hematopoietic stem-cell transplantation. Mechanistically, absence of NOD2 in monocytes and macrophages increases phagocytosis leading to enhanced fungal killing, conversely, NOD2 activation reduces the antifungal potential of these cells. Crucially, Nod2 deficiency results in resistance to Aspergillus infection in an in vivo model of pulmonary aspergillosis. Collectively, our data demonstrate that genetic deficiency of NOD2 plays a protective role during Aspergillus infection. Invasive aspergillosis (IA) is a severe infection that can occur in severely immunocompro- mised patients. Efficient immune recognition of Aspergillus is crucial to protect against infection, and previous studies suggested a role for NOD2 in this process. However, thorough investigation of the impact of NOD2 on susceptibility to aspergillosis is lacking. Common genetic variations in NOD2 has been associated with Crohn’s disease and here we investi- gated the influence of these genetic variations on the anti-Aspergillus host response. A NOD2 polymorphism reduced the risk of IA after hematopoietic stem-cell transplantation. Mechanistically, absence of NOD2 in monocytes and macrophages increases phagocytosis leading to enhanced fungal killing, conversely, NOD2 activation reduces the antifungal potential of these cells. Crucially, Nod2 deficiency results in resistance to Aspergillus infection in an in vivo model of pulmonary aspergillosis. Collectively, our data demonstrate that genetic deficiency of NOD2 plays a protective role during Aspergillus infection. 1 Cytokines & Inflammation, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris, France. 2 Department of Experimental Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications ARTICLE ARTICLE Results strategies. Nevertheless, several immune path plored for susceptibility to aspergillosis. One of these relatively unexplored recept NACHT-LRR receptors (NLRs), to which nucleotide-binding oligomerization domain belong. The NLR receptor Nlrp3 plays a role of inflammasome activation and subsequent mediated cytokine responses7. Two other NL and NOD2 are primarily involved in t peptidoglycan-derived moieties from bacteria tion of proinflammatory host responses8–12. A does not contain peptidoglycan, some that these NOD receptors might play a ro against aspergillosis13–16. In contrast to a p demonstrated a crucial role for NOD1 in ac epithelial cells by Aspergillus16, we recently re negatively modulates host defence by reducing and oxidative burst17. NOD2, another membe is highly expressed in lungs of mice infected w in THP1 cells, RAW macrophages and A549 c Aspergillus13,14. The NOD2 agonist Muramy can synergistically increase Aspergillus- levels13,14. NOD2 also may play a role in h fungal keratitis15,16. Recently, NOD2 was also role in the recognition of chitin18, a polysacch in the cell wall of all fungi. Polymorphisms i associated with host defence against infectiou ticular, strong associations between NOD2 p susceptibility to tuberculosis have been identi however, be noted that the strongest genet NOD2 is with Crohn’s disease23. Polymorphism autophagy and antigen presentation in ho bacteria24. Considering recent evidence sugge Table 1 Description of the SNPs in the NOD RefSNP Genome coordinates rs2066842 chr16:50710713 rs2066844 chr16:50712015 rs2066845 chr16:50722629 rs2066847 chr16:50729867 Publically available sequencing data from Pilot 1 of the 1000 Genom SNP single-nucleotide polymorphism, aa amino acid, P prolins, S serin allele frequency, HWE Hardy Weinberg Equilibrium NOD2 genetic variation decreases the risk of IA after HSCT. To investigate the relationship between genetic variability in NOD2 and susceptibility to IA, four nonsynonymous SNPs in the NOD2 coding sequence were analysed (Table 1). The probability of IA was assessed according to recipient or donor genotypes by esti- mating the cumulative incidence of infection among transplant recipients at 24 months after HSCT. Among the SNPs tested, the donor, but not recipient, P268S (rs2066842) SNP in NOD2 was associated with an increased risk of IA (Fig. 1a). Other poly- morphisms did not allow accurate risk estimations due to low (<0.05) allele frequencies in our study population. The cumulative incidence of IA for donor P268S was 32.7% for the CC genotype, 21.6% for CT and 20.0% for TT genotypes, respectively (Fig. 1a). Genetic deficiency of NOD2 confers resistance to invasive aspergillosis 3 Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany. 4 Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. 5 ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Campus de Gualtar, 4710-057 Braga, Portugal. 6 Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. 7 Département Infection et Epidémiologie, Unité Histopathologie Humaine et Modèles Animaux, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris, France. 8 Department of Gastroenterology and Hepatology, Radboud University Medical Center, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. 9 Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal. 10 Serviço de Hematologia e Transplantação de Medula, Hospital de Santa Maria, 1649-035 Lisboa, Portugal. 11 Serviço de Transplantação de Medula Óssea (STMO), Instituto Português de Oncologia do Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal. 12 Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands, Geert Grooteplein zuid 8, 6525GA Nijmegen, The Netherlands. 13 Department of Microbiology and Immunology, KU Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. 14 Department of Laboratory Medicine and National Reference Center for Medical Mycology, University Hospitals Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. 15 Department of Hematology, University Hospitals Leuven, Herestraat 49 Box 1030, 3000 Leuven, Belgium. These authors jointly supervised this work: Oumaima Ibrahim-Granet, Frank L. van de Veerdonk. Correspondence and requests for materials should be addressed to Frank L. van de Veerdonk. (email: Frank.vandeveerdonk@Radboudumc.nl) 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 H H umans are ubiquitously exposed to airborne spores of Aspergillus, but only severe immunocompromised patients are at risk of developing pulmonary invasive aspergillosis (IA)1. Patients undergoing hematopoietic stem cell transplantation (HSCT) have a distinctive elevated susceptibility to aspergillosis and infections in these patients are associated with a high mortality2. With increasing knowledge of the antifungal host response, it has become evident that not only the immu- nocompromised status of patients plays a role in susceptibility to infection, but also the genetic background of both the engrafted bone marrow and the recipient3. To provide a good risk strati- fication for the development of IA following HSCT, genetic susceptibility needs to be taken into account. Results The key contribution of the CC genotype to the risk of infection was further illustrated upon modelling a dominant mode of inheritance (cumulative incidence of IA, 32.7% for CC vs. 21.3% for CT and TT genotypes combined) (Fig. 1b). In a multivariate model accounting for age, gender, post-transplant neutropenia and acute graft-versus-host disease (GVHD)26, the donor CC genotype at P268S conferred a 2.1-fold increased risk of devel- oping IA after transplantation (95% CI, 1.15–4.47; p = 0.021; p-values calculated using Gray’s test). Collectively, these results highlight genetic variation at the NOD2 locus as a critical risk factor regulating susceptibility to IA after HSCT. p p y p g One of these relatively unexplored receptor families are the NACHT-LRR receptors (NLRs), to which the intracellular nucleotide-binding oligomerization domain (NOD) receptors belong. The NLR receptor Nlrp3 plays a role in IA via regulation of inflammasome activation and subsequently protective IL-1- mediated cytokine responses7. Two other NLR receptors NOD1 and NOD2 are primarily involved in the recognition of peptidoglycan-derived moieties from bacteria and in the induc- tion of proinflammatory host responses8–12. Although Aspergillus does not contain peptidoglycan, some evidence suggests that these NOD receptors might play a role in host defence against aspergillosis13–16. In contrast to a previous study that demonstrated a crucial role for NOD1 in activation of corneal epithelial cells by Aspergillus16, we recently reported that NOD1 negatively modulates host defence by reducing cytokine responses and oxidative burst17. NOD2, another member of the NLR family is highly expressed in lungs of mice infected with Aspergillus, and in THP1 cells, RAW macrophages and A549 cells stimulated with Aspergillus13,14. The NOD2 agonist Muramyl-dipeptide (MDP) can synergistically increase Aspergillus-induced cytokine levels13,14. NOD2 also may play a role in host defence against fungal keratitis15,16. Recently, NOD2 was also suggested to play a role in the recognition of chitin18, a polysaccharide that is present in the cell wall of all fungi. Polymorphisms in NOD2 have been associated with host defence against infectious diseases. In par- ticular, strong associations between NOD2 polymorphisms and susceptibility to tuberculosis have been identified19–22. It should, however, be noted that the strongest genetic association with NOD2 is with Crohn’s disease23. Polymorphisms in NOD2 impact autophagy and antigen presentation in host defence against bacteria24. Considering recent evidence suggesting a crucial role The NOD2 P268S SNP alters pulmonary cytokine levels in IA. Genetic deficiency of NOD2 confers resistance to invasive aspergillosis Common poly- morphisms in various pattern recognition receptor (PRR) path- ways are known to be associated with an increased risk for aspergillosis, which includes dectin-13,4, pentraxin-35 as well as many other receptors6. These findings help to predict suscept- ibility, yet also provide insight into the importance of these pathways in antifungal host defence. These studies, therefore, may also aid in the development of novel immune targeted treatment strategies. Nevertheless, several immune pathways remain unex- plored for susceptibility to aspergillosis. for the autophagy machinery in host defence against Aspergil- lus25, NOD2 is a candidate susceptibility gene for aspergillosis. l h h d h l d h d Although previous studies have revealed enhanced expression of NOD2 during aspergillosis and synergism with Aspergillus- induced cytokine responses, these studies did not thoroughly investigate whether NOD2 modulates anti-Aspergillus host defence. Additionally, it is unknown whether defective NOD2 signalling influences susceptibility to aspergillosis. Therefore, the present study investigates whether common polymorphisms in NOD2 or its complete deficiency influences susceptibility to IA, and whether it affects the immune response to Aspergillus. We demonstrate that genetic variation in NOD2 in humans and complete Nod2 deficiency in mice protects against IA. In line with this, NOD2 deficiency or its neutralization associates with increased antifungal activity of macrophages and monocytes, conversely NOD2 activation neutralizes fungal killing capacity of phagocytes. Our data collectively highlight a detrimental role for NOD2 receptor in anti-Aspergillus host defence. Table 1 Description of the SNPs in the NOD2 gene evaluated in our study RefSNP Genome coordinates aa change Alleles CEU MAF MAF in our study HWE rs2066842 chr16:50710713 P268S C > T 0.102 0.278 0.72 rs2066844 chr16:50712015 R702W C > T 0.014 0.027 0.77 rs2066845 chr16:50722629 G908R G > C 0.005 0.002 1.00 rs2066847 chr16:50729867 1007fs −> C 0.006 0.022 0.98 Publically available sequencing data from Pilot 1 of the 1000 Genomes Project (www.1000genomes.org) was used to determine MAF. Genome coordinates were extracted from the hg18 build SNP single-nucleotide polymorphism, aa amino acid, P prolins, S serine, R arginine, W tryptophan, G Glycine, fs frameshift, CEU Utah Residents (CEPH) with Northern and Western Ancestry, MAF minor allele frequency, HWE Hardy Weinberg Equilibrium NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Data are represented scatter dot plot with the median; with p-values were calculated using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs b Donor CC (N = 160, ref) CT+TT (N = 150, P = 0.03) Probability of IA 0.5 0.4 0.3 0.2 0.1 0.0 0 5 10 Months after transplantation 15 20 Donor TT (N = 25, P = 0.27) CC (N = 160, ref) CT (N = 125, P = 0.04) Probability of IA 0.5 0.4 0.3 0.2 0.1 0.0 0 5 10 Months after transplantation 15 20 0.5 a Recipient TT (N = 23, P = 0.70) CC (N = 154, ref) CT (N = 133, P = 0.93) 0.4 0.3 0.2 Probability of IA 0.1 0.0 0 5 10 Months after transplantation 15 20 b a IL-8 20,000 15,000 10,000 pg/mL 5000 0 CC CC+CT vs. TT p = 0.05 CT TT c 5000 IL-1β 4000 3000 2000 pg/mL pg/mL 1000 0 CC CC+CT vs. TT p = 0.78 CT TT IL-17A 25 20 15 10 5 0 pg/mL / L CC CC+CT vs. TT p = 0.24 CT TT 300 TNF pg/mL 200 100 20 10 0 CC CC+CT vs. TT p = 0.14 CT TT IL-10 25 20 15 10 5 0 pg/mL CC CC+CT vs. TT **p < 0.001 CT TT IL-6 5000 4000 3000 2000 pg/mL 1000 0 / L CC CC+CT vs. TT p = 0.07 CT TT c pg/mL CC+CT vs. TT **p < 0.001 Fig. 1 Genetic variation in donor P268S (rs2066842) confers resistance to IA after HSCT. Shown are the results obtained in a cohort comprising 310 Fig. 1 Genetic variation in donor P268S (rs2066842) confers resistance to IA after HSCT. Shown are the results obtained in a cohort comprising 310 eligible patients and respective donors. Cumulative incidence of IA according to (a) donor or recipient genotypes at rs2066842 or b a dominant genetic S (rs2066842) confers resistance to IA after HSCT. Shown are the results obtained in a cohort comprising 310 268S (rs2066842) confers resistance to IA after HSCT. Shown are the results obtained in a cohort comprising 310 eligible patients and respective donors. Cumulative incidence of IA according to (a) donor or recipient genotypes at rs2066842 or b a dominant genetic model of donor genotypes at rs2066842. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE 0.5 a c b Recipient Donor Donor TT (N = 23, P = 0.70) TT (N = 25, P = 0.27) CC (N = 154, ref) CC (N = 160, ref) CT (N = 133, P = 0.93) CT (N = 125, P = 0.04) CC (N = 160, ref) CT+TT (N = 150, P = 0.03) 0.4 0.3 0.2 Probability of IA Probability of IA 0.1 0.0 5000 300 TNF IL-6 IL-8 IL-17A IL-10 IL-1β 4000 3000 2000 pg/mL pg/mL 1000 0 5000 4000 3000 2000 pg/mL 1000 0 20,000 25 20 15 10 5 0 15,000 10,000 pg/mL pg/mL 25 20 15 10 5 0 pg/mL 5000 0 200 100 20 10 0 CC CC+CT vs. TT p = 0.78 CT TT CC CC+CT vs. TT p = 0.14 CT TT CC CC+CT vs. TT p = 0.07 CT TT CC CC+CT vs. TT p = 0.05 CT TT CC CC+CT vs. TT p = 0.24 CT TT CC CC+CT vs. TT **p < 0.001 CT TT 0.5 0.4 0.3 0.2 0.1 0.0 Probability of IA 0.5 0.4 0.3 0.2 0.1 0.0 0 5 10 Months after transplantation 15 20 0 5 10 Months after transplantation 15 20 0 5 10 Months after transplantation 15 20 Fig. 1 Genetic variation in donor P268S (rs2066842) confers resistance to IA after HSCT. Shown are the results obtained in a cohort comprising 310 eligible patients and respective donors. Cumulative incidence of IA according to (a) donor or recipient genotypes at rs2066842 or b a dominant genetic model of donor genotypes at rs2066842. In a, the blue line represents the carriers of the reference (ref) CC genotype, the red line carriers of the heterozygous CT genotype, and the yellow line represents carriers of the homozygous TT genotype. In the dominant model (b) red line represents the carriers of both the CT and TT genotypes. Data were censored at 24 months, and relapse and death were considered competing events. p-values were calculated using Gray’s test. c IL-1β, TNF, IL-6, IL-8, IL-17A, and IL-10 levels measured in the BAL of patients with aspergillosis and stratified based on the NOD2 rs2066842 donor genotypes. Each dot represent an individual patient, with black filled dots representing HSCT donor carriers of the reference CC genotype, half filled black/gray dots representing carriers of the heterozygous CT genotype, and gray dots representing carriers of the homozygous TT genotype. Results To assess whether the genotypes at P268S in NOD2 differentially regulate pulmonary inflammation in aspergillosis, cytokine levels in bronchoalveolar lavage (BAL) samples from patients with IA were assessed. Genotype-specific differences were observed, with patients transplanted with bonemarrow carrying the TT genotype displaying lower median concentrations of IL-10 and IL-8 than Table 1 Description of the SNPs in the NOD2 gene evaluated in our study RefSNP Genome coordinates aa change Alleles CEU MAF MAF in our study HWE rs2066842 chr16:50710713 P268S C > T 0.102 0.278 0.72 rs2066844 chr16:50712015 R702W C > T 0.014 0.027 0.77 rs2066845 chr16:50722629 G908R G > C 0.005 0.002 1.00 rs2066847 chr16:50729867 1007fs −> C 0.006 0.022 0.98 Publically available sequencing data from Pilot 1 of the 1000 Genomes Project (www.1000genomes.org) was used to determine MAF. Genome coordinates were extracted from the hg18 build SNP single-nucleotide polymorphism, aa amino acid, P prolins, S serine, R arginine, W tryptophan, G Glycine, fs frameshift, CEU Utah Residents (CEPH) with Northern and Western Ancestry, MAF minor allele frequency, HWE Hardy Weinberg Equilibrium Table 1 Description of the SNPs in the NOD2 gene evaluated in our study NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 2 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 In a, the blue line represents the carriers of the reference (ref) CC genotype, the red line carriers of the heterozygous CT genotype, and the yellow line represents carriers of the homozygous TT genotype. In the dominant model (b) red line represents the carriers of both the CT and TT genotypes. Data were censored at 24 months, and relapse and death were considered competing events. p-values were calculated using Gray’s test. c IL-1β, TNF, IL-6, IL-8, IL-17A, and IL-10 levels measured in the BAL of patients with aspergillosis and stratified based on the NOD2 rs2066842 donor genotypes. Each dot represent an individual patient, with black filled dots representing HSCT donor carriers of the reference CC genotype, half filled black/gray dots representing carriers of the heterozygous CT genotype, and gray dots representing carriers of the homozygous TT genotype. Data are represented scatter dot plot with the median; with p-values were calculated using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs Aspergillus (Supplementary Fig. 1), and homozygous carriers of these polymorphisms were not represented within our cohort. Aspergillus (Supplementary Fig. 1), and homozygous carriers of these polymorphisms were not represented within our cohort. Insertion of a cysteine at position 1007 (1007finsC) (rs2066847) induces a frameshift, which results in a defective NOD2 receptor, and homozygous carriage of this mutation results in complete NOD2 deficiency and is highly associated with Crohn’s disease27. Healthy individuals heterozygous for this mutation demonstrated significantly lower IL-1β and a trend toward lower TNF, but not IL-6 responses to Aspergillus (Fig. 2c). The decreased IL-1β correlated with significantly lower IL-17A responses in individuals carrying the Cysteine-insertion on one allele (Fig. 2d). Interestingly, Aspergillus-induced IFNγ or IL-22 production was not affected by this genotype (Fig. 2d). CC + CT carriers (0.41 vs. 2.6 pg/mL; and 1125 vs. 2560 pg/mL). In addition, a trend toward decreased IL-6 and TNF levels was also observed among patients transplanted with bonemarrow from TT carriers (Fig. 1c). Collectively, these findings point to a NOD2 genotype-determined alteration in cytokine production in response to Aspergillus infection. Insertion of a cysteine at position 1007 (1007finsC) (rs2066847) induces a frameshift, which results in a defective NOD2 receptor, and homozygous carriage of this mutation results in complete NOD2 deficiency and is highly associated with Crohn’s disease27. NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 fumigatus (2 × 106) following exposure for 24 h to (5 × 105) PBMCs results are stratified based on the e P268S (rs2066842; ref: CC n = 49, heterozygous: n = 45 and homozygous: TT n = 7) and (f) 1007finsC (rs2066847; ref n = 98 insC n = 7) genotypes. g, h Area under the curve (AUC) of relative light units (RLU) induced by luminol oxidation by reactive oxygen species (ROS) released by PBMCs, results are stratified based on the (g) P268S (rs2066842; reference: CC n = 47, heterozygous: n = 50 and homozygous: TT n = 9) and (h) 1007finsC (rs2066847; ref n = 112 insC n = 5) genotypes. Data are represented scatter dot plot with the median. Each dot represent an individual patient, with (a, b, e, g) black filled dots representing carriers of the ancestral (reference) CC genotype, half-filled black/gray dots representing carriers of the heterozygous CT genotype, and gray dots representing carriers of the homozygous TT genotype, and (c, d, f, h) black filled dots representing carriers of the reference (ref) genotype without insertion and half-filled black/gray dots representing carriers of one Cysteine insertion (insC). The means were compared using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs Human NOD2 deficiency reduces Aspergillus-induced cyto- kines. To further investigate the importance of NOD2 in Asper- gillus-induced cytokine response, we analysed responses of primary human PBMCs within a background of complete NOD2 deficiency. PBMCs from patients with Crohn’s disease, homo- zygous for the 1007finsC polymorphism and thus deficient for the NOD2 receptor, were stimulated with A. fumigatus. NOD2- deficient PBMCs demonstrated significantly lower IL-1β and TNF responses compared to controls (Fig. 3a). NOD2 deficient PBMCs also showed a significant reduction in production of the T-helper cytokines IL-22 and Interferon(IFN)γ and a trend toward decreased IL-17A induced by conidia (Fig. 3b). These reduced cytokine responses correlated with a reduced capacity to expand populations of IL-17A+, IL-22+, and IFNγ+ CD4 T-cells (Fig. 3c). Similar to individuals with heterozygous 1007insC mutations, the homozygous individuals demonstrated a trend toward improved fungal killing (Fig. 3d). However, no change in the capacity to induce ROS by zymosan or Aspergillus was observed (Fig. 3e). eight out of nine Nod2−/−mice survived the infection, despite having similar weight loss as WT mice during the first 3 days of infection (Fig. 4b). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 e, f Fungal killing capacity of human PBMCs assessed as CFU remaining of A. fumigatus (2 × 106) following exposure for 24 h to (5 × 105) PBMCs results are stratified based on the e P268S (rs2066842; ref: CC n = 49, heterozygous: n = 45 and homozygous: TT n = 7) and (f) 1007finsC (rs2066847; ref n = 98 insC n = 7) genotypes. g, h Area under the curve (AUC) of relative light units (RLU) induced by luminol oxidation by reactive oxygen species (ROS) released by PBMCs, results are stratified based on the (g) P268S (rs2066842; reference: CC n = 47, heterozygous: n = 50 and homozygous: TT n = 9) and (h) 1007finsC (rs2066847; ref n = 112 insC n = 5) genotypes. Data are represented scatter dot plot with the median. Each dot represent an individual patient, with (a, b, e, g) black filled dots representing carriers of the ancestral (reference) CC genotype, half-filled black/gray dots representing carriers of the heterozygous CT genotype, and gray dots representing carriers of the homozygous TT genotype, and (c, d, f, h) black filled dots representing carriers of the reference (ref) genotype without insertion and half-filled black/gray dots representing carriers of one Cysteine insertion (insC). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 fumigatus (2 × 106) following exposure for 24 h to (5 × 105) PBMCs results are stratified based on the e P268S (rs2066842; ref: CC n = 49, heterozygous: n = 45 and homozygous: TT n = 7) and (f) 1007finsC (rs2066847; ref n = 98 insC n = 7) genotypes. g, h Area under the curve (AUC) of relative light units (RLU) induced by luminol oxidation by reactive oxygen species (ROS) released by PBMCs, results are stratified based on the (g) P268S (rs2066842; reference: CC n = 47, heterozygous: n = 50 and homozygous: TT n = 9) and (h) 1007finsC (rs2066847; ref n = 112 insC n = 5) genotypes. Data are represented scatter dot plot with the median. Each dot represent an individual patient, with (a, b, e, g) black filled dots representing carriers of the ancestral (reference) CC genotype, half-filled black/gray dots representing carriers of the heterozygous CT genotype, and gray dots representing carriers of the homozygous TT genotype, and (c, d, f, h) black filled dots representing carriers of the reference (ref) genotype without insertion and half-filled black/gray dots representing carriers of one Cysteine insertion (insC). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 The means were compared using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs IL-1β IL-1β TNF IL-17A IL-22 IL-17A IL-22 rs2066847 Killing rs2066842 rs2066847 rs2066847 ROS IFNγ IFNγ TNF IL-6 IL-6 rs2066842 Killing rs2066842 ROS 15,000 a c d e f g h b 3000 3000 2000 1000 0 10,000 8000 6000 4000 2000 0 2000 1000 0 30,000 ns ns ns ns ns ns * * ** ** * 20,000 10,000 0 p = 0.07 p = 0.09 p = 0.32 p = 0.97 p = 0.32 p = 0.51 p = 0.30 10,000 5000 pg/mL pg/mL pg/mL pg/mL 3000 10,000 8000 6000 4000 2000 0 2000 1000 0 pg/mL 3000 2000 1000 0 pg/mL pg/mL pg/mL 2000 15,000 30,000 2000 100 3 × 107 2 × 107 1 × 107 0 90 80 70 60 1500 1000 500 0 20,000 10,000 0 10,000 5000 0 Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC 1000 1500 500 0 pg/mL pg/mL pg/mL pg/mL % Killing 100 90 80 70 60 % Killing AUC (RLU) 3 × 107 2 × 107 1 × 107 0 AUC (RLU) 0 CC CC vs CT + TT = ** CC vs CT + TT p = 0.06 CT TT CC CC vs CT + TT p = 0.80 CT TT CC CC vs CT + TT p = 0.5 CT TT CC CC vs CT + TT p = 0.39 CT TT CC CT TT CC vs CT + TT p = 0.29 CC CT TT CC vs CT + TT p = 0.37 CC CT TT CC vs CT + TT p = 0.43 CC CT TT Fig. 2 Human NOD2 polymorphisms influence Aspergillus-induced cytokine responses and fungal killing. a–d IL-1β, TNF, IL-6, IL-17A, IL-22, and IFNγ levels measured in culture supernatants of PBMCs stimulated with (a, c) live Aspergillus conidia for 24 h or (b, d) heat-inactivated (HI) Aspergillus conidia for 7 days. The PBMCs of individuals with various genotypes of the NOD2 gene were compared. These genotypes included (a, b) the P268S mutation (rs2066842; reference: CC n = 36, heterozygous: CT n = 28 and homozygous: TT n = 4) and (c, d) the 1007finsC mutation (rs2066847; reference n = 62 and heterozygous: insC n = 4). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 The means were compared using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs IL-6 c ns 2000 1000 1500 500 0 pg/mL pg/mL 06 CC vs CT + TT p = 0.29 CC CT TT rs2066842 Killing rs2066842 ROS e g ns ns 100 3 × 107 2 × 107 1 × 107 0 90 80 70 60 % Killing AUC (RLU) CC vs CT + TT p = 0.37 CC CT TT CC vs CT + TT p = 0.43 CC CT TT IL-1β 15,000 a p = 0.07 p = 0.30 10,000 5000 pg/mL pg/mL 0 CC CC vs CT + TT = ** CT TT TNF 30,000 ns 20,000 10,000 0 pg/mL pg/mL CC vs CT + TT p = 0.06 CC CT TT a rs2066847 Killing rs2066847 ROS f h * p = 0.32 Ref InsC Ref InsC 100 90 80 70 60 % Killing 3 × 107 2 × 107 1 × 107 0 AUC (RLU) IL-17A IL-22 rs2066847 IFNγ d ** p = 0.32 p = 0.97 3000 10,000 8000 6000 4000 2000 0 2000 1000 0 pg/mL 3000 2000 1000 0 pg/mL pg/mL Ref InsC Ref InsC Ref InsC 0.39 IL-22 rs2066842 IFNγ d 3000 2000 1000 0 10,000 8000 6000 4000 2000 0 ns ns pg/mL CC CC vs CT + TT p = 0.5 CT TT CC CC vs CT + TT p = 0.39 CT TT IL-17A b 3000 2000 1000 0 ** * pg/mL pg/mL CC CC vs CT + TT p = 0.80 CT TT b d rs2066847 rs2066842 Fig. 2 Human NOD2 polymorphisms influence Aspergillus-induced cytokine responses and fungal killing. a–d IL-1β, TNF, IL-6, IL-17A, IL-22, and IFNγ levels measured in culture supernatants of PBMCs stimulated with (a, c) live Aspergillus conidia for 24 h or (b, d) heat-inactivated (HI) Aspergillus conidia for 7 days. The PBMCs of individuals with various genotypes of the NOD2 gene were compared. These genotypes included (a, b) the P268S mutation (rs2066842; reference: CC n = 36, heterozygous: CT n = 28 and homozygous: TT n = 4) and (c, d) the 1007finsC mutation (rs2066847; reference n = 62 and heterozygous: insC n = 4). e, f Fungal killing capacity of human PBMCs assessed as CFU remaining of A. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Healthy individuals heterozygous for this mutation demonstrated significantly lower IL-1β and a trend toward lower TNF, but not IL-6 responses to Aspergillus (Fig. 2c). The decreased IL-1β correlated with significantly lower IL-17A responses in individuals carrying the Cysteine-insertion on one allele (Fig. 2d). Interestingly, Aspergillus-induced IFNγ or IL-22 production was not affected by this genotype (Fig. 2d). NOD2 variants alter A. fumigatus-induced cytokine responses. To examine the impact of NOD2 variation on host defence against Aspergillus, the impact of the NOD2 genetic variants on Aspergillus immune recognition and cytokine production was investigated. In vitro Aspergillus-induced cytokine responses of primary human PBMCs were stratified based on P268S (rs2066842), G908R (rs2066845), and R702W (rs2066844) gen- otypes, to investigate their influence on cytokines responses to A. fumigatus. The 1007insC frameshift mutation enhances fungal killing. For the P268S and 1007insC polymorphisms the impact on fungal killing capacity was evaluated. Although, the P268S polymorph- ism did not significantly impact Aspergillus killing (Fig. 2e), PBMCs of healthy individuals carrying the Cysteine-insertion (rs2066847) on one allele had a significantly increased capacity to neutralize Aspergillus-conidia (Fig. 2f). Production of reactive oxygen species (ROS) is highly important for host defence against aspergillosis, especially when considering that CGD patients that cannot produce ROS are highly susceptible to aspergillosis28. However, oxidative burst in response to Aspergillus was not influenced by the different NOD2 genotypes (Fig. 2g, h). Individuals carrying the T-allele at P268S, which was associated with a reduced susceptibility to aspergillosis in patients (Fig. 1), induced significantly lower IL-1β and demonstrated a trend toward lower TNF production in response to Aspergillus stimulation (Fig. 2a). Additionally, the TT-genotype was associated with significantly lower IL-17A responses compared with individuals carrying the CC or CT genotypes (Fig. 2b). Heterozygous carriers of the G908R and R702W polymorphisms did not show significantly altered cytokine responses to 3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 IL-1β IL-1β TNF IL-17A IL-22 IL-17A IL-22 rs2066847 Killing rs2066842 rs2066847 rs2066847 ROS IFNγ IFNγ TNF IL-6 IL-6 rs2066842 Killing rs2066842 ROS 15,000 a c d e f g h b 3000 3000 2000 1000 0 10,000 8000 6000 4000 2000 0 2000 1000 0 30,000 ns ns ns ns ns ns * * ** ** * 20,000 10,000 0 p = 0.07 p = 0.09 p = 0.32 p = 0.97 p = 0.32 p = 0.51 p = 0.30 10,000 5000 pg/mL pg/mL pg/mL pg/mL 3000 10,000 8000 6000 4000 2000 0 2000 1000 0 pg/mL 3000 2000 1000 0 pg/mL pg/mL pg/mL 2000 15,000 30,000 2000 100 3 × 107 2 × 107 1 × 107 0 90 80 70 60 1500 1000 500 0 20,000 10,000 0 10,000 5000 0 Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC Ref InsC 1000 1500 500 0 pg/mL pg/mL pg/mL pg/mL % Killing 100 90 80 70 60 % Killing AUC (RLU) 3 × 107 2 × 107 1 × 107 0 AUC (RLU) 0 CC CC vs CT + TT = ** CC vs CT + TT p = 0.06 CT TT CC CC vs CT + TT p = 0.80 CT TT CC CC vs CT + TT p = 0.5 CT TT CC CC vs CT + TT p = 0.39 CT TT CC CT TT CC vs CT + TT p = 0.29 CC CT TT CC vs CT + TT p = 0.37 CC CT TT CC vs CT + TT p = 0.43 CC CT TT Fig. 2 Human NOD2 polymorphisms influence Aspergillus-induced cytokine responses and fungal killing. a–d IL-1β, TNF, IL-6, IL-17A, IL-22, and IFNγ levels measured in culture supernatants of PBMCs stimulated with (a, c) live Aspergillus conidia for 24 h or (b, d) heat-inactivated (HI) Aspergillus conidia for 7 days. The PBMCs of individuals with various genotypes of the NOD2 gene were compared. These genotypes included (a, b) the P268S mutation (rs2066842; reference: CC n = 36, heterozygous: CT n = 28 and homozygous: TT n = 4) and (c, d) the 1007finsC mutation (rs2066847; reference n = 62 and heterozygous: insC n = 4). e, f Fungal killing capacity of human PBMCs assessed as CFU remaining of A. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE 30,000 a c d e b 5000 2500 15,000 3000 2000 1000 0 10,000 5000 0 p = 0.07 p = 0.09 p = 0.46 p = 0.57 p = 0.99 p = 0.89 2000 1500 1000 500 0 4000 3000 2000 1000 0 * * * * ** ** * * * ** ** * * 20,000 pg/mL pg/mL pg/mL pg/mL pg/mL 10,000 0 40 100 95 90 % Killing AUC (RLU) Killing ROS 85 80 0 1 × 107 2 × 107 3 × 107 4 × 107 5 × 107 1 × 108 2 × 108 3 × 108 4 × 108 5 × 108 30 20 % Positive CD4 cells 10 0 Co Co Co NOD2 –/– NOD2 –/– NOD2 –/– Co NOD2 –/– Live conidia IL-17A IL-22 IFNγ IFNγ IL-1β TNF IL-17A IL-22 HI conidia HI hyphae Live conidia HI conidia HI hyphae HI conidia HI conidia Control Zymosan HI hyphae HI conidia HI hyphae HI conidia HI hyphae Fig. 3 NOD2-deficient individuals have impaired cytokine responses in response to Aspergillus. a IL-1β and TNF levels in culture supernatants of PBMCs from healthy controls (black dots) and NOD2-deficient patients (gray dots) that were stimulated for 24 h with A. fumigatus live conidia, HI conidia or HI hyphae (n = 11 controls and n = 9 patients for IL-1β and n = 9 controls and n = 8 patients for TNF). b IL-17A, IL-22, and IFNγ levels after 7 days of stimulation with HI conidia or HI hyphae (IL-17A n = 7 controls and n = 6 patients; IL-22 and IFNγ n = 10 controls, n = 8 patients). c IL-17A+, IL-22+, and IFNγ+ CD4 T-cell populations (n = 8 controls and n = 5 patients) after 7 days stimulation with HI conidia shown as the percentage of total CD4 cells. d The fungal killing capacity of PBMCs (5 × 105) from healthy controls and NOD2-deficient patients (n = 12 controls, n = 6 patients) counted as CFU remaining after 24-h stimulation with live A. fumigatus (2 × 106). e The area under the curve of the reactive oxygen species release of PBMCs from healthy controls and NOD2-deficient patients (controls n = 8, patients n = 4) in response to live Aspergillus conidia (1 × 107/mL) and zymosan (150 µg/mL) measured by luminescence signal from luminol conversion over 1 h. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 e The area under the curve of the reactive oxygen species release of PBMCs from healthy controls and NOD2-deficient patients (controls n = 8, patients n = 4) in response to live Aspergillus conidia (1 × 107/mL) and zymosan (150 µg/mL) measured by luminescence signal from luminol conversion over 1 h. Data are represented as scatter dot plot with median and means were compared using the Mann–Whitney U test rarely displayed inflammatory infiltrates and when present small (Fig. 5a I, circle and arrowhead; II, arrow). Severe fungal invasion was observed in WT mice (Fig. 5a III) with a high density of hyphae that invaded blood vessels (Fig. 5a III arrow). In contrast, fungi were rarely observed in lungs of Nod2−/−mice, only conidia (Fig. 5a III arrow), without invasion of the parenchyma or blood vessels. Macrophages were observed in the lesions, either ran- domly distributed (Fig. 5a IV, wild-type mice) or gathered in the small infiltrates (Fig. 5a IV, Nod2−/−mice). Although the immune suppression drastically decreased the number of F4/80+ cells no differences were observed between the groups (Fig. 5a IV). indicate destruction of nasal mucosa (Fig. 6a, enlarged in Fig. 6b), and invasion of fungi (Fig. 6c). Nasal sinuses of Nod2−/−mice did not demonstrate any signs of destruction (Fig. 6d, e) or presence of fungi (Fig. 6f). NOD2 augments Aspergillus-induced cytokine responses. Since NOD2 genetic variation and its complete deficiency correlated with a decreased cytokine release, the capacity of NOD2 signalling to boost Aspergillus-induced cytokine responses was investigated. Co-stimulation of NOD2 by MDP augmented Aspergillus-induced IL-1β and TNF responses (Fig. 7a). This could, however, not be achieved in cells of Crohn’s disease patients carrying the 1007finsC mutation (Fig. 7b). Similarly, cytokine responses to A. fumigatus by cells of Nod2−/−mice were investigated. Although BMDMs of Nod2−/−mice did not demonstrate altered IL-6, KC and TNF responses (Fig. 7c), splenocytes of Nod2−/−mice showed a reduced capacity to mount IL-6, KC, and TNF responses (Fig. 7d) Using morphometric analysis, the average number of lesions per section and the affected area was quantified. WT mice had a trend towards a higher average number of lesions per section (Fig. 5b). Moreover, the affected area of the lesions was significantly larger in WT mice (Fig. 5b). g y g g Additional histology slides confirmed our morphometric analy- sis, as WT mice displayed marked lung lesions characterized by large foci of ischaemic necrosis (Fig. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Data are represented as scatter dot plot with median and means were compared using the Mann–Whitney U test 5000 4000 3000 2000 1000 0 * * * pg/mL TNF Live conidia HI conidia HI hyphae b 2500 p = 0.07 p = 0.89 2000 1500 1000 500 0 pg/mL IL-17A HI conidia HI hyphae 30,000 a * ** ** 20,000 pg/mL pg/mL 10,000 0 Live conidia IL-1β HI conidia HI hyphae b 15,000 3000 2000 1000 0 10,000 5000 0 ** ** * * pg/mL pg/mL IFNγ IL-22 HI conidia HI hyphae HI conidia HI hyphae a d p = 0.09 100 95 90 % Killing Killing 85 80 Co NOD2 –/– c * * * 40 30 20 % Positive CD4 cells 10 0 Co Co Co NOD2 –/– NOD2 –/– NOD2 –/– IL-17A IL-22 IFNγ e p = 0.46 p = 0.57 p = 0.99 AUC (RLU) ROS 0 1 × 107 2 × 107 3 × 107 4 × 107 5 × 107 1 × 108 2 × 108 3 × 108 4 × 108 5 × 108 HI conidia Control Zymosan d e c Fig. 3 NOD2-deficient individuals have impaired cytokine responses in response to Aspergillus. a IL-1β and TNF levels in culture supernatants of PBMCs from healthy controls (black dots) and NOD2-deficient patients (gray dots) that were stimulated for 24 h with A. fumigatus live conidia, HI conidia or HI hyphae (n = 11 controls and n = 9 patients for IL-1β and n = 9 controls and n = 8 patients for TNF). b IL-17A, IL-22, and IFNγ levels after 7 days of stimulation with HI conidia or HI hyphae (IL-17A n = 7 controls and n = 6 patients; IL-22 and IFNγ n = 10 controls, n = 8 patients). c IL-17A+, IL-22+, and IFNγ+ CD4 T-cell populations (n = 8 controls and n = 5 patients) after 7 days stimulation with HI conidia shown as the percentage of total CD4 cells. d The fungal killing capacity of PBMCs (5 × 105) from healthy controls and NOD2-deficient patients (n = 12 controls, n = 6 patients) counted as CFU remaining after 24-h stimulation with live A. fumigatus (2 × 106). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Although Nod2−/−mice demonstrated severe symptoms such as hunching, head tilting, and circling, symptoms that have been described in the in vivo aspergillosis mouse model30, they survived the infection, in contrast to WT mice. Bioluminescence imaging revealed that Nod2−/−mice rapidly cleared the luciferase-expressing Aspergillus, whereas WT mice developed a fungal infection as indicated by a significantly higher luminescence signal on day 3 post infection (pi) (Fig. 4c, d). After day 3 pi the luminescence could not be reliably compared between groups due to mice dropping out of the experiment (Supplementary Fig. 2), and severe hypoxia in critically ill mice that influences bioluminescence readout. For assessment of his- topathological damage in the lungs, inflammation and fungal burden, mice were sacrificed on day 3 pi. The decreased biolu- minescence signal in the lungs of Nod2−/−mice correlated with the fact that almost no Aspergillus DNA could be detected in the lung homogenates of Nod2−/−mice (3 out of 8 mice were PCR positive with low values). However, in the lung homogenates of WT mice, Aspergillus PCR was positive for 5 out of 8 mice (Fig. 4e). Nod2−/−mice are less susceptible to IA. Since NOD2 genetic variation was associated with a reduced risk of IA, the impact of full Nod2 deficiency on susceptibility to aspergillosis was vali- dated in an experimental model of IA. Wild-type (WT) C57BL/6 and Nod2-deficient (Nod2−/−) C57BL/6 mice were immuno- suppressed using cyclophosphamide and subsequently subjected to lethal Aspergillus infection29. Nod2−/−mice demonstrated a significantly improved 14-day survival, compared to WT mice (Fig. 4a). During infection, WT mice decline in bodyweight and seven out of eleven mice did not survive the infection whereas Nod2−/−mice show reduced pulmonary histopathological damage. Using histopathological analysis differences inflamma- tory and pathological damage to the lungs and sinuses of WT and Nod2−/−mice were assessed. Within the lungs, WT mice dis- played multifocal large areas of ischaemic necrosis (Fig. 5a I, circles and arrowheads), with fibrinous thrombi and destruction of blood vessels (Fig. 5a II, arrow). In contrast, Nod2−/−mice NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 4 4 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE Survival Weightloss Luminescence Fungal burden 100 a d b c e 0 1,000,000 10,000 p = 0.30 1000 100 rDNA copies/mg tissue 10 1 ** RLU/sec 100,000 1 2 Day 3 10 20 % weightloss 30 –1 0 1 Day 2 3 80 60 Percent survival 40 20 0 –4 –3 –2 –1 0 1 2 3 4 5 Time WT vs. WT WT WT D1 40000 30000 20000 10000 p/s/cm2/sr Color bar Min v= 2.00e3 Max = 4.00e4 D2 D3 Nod2 –/–= * Nod2 –/– Nod2 –/– Nod2 –/– 6 n = 9 n = 12 7 8 9 10 11 12 13 14 Fig. 4 Nod2−/−deficient mice have a reduced susceptibility to aspergillosis. Comparison of the susceptibility of wild-type mice (WT; black lines with circles) and Nod2-deficient mice (Nod2−/−; blue lines with squares) to invasive aspergillosis. a Kaplan–Meier survival curve of cyclophosphamide immunosuppressed WT (n = 12) and Nod2−/−(n = 9) mice infected intranasally with 5 × 104 conidia. p-values of the Kaplan–Meier curve were determined with the use of the log-rank test. Data represent the cumulative data of four separate experiments. b Percentage weight loss following cyclophosphamide immunosuppression and intranasal Aspergillus infection (5 × 104/mouse) in WT (n = 20) and Nod2−/−(n = 17) mice (p = 0.3515) (c, d) Luminescence signal at day 1 to 3 post infection from the luminescent Aspergillus originating from lung and sinus regions in WT (n = 20) and Nod2−/−(n = 17) mice. Curves were compared by repeated measurements two-way ANOVA. e Fungal burden as determined by amplification of Aspergillus ITS2 regions from lung homogenates. Data in graphs are represented as mean ± SEM or in scatterplots with a line indicating the median. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 The means were compared using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs, luminescence and weight curves were compared for significance using a Weightloss b 0 10 20 % weightloss 30 –1 0 1 Day 2 3 Weightloss Luminescence Fungal burden b c e 0 1,000,000 10,000 p = 0.30 1000 100 rDNA copies/mg tissue 10 1 ** RLU/sec 100,000 1 2 Day 3 10 20 % weightloss 30 –1 0 1 Day 2 3 WT WT Nod2 –/– Nod2 –/– Luminescence Fungal burden c e 1,000,000 10,000 p = 0.30 1000 100 rDNA copies/mg tissue 10 1 ** RLU/sec 100,000 1 2 Day 3 WT WT Nod2 –/– Nod2 –/– Survival 100 a 80 60 Percent survival 40 20 0 –4 –3 –2 –1 0 1 2 3 4 5 Time WT vs. Nod2 –/–= * 6 n = 9 n = 12 7 8 9 10 11 12 13 14 Fungal burden e 10,000 p = 0.30 1000 100 rDNA copies/mg tissue 10 1 WT Nod2 –/– b b e c e a d WT D1 40000 30000 20000 10000 p/s/cm2/sr Color bar Min v= 2.00e3 Max = 4.00e4 D2 D3 Nod2 –/– d d WT D1 40000 30000 20000 10000 p/s/cm2/sr Color bar Min v= 2.00e3 Max = 4.00e4 D2 D3 Nod2 –/– WT 40000 30000 20000 10000 p/s/cm2/sr Color bar Min v= 2.00e3 Max = 4.00e4 D2 D3 Fig. 4 Nod2−/−deficient mice have a reduced susceptibility to aspergillosis. Comparison of the susceptibility of wild-type mice (WT; black lines with circles) and Nod2-deficient mice (Nod2−/−; blue lines with squares) to invasive aspergillosis. a Kaplan–Meier survival curve of cyclophosphamide immunosuppressed WT (n = 12) and Nod2−/−(n = 9) mice infected intranasally with 5 × 104 conidia. p-values of the Kaplan–Meier curve were determined with the use of the log-rank test. Data represent the cumulative data of four separate experiments. b Percentage weight loss following cyclophosphamide immunosuppression and intranasal Aspergillus infection (5 × 104/mouse) in WT (n = 20) and Nod2−/−(n = 17) mice (p = 0.3515) (c, d) Luminescence signal at day 1 to 3 post infection from the luminescent Aspergillus originating from lung and sinus regions in WT (n = 20) and Nod2−/−(n = 17) mice. Curves were compared by repeated measurements two-way ANOVA. e Fungal burden as determined by amplification of Aspergillus ITS2 regions from lung homogenates. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 5c I: left of the black line) with destruction of the bronchi/bronchiole epithelium (Fig. 5c I, black arrowheads), fungal invasion of lung parenchyma (Fig. 5c II top row), destruction of alveoli (Fig. 5c III top row) and invasion of blood vessels (Fig. 5c IV top row). Similar lesions were observed in other WT mice (Fig. 5c second row) with invasion of blood vessels (Fig. 5c III second row) and hyphae crossing the bronchiole epithelium lining (Fig. 5c IV second row, black arrowhead). In contrast, Nod2−/−mice displayed no or minimal lesions (Fig. 5c third and fourth row). At a low magnification, no lesions could be observed (Fig. 5c I, II fourth row), whereas at a high magnification), few hyphae could be detected in the alveoli/alveolar walls (Fig. 5c III, IV fourth row, black arrowheads). NOD2 inhibits phagocytosis and killing of A. fumigatus. The reduced susceptibility of Nod2−/−mice and patients with NOD2 genetic variants may be explained by enhanced killing capacity of myeloid cells due to their NOD2 deficiency, as monocytes from NOD2-deficient individuals demonstrated a trend toward Aspergillus killing (Fig. 3d). BMDMs from WT and Nod2−/− mice were compared for their fungal killing capacity, and Nod2−/−BMDMs proved to be more efficient at eradicating live Aspergillus conidia (Fig. 8a). Subsequently, NOD2 gene expression was silenced in human monocyte-derived macrophages (MDMs) to validate that the absence of NOD2 also positively influences fungal killing in human cells. Treatment of MDMs with NOD2 targeting siRNA augmented fungal killing capacity (Fig. 8b). Since WT mice displayed invasive sinusitis, whereas nasal sinus lesions were absent in Nod2−/−mice (Fig. 6). Arrowheads NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 5 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 nced CLEC7A mRNA expression (Fig. 8j). Conversely, MDP ulation reduced surface dectin-1 expression on human Ms (Fig 8k) of healthy volunteers that were wild type for the inv NOD2 SNPs were compared with three NOD2-deficient Similarly fungal killing was assessed in murine BMDM I a b c 1 mm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 200 μm 200 μm 200 μm IHC F4/80 1 mm 200 μm 200 μm 200 μm IHC F4/80 II III IV I II III IV Lesions quantity Number of lesions/section Lesion area (μm2) Lesions size p=0.05 6 4 2 0 1 10 103 104 105 106 107 * WT Nod2–/– WT Nod2–/– WT Nod2–/– WT Nod2–/– 5 Nod2−/−mice show reduced histological damage and fungal burden following Aspergillus infection. a Histology of lung sections of wild −/−mice at day 3 pi, stained in HE (I, II), Grocott’s Methenamine Silver (III) or labelled using anti-F4/80 antibody (specific for macroph erstained with Haematoxylin staining. Scale bars represent 1 mm (I) and 200 μm (II–IV). b Morphometric analysis of the lesions in the w ons using Image J software to quantify the lesions in number and size. c Representative lung sections of two additional WT and Nod2−/−mic (I) and Grocott’s Methenamine Silver (II–IV). Scale bars represent 200 μm (I, II) and 50 μm (III, IV), means were compared for significance n-Whitney U test URE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ART I a 1 mm 200 μm 200 μm 200 μm IHC F4/80 1 mm 200 μm 200 μm 200 μm IHC F4/80 II III IV WT Nod2–/– a b Lesions quantity Number of lesions/section Lesion area (μm2) Lesions size p=0.05 6 4 2 0 1 10 103 104 105 106 107 * WT Nod2–/– WT Nod2–/– b Lesions quantity Number of lesions/section Lesion area (μm2) Lesions size p=0.05 6 4 2 0 1 10 103 104 105 106 107 * WT Nod2–/– WT Nod2–/– c 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm I II III IV WT Nod2–/– Fig. 5 Nod2−/−mice show reduced histological damage and fungal burden following Aspergillus infection. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Similarly, silencing NOD2 in human MDMs slightly NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 6 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Data in graphs are represented as mean ± SEM or in scatterplots with a line indicating the median. The means were compared using the Mann–Whitney U test, p-values of statistical tests are shown within the graphs, luminescence and weight curves were compared for significance using a two-way repeated measurements ANOVA (Fig. 8e). Conversely, MDP-stimulated MDMs demonstrate a reduced phagocytosis of FITC-labelled conidia (Fig. 8f). the absence of NOD2 positively influences fungal killing we hypothesized that NOD2 activation might impair antifungal host defence. Human MDMs were, therefore, pre-exposed to the NOD2 agonist MDP and subsequently fungal killing capacity was examined. In line with the observation that NOD2 deficiency and silencing is associated with increased Aspergillus killing capacity, NOD2 activation conversely reduced the capacity of human MDMs to kill Aspergillus spores (Fig. 8c). p g y g Although no influence of human NOD2 deficiency on ROS production was found (Fig. 3e), we wanted to validate that ROS production was indeed not influenced by NOD2 deficiency and NOD2 stimulation. BMDMs of WT and Nod2−/− mice stimulated with zymosan demonstrated a similar capacity to produce ROS (Fig. 8g). NOD2 stimulation of human MDMs also did not influence ROS production in response to zymosan stimulation (Fig. 8h). These data suggest that the observed increased killing in the setting of NOD2 deficiency is due to enhanced phagocytosis and not via increased ROS production in contrast to NOD1 deficiency17. Several antifungal mechanisms could account for the observed increased killing capacity of Aspergillus in monocytes and macrophages. Phagocytosis and ROS production are well- established factors that influence the fungal killing capacity. Therefore, these two possible mechanisms were systematically addressed to explain increased killing. Nod2−/− BMDMs demonstrated an enhanced capacity to engulf FITC-labelled A. fumigatus conidia, illustrated by a higher percentage FITC- positive macrophages and an overall higher mean fluorescence intensity (MFI) of the macrophages (Fig. 8d), indicating that more conidia were engulfed and more cells were actively engulfing conidia. Similarly, human MDMs in which NOD2 was silenced showed a trend towards an increased phagocytosis NOD2 negatively regulates dectin-1 expression. One of the most crucial receptors for A. fumigatus recognition and engulfment is dectin-1. Therefore, we investigated whether NOD2 influenced the expression of dectin-1. Nod2−/−BMDMs showed an increased expression of Clec7a, the gene encoding dectin-1 (Fig. 8i). NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 To verify that MDP did not have off-target effects negatively influencing fungal killing, phagocytosis, and dectin-1 expression, monocytes 7 7 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 NASAL SINUS Wild-type Nod2–/– 500 μm 200 μm 100 μm 500 μm 200 μm 100 μm a b c d e f Fig. 6 histology of nasal sinuses Histology of Nasal Sinuses of (a–c) wild-type and (d–f) Nod2−/−mice at day 3 pi, stained by HE staining at (a, d) ×2 and (b, e) ×10 magnification and (c, f) Grocott’s Methenamine Silver staining at ×20 magnification. Scale bars represent (a, d) 500 μm, (b, e) 200 μm, and (c, f) 100 μm Fig. 6 histology of nasal sinuses Histology of Nasal Sinuses of (a–c) wild-type and (d–f) Nod2−/−mice at day 3 pi, stained by HE staining at (a, d) ×2 and (b, e) ×10 magnification and (c, f) Grocott’s Methenamine Silver staining at ×20 magnification. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Scale bars represent (a, d) 500 μm, (b, e) 200 μm, and (c, f) 100 *** TNF Co HK conidia MDP HK conidia + MDP 8000 6000 4000 2000 0 pg/mL IL-1β Co HK conidia MDP HK conidia + MDP 10,000 8000 6000 4000 2000 0 p = 1.00 pg/mL b 10,000 *** IL-1β 8000 6000 4000 2000 0 Co HK conidia MDP HK conidia + MDP pg/mL a 10,000 *** *** IL-1β TNF 8000 6000 4000 2000 0 Co HK conidia MDP HK conidia + MDP Co HK conidia MDP HK conidia + MDP 8000 6000 4000 2000 0 pg/mL pg/mL a TNF IL-1β Co HK conidia MDP HK conidia + MDP Co HK conidia MDP HK conidia + MDP 10,000 8000 6000 4000 2000 0 8000 6000 4000 p = 0.49 p = 1.00 2000 0 pg/mL pg/mL b TNF Co HK conidia MDP HK conidia + MDP 8000 6000 4000 p = 0.49 2000 0 pg/mL 10,000 *** *** * IL-1β TNF TNF TNF KC Splenocytes BMDMs IL-6 TNF KC IL-6 IL-1β 8000 6000 4000 2000 0 Co HK conidia MDP HK conidia + MDP Co HK conidia MDP HK conidia + MDP Co HK conidia MDP HK conidia + MDP Co HK conidia MDP HK conidia + MDP 10,000 8000 6000 4000 2000 0 8000 6000 4000 2000 0 8000 6000 4000 p = 0.49 p = 1.00 p = 0.06 2000 0 400 300 pg/mL pg/mL pg/mL pg/mL pg/mL pg/mL pg/mL pg/mL pg/mL pg/mL 200 100 0 WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– 400 300 200 100 0 500 400 300 200 100 0 50 30 20 10 0 40 30 20 10 0 20 15 10 5 0 a b d c Fig. 7 NOD2 activation positively regulates cytokine production. a, b Aspergillus-induced IL-1β and TNF levels in the culture supernatants of human PBMCs (5 × 105) of (a) healthy volunteers (n = 13) represented as black dots or (b) NOD2-deficient patients (n = 6) represented as grey dots in the presence or absence of (10 μg/mL) MDP. Data is represented as scatter dot plot with median and means were compared using the Wilcoxon signed rank test was paired comparisons. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 a Histology of lung sections of wild-type and Nod2−/−mice at day 3 pi, stained in HE (I, II), Grocott’s Methenamine Silver (III) or labelled using anti-F4/80 antibody (specific for macrophages), counterstained with Haematoxylin staining. Scale bars represent 1 mm (I) and 200 μm (II–IV). b Morphometric analysis of the lesions in the whole lung sections using Image J software to quantify the lesions in number and size. c Representative lung sections of two additional WT and Nod2−/−mice, stained in HE (I) and Grocott’s Methenamine Silver (II–IV). Scale bars represent 200 μm (I, II) and 50 μm (III, IV), means were compared for significance using the Mann-Whitney U test c 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 200 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm 50 μm I II III IV WT Nod2–/– c Fig. 5 Nod2−/−mice show reduced histological damage and fungal burden following Aspergillus infection. a Histology of lung sections of wild-type and Nod2−/−mice at day 3 pi, stained in HE (I, II), Grocott’s Methenamine Silver (III) or labelled using anti-F4/80 antibody (specific for macrophages), counterstained with Haematoxylin staining. Scale bars represent 1 mm (I) and 200 μm (II–IV). b Morphometric analysis of the lesions in the whole lung sections using Image J software to quantify the lesions in number and size. c Representative lung sections of two additional WT and Nod2−/−mice, stained in HE (I) and Grocott’s Methenamine Silver (II–IV). Scale bars represent 200 μm (I, II) and 50 μm (III, IV), means were compared for significance using the Mann-Whitney U test enhanced CLEC7A mRNA expression (Fig. 8j). Conversely, MDP stimulation reduced surface dectin-1 expression on human MDMs (Fig. 8k). of healthy volunteers that were wild type for the investigated NOD2 SNPs were compared with three NOD2-deficient patients. Similarly, fungal killing was assessed in murine BMDMs. MDP significantly reduced in murine BMDMs (Fig. 9a) and in human monocytes fungal killing (Fig. 9b), phagocytosis (Fig. 9c), and dectin-1 expression (Fig. 9d), whereas in the cells of Nod2−/−mice or NOD2-deficient patients no effect of MDP could be detected. MDP inhibits antifungal immunity in WT cells. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 c, d Aspergillus-induced IL-6, KC, and TNF levels in the culture supernatants of murine (c) BMDMs and (d) splenocytes of wild-type (WT, black dots) and Nod2-deficient (Nod2−/−, grey dots) mice. Data are represented scatterplots with a line indicating the median and means were compared using the Mann–Whitney U test b b a TNF pg/mL WT Nod2 –/– 400 300 200 100 0 * IL-6 pg/mL WT Nod2 –/– 50 40 30 20 10 0 d BMDMs KC IL-6 400 300 pg/mL pg/mL 200 100 0 WT Nod2 –/– WT Nod2 –/– 500 400 300 200 100 0 c BMDMs TNF KC IL-6 400 300 pg/mL pg/mL pg/mL 200 100 0 WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– 400 300 200 100 0 500 400 300 200 100 0 c KC Splenocytes pg/mL WT Nod2 –/– 30 20 10 0 * TNF KC Splenocytes IL-6 p = 0.06 pg/mL pg/mL pg/mL WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– 50 30 20 10 0 40 30 20 10 0 20 15 10 5 0 d TNF KC Splenocytes p = 0.06 pg/mL pg/mL WT Nod2 –/– WT Nod2 –/– 30 20 10 0 20 15 10 5 0 d TNF p = 0.06 pg/mL WT Nod2 –/– 20 15 10 5 0 c Fig. 7 NOD2 activation positively regulates cytokine production. a, b Aspergillus-induced IL-1β and TNF levels in the culture supernatants of human PBMCs (5 × 105) of (a) healthy volunteers (n = 13) represented as black dots or (b) NOD2-deficient patients (n = 6) represented as grey dots in the presence or absence of (10 μg/mL) MDP. Data is represented as scatter dot plot with median and means were compared using the Wilcoxon signed rank test was paired comparisons. c, d Aspergillus-induced IL-6, KC, and TNF levels in the culture supernatants of murine (c) BMDMs and (d) splenocytes of wild-type (WT, black dots) and Nod2-deficient (Nod2−/−, grey dots) mice. Data are represented scatterplots with a line indicating the median and means were compared using the Mann–Whitney U test NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 100 a b c f h k d e j g i Fungal killing Phagocytosis ROS release Dectin-1 expression mRNA expression NOD2 CLEC7A Clec7a mRNA *** ** ** ** ** * * * ** 80 400,000 50 40 30 20 Relative expression 10 0 6 × 10 6 4 × 10 6 2 × 10 6 0 300,000 200,000 MFI FITC RLU 1.5 × 10 5 1.0 × 10 5 5.0 × 10 4 0.0 RLU 100,000 0 Phagocytosing cells Fluorescence intensity p = 0.39 p = 0.09 p = 0.07 p = 0.43 p = 0.06 60 40 20 0 80 150,000 4 3 2 1 0 100,000 50,000 0 60 40 20 0 80 60 40 20 0 80 60 Percentage killing Percentage FITC + cells Percentage FITC + cells MFI 150,000 40000 ** Surface Dectin-1 30000 20000 10000 0 100,000 50,000 0 MFI MFI Fold change Percentage FITC + cells Percentage killing Percentage killing 40 Murine BMDMs Nod2 knockout NOD2 silencing NOD2 stimulation Humsn MDMs 20 0 WT Scrambled siNOD2 RPMI RPMI RPMI RPMI CO MDP MDP MDP MDP MDP (NOD2) (NOD2) (NOD2) (NOD2) (NOD2) Scrambled Scrambled Scrambled Scrambled siNOD2 siNOD2 siNOD2 siNOD2 Nod2 –/– WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– WT Nod2 –/– 100 80 60 40 20 0 100 80 60 40 20 0 ig. 8 NOD2 negatively regulates, fungal killing, phagocytosis, and dectin-1 expression. a–c The fungal killing capacity of macrophages (1 × 105) assessed by FU remaining of A. fumigatus (2 × 106) following exposure for 24 h, in (a) wild-type and Nod2−/−BMDMs (n = 16 WT, n = 12 Nod2−/−). b human GM- SF differentiated MDMs treated (n = 9) for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and c human GM-CSF differentiated MDMs (n = 9) eated for 48 h with the NOD2 ligand (10 μg/mL) MDP. Phagocytosis efficiency assessed as percentage of macrophages that engulfed FITC-labelled A. umigatus conidia and mean fluorescence intensity of the total macrophage population in (d) wild-type and Nod2−/−BMDMs (n = 16 wt, n = 12 od2−/−), (e) human GM-CSF differentiated MDMs (n = 9) treated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (f) human GM-CSF ifferentiated MDMs (n = 6) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Means were compared using the Mann–Whitney U test for murine BMDMs (a, d, g, i) and the Wilcoxon signed-rank test was paired comparisons following siRNA treatment (b, e, j), or MDP stimulation (c, f, h, k) Fig. 8 NOD2 negatively regulates, fungal killing, phagocytosis, and dectin-1 expression. a–c The fungal killing capacity of macrophages (1 × 105) assessed by CFU remaining of A. fumigatus (2 × 106) following exposure for 24 h, in (a) wild-type and Nod2−/−BMDMs (n = 16 WT, n = 12 Nod2−/−). b human GM- CSF differentiated MDMs treated (n = 9) for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and c human GM-CSF differentiated MDMs (n = 9) treated for 48 h with the NOD2 ligand (10 μg/mL) MDP. Phagocytosis efficiency assessed as percentage of macrophages that engulfed FITC-labelled A. fumigatus conidia and mean fluorescence intensity of the total macrophage population in (d) wild-type and Nod2−/−BMDMs (n = 16 wt, n = 12 Nod2−/−), (e) human GM-CSF differentiated MDMs (n = 9) treated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (f) human GM-CSF differentiated MDMs (n = 6) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP. g, h The area under the curve of the reactive oxygen species release of (g) wild-type (n = 6) and Nod2−/−(n = 6) BMDMs or (h) human MDMs (n = 5) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP in response to zymosan (150 µg/mL) measured by luminescence signal from luminol conversion over 1 h. i Dectin-1 (Clec7a) expression assessed by qPCR in wild-type and Nod2−/−BMDMs (n = 14 wt, n = 10 Nod2−/−), (j) NOD2 (n = 8) and CLEC7A (n = 6) mRNA expression in human GM-CSF differentiated MDMs treated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (k) Surface dectin-1 expression measured by flow cytometry on human GM-CSF differentiated MDMs treated for 28 h with the NOD2 ligand (10 μg/mL) MDP. Data is represented as scatter dot plot with median with (a, d, g) black dots representing wild-type mice and grey dots representing Nod2 deficient mice, (b, e, j) black squares representing human macrophages treated with scrambled siRNA and grey squares human macrophages treated with NOD2 targeting siRNA, and black triangles representing MDMs without MDP pre- treatment and grey triangles MDMs with MDP pre-treatment. Discussion in PRRs is common in the general population, however, in hematopoietic stem cell transplant patients (HSCT), such varia- tions can drastically impact susceptibility to IA6. The only intracellular PRRs explored to date, NLRP3 and NOD1 belonging to the NLRs, provide evidence that this class of receptors can modulate host responses against A. fumigatus7,17. However, one of the most well known NLRs that is directly linked with PRRs are key players in activating the antifungal host response during invasive aspergillosis (IA) by inducing cytokine responses and facilitating phagocytosis with subsequent fungal killing. PRRs on the cell surface, such as Toll-like receptors and C-type lectin receptors, have been extensively described in inducing these responses in host defence against Aspergillus31. Genetic variation 8 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 g, h The area under the curve of the reactive oxygen species release f (g) wild-type (n = 6) and Nod2−/−(n = 6) BMDMs or (h) human MDMs (n = 5) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP in response to ymosan (150 µg/mL) measured by luminescence signal from luminol conversion over 1 h. i Dectin-1 (Clec7a) expression assessed by qPCR in wild-type nd Nod2−/−BMDMs (n = 14 wt, n = 10 Nod2−/−), (j) NOD2 (n = 8) and CLEC7A (n = 6) mRNA expression in human GM-CSF differentiated MDMs eated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (k) Surface dectin-1 expression measured by flow cytometry on human GM-CSF ifferentiated MDMs treated for 28 h with the NOD2 ligand (10 μg/mL) MDP. Data is represented as scatter dot plot with median with (a, d, g) black dots epresenting wild-type mice and grey dots representing Nod2 deficient mice, (b, e, j) black squares representing human macrophages treated with crambled siRNA and grey squares human macrophages treated with NOD2 targeting siRNA, and black triangles representing MDMs without MDP pre- eatment and grey triangles MDMs with MDP pre-treatment. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 8 NOD2 negatively regulates, fungal killing, phagocytosis, and dectin-1 expression. a–c The fungal killing capacity of Fig. 8 NOD2 negatively regulates, fungal killing, phagocytosis, and dectin-1 expression. a–c The fungal killing capacity of macrophages (1 × 105) assessed by CFU remaining of A. fumigatus (2 × 106) following exposure for 24 h, in (a) wild-type and Nod2−/−BMDMs (n = 16 WT, n = 12 Nod2−/−). b human GM- CSF differentiated MDMs treated (n = 9) for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and c human GM-CSF differentiated MDMs (n = 9) treated for 48 h with the NOD2 ligand (10 μg/mL) MDP. Phagocytosis efficiency assessed as percentage of macrophages that engulfed FITC-labelled A. fumigatus conidia and mean fluorescence intensity of the total macrophage population in (d) wild-type and Nod2−/−BMDMs (n = 16 wt, n = 12 Nod2−/−), (e) human GM-CSF differentiated MDMs (n = 9) treated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (f) human GM-CSF differentiated MDMs (n = 6) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP. g, h The area under the curve of the reactive oxygen species release of (g) wild-type (n = 6) and Nod2−/−(n = 6) BMDMs or (h) human MDMs (n = 5) treated for 24 h with the NOD2 ligand (10 μg/mL) MDP in response to zymosan (150 µg/mL) measured by luminescence signal from luminol conversion over 1 h. i Dectin-1 (Clec7a) expression assessed by qPCR in wild-type and Nod2−/−BMDMs (n = 14 wt, n = 10 Nod2−/−), (j) NOD2 (n = 8) and CLEC7A (n = 6) mRNA expression in human GM-CSF differentiated MDMs treated for 48 h with siRNA targeting NOD2 or non-targeting siRNA, and (k) Surface dectin-1 expression measured by flow cytometry on human GM-CSF differentiated MDMs treated for 28 h with the NOD2 ligand (10 μg/mL) MDP. Data is represented as scatter dot plot with median with (a, d, g) black dots representing wild-type mice and grey dots representing Nod2 deficient mice, (b, e, j) black squares representing human macrophages treated with scrambled siRNA and grey squares human macrophages treated with NOD2 targeting siRNA, and black triangles representing MDMs without MDP pre- treatment and grey triangles MDMs with MDP pre-treatment. NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Means were compared using the Mann–Whitney U test for murine BMDMs (a, d, g, i) and he Wilcoxon signed rank test was paired comparisons following siRNA treatment (b e j) or MDP stimulation (c f h k) | / 100 a d Fungal killing P *** ** 80 Phagocytosing cells 60 40 20 0 80 60 Percentage killing Percentage FITC + cells 40 Murine BMDMs Nod2 knockout 20 0 WT Nod2 –/– WT Nod2 –/– Phagocytosis ** 400,000 300,000 200,000 MFI FITC 100,000 0 Fluorescence intensity WT Nod2 –/– d P ** 80 Phagocytosing cells 60 40 20 0 Percentage FITC + cells WT Nod2 –/– 100 a d Fungal killing *** 80 60 Percentage killing Percentage FITC + cells 40 Murine BMDMs Nod2 knockout 20 0 WT Nod2 –/– g ROS release 6 × 10 6 4 × 10 6 2 × 10 6 0 RLU p = 0.39 WT Nod2 –/– i Dectin-1 expression Clec7a mRNA ** 50 40 30 20 Relative expression 10 0 WT Nod2 –/– g g Relative expression j mRNA expression NOD2 CLEC7A ** p = 0.06 4 3 2 1 0 Fold change Scrambled Scrambled siNOD2 siNOD2 b ** Percentage killing NOD2 silencing msn MDMs Scrambled siNOD2 100 80 60 40 20 0 e p = 0.09 80 60 40 20 0 Percentage FITC + cells Scrambled siNOD2 e e Percentage FITC + cells p = 0.07 150,000 100,000 50,000 0 MFI Scrambled siNOD2 Percentage FITC + cells MFI f * 80 60 40 20 0 Percentage FITC + cells RPMI MDP (NOD2) c f * * 80 60 40 20 0 Percentage FITC + cells Percentage killing NOD2 stimulation Hums RPMI RPMI MDP MDP (NOD2) (NOD2) 100 80 60 40 20 0 * 150,000 100,000 50,000 0 MFI RPMI MDP (NOD2) c f * Percentage FITC + cells Percentage killing NOD2 stimulation RPMI MDP (NOD2) 100 80 60 40 20 0 h k 1.5 × 10 5 1.0 × 10 5 5.0 × 10 4 0.0 RLU p = 0.43 40000 ** Surface Dectin-1 30000 20000 10000 0 MFI RPMI CO MDP MDP (NOD2) (NOD2) h k 1.5 × 10 5 1.0 × 10 5 5.0 × 10 4 0.0 RLU p = 0.43 MFI CO MDP (NOD2) f h k k 40000 ** Surface Dectin-1 30000 20000 10000 0 MFI RPMI MDP (NOD2) c Fig. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Nevertheless, we observed that NOD2 polymorphisms, as well as the complete deficiency of the receptor, were associated with decreased Aspergillus-induced pro-inflammatory cyto- kine responses. NOD2 stimulation augments Aspergillus-induced cytokine responses. It has been widely described that excessive inflammation, and in particular IL-17-mediated inflammation, can result in detrimental immunopathology during Aspergillus infections in mice36–39, but this is primarily observed in situations where the immune system is largely functional such as cystic fibrosis, allergic bronchopulmoary aspergillosis, corticosteroid, and fully immunocompetent models. Although reduced cytokine- driven inflammation can contribute to less damage in certain aspergillosis models, a lower capacity to mount early cytokine response is also known to be a primary risk factor for suscept- ibility40. Based on our data, we can only conclude that NOD2 has a potential to modify Aspergillus-induced cytokines in vitro, but it needs to be elucidated whether this in any way contributes to the observed protection in HSCT patients with NOD2 variants and Nod2−/−mice. Functionally, we demonstrate that in particular the 1007finsC polymorphism impacts the response of primary immune cells to Aspergillus, namely in cytokine signalling and fungal killing, whereas we only observed an effect of the P268S polymorphism on cytokine responses. Immunosuppression and cytostatic drugs needed for the treatment of cancer and autoimmune disorders makes patients highly susceptible to invasive fungal infections such as IA. Cyclophosphamide is a drug used to treat hematological malig- nancies or to suppress the immune system to preventgraft rejection and renders mice highly susceptible to develop infec- tions with Aspergillus fumigatus. This immunosuppression allows a low dose of intranasally administered conidia to cause an invasive infection that is lethal within days, which in immuno- competent mice would have been efficiently cleared30. Nod2- deficient mice were resistant against aspergillosis despite being immunosuppressed and showing severe symptoms of aspergillo- sis such as weight loss, hunching, head tilting, and circling30. The protection observed in Nod2−/−mice was associated with reduced fungal burden and reduced histopathological damage to the lungs. A deficiency in PRRs being protective against lethal aspergillosis is a striking observation. Especially since it is chal- lenging to protect immunosuppressed mice even with available potent antifungal therapies, which often requires combinational therapies to achieve survival of these mice33,34. What could then be the mechanism of protection in the setting of genetic NOD2 deficiency? Carriage of the 1007finsC poly- morphism correlates with an increased fungal killing capacity. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Means were compared using the Wilcoxon signed-rank test for paired comparisons except for the comparison of WT with Nod2-/- cells which were compared using the Mann-Whitney U test b c 100 40 30 20 %FITC positive monocytes 10 0 90 80 70 60 50 40 * * Monocyte fungal killing Phagocytosing cells % Killing CO CO MDP NOD2–/– PT NOD2–/– PT MDP CO CO MDP NOD2–/– PT NOD2–/– PT MDP b 100 90 80 70 60 50 40 * Monocyte fungal killing % Killing CO CO MDP NOD2–/– PT NOD2–/– PT MDP c 40 30 20 %FITC positive monocytes 10 0 * Phagocytosing cells CO CO MDP NOD2–/– PT NOD2–/– PT MDP 40,000 30,000 20,000 MFI FITC 10,000 0 * Phagocytosis CO CO MDP NOD2 –/– PT NOD2–/– PT MDP 100 a p = 0.43 * * BMDM fungal killing 80 60 % Killing 40 20 0 WT WT MDP Nod2–/– Nod2–/– MDP d 8000 6000 4000 Dectin-1 MFI 2000 0 * Dectin-1 expression CO CO MDP NOD2–/– PT NOD2–/– PT MDP d b c Fig. 9 MDP negatively affects antifungal host response only in the presence of functional NOD2. a, b The fungal killing capacity of (a) murine BMDMs (n = 8 wt and n = 6 Nod2−/−) and (b) human monocytes (1 × 105) assessed by CFU remaining of A. fumigatus (2 × 106) following exposure for 24 h. c Phagocytosis efficiency assessed as percentage of monocytes that engulfed FITC-labelled A. fumigatus conidia and mean fluorescence intensity of the total macrophage population, (d) surface dectin-1 expression measured by flow cytometry in cells of healthy controls (co) (n = 6) as well as NOD2-deficient patients (NOD2−/−PT) (n = 3). Data are represented as scatterplot with median, black dots represent wild-type and grey dots represent NOD2-deficient cells. Means were compared using the Wilcoxon signed-rank test for paired comparisons except for the comparison of WT with Nod2-/- cells which were compared using the Mann-Whitney U test for 1007finsC and G908R polymorphisms32, a strong trend (p = 0.05) towards a reduced presence of the mutated R702W allele was observed in IA patients32. reduced pulmonary inflammation35. We observed that some cytokines have lower levels in the BAL of aspergillosis patients having the TT-genotype at P268S (rs2066842). This might indi- cate a less severe infection that may be related to enhanced fungal killing. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 100 a b c d 100 40 40,000 8000 6000 4000 Dectin-1 MFI 2000 0 30,000 20,000 MFI FITC 10,000 0 30 20 %FITC positive monocytes 10 0 90 80 70 60 50 40 p = 0.43 * * * * * * BMDM fungal killing Monocyte fungal killing Phagocytosing cells Phagocytosis Dectin-1 expression 80 60 % Killing % Killing 40 20 0 WT CO CO MDP NOD2–/– PT NOD2–/– PT MDP CO CO MDP NOD2–/– PT NOD2–/– PT MDP CO CO MDP NOD2 –/– PT NOD2–/– PT MDP CO CO MDP NOD2–/– PT NOD2–/– PT MDP WT MDP Nod2–/– Nod2–/– MDP Fig. 9 MDP negatively affects antifungal host response only in the presence of functional NOD2. a, b The fungal killing capacity of (a) murine BMDMs (n = 8 wt and n = 6 Nod2−/−) and (b) human monocytes (1 × 105) assessed by CFU remaining of A. fumigatus (2 × 106) following exposure for 24 h. c Phagocytosis efficiency assessed as percentage of monocytes that engulfed FITC-labelled A. fumigatus conidia and mean fluorescence intensity of the total macrophage population, (d) surface dectin-1 expression measured by flow cytometry in cells of healthy controls (co) (n = 6) as well as NOD2-deficient patients (NOD2−/−PT) (n = 3). Data are represented as scatterplot with median, black dots represent wild-type and grey dots represent NOD2-deficient cells. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Means were compared using the Mann–Whitney U test for murine BMDMs (a, d, g, i) and the Wilcoxon signed-rank test was paired comparisons following siRNA treatment (b, e, j), or MDP stimulation (c, f, h, k) immunodysregulation that leads to disease23, namely NOD2, remains largely unexplored in the context of anti-Aspergillus host defence13–16, Here, we systematically addressed the role of NOD2 in susceptibility to Aspergillus infection. effect on antifungal immunity. A potential limitation of our study is the lack of association for other NOD2 polymorphisms even- tually with more noticeable loss-of-function phenotypes. This may, however, be explained by the low allele frequency of such variants, which do not allow accurate risk estimations. A previous study also investigated NOD2 polymorphisms in association with aspergillosis in HSCT patients. Although in this study a lack of association due to the low frequency of the variants was observed We report an association between NOD2 genetic variation, Nod2 deficiency and decreased susceptibility to IA. Specifically, the TT-genotype at P268S confers resistance to IA after HSCT, a finding highlighting a potential NOD2-dependent detrimental NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 9 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 An alternative explanation for the different phenotypes observed with NOD1 and NOD2 is that one, or both, of these receptors, can, in addi- tion to RICK, induces an alternative-signalling cascade. Of note, it has previously been demonstrated that NOD2 can signal through the intracellular adaptor CARD954, which has a strong associa- tion with antifungal host response55,56. It is tempting to speculate that the detrimental effect of NOD2 may be due to sequestering CARD9 from other receptors requiring CARD9 as a signalling adaptor, such as dectin-157, dectin-258. Further studies using NOD1/NOD2, RICK, and NOD2/CARD9 knockout mice and co- precipitations would be required to investigate how the molecular pathways of NOD1 and NOD2 intertwine to mediate detrimental effects on the antifungal host response against Aspergillus. One of the crucial PRRs for phagocytosis of A. fumigatus is the c-type lectin receptor dectin-142,43. On the one hand, when we studied the expression of dectin-1 in the setting of Nod2 defi- ciency or silencing we observed that when phagocytosis was increased this correlated with increased dectin-1 expression. On the other hand NOD2 stimulation with MDP decreased surface dectin-1 expression. The observed correlation between increased dectin-1 expression and increased phagocytosis and killing within the setting of NOD2 deficiency, may argue for a role for dectin-1, but does not exclude that other mechanisms are still playing a role in the observed protection. p Although it has previously been shown that other fungi such as Candida albicans are not recognized by NOD244,45, the fungal cell wall component chitin/chitosan that is present in both Aspergillus and Candida has been suggested to be a ligand for NLRs18,46. Chitosan activates NLRP3 and thereby activates the inflammasome and induces IL-1β production, whereas chitin did not activate NLRP346. Chitin induces IL-10 dependent on TLR9, mannose receptor and NOD218. These data suggest that NOD2 plays a role in the recognition of fungal molecules such as chitin. However, a different study demonstrated that chitin-induced IL-1Ra production in human PBMCs is independent of NOD247. In addition, chitin can synergize with the NOD2 ligand MDP to augment IL-1β and TNF responses47, similar to our current observation that Aspergillus synergizes with MDP stimulation. Although this underlines that chitin and possibly other fungal cell wall molecules synergize with NOD2 signalling to augment cytokine responses, further studies are required to identify the PAMPs in Aspergillus that are recognized by NOD2. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Comparing WT and Nod2- deficient murine cells and silencing of the same human cells making them NOD2 deficient practically eliminates these donor factors that contribute to variability of phagocytosis. To prove that NOD2 influences phagocytosis in human cells we made use of the following knowledge. NOD2 is a receptor for derivates of bacterial peptidoglycan, such as MDP, which is present in the peptidoglycan of both gram positive and negative bacteria8,10,11. When we studied killing and phagocytosis of Aspergillus in the presence or absence of MDP we observed that NOD2 stimulation indeed decreases phagocytosis and killing. By performing these experiments in cells isolated form NOD2-deficient patients we show that MDP in these cells did not influence phagocytosis and killing. These data strengthen the conclusion that NOD2 nega- tively influences phagocytosis and killing of Aspergillus and supports the concept that genetic NOD2 deficiency could confer protection against invasive aspergillosis by an increased capacity of NOD2-deficient cells to control fungal burden in the host. independent way. This could provide a rationale for treating patients that are immunosuppressed, either due to primary immunodeficiency such as chronic granulomatous disease that lack ROS or in patients that receive corticosteroids that suppress immune cells to produce ROS. Moreover, the effects of NOD2 deficiency are in sharp contrast with NOD1 deficiency. NOD1- deficient cells show increased cytokine production in response to Aspergillus. This might be beneficial, but could also be detri- mental during the natural course of aspergillosis. Moreover, the oxidative burst is significantly higher under NOD1 deficient conditions and is decreased by NOD1 stimulation17, whereas in NOD2 we do not find an association with altered ROS produc- tion. NOD1 and NOD2 are closely related and interact with each other, therefore one would expect they behave similar in anti- Aspergillus host defence, but here we demonstrate clear different roles for NOD2 than the previous effects described for NOD117. A potential explanation for the different phenotypes observed with NOD1 and NOD2 deficiency is that Aspergillus PAMPs may have different affinities for the two different receptors or that different PAMPs bind and/or activate the receptors. Binding of the receptors by different PAMPs could lead to the fact that both receptors compete for the downstream adapter RICK, which was previously proposed to explain differential regulation of inflam- mation by NOD1 and NOD2 in arthritis53. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 In addition, Nod2-deficient mice demonstrated improved fungal clearance compared to WT mice, which was associated with an absence of histological damage and fungal outgrowth within the lungs. In addition Nod2 deficiency in murine BMDMs or NOD2 silencing in human MDMs augments fungal killing, whereas NOD2 stimulation by MDP in human MDMs or monocytes suppresses fungal killing. Subsequently, we systematically addressed whether phagocytosis capacity and/or ROS production, which are well-established mechanisms needed for the killing of Aspergillus, would be altered in NOD2-deficient cells. We observed no effect on the ROS production. However, observed that NOD2 negatively regulates phagocytosis. Silencing of NOD2 gene expression slightly enhanced engulfment of A. fumigatus conidia, whereas NOD2 stimulation suppressed the phagocytic capacity of human MDMs and monocytes. Nod2−/−BMDMs were more efficient at engulfing A. fumigatus conidia than their WT counterparts. This is in line with a previous report showing that NOD2 polymorphisms improve phagocytosis of the p The fact that we observe protection of Nod2 deficiency in an immunocompromised mouse model raises the question which cells are responsible for the protection. We observed resident macrophages, that remain in the lung even after immunosup- pressive therapy, which could potentially mediate fungal killing. In the HSCT patients, the NOD2 P268S polymorphism was only associated with a reduced incidence of aspergillosis in the donor genotype. The donor genotype will represent the genotype of the patient’s myeloid cells following transplantation suggesting that the protective effect of NOD2 genetic variation lies within the myeloid compartment. Furthermore, we observe that NOD2 negatively affects the antifungal capacity of various types of myeloid cells, including murine BMDMs, human MDMs and human monocytes. Interestingly, Staphylococcus aureus pneumonia in Nod2- deficient mice was less severe than in wild-type animals due to NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 10 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 gram-negative bacterium Escherichia coli41. However, in NOD2- deficient patients, we did not observe augmented phagocytosis compared to healthy donor cells. At first sight this might argue against a role for NOD2 in phagocytosis, however, it needs to be taken into account that the rate of phagocytosis is already variable between humans. This is most likely explained by a different genetic background and, in the case of our patients, maybe even immunosuppressive medication. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 Moreover, NOD2 may not be directly involved in recognizing Aspergillus, but rather coordinate the responses that are induced by other (membrane-bound) PRRs, for example, the orchestration of phagosome composition. NOD2 synergizes with TLR signalling to yield more potent inflammatory responses48–52. Selective modulation of signals from PRRs that recognize Aspergillus is a possible mechanism by which the NOD receptors regulate the host response to A. fumigatus. g g p g NOD2 deficiency mediates protection against Aspergillus in mice, and polymorphisms in NOD2 alter the susceptibility of HSCT patients to develop aspergillosis. These effects are in the context where NOD2 seems to play a role in the induction of innate and adaptive cytokine responses against Aspergillus in humans. The absence of NOD2, however, strongly correlates with an enhancement of fungal killing and phagocytosis, which is independent of ROS. This makes NOD2 an attractive therapeutic target in the treatment of invasive aspergillosis. Study design. A total of 310 consecutive haematological patients of European descent undergoing allogeneic HSCT at Instituto Português de Oncologia, Porto, and at the Hospital de Santa Maria, Lisbon, between 2010 and 2014, and respective donors, were included in the genetic association study. The demographic and clinical characteristics of the patients were as previously described26 and are pre- sented in Supplementary Table 2. Exclusion criteria were the development of fungal infection other than that caused by Aspergillus spp., and pre-transplant fungal infection. It should be noted that this cohort was previously successfully used for identification of genes conferring increased susceptibility to aspergillosis26. The sample size was estimated to provide a power of 80% (1 −β = 0.80) with a type I error below 5% (α = 0.05) for genetic variants with minor allele frequencies between 10 and 20% conferring a relative risk of 2.0. NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications ARTICLE After 24 h at 37 °C, the cells were washed in water and plated in serial dilution on Sabouraud agar plates. CFUs were counted after 24 h at 37 °C. Aspergillus fumigatus strains. A clinical isolate of Aspergillus fumigatus V05–27 was used for all ex vivo and in vitro stimulations60. Aspergillus was grown for 7 days at 37 °C on Sabouraud dextrose agar slants poured in T150 cell culture flasks (Corning). Abundant conidia were produced under these conditions. To harvest conidia phosphate-buffered saline (PBS) with 0.05% Tween 80 was poured on the slants and the surface was gently scraped using a cell scraper. To remove hyphae and debris, the conidial suspension was filtered through four layers of sterile gauze. Conidia were counted using a Bürker counting chamber, stored at −20 °C or heat inactivated for 30 min at 90 °C. A concentration of 1 × 107/mL was used in the experiments unless otherwise indicated. To obtain hyphal fragments, a suspension of 1 × 107/mL conidia was made in RPMI1640. After 10 h of incubation at 37 °C, the tubes were centrifuged at 1550 × g for 10 min, and the pellet, containing almost exclusively hyphae, was washed twice in PBS and heat inactivated for 30 min at 90 ° C. Phagocytosis assays. Human CD14+ monocytes, human MDMs, or BMDMs were plated in 24 flat bottom plates at 5 × 105 cells/well. Cells were allowed to phagocytose 5 × 106 (MOI 1:10) heat inactivated FITC-labelled conidia for 4 h. Subsequently the fluorescence signal of extracellular non-phagocytosed conidia was quenched using 0.2% trypan blue. The cells were measured on a Cytoflex flow cytometer (Beckman Coulter) and the data were analysed using Kaluza software (Beckman Coulter). The monocytes that phagocytosed one or more conidia were enumerated by their positivity for the FITC signal, and could be divided into a FITC negative (monocytes that did not engulf conidia) and a FITC positive (monocytes that engulfed conidia) population. Phagocytosis efficiency was assessed as the mean fluorescence intensity of FITC+ macrophage population (Supple- mentary Figure 5). Heat-inactivated Aspergillus conidia (1 × 107/mL) were FITC-labelled by incubation with FITC at a final concentration of 0.1 mg/mL (SIGMA) in 0.05 M Na carbonate buffer (pH 10.2) at 37 °C for 1 h. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 of 2.5. No patients were excluded in these studies. All cytokine and killing assays were performed by a researcher blinded for the genotype. corticosteroid immunosuppressed mouse models of aspergillosis62, the 2/7/1 strain demonstrated a similar virulence as observed for its parental strain CBS144.8563,64. corticosteroid immunosuppressed mouse models of aspergillosis62, the 2/7/1 strain demonstrated a similar virulence as observed for its parental strain CBS144.8563,64. PBMC isolation and stimulation. Venous blood was drawn into 10 mL EDTA tubes. Blood was diluted in PBS (1:1) and fractions were separated by Ficoll (Ficoll- Paque Plus, GE healthcare, Zeist, The Netherlands) density gradient centrifugation according to the protocol supplied by the manufacturer. Cells were washed twice with PBS and resuspended in RPMI-1640+ (RPMI1640 Dutch modification sup- plemented with 50 µg/mL gentamycin, 2 mM L-glutamine and 1 mM pyruvate; Gibco, Invitrogen, Breda, The Netherlands). Ethics statement. For the genetic association study, approval was obtained from the Ethics Subcommittee for Life and Health Sciences of the University of Minho, Portugal (125/014 and 014/015), the Ethics Committee for Health of the Instituto Português de Oncologia—Porto, Portugal (26/015), the Ethics Committee of the Lisbon Academic Medical Center, Portugal (632/014), and the National Com- mission for the Protection of Data, Portugal (1950/015). For the functional genomics study and patient studies, drawing of blood samples from patients and healthy volunteers was approved by the local ethical board at the Radboud University Nijmegen (Arnhem-Nijmegen Medical Ethical Committee). PBMCs were plated in 96-well round-bottom plates (Corning, NY, USA) at a final concentration of 2.5 × 106 cells/mL and in a total volume of 200 μL. The individuals in the functional genomic cohort were stimulated with medium (negative control) or live Aspergillus at a final concentration of 1 × 107/mL for 24 h or HI A. fumigatus conidia for 7 days (to prevent outgrowth of the fungus influencing the results). The NOD2-deficient patients were stimulated in the presence of 10% serum with the culture medium, live A. fumigatus conidia (1 × 107/mL), HI conidia (1 × 107/mL) or HI hyphae (derived from 1 × 107/mL conidia). PBMCs in co-stimulation experiments were exposed to 10 μg/mL MDP and subsequently stimulated with medium, HI conidia (1 × 107/mL). After stimulation culture supernatants were collected and stored at −20 °C until cytokine measurement. ARTICLE Most patients received anti-inflammatory therapy for treatment of their Crohn’s disease; Patient 1 Mesalazine 1dd 1000 mg, Patient 2 No immunomodulation, Patient 3 Adalimumab 1 × 2 weeks 40 mg sub cutaneous, Patient 4 mesalazine 3dd 1 g and azathioprine 1dd 200 mg, Patient 5 infliximab every 8 weeks 300 mg iv, Patients 6–9 unknown. Nine patients with Crohn’s disease that were homozygous for the 1007finsC polymorphism were included for studying NOD2 deficiency. Most patients received anti-inflammatory therapy for treatment of their Crohn’s disease; Patient 1 Mesalazine 1dd 1000 mg, Patient 2 No immunomodulation, Patient 3 g, , Adalimumab 1 × 2 weeks 40 mg sub cutaneous, Patient 4 mesalazine 3dd 1 g and azathioprine 1dd 200 mg, Patient 5 infliximab every 8 weeks 300 mg iv, Patients 6–9 unknown. The surface dectin-1 expression on human MDMs was assessed following stimulation of with MDP as described above. MDMs were stained in a final volume of 50 μL with FITC-conjugated anti-human CD14 monoclonal antibody (BD; clone TUK 4, dilution 1:20), KromeOrange-conjugated anti-human CD45 monoclonal antibody (Beckman Coulter; clone J.33, dilution 1:10) and APC-conjugated anti- human dectin-1 monoclonal antibody (R&D, clone 259931, dilution 1:10). CD14+ cells were gated within the population of CD45+ cells and subsequently, the Mean fluorescence intensity (MFI) of Dectin-1 was assessed on the CD14+/CD45+ cells (Supplementary Figure 4). The cells were measured on a Cytoflex flow cytometer (Beckman Coulter) and the data were analysed using Kaluza software (Beckman Coulter). Genotyping. DNA was isolated using the Gentra Pure Gene Blood kit (Qiagen), in accordance with the manufacturer’s protocol. Genotyping was performed using KASPar assays (LGC Genomics, Hertfordshire, UK) in an Applied Biosystems 7500 Fast Real-Time PCR system for the patient cohort. Mean call rate was >97% for all genotyped SNPs. Quality control for the genotyping results was achieved with negative controls, common and rare homozygous controls (whenever available), and retesting of samples with indeterminate results. Details of the MAF of the polymorphisms in our cohort are provided in Table 1 and linkage disequilibrium for all genotyped SNPs is shown in Supplementary Table 1. Aspergillus killing assays. Freshly isolated PBMCs (5 × 105), human GM-CSF monocyte-derived macrophages (2 × 105) or murine BMDMs (2 × 105) were exposed to Aspergillus conidia (2 × 106) in 96 well plates a final volume of 200 μL. ARTICLE For assessment of BAL cytokine levels approval was obtained from the Ethics Subcommittee for Life and Health Sciences of the University of Minho, Portugal (126/014), and the Ethics Committee of the University Hospitals of Leuven, Belgium. g All patients and healthy volunteers provided written informed consent. Mice were cared for in accordance with Institut Pasteur guidelines, in compliance with European animal welfare regulation. This study was approved by the ethical committee for animal experimentation CETEA (Comité d’éthique en experimentation animale, Project license number 2013-0020). Animal studies were conducted under protocols approved by St. Jude Children’s Research Hospital Committee on Use and Care of Animals (protocol no 482-100265-1-/13). Flow cytometry. Flow cytometry for Aspergillus-induced IL-17A+, IL-22+, and IFNγ+ T-cells was performed as described previously65. Following 7 day Asper- gillus-stimulations, culture supernatants were removed and PBMCs were re- stimulated 4–6 h with PMA (50 ng/mL; Sigma-Aldrich), ionomycin (1 mg/mL; Sigma-Aldrich), and GolgiPlug (BD Biosciences) according to the protocols sup- plied by the manufacturers. Cells were stained extracellular in a total volume of 50 μL using PE-Cy7–conjugated anti-CD4 monoclonal antibody (eBiosciences, clone RM4–5, dilution 1:20). Subsequently, the cells were fixed and permeabilized with Cytofix/Cytoperm solution (eBioscience) according to the protocol supplied by the manufacturer. Following permeabilization the cells were stained intra- cellularly with Alexa 647-conjugated anti-IL-17A monoclonal antibody (BD Biosciences, Clone TC11-18H10, dilution 1:6), PE-conjugated anti-IL-22 mono- clonal antibody (R&D Systems, Clone 142928, dilution 1:12), and FITC-conjugated anti-IFNγ monoclonal antibody (eBioscience, clone 4s.B3, dilution 1:300) according to the protocols supplied by the manufacturer’s. The cells were measured on an FC500 flow cytometer (Beckman Coulter) and the data were analysed using CXP analysis software v2.2 (Beckman Coulter). Healthy controls and NOD2 deficient patients. Venous blood samples from healthy controls and patients were obtained and were analysed for polymorphisms in NOD2 gene (P268S rs2066842, G908R rs2066845, R702W rs2066844 and 1007finsC, rs2066847). DNA was isolated from whole blood by using the isolation Gentra Pure Gene Blood kit (Qiagen), according to the manufacturer’s protocol. Gene fragments were amplified and genotyped using commercially available TaqMan SNP Genotyping Assays (Applied Biosystems) according to the manu- facturer’s protocol on the StepOnePlus system (Applied Biosystems). Quality control was performed by the incorporation of positive and negative controls and duplication of random samples across different plates. p p p Nine patients with Crohn’s disease that were homozygous for the 1007finsC polymorphism were included for studying NOD2 deficiency. Methods St d d i Study design. A total of 310 consecutive haematological patients of European descent undergoing allogeneic HSCT at Instituto Português de Oncologia, Porto, and at the Hospital de Santa Maria, Lisbon, between 2010 and 2014, and respective donors, were included in the genetic association study. The demographic and clinical characteristics of the patients were as previously described26 and are pre- sented in Supplementary Table 2. Exclusion criteria were the development of fungal infection other than that caused by Aspergillus spp., and pre-transplant fungal infection. It should be noted that this cohort was previously successfully used for identification of genes conferring increased susceptibility to aspergillosis26. The sample size was estimated to provide a power of 80% (1 −β = 0.80) with a type I error below 5% (α = 0.05) for genetic variants with minor allele frequencies between 10 and 20% conferring a relative risk of 2.0. For the functional genomics study, similarly, the cohort was previously successfully used for identification of polymorphisms that lead to reduced cytokine responses59. The functional genomics cohort consisted of 200 healthy volunteers, of which approximately 80 (variable per genotype) were included in the current study. Individuals of which the genotype could not reliably be determined using SNP assays, and individuals that were not assessed for cytokine production were excluded from the analysis. The sample size of 80 healthy individuals was estimated to provide a power of 70% (1 −β = 0.70) with a type I error below 5% (α = 0.05) for genetic variants with a minor allele frequencies of 20% conferring an odds ratio p f g Collectively our data highlight a detrimental effect for NOD2 on antifungal host defence against A. fumigatus. This places NOD2 in a unique position in anti-Aspergillus host defence. It has the capacity to increase phagocytosis and killing in a ROS 11 ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 primers 5′-GGGCGAATCACAGATTGAATC-3′, 5′-GCGGTTCCAAACGTAC CAA-3′ and probe LC610-TTTTTATGTGTCCGCCACCATCTGGATC-BBQ. For the ITS2 detection, a two-fold dilution series of the cloned PCR product was included to calculate the number of copies per reaction. Quantitative reverse transcriptase PCR for CLEC7A expression. RNA was isolated according to the protocol supplied with the TRIzol reagent. Isolated mRNA (1 µg) was reverse transcribed into cDNA using the iScript cDNA synthesis kit (BIORAD). Quantitative real-time PCR (qPCR) was performed using Power SYBR Green PCR master mix (Applied Biosystems) and following primers (all manufactured by Biolegio) for human samples hNOD2 Fwd 5′-CCCTGCAGC TGGACTACAACT-3′ and Rev 5′-AGATGCCTCGGTCTGAGATATTG-3′, hGAPDH Fwd 5′-AGGGGAGATTCAGTGTGGTG-3′ and Rev 5′-CGACCACTT TGTCAAGCTCA-3′ hCLEC7A Fwd 5′-ACAATGCTGGCAACTGGGCT-3′ and Rev 5′-GCCGAGAAAGGCCTATCCAAAA-3′ and the following primer sets form mouse samples mClec7a Fwd 5′-AGGTTTTTCTCAGCCTTGC CTTC-3′ and Rev 5′-GGGAGCAGTGTCTCTTACTTCC-3′, mGapdh Fwd 5′-AG GTCGGTGTGAACGGATTTG-3′ and Rev 5′-TGTAGACCATGTAGTTGAGGT CA-3′. PCR was performed using an Applied Biosystems StepONE PCR system using PCR conditions 2 min 50 °C, 10 min 95 °C followed by 40 cycles at 95 °C for 15 s and 60 °C for 1 min. The RNA genes of interest were corrected for differences i l di t ti i th i l f th h k i t i GAPDH Quantitative reverse transcriptase PCR for CLEC7A expression. RNA was isolated according to the protocol supplied with the TRIzol reagent. Isolated mRNA (1 µg) was reverse transcribed into cDNA using the iScript cDNA synthesis kit (BIORAD). Quantitative real-time PCR (qPCR) was performed using Power SYBR Green PCR master mix (Applied Biosystems) and following primers (all manufactured by Biolegio) for human samples hNOD2 Fwd 5′-CCCTGCAGC TGGACTACAACT-3′ and Rev 5′-AGATGCCTCGGTCTGAGATATTG-3′, hGAPDH Fwd 5′-AGGGGAGATTCAGTGTGGTG-3′ and Rev 5′-CGACCACTT TGTCAAGCTCA-3′ hCLEC7A Fwd 5′-ACAATGCTGGCAACTGGGCT-3′ and Rev 5′-GCCGAGAAAGGCCTATCCAAAA-3′ and the following primer sets form mouse samples mClec7a Fwd 5′-AGGTTTTTCTCAGCCTTGC Quantitative reverse transcriptase PCR for CLEC7A expression. RNA was isolated according to the protocol supplied with the TRIzol reagent. Isolated mRNA (1 µg) was reverse transcribed into cDNA using the iScript cDNA synthesis kit (BIORAD). Quantitative real-time PCR (qPCR) was performed using Power SYBR Green PCR master mix (Applied Biosystems) and following primers (all manufactured by Biolegio) for human samples hNOD2 Fwd 5′-CCCTGCAGC TGGACTACAACT-3′ and Rev 5′-AGATGCCTCGGTCTGAGATATTG-3′, Histology. Sinuses and lungs were removed and immediately fixed in 10% neutral- buffered formalin. After fixation, sinuses were decalcified for 1 month, using a chelating agent (ethylenediaminetetracetic acid—EDTA) in order to allow routine processing of paraffin while preserving high-quality morphology. ARTICLE In vivo experiments. Mice for in vivo experiments were supplied by the breeding centre R. Janvier (Le Genest Saint-Isle, France). All mice were housed under specific pathogen-free conditions in IVC cages, and fed standard chow and water ad libitum. For the survival experiment in an immunosuppressed background C57BL/6 wild-type (6male/7female), and C57BL/6 Nod2−/−(7male/2female) mice (28 to 31 g, 10 weeks old) were used. An estimated power of 80% (1 −β = 0.80) with a type I error below 5% (α = 0.05) for a relative risk of 1.8 was estimated based on a median survival of 4 days in the control group. Mice were separated between genotypes into cages without further randomization and immunosuppressed at day 4 and day 1 before infection by intraperitoneal injection of 200 µL cyclopho- sphamide (Sigma Aldrich) at 4 mg/mL. At the day of infection, mice were anaes- thetized by intramuscular injection (150 µL) of ketamine (10 mg/mL) and xylazine (10 mg/mL) hair was shaved from the ventral lung area and subsequently, mice were inoculated intranasally with 5 × 104 luciferase expressing A. fumigatus 2/7/1 conidia29 in 25 µL PBS. In vivo experiments. Mice for in vivo experiments were supplied by the breeding centre R. Janvier (Le Genest Saint-Isle, France). All mice were housed under specific pathogen-free conditions in IVC cages, and fed standard chow and water ad libitum. For the survival experiment in an immunosuppressed background C57BL/6 wild-type (6male/7female), and C57BL/6 Nod2−/−(7male/2female) mice (28 to 31 g, 10 weeks old) were used. An estimated power of 80% (1 −β = 0.80) with a type I error below 5% (α = 0.05) for a relative risk of 1.8 was estimated based on a median survival of 4 days in the control group. Mice were separated between genotypes into cages without further randomization and immunosuppressed at day 4 and day 1 before infection by intraperitoneal injection of 200 µL cyclopho- h d ( ld h) h d f f Cytokine measurements. The levels of cytokines in human BAL samples were quantified using the Human Premixed Multi-Analyte Kit (R&D Systems, MN, USA). The cytokine levels in culture supernatants of human PBMCs were measured using commercially available ELISA assays according to the pro- tocol supplied by the manufacturer. IL-1β, TNF, IL-6, IL-17A, and IL-22 assays were from R&D systems and IFNγ was from Sanquin (Amsterdam, The Nether- lands). ARTICLE Mouse IL-1β, TNF, IL-6, KC, IL-17A, IL-22, and IFNγ in splenocyte stimulations were measured using the Luminex multiplex platform (Millipore, Billerica, MA). Statistical analysis. For the genetic association study, the probability of IA according to NOD2 genotypes was determined using the cumulative incidence method and compared using Gray’s test66. Cumulative incidences of infection at 24 months were computed with the cmprsk package for R version 2.10.167, with censoring of data at the date of last follow-up visit and relapse and death as competing events. The clinical and genetic variables achieving a p-value ≤0.15 in the univariate analysis were entered one by one in a pairwise model together and kept in the final model if they remained significant (p ≤0.05). Multivariate analysis was performed using the sub-distribution regression model of Fine and Gray with the cmprsk package for R68. µ In all experiments, survival and weight was monitored in an unblinded fashion during the course of infection. For histological assessment female C57BL/6 wild-type and C57BL/6 Nod2−/− mice (19 to 22 g, 8 weeks old) were used. With 8 mice per group in two separate experiments a power was estimated of 80% (1 −β = 0.80) with a type I error below 5% (α = 0.05) for a variance of 5%. They received similar immunosuppression regimen and were similarly infected as the mice for survival. Weight and bioluminescence were monitored daily during the course of infection. At day 3 the mice were euthanized. Data are presented as scatterplots representing individual data points and a line indicating the median value or as graphs ±SEM. Data from functional genomic experiments, in vitro experiments and in vivo experiments was subjected to D’Agostino & Pearson omnibus normality test and was not normally distributed. No samples/animals were excluded from analysis in the in vivo experiments. For in vitro experiments all data points are shown without exclusion. In the functional genomic experiments only healthy individuals whose genotype could not accurately be determined were excluded from the studies. Unless otherwise indicated the Mann-Whitney U test was used to determine statistical significant differences between experimental groups and for paired analysis such as with MDP stimulation or siRNA treatment the paired Wilcoxon signed-rank test was used with *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. All data were analysed using GraphPad Prism v6.0. Bioluminescence imaging. ARTICLE Sinus and lung samples were then embedded in paraffin and cut into 4 µm thick sections. Serial sections were stained with haematoxylin and eosin (HE) for assessment histological lesions, Grocott’s methenamine silver for fungal detection. , hGAPDH Fwd 5′-AGGGGAGATTCAGTGTGGTG-3′ and Rev 5′-CGACCACTT TGTCAAGCTCA-3′ hCLEC7A Fwd 5′-ACAATGCTGGCAACTGGGCT-3′ and Rev 5′-GCCGAGAAAGGCCTATCCAAAA-3′ and the following primer sets form mouse samples mClec7a Fwd 5′-AGGTTTTTCTCAGCCTTGC p CTTC-3′ and Rev 5′-GGGAGCAGTGTCTCTTACTTCC-3′, mGapdh Fwd 5′-AG GTCGGTGTGAACGGATTTG-3′ and Rev 5′-TGTAGACCATGTAGTTGAGGT CA-3′. PCR was performed using an Applied Biosystems StepONE PCR system using PCR conditions 2 min 50 °C, 10 min 95 °C followed by 40 cycles at 95 °C for 15 s and 60 °C for 1 min. The RNA genes of interest were corrected for differences in loading concentration using the signal of the housekeeping protein GAPDH. g For morphometric analysis, fields at a magnification of ×50, covering the entire lung sections of WT and Nod2−/−mice at day 2 post infection were selected and analysed using ImageJ software (http://rsbweb.nih.gov/ij/). We used the software to count the number of lesion foci per lung section, considering ischaemic necrosis foci for wild-type mice and small macrophage infiltrates for Nod2−/−mice since ischaemic necrosis was not observed in these mice. Using the software we also measured the size of ischaemic necrosis and macrophage infiltrate foci. Results were expressed as the number and surface of lung lesions, relative to the total lung sections. NOD2 silencing. Freshly isolated PBMCs were differentiated to macrophages using 6-day differentiation in 10% human serum supplemented with 5 ng/mL GM-CSF (R&D systems). After differentiation (1 × 105) macrophages were seeded in 96 well plates and left for 2 h at 37 °C to subsequently transfect them with 25 nM NOD2 targeting siRNA (on target) or scrambled (non-target) control siRNA (smart pool, Thermo Scientific) for 24 h at 37 °C (Dharmafect, Thermo Scientific). Subse- quently, the culture medium was refreshed and cells were used for killing and phagocytosis assays and PCR analysis. To detect the presence of macrophages within the lung tissue, immunohistochemistry analysis was performed using a rat anti-mouse F4/80 monoclonal antibody (AbD Serotec, MCA497G, clone CI:A3-1, diluted 1:400), in sterile phosphate-buffered saline and incubated overnight at 4 °C. The primary antibody was visualized with the N-Histofine rat (Microm) according to the manufacturer’s protocol. The colour was developed with 3-Amino-9- EthylCarbazole (AEC chromogen, Sigma). The sections were then counterstained with Meyer’s haematoxylin and cover-slipped for microscopic observation. ARTICLE Bioluminescence imaging was acquired at day 1 post- infection (pi) and was continued on days 2, 3, 4, 6, and 8 pi. Images were acquired using an IVIS 100 system (PerkinElmer) according to the manufacturer’s instructions. Analysis and acquisition were performed using Living Image software, version 2.6 (Xenogen). A volume of 100 μL of PBS containing 3.33 mg D-luciferin was injected intraperitoneally before each measurement. During image acquisition, mice were anesthetized using a constant flow of 2.5% isoflurane mixed with oxygen by means of an XGI-8 gas anaesthesia system (Xenogen), which allowed control over the duration of anaesthesia. Images were acquired for 5 min62. Quantification of photons per second emitted by each organ was performed by defining regions of interest corresponding to the respective organs of interest (sinus and thorax region), using the Xenogen software Living Image, version 3.0. Data availability. The authors declare that the data supporting the findings of this study are available within the paper and its Supplementary Information Files. All relevant data are available by request from the authors, with the restriction of data that would compromise patient confidentiality. Aspergillus PCR. Lung homogenates were obtained following disruption in saline using the Retsch Mixer Mill 301 homogenizer. The fungal burden was determined by amplification of Aspergillus ITS2 regions. Briefly, Homogenized tissue samples were used for DNA isolation by using the automated MagNA Pure system and the MagNA Pure LC Total Nucleic Acid Isolation Kit according to manufacturers protocol (Roche Applied Science). PhHV was added to all samples as an internal isolation control. The concentration of total isolated DNA was measured by using the Quantus Fluorometer (Promega). Aspergillus loads were determined by real- time PCR using the LC480 instrument and the probes master kit (Roche Applied Science). Thermocycling conditions were as follows: 37 °C for 10 min, 95 °C for 10 min, and 50 cycles: 95 °C for 15 s, and 60 °C for 45 s. The rDNA ITS2 region of Aspergillus fumigatus was detected by using primers 5′-GCGTCATTGCTGCCC TCAAGC-3′, 5′-ATATGCTTAAGTTCAGCGGGT-3′ and probe Cy5-TCCTCGA GCGTATGGGGCTT-BBQ. The PhHV isolation control was detected by using Received: 25 September 2017 Accepted: 23 May 2018 Received: 25 September 2017 Accepted: 23 May 2018 Ben-Ami, R., Lewis, R. E. & Kontoyiannis, D. P. Enemy of the (immunosuppressed) state: an update on the pathogenesis of Aspergillus fumigatus infection. Br. J. Haematol. 150, 406–417 (2010). ARTICLE Unbound FITC was washed away by centrifugation three times in PBS–0.1% Tween 20, and labelled conidia were resuspended in RPMI1640, counted and adjusted to a concentration of (4 × 108/ mL)61. For in vivo experiments the luciferase-expressing Aspergillus fumigatus 2/7/ 1 strain was used29, this strain contains two genomic lucOpt integrations under control of the Aspergillus gpdA promotor that regulates stable luciferase expression62. The strain has a similar antifungal susceptibility as its parental CBS144.85 strain and demonstrates no growth defects under various in vitro cultivation conditions such as different temperatures and carbon sources29. In ROS induction. The induction of ROS was measured by oxidation luminol (5-amino-2,3,dihydro-1,4-phtalazinedione). PBMCs (5 × 105), murine BMDMs (1 × 105), human MDMs (1 × 105) were resuspended in HBSS and put in dark 96-well plates. Cells were exposed to HBSS, A. fumigatus germs (1 × 107/mL; PBMCs only) or Zymosan (150 µg/mL). 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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/. 68. Scrucca, L., Santucci, A. & Aversa, F. Regression modeling of competing risk using R: an in depth guide for clinicians. Bone Marrow Transplant. 45, 1388–1395 (2010). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 14 NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04912-3 FEDER-000013), and the Fundação para a Ciência e Tecnologia (FCT) (IF/00735/2014 to A.C. and SFRH/BPD/96176/2013 to C.C.). 58. Bi, L. et al. 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Aspergillus fumigatus evades immune recognition during germination through loss of Toll-like receptor-4-mediated signal transduction. J. Infect. Dis. 188, 320–326 (2003). f 61. Chai, L. Y. et al. Modulation of Toll-like receptor 2 (TLR2) and TLR4 responses by Aspergillus fumigatus. Infect. Immun. 77, 2184–2192 (2009). sponses by Aspergillus fumigatus. Infect. Immun. 77, 2184–2192 ( 62. Brock, M. et al. Bioluminescent Aspergillus fumigatus, a new tool for drug efficiency testing and in vivo monitoring of invasive aspergillosis. Appl. Environ. Microbiol. 74, 7023–7035 (2008). © The Author(s) 2018 Acknowledgements We thank C. Wertz and M. Fanton D’Andon for providing Nod2-deficient mice, M. Schlotter for organizing patient inclusion, B. Rösler for assistance with flowcytometry. We also thank the NOD2-deficient patients for contributing to our study by providing blood samples. M.S.G. was supported by the Erasmus lifelong learning program. F.L.v.d. V. was supported by the E-rare project EURO-CMC. M.O. was supported by the NWO, 016.176.006). A.C. and C.C. were supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agree- ment, through the European Regional Development Fund (FEDER) (NORTE-01-0145- 15 NATURE COMMUNICATIONS | (2018) 9:2636 | DOI: 10.1038/s41467-018-04912-3 | www.nature.com/naturecommunications 15